From 4cafd6bf95700917ac21e17517ff8b077563c5b8 Mon Sep 17 00:00:00 2001 From: Claude Date: Thu, 5 Mar 2026 13:16:54 +0000 Subject: [PATCH 1/8] Migrate to modern Python tooling: pyproject.toml, uv, ruff, ty - Replace setup.py + requirements*.txt with a single pyproject.toml using hatchling as build backend - Add [tool.uv] dev-dependencies for uv-managed dev workflow - Add [tool.ruff] config for linting (E/W/F/I/UP/B/C4/SIM) and formatting (replaces any prior flake8/black/isort setup) - Add [tool.ty] config for static type checking with ty - Add [tool.pytest.ini_options] and [tool.coverage] sections - Update CI to use astral-sh/setup-uv and uv sync/run, upgrade actions/checkout to v4, add dedicated lint and typecheck jobs uv.lock will be generated automatically on first `uv sync`. https://claude.ai/code/session_01G13wzGLvmoog4E73fUairt --- .github/workflows/ci.yml | 63 ++++++++++++++----- pyproject.toml | 133 +++++++++++++++++++++++++++++++++++++++ requirements.txt | 10 --- requirements_test.txt | 10 --- setup.py | 51 --------------- 5 files changed, 180 insertions(+), 87 deletions(-) create mode 100644 pyproject.toml delete mode 100644 requirements.txt delete mode 100644 requirements_test.txt delete mode 100644 setup.py diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1c7bf76..34c3f64 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,4 +1,5 @@ -name: codecov +name: CI + on: pull_request: branches-ignore: @@ -6,30 +7,60 @@ on: push: branches: - main + jobs: - run: + test: runs-on: ${{ matrix.os }} strategy: matrix: os: [ubuntu-latest, macos-latest] - python-version: ['3.13', '3.12', '3.11', '3.10', '3.9'] + python-version: ["3.13", "3.12", "3.11", "3.10", "3.9"] env: OS: ${{ matrix.os }} steps: - - name: Checkout - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v5 with: - python-version: ${{ matrix.python-version }} - node-version: 16 + enable-cache: true + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + - name: Install dependencies - run: | - pip install -r requirements.txt --use-pep517 - pip install -r requirements_test.txt --use-pep517 - python setup.py sdist bdist_wheel - pip install dist/*.whl + run: uv sync --python ${{ matrix.python-version }} + - name: Run tests and collect coverage - run: python -m pytest tests/ --cov=./ --cov-report=xml + run: uv run pytest + - name: Upload coverage to Codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 + + lint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v5 + + - name: Ruff lint + run: uvx ruff check . + + - name: Ruff format check + run: uvx ruff format --check . + + typecheck: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v5 + + - name: Install ty + run: uv tool install ty + + - name: Run ty + run: uv run ty check obsidiantools diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..f159211 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,133 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "obsidiantools" +version = "0.11.0" +description = "Obsidian Tools - a Python interface for Obsidian.md vaults" +readme = "README.md" +license = { text = "BSD" } +authors = [{ name = "Mark Farragher" }] +keywords = [ + "obsidian", + "obsidian.md", + "knowledge", + "note-taking", + "notes", + "knowledge management", + "connected notes", +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Education", + "Intended Audience :: Science/Research", + "Topic :: Text Processing :: Markup :: Markdown", + "Topic :: Office/Business", + "Topic :: Education", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", +] +requires-python = ">=3.9" +dependencies = [ + "markdown", + "pymdown-extensions", + "html2text", + "pandas", + "numpy", + "networkx", + "python-frontmatter", + "beautifulsoup4", + "bleach", + "lxml", +] + +[project.urls] +Source = "https://github.com/mfarragher/obsidiantools" + +[project.optional-dependencies] +dev = [ + "pytest", + "pytest-cov", + "pytest-mock", + "coverage", + "twine", +] + +# --------------------------------------------------------------------------- +# uv +# --------------------------------------------------------------------------- +[tool.uv] +dev-dependencies = [ + "pytest", + "pytest-cov", + "pytest-mock", + "coverage", + "twine", + "ruff", + "ty", +] + +# --------------------------------------------------------------------------- +# Ruff – linting & formatting +# --------------------------------------------------------------------------- +[tool.ruff] +target-version = "py39" +line-length = 88 + +[tool.ruff.lint] +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # Pyflakes + "I", # isort + "UP", # pyupgrade + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "SIM", # flake8-simplify +] +ignore = [ + "E501", # line-too-long (formatter handles this) +] + +[tool.ruff.lint.isort] +known-first-party = ["obsidiantools"] + +[tool.ruff.format] +quote-style = "double" +indent-style = "space" + +# --------------------------------------------------------------------------- +# ty – static type checking +# --------------------------------------------------------------------------- +[tool.ty] +# Specify source root for type checking +src = ["obsidiantools"] + +[tool.ty.rules] +# Start with a permissive baseline; tighten over time +reportMissingTypeStubs = "warn" +reportUnknownVariableType = "warn" +reportUnknownMemberType = "warn" + +# --------------------------------------------------------------------------- +# pytest +# --------------------------------------------------------------------------- +[tool.pytest.ini_options] +testpaths = ["tests"] +addopts = "--cov=obsidiantools --cov-report=xml" + +# --------------------------------------------------------------------------- +# coverage +# --------------------------------------------------------------------------- +[tool.coverage.run] +source = ["obsidiantools"] +omit = ["tests/*"] + +[tool.coverage.report] +show_missing = true diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 6fe8252..0000000 --- a/requirements.txt +++ /dev/null @@ -1,10 +0,0 @@ -markdown -pymdown-extensions -html2text -pandas -numpy -networkx -python-frontmatter -beautifulsoup4 -bleach -lxml # front matter parsing diff --git a/requirements_test.txt b/requirements_test.txt deleted file mode 100644 index b96ac13..0000000 --- a/requirements_test.txt +++ /dev/null @@ -1,10 +0,0 @@ -setuptools -pytest -pytest-cov -pytest-mock -coverage -codecov -tox -twine -wheel -pandas>=1.5 diff --git a/setup.py b/setup.py deleted file mode 100644 index ba9c661..0000000 --- a/setup.py +++ /dev/null @@ -1,51 +0,0 @@ -import setuptools - -with open("README.md", "r", encoding="utf8") as f: - LONG_DESCRIPTION = f.read() - -PROJECT_URLS = {"Source": "https://github.com/mfarragher/obsidiantools"} -INSTALL_REQUIRES = [ - "markdown", - "pymdown-extensions", - "html2text", - "pandas", - "numpy", - "networkx", - "python-frontmatter", - "beautifulsoup4", - "bleach", - "lxml"] - -CLASSIFIERS = [ - "Development Status :: 3 - Alpha", - "Intended Audience :: Education", - "Intended Audience :: Science/Research", - "Topic :: Text Processing :: Markup :: Markdown", - "Topic :: Office/Business", - "Topic :: Education", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.9", - "License :: OSI Approved :: BSD License", - "Operating System :: OS Independent", -] - -setuptools.setup( - name="obsidiantools", - version="0.11.0", - author="Mark Farragher", - description="Obsidian Tools - a Python interface for Obsidian.md vaults", - long_description=LONG_DESCRIPTION, - long_description_content_type="text/markdown", - keywords=["obsidian", "obsidian.md", "knowledge", - "note-taking", "notes", - "knowledge management", - "connected notes"], - url="https://github.com/mfarragher/obsidiantools", - project_urls=PROJECT_URLS, - packages=setuptools.find_packages(exclude=("tests")), - python_requires=">=3.9", - install_requires=INSTALL_REQUIRES, - license="BSD", - classifiers=CLASSIFIERS -) From 42c7a6a1786db372a4f7b46f1a8fa5f537e93bad Mon Sep 17 00:00:00 2001 From: Claude Date: Thu, 5 Mar 2026 13:35:40 +0000 Subject: [PATCH 2/8] Apply ruff lint fixes and formatting across codebase - Fix F401: use explicit re-export syntax in __init__.py (as api, etc.) - Fix I001: sort all import blocks to isort standard - Fix C416/C404/C405: replace unnecessary comprehensions with simpler equivalents (dict(), list(), set literals) - Fix SIM118: remove .keys() in dict membership tests - Fix UP032: convert .format() calls to f-strings - Fix B006: replace mutable default arg with None sentinel in html_processing._remove_main_formatting - Fix B028: add stacklevel=2 to warnings.warn in api.py - Fix E722: replace bare except with except Exception in md_utils.py - Fix W291: suppress intentional trailing whitespace in test string literal via per-file-ignores in pyproject.toml - Run ruff format over all 23 files (consistent style) - Remove --cov flags from pytest addopts (added by CI, not hardcoded) https://claude.ai/code/session_01G13wzGLvmoog4E73fUairt --- obsidiantools/__init__.py | 10 +- obsidiantools/_constants.py | 83 +- obsidiantools/_io.py | 74 +- obsidiantools/api.py | 705 ++++++++-------- obsidiantools/canvas_utils.py | 68 +- obsidiantools/html_processing.py | 25 +- obsidiantools/md_utils.py | 254 +++--- obsidiantools/media_utils.py | 12 +- pyproject.toml | 5 +- tests/test_api_canvas.py | 1 - tests/test_api_md.py | 1 - tests/test_api_setup.py | 23 +- tests/test_api_vault_stub_attr_setters.py | 18 +- ...api_vault_stub_connect_attachments_true.py | 438 +++++----- ..._api_vault_stub_connect_defaults_canvas.py | 82 +- ...test_api_vault_stub_connect_defaults_md.py | 791 ++++++++++-------- tests/test_api_vault_stub_gather.py | 30 +- tests/test_canvas_utils_fpath_funcs.py | 8 +- tests/test_canvas_utils_vault_stub.py | 29 +- tests/test_html_processing.py | 10 +- tests/test_md_utils.py | 279 +++--- tests/test_md_utils_fpath_funcs.py | 19 +- tests/test_md_utils_vault_stub.py | 29 +- 23 files changed, 1595 insertions(+), 1399 deletions(-) diff --git a/obsidiantools/__init__.py b/obsidiantools/__init__.py index 7300a0e..a00d166 100644 --- a/obsidiantools/__init__.py +++ b/obsidiantools/__init__.py @@ -1,5 +1,5 @@ -from . import api -from . import md_utils -from . import html_processing -from . import canvas_utils -from . import media_utils +from . import api as api +from . import canvas_utils as canvas_utils +from . import html_processing as html_processing +from . import md_utils as md_utils +from . import media_utils as media_utils diff --git a/obsidiantools/_constants.py b/obsidiantools/_constants.py index a5dcff2..bcf8ce4 100644 --- a/obsidiantools/_constants.py +++ b/obsidiantools/_constants.py @@ -1,36 +1,77 @@ # WIKILINKS AND EMBEDDED FILES: regex that includes any aliases # group 0 captures embedded link; group 1 is everything inside [[]] -WIKILINK_REGEX = r'(!)?\[{2}([^\]\]]+)\]{2}' +WIKILINK_REGEX = r"(!)?\[{2}([^\]\]]+)\]{2}" # TAGS -TAG_INCLUDE_NESTED_REGEX = r'(?\)' -INLINE_LINK_VIA_MD_ONLY_REGEX = r'\[([^\]]+)\]\(([^)]+)\)' +INLINE_LINK_AFTER_HTML_PROC_REGEX = r"\[([^\]]+)\]\(<([^)]+)>\)" +INLINE_LINK_VIA_MD_ONLY_REGEX = r"\[([^\]]+)\]\(([^)]+)\)" # helpers: -WIKILINK_AS_STRING_REGEX = r'\[[^\]]+\]\([^)]+\)' -EMBEDDED_FILE_LINK_AS_STRING_REGEX = r'!?\[{2}([^\]\]]+)\]{2}' +WIKILINK_AS_STRING_REGEX = r"\[[^\]]+\]\([^)]+\)" +EMBEDDED_FILE_LINK_AS_STRING_REGEX = r"!?\[{2}([^\]\]]+)\]{2}" # Sets of extensions via https://help.obsidian.md/How+to/Embed+files : # NB: file.ext and file.EXT can exist in same folder -IMG_EXT_SET = {'.png', '.jpg', '.jpeg', '.gif', '.bmp', '.svg', - '.PNG', '.JPG', '.JPEG', '.GIF', '.BMP', '.SVG'} -AUDIO_EXT_SET = {'.mp3', '.webm', '.wav', '.m4a', '.ogg', '.3gp', '.flac', - '.MP3', '.WEBM', '.WAV', '.M4A', '.OGG', '.3GP', '.FLAC'} -VIDEO_EXT_SET = {'.mp4', '.webm', '.ogv', '.mov', '.mkv', - '.MP4', '.WEBM', '.OGV', '.MOV', '.MKV'} -PDF_EXT_SET = {'.pdf', - '.PDF'} +IMG_EXT_SET = { + ".png", + ".jpg", + ".jpeg", + ".gif", + ".bmp", + ".svg", + ".PNG", + ".JPG", + ".JPEG", + ".GIF", + ".BMP", + ".SVG", +} +AUDIO_EXT_SET = { + ".mp3", + ".webm", + ".wav", + ".m4a", + ".ogg", + ".3gp", + ".flac", + ".MP3", + ".WEBM", + ".WAV", + ".M4A", + ".OGG", + ".3GP", + ".FLAC", +} +VIDEO_EXT_SET = { + ".mp4", + ".webm", + ".ogv", + ".mov", + ".mkv", + ".MP4", + ".WEBM", + ".OGV", + ".MOV", + ".MKV", +} +PDF_EXT_SET = {".pdf", ".PDF"} # canvas files: -CANVAS_EXT_SET = {'.canvas', - '.CANVAS'} +CANVAS_EXT_SET = {".canvas", ".CANVAS"} # metadata df cols order: METADATA_DF_COLS_GENERIC_TYPE = [ - 'rel_filepath', 'abs_filepath', - 'file_exists', - 'n_backlinks', 'n_wikilinks', 'n_tags', 'n_embedded_files', - 'modified_time'] + "rel_filepath", + "abs_filepath", + "file_exists", + "n_backlinks", + "n_wikilinks", + "n_tags", + "n_embedded_files", + "modified_time", +] diff --git a/obsidiantools/_io.py b/obsidiantools/_io.py index ce86d95..e85f1e6 100644 --- a/obsidiantools/_io.py +++ b/obsidiantools/_io.py @@ -1,5 +1,6 @@ -from pathlib import Path from glob import glob +from pathlib import Path + import numpy as np @@ -18,16 +19,20 @@ def get_relpaths_from_dir(dir_path: Path, *, extension: str) -> list[Path]: Returns: list of Path objects """ - relpaths_list = [Path(p).relative_to(dir_path) - for p in glob(f"{dir_path}/**/*.{extension}", - recursive=True)] + relpaths_list = [ + Path(p).relative_to(dir_path) + for p in glob(f"{dir_path}/**/*.{extension}", recursive=True) + ] return relpaths_list -def get_relpaths_matching_subdirs(dir_path: Path, *, - extension: str, - include_subdirs: list = None, - include_root: bool = True) -> list[Path]: +def get_relpaths_matching_subdirs( + dir_path: Path, + *, + extension: str, + include_subdirs: list = None, + include_root: bool = True, +) -> list[Path]: """Get list of relative paths for {extension} files in a given directory, filtered to include specified subdirectories (with include_subdirs kwarg). The default arguments align with get_relpaths_from_dir @@ -61,34 +66,35 @@ def get_relpaths_matching_subdirs(dir_path: Path, *, # forward slash consistently here. if include_subdirs: - include_subdirs_final = [str(Path(i).as_posix()) - for i in include_subdirs] + include_subdirs_final = [str(Path(i).as_posix()) for i in include_subdirs] if not include_subdirs and include_root: - return get_relpaths_from_dir(dir_path, - extension=extension) + return get_relpaths_from_dir(dir_path, extension=extension) elif not include_subdirs and not include_root: - return [i for i in get_relpaths_from_dir(dir_path, - extension=extension) - if str(i.parent.as_posix()) != '.'] + return [ + i + for i in get_relpaths_from_dir(dir_path, extension=extension) + if str(i.parent.as_posix()) != "." + ] else: if include_root: - return [i for i in get_relpaths_from_dir(dir_path, - extension=extension) - if str(i.parent.as_posix()) - in include_subdirs_final + ['.']] + return [ + i + for i in get_relpaths_from_dir(dir_path, extension=extension) + if str(i.parent.as_posix()) in include_subdirs_final + ["."] + ] else: - return [i for i in get_relpaths_from_dir(dir_path, - extension=extension) - if str(i.parent.as_posix()) - in include_subdirs_final] + return [ + i + for i in get_relpaths_from_dir(dir_path, extension=extension) + if str(i.parent.as_posix()) in include_subdirs_final + ] -def _get_valid_filepaths_by_ext_set(dirpath: Path, *, - exts: set[str]): - all_files = [p.relative_to(dirpath) - for p in Path(dirpath).glob("**/*") - if p.suffix in exts] +def _get_valid_filepaths_by_ext_set(dirpath: Path, *, exts: set[str]): + all_files = [ + p.relative_to(dirpath) for p in Path(dirpath).glob("**/*") if p.suffix in exts + ] return all_files @@ -98,15 +104,13 @@ def _get_shortest_path_by_filename(relpaths_list: list[Path]) -> dict[str, Path] # get indices of dupe 'filename w/ ext': _, inverse_ix, counts = np.unique( - np.array(all_file_names_list), - return_inverse=True, - return_counts=True, - axis=0) + np.array(all_file_names_list), return_inverse=True, return_counts=True, axis=0 + ) dupe_names_ix = np.where(counts[inverse_ix] > 1)[0] # get shortest paths via mask: shortest_paths_arr = np.array(all_file_names_list, dtype=object) shortest_paths_arr[dupe_names_ix] = np.array( - [str(fpath) - for fpath in relpaths_list])[dupe_names_ix] - return {fn: path for fn, path in zip(shortest_paths_arr, relpaths_list)} + [str(fpath) for fpath in relpaths_list] + )[dupe_names_ix] + return dict(zip(shortest_paths_arr, relpaths_list)) diff --git a/obsidiantools/api.py b/obsidiantools/api.py index 5f02bde..31b51f1 100644 --- a/obsidiantools/api.py +++ b/obsidiantools/api.py @@ -1,39 +1,51 @@ import warnings +from collections import Counter +from itertools import chain +from pathlib import Path + import networkx as nx import numpy as np import pandas as pd -from collections import Counter -from pathlib import Path -from itertools import chain -# init -from .md_utils import (get_md_relpaths_matching_subdirs) -from .canvas_utils import (get_canvas_relpaths_matching_subdirs, - _get_all_valid_canvas_file_relpaths) -# connect -from .md_utils import (_get_md_front_matter_and_content, - _get_html_from_md_content, - _get_md_links_from_source_text, - _get_unique_md_links_from_source_text, - _get_unique_wikilinks_from_source_text, - _get_all_wikilinks_from_source_text, - _get_all_embedded_files_from_source_text, - get_tags, - _get_all_latex_from_html_content) from ._constants import METADATA_DF_COLS_GENERIC_TYPE from ._io import _get_shortest_path_by_filename -from .media_utils import _get_all_valid_media_file_relpaths -# gather: -from .md_utils import (get_source_text_from_html, - _get_readable_text_from_html) + # canvas: -from .canvas_utils import (get_canvas_content, - get_canvas_graph_detail) +from .canvas_utils import ( + _get_all_valid_canvas_file_relpaths, + get_canvas_content, + get_canvas_graph_detail, + get_canvas_relpaths_matching_subdirs, +) + +# init +# connect +# gather: +from .md_utils import ( + _get_all_embedded_files_from_source_text, + _get_all_latex_from_html_content, + _get_all_wikilinks_from_source_text, + _get_html_from_md_content, + _get_md_front_matter_and_content, + _get_md_links_from_source_text, + _get_readable_text_from_html, + _get_unique_md_links_from_source_text, + _get_unique_wikilinks_from_source_text, + get_md_relpaths_matching_subdirs, + get_source_text_from_html, + get_tags, +) +from .media_utils import _get_all_valid_media_file_relpaths class Vault: - def __init__(self, dirpath: Path, *, - include_subdirs: list[str] = None, include_root: bool = True): + def __init__( + self, + dirpath: Path, + *, + include_subdirs: list[str] = None, + include_root: bool = True, + ): """A Vault object lets you dig into your Obsidian vault, by giving you a toolkit for analysing its contents. Specify a dirpath to instantiate the class. This class is intended to support multiple @@ -132,18 +144,20 @@ def __init__(self, dirpath: Path, *, canvas_graph_detail_index """ if not isinstance(dirpath, Path): - raise TypeError("Specify a pathlib.Path for the dirpath argument (not other types like strings)") + raise TypeError( + "Specify a pathlib.Path for the dirpath argument (not other types like strings)" + ) # args: self._dirpath = dirpath self._attachments = None # connect() self._md_file_index = self._get_md_relpaths_by_name( - include_subdirs=include_subdirs, - include_root=include_root) + include_subdirs=include_subdirs, include_root=include_root + ) self._canvas_file_index = self._get_canvas_relpaths_by_name( - include_subdirs=include_subdirs, - include_root=include_root) + include_subdirs=include_subdirs, include_root=include_root + ) self._is_connected = False self._is_gathered = False @@ -443,25 +457,26 @@ def canvas_content_index(self, value) -> dict[str, str]: self._canvas_content_index = value @property - def canvas_graph_detail_index(self) -> \ - dict[str, tuple[nx.MultiDiGraph, - dict[str, tuple[int, int]], - dict[tuple[str, str], str]] - ]: + def canvas_graph_detail_index( + self, + ) -> dict[ + str, + tuple[nx.MultiDiGraph, dict[str, tuple[int, int]], dict[tuple[str, str], str]], + ]: """dict of tuple: 'shortest path when possible' filepath with canvas ext (k), to canvas graph detail tuple (v).""" return self._canvas_graph_detail_index @canvas_graph_detail_index.setter - def canvas_graph_detail_index(self, value) -> \ - dict[str, tuple[nx.MultiDiGraph, - dict[str, tuple[int, int]], - dict[tuple[str, str], str]] - ]: + def canvas_graph_detail_index( + self, value + ) -> dict[ + str, + tuple[nx.MultiDiGraph, dict[str, tuple[int, int]], dict[tuple[str, str], str]], + ]: self._canvas_graph_detail_index = value - def connect(self, *, show_nested_tags: bool = False, - attachments=False): + def connect(self, *, show_nested_tags: bool = False, attachments=False): """connect your notes together by representing the vault as a Networkx graph object, G. @@ -501,19 +516,17 @@ def connect(self, *, show_nested_tags: bool = False, # loop through md files: for f, relpath in self._md_file_index.items(): self._connect_update_based_on_new_relpath( - relpath, note=f, - show_nested_tags=show_nested_tags) + relpath, note=f, show_nested_tags=show_nested_tags + ) # canvas content: # loop through canvas files: self._canvas_content_index = {} self._canvas_graph_detail_index = {} for f, relpath in self._canvas_file_index.items(): - content_c = get_canvas_content( - self._dirpath / relpath) + content_c = get_canvas_content(self._dirpath / relpath) self._canvas_content_index[f] = content_c - G_c, pos_c, edge_labels_c = get_canvas_graph_detail( - content_c) + G_c, pos_c, edge_labels_c = get_canvas_graph_detail(content_c) self._canvas_graph_detail_index[f] = G_c, pos_c, edge_labels_c # set these up before graph is created: @@ -521,8 +534,7 @@ def connect(self, *, show_nested_tags: bool = False, self._set_media_file_attrs() # graph setup: - graph_data_dict = self.__get_graph_data_dict( - attachments=attachments) + graph_data_dict = self.__get_graph_data_dict(attachments=attachments) G = nx.MultiDiGraph(graph_data_dict) self._graph = G self._set_graph_related_attributes() @@ -537,79 +549,76 @@ def connect(self, *, show_nested_tags: bool = False, return self # fluent - def _connect_update_based_on_new_relpath(self, relpath: Path, *, - note: str, - show_nested_tags: bool): + def _connect_update_based_on_new_relpath( + self, relpath: Path, *, note: str, show_nested_tags: bool + ): """Individual file read & associated attrs update for the connect method.""" exclude_canvas = not self._attachments # MAIN file read: front_matter, content = _get_md_front_matter_and_content( - self._dirpath / relpath) + self._dirpath / relpath + ) html = _get_html_from_md_content(content) - src_txt = get_source_text_from_html( - html, remove_code=True) + src_txt = get_source_text_from_html(html, remove_code=True) # info from core text: - self._md_links_index[note] = ( - _get_md_links_from_source_text(src_txt)) - self._unique_md_links_index[note] = ( - _get_unique_md_links_from_source_text(src_txt)) + self._md_links_index[note] = _get_md_links_from_source_text(src_txt) + self._unique_md_links_index[note] = _get_unique_md_links_from_source_text( + src_txt + ) self._embedded_files_index[note] = ( - _get_all_embedded_files_from_source_text( - src_txt, remove_aliases=True) + _get_all_embedded_files_from_source_text(src_txt, remove_aliases=True) # (aliases are redundant for connect method) - ) - self._wikilinks_index[note] = ( - _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=True, - exclude_canvas=exclude_canvas)) - self._unique_wikilinks_index[note] = ( - _get_unique_wikilinks_from_source_text( - src_txt, remove_aliases=True, - exclude_canvas=exclude_canvas)) + ) + self._wikilinks_index[note] = _get_all_wikilinks_from_source_text( + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ) + self._unique_wikilinks_index[note] = _get_unique_wikilinks_from_source_text( + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ) # info from html: - self._math_index[note] = (_get_all_latex_from_html_content( - html)) + self._math_index[note] = _get_all_latex_from_html_content(html) # split out front matter: self._front_matter_index[note] = front_matter # MORE file reads needed for extra info: self._tags_index[note] = get_tags( - self._dirpath / relpath, - show_nested=show_nested_tags) + self._dirpath / relpath, show_nested=show_nested_tags + ) def _set_media_file_attrs(self): - (embedded_files_by_short_path, - non_embedded_files_by_short_path, - nonexistent_files_by_short_path) = ( - self._get_media_file_dicts_tuple()) + ( + embedded_files_by_short_path, + non_embedded_files_by_short_path, + nonexistent_files_by_short_path, + ) = self._get_media_file_dicts_tuple() # only set media file index once: if not self._media_file_index: - files_ix = {**embedded_files_by_short_path, - **non_embedded_files_by_short_path} + files_ix = { + **embedded_files_by_short_path, + **non_embedded_files_by_short_path, + } self._media_file_index = files_ix # these attrs can be set again, once graph is created: - self._nonexistent_media_files = list( - nonexistent_files_by_short_path.keys()) - self._isolated_media_files = list( - non_embedded_files_by_short_path.keys()) + self._nonexistent_media_files = list(nonexistent_files_by_short_path.keys()) + self._isolated_media_files = list(non_embedded_files_by_short_path.keys()) def _set_canvas_file_attrs(self): - (linked_files_by_short_path, - non_linked_files_by_short_path, - nonexistent_files_by_short_path) = ( - self._get_canvas_file_dicts_tuple()) - - self._nonexistent_canvas_files = list( - nonexistent_files_by_short_path.keys()) - self._isolated_canvas_files = list( - non_linked_files_by_short_path.keys()) - - def _get_media_file_dicts_tuple(self) \ - -> tuple[dict[str, Path], dict[str, Path], dict[str, Path]]: + ( + linked_files_by_short_path, + non_linked_files_by_short_path, + nonexistent_files_by_short_path, + ) = self._get_canvas_file_dicts_tuple() + + self._nonexistent_canvas_files = list(nonexistent_files_by_short_path.keys()) + self._isolated_canvas_files = list(non_linked_files_by_short_path.keys()) + + def _get_media_file_dicts_tuple( + self, + ) -> tuple[dict[str, Path], dict[str, Path], dict[str, Path]]: """Return (existent files embedded, existent files not embedded, nonexistent files embedded). @@ -621,17 +630,19 @@ def _get_media_file_dicts_tuple(self) \ # detail on all embedded files AND ones that exist: all_files_embedded_in_notes = list( - chain.from_iterable(self._embedded_files_index.values())) - media_file_relpaths_existent = _get_all_valid_media_file_relpaths( - self._dirpath) + chain.from_iterable(self._embedded_files_index.values()) + ) + media_file_relpaths_existent = _get_all_valid_media_file_relpaths(self._dirpath) return self.__get_file_dicts_tuple( all_files_embedded_in_notes, links_index=self._embedded_files_index, existing_file_relpaths=media_file_relpaths_existent, - file_type='media') + file_type="media", + ) - def _get_canvas_file_dicts_tuple(self) \ - -> tuple[dict[str, Path], dict[str, Path], dict[str, Path]]: + def _get_canvas_file_dicts_tuple( + self, + ) -> tuple[dict[str, Path], dict[str, Path], dict[str, Path]]: """Return (existent files linked, existent files not linked, nonexistent files linked). @@ -643,96 +654,110 @@ def _get_canvas_file_dicts_tuple(self) \ # detail on all linked files AND ones that exist: all_files_linked_in_notes = list( - chain.from_iterable(self._wikilinks_index.values())) + chain.from_iterable(self._wikilinks_index.values()) + ) canvas_file_relpaths_existent = _get_all_valid_canvas_file_relpaths( - self._dirpath) + self._dirpath + ) return self.__get_file_dicts_tuple( all_files_linked_in_notes, links_index=self._wikilinks_index, existing_file_relpaths=canvas_file_relpaths_existent, - file_type='canvas') + file_type="canvas", + ) - def __get_file_dicts_tuple(self, linked_files_list: list[str], *, - links_index: dict[list[str]], - existing_file_relpaths: list[Path], - file_type: str): + def __get_file_dicts_tuple( + self, + linked_files_list: list[str], + *, + links_index: dict[list[str]], + existing_file_relpaths: list[Path], + file_type: str, + ): # get shortest path for each 'linked' file of chosen type; # check whether each exists - shortest_names_existent = _get_shortest_path_by_filename( - existing_file_relpaths) + shortest_names_existent = _get_shortest_path_by_filename(existing_file_relpaths) # for nonexistent files, don't want to catch other types: short_names_not_wanted_set = ( set(shortest_names_existent) .union(set(self._nonexistent_notes)) - .union(set(self._md_file_index))) - if file_type == 'canvas': + .union(set(self._md_file_index)) + ) + if file_type == "canvas": other_fpaths_not_wanted_set = _get_all_valid_media_file_relpaths( - self._dirpath) - elif file_type == 'media': + self._dirpath + ) + elif file_type == "media": other_fpaths_not_wanted_set = _get_all_valid_canvas_file_relpaths( - self._dirpath) + self._dirpath + ) else: raise ValueError('Value for type is either "canvas" or "media".') shortest_names_nonexistent = { - fn: Path(fn) for fn in chain(*links_index.values()) + fn: Path(fn) + for fn in chain(*links_index.values()) if fn not in short_names_not_wanted_set - and Path(fn) not in other_fpaths_not_wanted_set} - shortest_names = {**shortest_names_existent, - **shortest_names_nonexistent} + and Path(fn) not in other_fpaths_not_wanted_set + } + shortest_names = {**shortest_names_existent, **shortest_names_nonexistent} # SETS # existent files (either linked or not): - set_files_existent_linked = ( - set(shortest_names_existent) - .intersection(set(linked_files_list))) - set_files_existent_not_linked = ( - set(shortest_names_existent) - .difference(set_files_existent_linked)) - # nonexistent files: - set_files_nonexistent_linked = ( + set_files_existent_linked = set(shortest_names_existent).intersection( set(linked_files_list) - .intersection(set(shortest_names_nonexistent))) + ) + set_files_existent_not_linked = set(shortest_names_existent).difference( + set_files_existent_linked + ) + # nonexistent files: + set_files_nonexistent_linked = set(linked_files_list).intersection( + set(shortest_names_nonexistent) + ) # DICTS # existent files (either linked or not): linked_files_by_short_path = { short_path: rel_path for short_path, rel_path in shortest_names.items() - if short_path in set_files_existent_linked} + if short_path in set_files_existent_linked + } non_linked_files_by_short_path = { short_path: rel_path for short_path, rel_path in shortest_names.items() - if short_path in set_files_existent_not_linked} + if short_path in set_files_existent_not_linked + } # nonexistent files: nonexistent_files_by_short_path = { short_path: np.nan - for short_path in shortest_names_nonexistent.keys() - if short_path in set_files_nonexistent_linked} - - return (linked_files_by_short_path, - non_linked_files_by_short_path, - nonexistent_files_by_short_path) + for short_path in shortest_names_nonexistent + if short_path in set_files_nonexistent_linked + } + + return ( + linked_files_by_short_path, + non_linked_files_by_short_path, + nonexistent_files_by_short_path, + ) def _get_backlink_counts_for_media_files_only(self) -> dict[str, int]: dict_out = dict.fromkeys(self._media_file_index.keys(), 0) - dict_counts = dict( - Counter(list(chain(*self._embedded_files_index.values())))) + dict_counts = dict(Counter(list(chain(*self._embedded_files_index.values())))) # merge counts into dict_out: dict_out = {**dict_out, **dict_counts} return dict_out def _get_backlink_counts_for_canvas_files_only(self) -> dict[str, int]: if not self._attachments: - raise AttributeError('Set attachments=True in connect() to get backlink counts for canvas files.') + raise AttributeError( + "Set attachments=True in connect() to get backlink counts for canvas files." + ) dict_out = dict.fromkeys(self._canvas_file_index.keys(), 0) - dict_counts = dict( - Counter(list(chain(*self._wikilinks_index.values())))) + dict_counts = dict(Counter(list(chain(*self._wikilinks_index.values())))) # merge counts into dict_out: dict_out = {**dict_out, **dict_counts} return dict_out - def __get_graph_data_dict(self, *, attachments=False) -> \ - dict[str, list[str]]: + def __get_graph_data_dict(self, *, attachments=False) -> dict[str, list[str]]: """Get the dict {k: v} of the graph's data: where k is a note name and v is a list of the 'wikilinks' in a note. @@ -762,27 +787,32 @@ def __get_graph_data_dict(self, *, attachments=False) -> \ # attachments include 'media' files and canvas files: # i) use wikilinks & embedded file info for graph edges: d_out = { - n: (self._wikilinks_index.get(n, []) + n: ( + self._wikilinks_index.get(n, []) + self._embedded_files_index.get(n, []) + ) + for n in ( + set( + list(self._wikilinks_index.keys()) + + list(self._embedded_files_index.keys()) ) - for n in (set(list(self._wikilinks_index.keys()) - + list(self._embedded_files_index.keys()))) + ) } # ii) add isolated media files & canvas files as nodes: isolated_files_dict = { - short_path: [] for short_path - in [*self._isolated_media_files, - *self._isolated_canvas_files]} - d_out = {**d_out, - **isolated_files_dict} + short_path: [] + for short_path in [ + *self._isolated_media_files, + *self._isolated_canvas_files, + ] + } + d_out = {**d_out, **isolated_files_dict} return d_out def _set_graph_related_attributes(self): - self._backlinks_index = self._get_backlinks_index( - graph=self._graph) + self._backlinks_index = self._get_backlinks_index(graph=self._graph) self._nonexistent_notes = self._get_nonexistent_notes() - self._isolated_notes = self._get_isolated_notes( - graph=self._graph) + self._isolated_notes = self._get_isolated_notes(graph=self._graph) def gather(self, *, tags: list[str] = None): """gather the content of your notes so that all the plaintext is @@ -807,30 +837,25 @@ def gather(self, *, tags: list[str] = None): and produces a one-line string. """ for f, relpath in self._md_file_index.items(): - self._gather_update_based_on_new_relpath( - relpath, - note=f, tags=tags) + self._gather_update_based_on_new_relpath(relpath, note=f, tags=tags) self._is_gathered = True return self # fluent - def _gather_update_based_on_new_relpath(self, relpath: Path, *, - note: str, tags: list[str]): + def _gather_update_based_on_new_relpath( + self, relpath: Path, *, note: str, tags: list[str] + ): """Individual file read & associated attrs update for the gather method.""" # MAIN file read: - _, content = _get_md_front_matter_and_content( - self._dirpath / relpath) + _, content = _get_md_front_matter_and_content(self._dirpath / relpath) html = _get_html_from_md_content(content) # (also remove LaTeX for source text:) - src_txt = get_source_text_from_html( - html, remove_code=True, remove_math=True) + src_txt = get_source_text_from_html(html, remove_code=True, remove_math=True) # 'source' text will not remove any content, but 'readable' will: self._source_text_index[note] = src_txt - self._readable_text_index[note] = ( - _get_readable_text_from_html( - html, tags=tags)) + self._readable_text_index[note] = _get_readable_text_from_html(html, tags=tags) def get_backlinks(self, note_name: str) -> list[str]: """Get backlinks for a note (given its name). @@ -849,10 +874,10 @@ def get_backlinks(self, note_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if note_name not in self._graph.nodes: - raise ValueError('"{}" not found in graph.'.format(note_name)) + raise ValueError(f'"{note_name}" not found in graph.') else: return self._backlinks_index[note_name] @@ -867,10 +892,10 @@ def get_backlink_counts(self, note_name: str) -> dict[str, int]: dict of integers >= 1 """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if note_name not in self._graph.nodes: - raise ValueError('"{}" not found in graph.'.format(note_name)) + raise ValueError(f'"{note_name}" not found in graph.') else: backlinks = self.get_backlinks(note_name) return dict(Counter(backlinks)) @@ -890,10 +915,12 @@ def get_wikilinks(self, file_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have wikilinks.'.format(file_name)) + raise ValueError( + f'"{file_name}" does not exist so it cannot have wikilinks.' + ) else: return self._wikilinks_index[file_name] @@ -908,10 +935,10 @@ def get_wikilink_counts(self, note_name: str) -> dict[str, int]: dict of integers >= 1 """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if note_name not in self._graph.nodes: - raise ValueError('"{}" not found in graph.'.format(note_name)) + raise ValueError(f'"{note_name}" not found in graph.') else: wikilinks = self.get_wikilinks(note_name) return dict(Counter(wikilinks)) @@ -931,10 +958,12 @@ def get_embedded_files(self, file_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have embedded files.'.format(file_name)) + raise ValueError( + f'"{file_name}" does not exist so it cannot have embedded files.' + ) else: return self._embedded_files_index[file_name] @@ -953,10 +982,12 @@ def get_md_links(self, file_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have md links.'.format(file_name)) + raise ValueError( + f'"{file_name}" does not exist so it cannot have md links.' + ) else: return self._md_links_index[file_name] @@ -975,9 +1006,11 @@ def get_front_matter(self, file_name: str) -> list[dict]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have front matter.'.format(file_name)) + raise ValueError( + f'"{file_name}" does not exist so it cannot have front matter.' + ) else: return self._front_matter_index[file_name] @@ -998,9 +1031,9 @@ def get_tags(self, file_name: str) -> list[str]: list """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') + raise AttributeError("Connect notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have tags.'.format(file_name)) + raise ValueError(f'"{file_name}" does not exist so it cannot have tags.') else: return self._tags_index[file_name] @@ -1020,9 +1053,9 @@ def get_source_text(self, file_name: str) -> str: str """ if not self._is_gathered: - raise AttributeError('Gather notes before calling the function') + raise AttributeError("Gather notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have text.'.format(file_name)) + raise ValueError(f'"{file_name}" does not exist so it cannot have text.') else: return self._source_text_index[file_name] @@ -1046,9 +1079,9 @@ def get_readable_text(self, file_name: str) -> str: str """ if not self._is_gathered: - raise AttributeError('Gather notes before calling the function') + raise AttributeError("Gather notes before calling the function") if file_name not in self._md_file_index: - raise ValueError('"{}" does not exist so it cannot have text.'.format(file_name)) + raise ValueError(f'"{file_name}" does not exist so it cannot have text.') else: return self._readable_text_index[file_name] @@ -1068,8 +1101,7 @@ def _get_canvas_relpaths(self, **kwargs) -> list[Path]: Returns: list """ - return get_canvas_relpaths_matching_subdirs(self._dirpath, - **kwargs) + return get_canvas_relpaths_matching_subdirs(self._dirpath, **kwargs) def __get_relpaths_by_name(self, *, extension, **kwargs) -> dict[str, Path]: """Return k,v pairs @@ -1081,14 +1113,12 @@ def __get_relpaths_by_name(self, *, extension, **kwargs) -> dict[str, Path]: """ # get note names (for k) and relpaths (for v): # keep or remove ext, based on how the file refs appear in wikilinks: - if extension == 'md': - relpaths_list = self._get_md_relpaths( - **kwargs) + if extension == "md": + relpaths_list = self._get_md_relpaths(**kwargs) # remove .md ext: all_file_names_list = [f.stem for f in relpaths_list] - if extension == 'canvas': - relpaths_list = self._get_canvas_relpaths( - **kwargs) + if extension == "canvas": + relpaths_list = self._get_canvas_relpaths(**kwargs) # keep .canvas ext: all_file_names_list = [f.name for f in relpaths_list] @@ -1097,39 +1127,35 @@ def __get_relpaths_by_name(self, *, extension, **kwargs) -> dict[str, Path]: np.array(all_file_names_list), return_inverse=True, return_counts=True, - axis=0) + axis=0, + ) dupe_names_ix = np.where(counts[inverse_ix] > 1)[0] # get shortest paths via mask: shortest_paths_arr = np.array(all_file_names_list, dtype=object) - if extension == 'md': + if extension == "md": shortest_paths_arr[dupe_names_ix] = np.array( - [str(fpath.with_suffix('')) - for fpath in relpaths_list])[dupe_names_ix] - if extension == 'canvas': + [str(fpath.with_suffix("")) for fpath in relpaths_list] + )[dupe_names_ix] + if extension == "canvas": shortest_paths_arr[dupe_names_ix] = np.array( - [str(fpath) - for fpath in relpaths_list])[dupe_names_ix] + [str(fpath) for fpath in relpaths_list] + )[dupe_names_ix] - dict_out = {n: p for n, p in zip(shortest_paths_arr, relpaths_list)} - return dict_out + return dict(zip(shortest_paths_arr, relpaths_list)) def _get_md_relpaths_by_name(self, **kwargs) -> dict[str, Path]: - return self.__get_relpaths_by_name(extension='md', - **kwargs) + return self.__get_relpaths_by_name(extension="md", **kwargs) def _get_canvas_relpaths_by_name(self, **kwargs) -> dict[str, Path]: - return self.__get_relpaths_by_name(extension='canvas', - **kwargs) + return self.__get_relpaths_by_name(extension="canvas", **kwargs) @staticmethod - def _get_backlinks_index(*, - graph: nx.MultiDiGraph) -> dict[str, list[str]]: + def _get_backlinks_index(*, graph: nx.MultiDiGraph) -> dict[str, list[str]]: """Return k,v pairs where k is the md note name and v is list of ALL backlinks found in k""" - return {n: [n[0] for n in list(graph.in_edges(n))] - for n in graph.nodes} + return {n: [n[0] for n in list(graph.in_edges(n))] for n in graph.nodes} def get_note_metadata(self) -> pd.DataFrame: """Structured dataset of metadata on the vault's notes. This @@ -1144,64 +1170,69 @@ def get_note_metadata(self) -> pd.DataFrame: pd.DataFrame """ if not self._is_connected: - raise AttributeError('Connect notes before calling the function') - - ix_list = list(set(self._backlinks_index.keys()) - .difference(set(self._media_file_index)) - .difference(set(self._nonexistent_media_files)) - .difference(set(self._canvas_file_index)) - ) - - df = (pd.DataFrame(index=ix_list, - columns=METADATA_DF_COLS_GENERIC_TYPE) - .rename(columns={'file_exists': 'note_exists'}) - .rename_axis('note')) - df = (df.pipe(self._create_note_metadata_columns) - .pipe(self._clean_up_note_metadata_dtypes) - ) + raise AttributeError("Connect notes before calling the function") + + ix_list = list( + set(self._backlinks_index.keys()) + .difference(set(self._media_file_index)) + .difference(set(self._nonexistent_media_files)) + .difference(set(self._canvas_file_index)) + ) + + df = ( + pd.DataFrame(index=ix_list, columns=METADATA_DF_COLS_GENERIC_TYPE) + .rename(columns={"file_exists": "note_exists"}) + .rename_axis("note") + ) + df = df.pipe(self._create_note_metadata_columns).pipe( + self._clean_up_note_metadata_dtypes + ) return df - def _create_note_metadata_columns(self, - df: pd.DataFrame) -> pd.DataFrame: + def _create_note_metadata_columns(self, df: pd.DataFrame) -> pd.DataFrame: """pipe func for mutating df""" - df['rel_filepath'] = [self._md_file_index.get(f, np.nan) - for f in df.index.tolist()] - df['abs_filepath'] = np.where(df['rel_filepath'].notna(), - [self._dirpath / str(f) - for f in df['rel_filepath'].tolist()], - np.nan) - df['note_exists'] = np.where(df['rel_filepath'].notna(), - True, False) - df['n_backlinks'] = [len(self.get_backlinks(f)) for f in df.index] - df['n_wikilinks'] = np.where(df['note_exists'], - [len(self._wikilinks_index.get(f, [])) - for f in df.index.tolist()], - np.nan) - df['n_tags'] = np.where(df['note_exists'], - [len(self._tags_index.get(f, [])) - for f in df.index.tolist()], - np.nan) - df['n_embedded_files'] = np.where(df['note_exists'], - [len(self._embedded_files_index.get( - f, [])) - for f in df.index.tolist()], - np.nan) - df['modified_time'] = pd.to_datetime( - [f.lstat().st_mtime if not pd.isna(f) - else pd.NaT - for f in df['abs_filepath'].tolist()], - unit='s' + df["rel_filepath"] = [ + self._md_file_index.get(f, np.nan) for f in df.index.tolist() + ] + df["abs_filepath"] = np.where( + df["rel_filepath"].notna(), + [self._dirpath / str(f) for f in df["rel_filepath"].tolist()], + np.nan, + ) + df["note_exists"] = np.where(df["rel_filepath"].notna(), True, False) + df["n_backlinks"] = [len(self.get_backlinks(f)) for f in df.index] + df["n_wikilinks"] = np.where( + df["note_exists"], + [len(self._wikilinks_index.get(f, [])) for f in df.index.tolist()], + np.nan, + ) + df["n_tags"] = np.where( + df["note_exists"], + [len(self._tags_index.get(f, [])) for f in df.index.tolist()], + np.nan, + ) + df["n_embedded_files"] = np.where( + df["note_exists"], + [len(self._embedded_files_index.get(f, [])) for f in df.index.tolist()], + np.nan, + ) + df["modified_time"] = pd.to_datetime( + [ + f.lstat().st_mtime if not pd.isna(f) else pd.NaT + for f in df["abs_filepath"].tolist() + ], + unit="s", ) return df - def _clean_up_note_metadata_dtypes(self, - df: pd.DataFrame) -> pd.DataFrame: + def _clean_up_note_metadata_dtypes(self, df: pd.DataFrame) -> pd.DataFrame: """pipe func for mutating df""" - df['rel_filepath'] = np.where(df['rel_filepath'].notna(), - [Path(str(f)) - for f in df['rel_filepath']], - np.nan) - df['n_wikilinks'] = df['n_wikilinks'].astype(float) # for consistency + df["rel_filepath"] = np.where( + df["rel_filepath"].notna(), + [Path(str(f)) for f in df["rel_filepath"]], + np.nan, + ) + df["n_wikilinks"] = df["n_wikilinks"].astype(float) # for consistency return df def get_media_file_metadata(self) -> pd.DataFrame: @@ -1226,35 +1257,37 @@ def get_media_file_metadata(self) -> pd.DataFrame: Returns: pd.DataFrame """ - ix_list = [*list(self._media_file_index.keys()), - *self._nonexistent_media_files] - df = (pd.DataFrame(index=ix_list, - columns=METADATA_DF_COLS_GENERIC_TYPE) - .rename_axis('file')) + ix_list = [*list(self._media_file_index.keys()), *self._nonexistent_media_files] + df = pd.DataFrame( + index=ix_list, columns=METADATA_DF_COLS_GENERIC_TYPE + ).rename_axis("file") if not ix_list: return df else: df = df.pipe(self._create_media_file_metadata_columns) return df - def _create_media_file_metadata_columns(self, - df: pd.DataFrame) -> pd.DataFrame: + def _create_media_file_metadata_columns(self, df: pd.DataFrame) -> pd.DataFrame: """pipe func for mutating df""" - df['rel_filepath'] = [self._media_file_index.get(f, np.nan) - for f in df.index.tolist()] - df['abs_filepath'] = np.where(df['rel_filepath'].notna(), - [self._dirpath / str(f) - for f in df['rel_filepath'].tolist()], - np.nan) - df['file_exists'] = pd.Series( - np.logical_not(df.index.isin(self._nonexistent_media_files)), - index=df.index) - df['n_backlinks'] = self._get_backlink_counts_for_media_files_only() - df['modified_time'] = pd.to_datetime( - [f.lstat().st_mtime if not pd.isna(f) - else pd.NaT - for f in df['abs_filepath'].tolist()], - unit='s') + df["rel_filepath"] = [ + self._media_file_index.get(f, np.nan) for f in df.index.tolist() + ] + df["abs_filepath"] = np.where( + df["rel_filepath"].notna(), + [self._dirpath / str(f) for f in df["rel_filepath"].tolist()], + np.nan, + ) + df["file_exists"] = pd.Series( + np.logical_not(df.index.isin(self._nonexistent_media_files)), index=df.index + ) + df["n_backlinks"] = self._get_backlink_counts_for_media_files_only() + df["modified_time"] = pd.to_datetime( + [ + f.lstat().st_mtime if not pd.isna(f) else pd.NaT + for f in df["abs_filepath"].tolist() + ], + unit="s", + ) return df def get_canvas_file_metadata(self) -> pd.DataFrame: @@ -1280,39 +1313,44 @@ def get_canvas_file_metadata(self) -> pd.DataFrame: Returns: pd.DataFrame """ - ix_list = [*list(self._canvas_file_index.keys()), - *self._nonexistent_canvas_files] - df = (pd.DataFrame(index=ix_list, - columns=METADATA_DF_COLS_GENERIC_TYPE) - .rename_axis('file')) + ix_list = [ + *list(self._canvas_file_index.keys()), + *self._nonexistent_canvas_files, + ] + df = pd.DataFrame( + index=ix_list, columns=METADATA_DF_COLS_GENERIC_TYPE + ).rename_axis("file") if not ix_list: return df else: df = df.pipe(self._create_canvas_file_metadata_columns) return df - def _create_canvas_file_metadata_columns(self, - df: pd.DataFrame) -> pd.DataFrame: + def _create_canvas_file_metadata_columns(self, df: pd.DataFrame) -> pd.DataFrame: """pipe func for mutating df""" - df['rel_filepath'] = [self._canvas_file_index.get(f, np.nan) - for f in df.index.tolist()] - df['abs_filepath'] = np.where(df['rel_filepath'].notna(), - [self._dirpath / str(f) - for f in df['rel_filepath'].tolist()], - np.nan) - df['file_exists'] = pd.Series( + df["rel_filepath"] = [ + self._canvas_file_index.get(f, np.nan) for f in df.index.tolist() + ] + df["abs_filepath"] = np.where( + df["rel_filepath"].notna(), + [self._dirpath / str(f) for f in df["rel_filepath"].tolist()], + np.nan, + ) + df["file_exists"] = pd.Series( np.logical_not(df.index.isin(self._nonexistent_canvas_files)), - index=df.index) + index=df.index, + ) if self._attachments: - df['n_backlinks'] = ( - self._get_backlink_counts_for_canvas_files_only()) + df["n_backlinks"] = self._get_backlink_counts_for_canvas_files_only() else: - df['n_backlinks'] = np.nan - df['modified_time'] = pd.to_datetime( - [f.lstat().st_mtime if not pd.isna(f) - else pd.NaT - for f in df['abs_filepath'].tolist()], - unit='s') + df["n_backlinks"] = np.nan + df["modified_time"] = pd.to_datetime( + [ + f.lstat().st_mtime if not pd.isna(f) else pd.NaT + for f in df["abs_filepath"].tolist() + ], + unit="s", + ) return df def get_all_file_metadata(self) -> pd.DataFrame: @@ -1338,23 +1376,24 @@ def get_all_file_metadata(self) -> pd.DataFrame: Returns: pd.DataFrame """ - df = (self.get_note_metadata() - .rename(columns={'note_exists': 'file_exists'})) - df['graph_category'] = np.where( - df['file_exists'], 'note', 'nonexistent') + df = self.get_note_metadata().rename(columns={"note_exists": "file_exists"}) + df["graph_category"] = np.where(df["file_exists"], "note", "nonexistent") if not self._attachments: - warnings.warn('Only notes (md files) were used to build the graph. Set attachments=True in the connect method to show all file metadata.') + warnings.warn( + "Only notes (md files) were used to build the graph. Set attachments=True in the connect method to show all file metadata.", + stacklevel=2, + ) else: df_media = self.get_media_file_metadata() - df_media['graph_category'] = np.where( - df_media['file_exists'], 'attachment', 'nonexistent') + df_media["graph_category"] = np.where( + df_media["file_exists"], "attachment", "nonexistent" + ) df_canvas = self.get_canvas_file_metadata() - df_canvas['graph_category'] = np.where( - df_canvas['file_exists'], 'attachment', 'nonexistent') + df_canvas["graph_category"] = np.where( + df_canvas["file_exists"], "attachment", "nonexistent" + ) - df = (pd.concat( - [df, df_media, df_canvas]) - .rename_axis('file')) + df = pd.concat([df, df_media, df_canvas]).rename_axis("file") return df def _get_nonexistent_notes(self) -> list[str]: @@ -1362,18 +1401,18 @@ def _get_nonexistent_notes(self) -> list[str]: The comparison is done with sets but the result is returned as a list.""" - return list(set(self._backlinks_index.keys()) - # anything remaining that isn't a file is a non-e note: - .difference(set(self._md_file_index)) - .difference(set(self._media_file_index)) - .difference(set(self._nonexistent_media_files)) - .difference(set(self._canvas_file_index))) - - def _get_isolated_notes(self, *, - graph: nx.MultiDiGraph) -> list[str]: + return list( + set(self._backlinks_index.keys()) + # anything remaining that isn't a file is a non-e note: + .difference(set(self._md_file_index)) + .difference(set(self._media_file_index)) + .difference(set(self._nonexistent_media_files)) + .difference(set(self._canvas_file_index)) + ) + + def _get_isolated_notes(self, *, graph: nx.MultiDiGraph) -> list[str]: """Get notes that are not connected to any other notes in the vault, i.e. they have 0 wikilinks and 0 backlinks. These notes are retrieved from the graph.""" - return [fn for fn in nx.isolates(graph) - if fn in self._md_file_index] + return [fn for fn in nx.isolates(graph) if fn in self._md_file_index] diff --git a/obsidiantools/canvas_utils.py b/obsidiantools/canvas_utils.py index c40d009..f5fb757 100644 --- a/obsidiantools/canvas_utils.py +++ b/obsidiantools/canvas_utils.py @@ -1,10 +1,14 @@ import json -import networkx as nx from pathlib import Path + +import networkx as nx + from ._constants import CANVAS_EXT_SET -from ._io import (get_relpaths_from_dir, - get_relpaths_matching_subdirs, - _get_valid_filepaths_by_ext_set) +from ._io import ( + _get_valid_filepaths_by_ext_set, + get_relpaths_from_dir, + get_relpaths_matching_subdirs, +) def get_canvas_relpaths_from_dir(dir_path: Path) -> list[Path]: @@ -21,12 +25,12 @@ def get_canvas_relpaths_from_dir(dir_path: Path) -> list[Path]: Returns: list of Path objects """ - return get_relpaths_from_dir(dir_path, extension='canvas') + return get_relpaths_from_dir(dir_path, extension="canvas") -def get_canvas_relpaths_matching_subdirs(dir_path: Path, *, - include_subdirs: list = None, - include_root: bool = True) -> list[Path]: +def get_canvas_relpaths_matching_subdirs( + dir_path: Path, *, include_subdirs: list = None, include_root: bool = True +) -> list[Path]: """Get list of relative paths for canvas files in a given directory, filtered to include specified subdirectories (with include_subdirs kwarg). The default arguments align with get_canvas_relpaths_from_dir @@ -56,15 +60,14 @@ def get_canvas_relpaths_matching_subdirs(dir_path: Path, *, """ return get_relpaths_matching_subdirs( dir_path, - extension='canvas', + extension="canvas", include_subdirs=include_subdirs, - include_root=include_root) + include_root=include_root, + ) def _get_all_valid_canvas_file_relpaths(dirpath): - return (_get_valid_filepaths_by_ext_set( - dirpath, - exts=CANVAS_EXT_SET)) + return _get_valid_filepaths_by_ext_set(dirpath, exts=CANVAS_EXT_SET) def get_canvas_content(filepath: Path) -> dict: @@ -76,15 +79,14 @@ def get_canvas_content(filepath: Path) -> dict: Returns: dict """ - with open(filepath, encoding='utf-8') as f: + with open(filepath, encoding="utf-8") as f: json_as_dict = json.load(f) return json_as_dict -def get_canvas_graph_detail(canvas_content: dict) -> \ - tuple[nx.MultiDiGraph, - dict[str, tuple[int, int]], - dict[tuple[str, str], str]]: +def get_canvas_graph_detail( + canvas_content: dict, +) -> tuple[nx.MultiDiGraph, dict[str, tuple[int, int]], dict[tuple[str, str], str]]: """Get the content from a canvas in a NetworkX graph. With all the detail that is returned, it is possible to recreate the layout of the material in the canvas. @@ -104,22 +106,28 @@ def get_canvas_graph_detail(canvas_content: dict) -> \ edge_labels: list of labels for each edge in graph """ G = nx.MultiDiGraph() - nodes_list = [i.get('id') for i in canvas_content['nodes'] - if i.get('type') != 'group'] + nodes_list = [ + i.get("id") for i in canvas_content["nodes"] if i.get("type") != "group" + ] G.add_nodes_from(nodes_list) - graph_edges_list = [(i.get('fromNode'), i.get('toNode')) - for i in canvas_content['edges'] - if i.get('type') != 'group'] + graph_edges_list = [ + (i.get("fromNode"), i.get("toNode")) + for i in canvas_content["edges"] + if i.get("type") != "group" + ] G.add_edges_from(graph_edges_list) # y co-ord needs to be flipped to reflect app(?): - pos = {i.get('id'): (i.get('x'), -i.get('y')) - for i in canvas_content['nodes'] - if i.get('type') != 'group'} - - edge_labels = dict([((i.get('fromNode'), i.get('toNode')), - f"{i.get('label', '')}") - for i in canvas_content['edges']]) + pos = { + i.get("id"): (i.get("x"), -i.get("y")) + for i in canvas_content["nodes"] + if i.get("type") != "group" + } + + edge_labels = { + (i.get("fromNode"), i.get("toNode")): f"{i.get('label', '')}" + for i in canvas_content["edges"] + } return G, pos, edge_labels diff --git a/obsidiantools/html_processing.py b/obsidiantools/html_processing.py index f04ad86..a8e43b4 100644 --- a/obsidiantools/html_processing.py +++ b/obsidiantools/html_processing.py @@ -1,6 +1,6 @@ -from html2text import HTML2Text import bleach from bs4 import BeautifulSoup +from html2text import HTML2Text def _get_html2text_obj_with_config() -> HTML2Text: @@ -27,54 +27,53 @@ def _get_plaintext_from_html(html: str) -> str: def _remove_code(html: str) -> str: # exclude 'code' tags from link output: - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") soup = _remove_code_via_soup(soup) html_str = str(soup) return html_str def _remove_code_via_soup(soup): - for s in soup.select('code'): + for s in soup.select("code"): s.extract() return soup def _remove_del_text(html: str) -> str: - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") soup = _remove_del_text_via_soup(soup) html_str = str(soup) return html_str def _remove_del_text_via_soup(soup): - for s in soup.select('del'): + for s in soup.select("del"): s.extract() return soup -def _remove_main_formatting( - html: str, *, - tags: list[str] = ['p', 'h1', 'h2', 'h3', 'h4', 'h5', 'h6']) -> str: +def _remove_main_formatting(html: str, *, tags: list[str] | None = None) -> str: + if tags is None: + tags = ["p", "h1", "h2", "h3", "h4", "h5", "h6"] return bleach.clean(html, tags=tags, strip=True) def _remove_latex(html: str) -> str: - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") soup = _remove_latex_via_soup(soup) html_str = str(soup) return html_str def _remove_latex_via_soup(soup): - for s in soup.select('span', {'class': 'MathJax_Preview'}): + for s in soup.select("span", {"class": "MathJax_Preview"}): s.extract() return soup def _get_all_latex_from_html_content(html: str) -> list[str]: - soup = BeautifulSoup(html, 'html.parser') + soup = BeautifulSoup(html, "html.parser") - s_content = soup.find_all('span', {'class': 'MathJax_Preview'}, - string=True) + s_content = soup.find_all("span", {"class": "MathJax_Preview"}, string=True) latex_found_list = [i.string for i in s_content] return latex_found_list diff --git a/obsidiantools/md_utils.py b/obsidiantools/md_utils.py index c99a52e..f74c48d 100644 --- a/obsidiantools/md_utils.py +++ b/obsidiantools/md_utils.py @@ -1,23 +1,29 @@ import re -import yaml from pathlib import Path -from bs4 import BeautifulSoup -import markdown + import frontmatter -from ._constants import (WIKILINK_REGEX, - TAG_MAIN_ONLY_REGEX, TAG_INCLUDE_NESTED_REGEX, - WIKILINK_AS_STRING_REGEX, - EMBEDDED_FILE_LINK_AS_STRING_REGEX, - INLINE_LINK_AFTER_HTML_PROC_REGEX, - INLINE_LINK_VIA_MD_ONLY_REGEX) -from ._io import (get_relpaths_from_dir, - get_relpaths_matching_subdirs) -from .html_processing import (_get_plaintext_from_html, - _remove_code_via_soup, - _remove_latex_via_soup, - _remove_del_text_via_soup, - _remove_main_formatting, - _get_all_latex_from_html_content) +import markdown +import yaml +from bs4 import BeautifulSoup + +from ._constants import ( + EMBEDDED_FILE_LINK_AS_STRING_REGEX, + INLINE_LINK_AFTER_HTML_PROC_REGEX, + INLINE_LINK_VIA_MD_ONLY_REGEX, + TAG_INCLUDE_NESTED_REGEX, + TAG_MAIN_ONLY_REGEX, + WIKILINK_AS_STRING_REGEX, + WIKILINK_REGEX, +) +from ._io import get_relpaths_from_dir, get_relpaths_matching_subdirs +from .html_processing import ( + _get_all_latex_from_html_content, + _get_plaintext_from_html, + _remove_code_via_soup, + _remove_del_text_via_soup, + _remove_latex_via_soup, + _remove_main_formatting, +) def get_md_relpaths_from_dir(dir_path: Path) -> list[Path]: @@ -34,12 +40,12 @@ def get_md_relpaths_from_dir(dir_path: Path) -> list[Path]: Returns: list of Path objects """ - return get_relpaths_from_dir(dir_path, extension='md') + return get_relpaths_from_dir(dir_path, extension="md") -def get_md_relpaths_matching_subdirs(dir_path: Path, *, - include_subdirs: list = None, - include_root: bool = True) -> list[Path]: +def get_md_relpaths_matching_subdirs( + dir_path: Path, *, include_subdirs: list = None, include_root: bool = True +) -> list[Path]: """Get list of relative paths for markdown files in a given directory, filtered to include specified subdirectories (with include_subdirs kwarg). The default arguments align with get_md_relpaths_from_dir @@ -69,13 +75,13 @@ def get_md_relpaths_matching_subdirs(dir_path: Path, *, """ return get_relpaths_matching_subdirs( dir_path, - extension='md', + extension="md", include_subdirs=include_subdirs, - include_root=include_root) + include_root=include_root, + ) -def get_wikilinks(filepath: Path, *, - exclude_canvas: bool = True) -> list[str]: +def get_wikilinks(filepath: Path, *, exclude_canvas: bool = True) -> list[str]: """Get ALL wikilinks from a md file. The links' order of appearance in the file IS preserved in the output. @@ -99,8 +105,8 @@ def get_wikilinks(filepath: Path, *, src_txt = get_source_text_from_md_file(filepath, remove_code=True) wikilinks = _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=True, - exclude_canvas=exclude_canvas) + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ) return wikilinks @@ -123,13 +129,11 @@ def get_embedded_files(filepath: Path) -> list[str]: """ src_txt = get_source_text_from_md_file(filepath, remove_code=True) - files = _get_all_embedded_files_from_source_text( - src_txt, remove_aliases=True) + files = _get_all_embedded_files_from_source_text(src_txt, remove_aliases=True) return files -def get_unique_wikilinks(filepath: Path, *, - exclude_canvas: bool = True) -> list[str]: +def get_unique_wikilinks(filepath: Path, *, exclude_canvas: bool = True) -> list[str]: """Get UNIQUE wikilinks from a md file. The links' order of appearance in the file IS preserved in the output. @@ -151,8 +155,8 @@ def get_unique_wikilinks(filepath: Path, *, src_txt = get_source_text_from_md_file(filepath, remove_code=True) wikilinks = _get_unique_wikilinks_from_source_text( - src_txt, remove_aliases=True, - exclude_canvas=exclude_canvas) + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ) return wikilinks @@ -237,18 +241,21 @@ def get_tags(filepath: Path, *, show_nested: bool = False) -> list[str]: """ # get text from source file, but remove any '\#' and code: src_txt = get_source_text_from_md_file( - filepath, remove_code=True, - str_transform_func=_transform_md_file_string_for_tag_parsing) + filepath, + remove_code=True, + str_transform_func=_transform_md_file_string_for_tag_parsing, + ) # remove wikilinks so that '#' headers are not caught: src_txt = _remove_wikilinks_from_source_text(src_txt) tags = _get_tags_from_source_text(src_txt, show_nested=show_nested) return tags -def _get_md_front_matter_and_content(filepath: Path, *, - str_transform_func=None) -> tuple[dict, str]: +def _get_md_front_matter_and_content( + filepath: Path, *, str_transform_func=None +) -> tuple[dict, str]: """parse md file into front matter and note content""" - with open(filepath, encoding='utf-8') as f: + with open(filepath, encoding="utf-8") as f: try: file_string = f.read() if str_transform_func: @@ -264,16 +271,15 @@ def _get_md_front_matter_and_content(filepath: Path, *, # handle template {{}} chars in front matter: except yaml.constructor.ConstructorError: file_string_esc = file_string.translate( - str.maketrans({"{": r"\{", - "}": r"\}"})) + str.maketrans({"{": r"\{", "}": r"\}"}) + ) return frontmatter.parse(file_string_esc) # any others: - except: + except Exception: return {}, file_string -def _get_html_from_md_file(filepath: Path, *, - str_transform_func=None) -> str: +def _get_html_from_md_file(filepath: Path, *, str_transform_func=None) -> str: """md file -> html (without front matter). pymarkdown extensions are used and configured to reflect the Obsidian @@ -281,33 +287,37 @@ def _get_html_from_md_file(filepath: Path, *, to parse math, md_mermaid for mermaid diagram support, etc. """ _, md_content = _get_md_front_matter_and_content( - filepath, - str_transform_func=str_transform_func) + filepath, str_transform_func=str_transform_func + ) html = _get_html_from_md_content(md_content) return html def _get_html_from_md_content(md_content: str) -> str: """md content -> html (without front matter)""" - html = markdown.markdown(md_content, output_format='html', - extensions=['pymdownx.arithmatex', - 'pymdownx.superfences', - 'pymdownx.mark', - 'pymdownx.tilde', - 'pymdownx.saneheaders', - 'footnotes', - 'sane_lists', - 'tables'], - extension_configs={'pymdownx.tilde': - {'subscript': False}}) + html = markdown.markdown( + md_content, + output_format="html", + extensions=[ + "pymdownx.arithmatex", + "pymdownx.superfences", + "pymdownx.mark", + "pymdownx.tilde", + "pymdownx.saneheaders", + "footnotes", + "sane_lists", + "tables", + ], + extension_configs={"pymdownx.tilde": {"subscript": False}}, + ) return html -def get_source_text_from_html(html: str, *, - remove_code: bool = False, - remove_math: bool = False) -> str: +def get_source_text_from_html( + html: str, *, remove_code: bool = False, remove_math: bool = False +) -> str: """html (without front matter) -> ASCII plaintext""" - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") if remove_code: soup = _remove_code_via_soup(soup) if remove_math: @@ -316,33 +326,31 @@ def get_source_text_from_html(html: str, *, return _get_plaintext_from_html(new_str) -def get_source_text_from_md_file(filepath: Path, *, - remove_code: bool = False, - remove_math: bool = False, - str_transform_func=None) -> str: +def get_source_text_from_md_file( + filepath: Path, + *, + remove_code: bool = False, + remove_math: bool = False, + str_transform_func=None, +) -> str: """md file -> html (without front matter) -> ASCII plaintext""" # strip out front matter (if any): - html = _get_html_from_md_file( - filepath, - str_transform_func=str_transform_func) + html = _get_html_from_md_file(filepath, str_transform_func=str_transform_func) - return get_source_text_from_html(html, remove_code=remove_code, - remove_math=remove_math) + return get_source_text_from_html( + html, remove_code=remove_code, remove_math=remove_math + ) -def get_readable_text_from_md_file(filepath: Path, *, - tags: list[str] = None) -> str: +def get_readable_text_from_md_file(filepath: Path, *, tags: list[str] = None) -> str: """md file -> html -> plaintext with major formatting removed.""" # strip out front matter (if any): - html = _get_html_from_md_file( - filepath) - html = _get_readable_text_from_html( - html, tags=tags) + html = _get_html_from_md_file(filepath) + html = _get_readable_text_from_html(html, tags=tags) return html -def _get_readable_text_from_html(html: str, *, - tags: list[str] = None) -> str: +def _get_readable_text_from_html(html: str, *, tags: list[str] = None) -> str: # -str or regex- # wikilinks and md links as text: html = _replace_md_links_with_their_text(html) @@ -351,7 +359,7 @@ def _get_readable_text_from_html(html: str, *, # -bs4- # remove code and remove major formatting on text: - soup = BeautifulSoup(html, 'lxml') + soup = BeautifulSoup(html, "lxml") soup = _remove_code_via_soup(soup) soup = _remove_latex_via_soup(soup) soup = _remove_del_text_via_soup(soup) @@ -373,56 +381,61 @@ def _get_all_wikilinks_and_embedded_files(src_txt: str) -> list[str]: return link_matches_list -def _remove_aliases_from_wikilink_regex_matches(link_matches_list: list[str]) -> list[str]: - return [(i.replace('\\', '') - .split("|")[0].rstrip() # catch alias/alt-text - .split('#', 1)[0]) # catch links to headers - for i in link_matches_list] +def _remove_aliases_from_wikilink_regex_matches( + link_matches_list: list[str], +) -> list[str]: + return [ + ( + i.replace("\\", "") + .split("|")[0] + .rstrip() # catch alias/alt-text + .split("#", 1)[0] + ) # catch links to headers + for i in link_matches_list + ] -def _get_all_wikilinks_from_source_text(src_txt: str, *, - remove_aliases: bool = True, - exclude_canvas: bool = True) -> list[str]: +def _get_all_wikilinks_from_source_text( + src_txt: str, *, remove_aliases: bool = True, exclude_canvas: bool = True +) -> list[str]: matches_list = _get_all_wikilinks_and_embedded_files(src_txt) - link_matches_list = [g[1] for g in matches_list - if g[0] == ''] + link_matches_list = [g[1] for g in matches_list if g[0] == ""] if remove_aliases: link_matches_list = _remove_aliases_from_wikilink_regex_matches( - link_matches_list) + link_matches_list + ) # remove .md: - link_matches_list = [name.removesuffix('.md') - for name in link_matches_list] + link_matches_list = [name.removesuffix(".md") for name in link_matches_list] if exclude_canvas: - link_matches_list = [n for n in link_matches_list - if not n.endswith('.canvas')] + link_matches_list = [n for n in link_matches_list if not n.endswith(".canvas")] return link_matches_list -def _get_all_embedded_files_from_source_text(src_txt: str, *, - remove_aliases: bool = True) -> list[str]: +def _get_all_embedded_files_from_source_text( + src_txt: str, *, remove_aliases: bool = True +) -> list[str]: matches_list = _get_all_wikilinks_and_embedded_files(src_txt) - embedded_files_sublist = [g[1] for g in matches_list - if g[0] == '!'] + embedded_files_sublist = [g[1] for g in matches_list if g[0] == "!"] if remove_aliases: embedded_files_sublist = _remove_aliases_from_wikilink_regex_matches( - embedded_files_sublist) + embedded_files_sublist + ) return embedded_files_sublist def _get_all_latex_from_md_file(filepath: Path) -> list[str]: - return _get_all_latex_from_html_content( - _get_html_from_md_file(filepath)) + return _get_all_latex_from_html_content(_get_html_from_md_file(filepath)) -def _get_unique_wikilinks_from_source_text(src_txt: str, *, - remove_aliases: bool = True, - exclude_canvas: bool = True) -> list[str]: +def _get_unique_wikilinks_from_source_text( + src_txt: str, *, remove_aliases: bool = True, exclude_canvas: bool = True +) -> list[str]: wikilinks = _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=remove_aliases, - exclude_canvas=exclude_canvas) + src_txt, remove_aliases=remove_aliases, exclude_canvas=exclude_canvas + ) return list(dict.fromkeys(wikilinks)) @@ -434,22 +447,20 @@ def _get_all_md_link_info_from_source_text(src_txt: str) -> list[tuple[str]]: def _get_unique_md_links_from_source_text(src_txt: str) -> list[str]: - links_detail = _get_all_md_link_info_from_source_text( - src_txt) + links_detail = _get_all_md_link_info_from_source_text(src_txt) links_list = [link for _, link in links_detail] return list(dict.fromkeys(links_list)) def _remove_wikilinks_from_source_text(src_txt: str) -> str: - return re.sub(WIKILINK_REGEX, '', src_txt) + return re.sub(WIKILINK_REGEX, "", src_txt) def _transform_md_file_string_for_tag_parsing(txt: str) -> str: - return txt.replace('\\#', '') + return txt.replace("\\#", "") -def _get_tags_from_source_text(src_txt: str, *, - show_nested: bool = False) -> list[str]: +def _get_tags_from_source_text(src_txt: str, *, show_nested: bool = False) -> list[str]: if not show_nested: pattern = re.compile(TAG_MAIN_ONLY_REGEX) else: @@ -460,15 +471,18 @@ def _get_tags_from_source_text(src_txt: str, *, def _replace_wikilinks_with_their_text(src_txt: str) -> str: # get list of wikilinks as strings: - links_list = _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=False) + links_list = _get_all_wikilinks_from_source_text(src_txt, remove_aliases=False) # get links in their text format: - readable_text_list = [(i.replace('\\', '') - # get wikilinks w/o alias, otherwise alias: - .split("|")[-1] - .strip()) - for i in links_list] + readable_text_list = [ + ( + i.replace("\\", "") + # get wikilinks w/o alias, otherwise alias: + .split("|")[-1] + .strip() + ) + for i in links_list + ] # loop over txt content to replace "[[...]]" wikilinks w/ readable text: out_str = src_txt @@ -502,10 +516,10 @@ def _remove_embedded_file_links_from_text(src_txt: str) -> str: # get list of embedded file links as strings: links_list = re.findall(EMBEDDED_FILE_LINK_AS_STRING_REGEX, src_txt) # add in the ![[...]] chars: - links_list = ["".join(['![[', i, ']]']) for i in links_list] + links_list = ["".join(["![[", i, "]]"]) for i in links_list] # remove from text: out_str = src_txt for i in links_list: - out_str = out_str.replace(i, '') + out_str = out_str.replace(i, "") return out_str diff --git a/obsidiantools/media_utils.py b/obsidiantools/media_utils.py index 63fa54f..f6c27b4 100644 --- a/obsidiantools/media_utils.py +++ b/obsidiantools/media_utils.py @@ -1,12 +1,8 @@ -from pathlib import Path -import numpy as np -from ._constants import (IMG_EXT_SET, AUDIO_EXT_SET, - VIDEO_EXT_SET, PDF_EXT_SET) +from ._constants import AUDIO_EXT_SET, IMG_EXT_SET, PDF_EXT_SET, VIDEO_EXT_SET from ._io import _get_valid_filepaths_by_ext_set def _get_all_valid_media_file_relpaths(dirpath): - return (_get_valid_filepaths_by_ext_set( - dirpath, - exts=(IMG_EXT_SET | AUDIO_EXT_SET - | VIDEO_EXT_SET | PDF_EXT_SET))) + return _get_valid_filepaths_by_ext_set( + dirpath, exts=(IMG_EXT_SET | AUDIO_EXT_SET | VIDEO_EXT_SET | PDF_EXT_SET) + ) diff --git a/pyproject.toml b/pyproject.toml index f159211..20ea001 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -95,6 +95,10 @@ ignore = [ "E501", # line-too-long (formatter handles this) ] +[tool.ruff.lint.per-file-ignores] +# Trailing whitespace is intentional inside expected-value string literals +"tests/test_md_utils.py" = ["W291"] + [tool.ruff.lint.isort] known-first-party = ["obsidiantools"] @@ -120,7 +124,6 @@ reportUnknownMemberType = "warn" # --------------------------------------------------------------------------- [tool.pytest.ini_options] testpaths = ["tests"] -addopts = "--cov=obsidiantools --cov-report=xml" # --------------------------------------------------------------------------- # coverage diff --git a/tests/test_api_canvas.py b/tests/test_api_canvas.py index b468c03..0bd4f47 100644 --- a/tests/test_api_canvas.py +++ b/tests/test_api_canvas.py @@ -1,6 +1,5 @@ import pytest - from obsidiantools.api import Vault diff --git a/tests/test_api_md.py b/tests/test_api_md.py index 742b0ce..c308b9c 100644 --- a/tests/test_api_md.py +++ b/tests/test_api_md.py @@ -1,6 +1,5 @@ import pytest - from obsidiantools.api import Vault diff --git a/tests/test_api_setup.py b/tests/test_api_setup.py index cc14155..7cb726f 100644 --- a/tests/test_api_setup.py +++ b/tests/test_api_setup.py @@ -1,6 +1,5 @@ -import pytest import networkx as nx - +import pytest from obsidiantools.api import Vault @@ -44,7 +43,7 @@ def test_vault_instantiation_needs_directory(): def test_type_error_is_raised_for_string_dirpath(): - actual_vault_dirpath = 'home/digital-garden' + actual_vault_dirpath = "home/digital-garden" with pytest.raises(TypeError): Vault(actual_vault_dirpath) @@ -73,22 +72,22 @@ def test_connect(mock_initial_vault): def test_functions_to_fail_for_unconnected_vault(mock_initial_vault): # catch functions that require attributes set via connect method with pytest.raises(AttributeError): - mock_initial_vault.get_backlinks('A note that would not exist') + mock_initial_vault.get_backlinks("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_backlink_counts('A note that would not exist') + mock_initial_vault.get_backlink_counts("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_wikilinks('A note that would not exist') + mock_initial_vault.get_wikilinks("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_wikilink_counts('A note that would not exist') + mock_initial_vault.get_wikilink_counts("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_tags('A note that would not exist') + mock_initial_vault.get_tags("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_embedded_files('A note that would not exist') + mock_initial_vault.get_embedded_files("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_math_index('A note that would not exist') + mock_initial_vault.get_math_index("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_front_matter('A note that would not exist') + mock_initial_vault.get_front_matter("A note that would not exist") with pytest.raises(AttributeError): - mock_initial_vault.get_md_links('A note that would not exist') + mock_initial_vault.get_md_links("A note that would not exist") with pytest.raises(AttributeError): mock_initial_vault.get_note_metadata() diff --git a/tests/test_api_vault_stub_attr_setters.py b/tests/test_api_vault_stub_attr_setters.py index f941134..e4adc89 100644 --- a/tests/test_api_vault_stub_attr_setters.py +++ b/tests/test_api_vault_stub_attr_setters.py @@ -1,7 +1,7 @@ -import pytest from pathlib import Path -import networkx as nx +import networkx as nx +import pytest from obsidiantools.api import Vault @@ -11,15 +11,15 @@ @pytest.fixture def actual_connected_vault(): - return Vault(WKD / 'tests/vault-stub').connect().gather() + return Vault(WKD / "tests/vault-stub").connect().gather() def test_attr_setters_main_setup(actual_connected_vault): actual_connected_vault.md_file_index = {} assert actual_connected_vault.md_file_index == {} - actual_connected_vault.canvas_file_index = {'New.canvas': ''} - assert actual_connected_vault.canvas_file_index == {'New.canvas': ''} + actual_connected_vault.canvas_file_index = {"New.canvas": ""} + assert actual_connected_vault.canvas_file_index == {"New.canvas": ""} def test_attr_setters_md_connect_related(actual_connected_vault): @@ -86,11 +86,11 @@ def test_attr_setters_md_connect_related(actual_connected_vault): def test_attr_setters_md_gather_related(actual_connected_vault): - actual_connected_vault.source_text_index = {'Isolated note': '`new text`'} - assert actual_connected_vault.source_text_index == {'Isolated note': '`new text`'} + actual_connected_vault.source_text_index = {"Isolated note": "`new text`"} + assert actual_connected_vault.source_text_index == {"Isolated note": "`new text`"} - actual_connected_vault.readable_text_index = {'Isolated note': 'Test'} - assert actual_connected_vault.readable_text_index == {'Isolated note': 'Test'} + actual_connected_vault.readable_text_index = {"Isolated note": "Test"} + assert actual_connected_vault.readable_text_index == {"Isolated note": "Test"} def test_attr_setters_canvas_connect_related(actual_connected_vault): diff --git a/tests/test_api_vault_stub_connect_attachments_true.py b/tests/test_api_vault_stub_connect_attachments_true.py index 173fb70..4cc8494 100644 --- a/tests/test_api_vault_stub_connect_attachments_true.py +++ b/tests/test_api_vault_stub_connect_attachments_true.py @@ -1,10 +1,10 @@ -import pytest +from pathlib import Path + import numpy as np import pandas as pd -from pathlib import Path +import pytest from pandas.testing import assert_series_equal - from obsidiantools.api import Vault # NOTE: run the tests from the project dir. @@ -13,160 +13,170 @@ @pytest.fixture def actual_connected_vault(): - return (Vault(WKD / 'tests/vault-stub') - .connect(attachments=True)) + return Vault(WKD / "tests/vault-stub").connect(attachments=True) @pytest.fixture def expected_note_metadata_dict(): return { - 'rel_filepath': {'Sussudio': Path('Sussudio.md'), - 'Isolated note': Path('Isolated note.md'), - 'Brevissimus moenia': Path('lipsum/Brevissimus moenia.md'), - 'Ne fuit': Path('lipsum/Ne fuit.md'), - 'Alimenta': Path('lipsum/Alimenta.md'), - 'Vulnera ubera': Path('lipsum/Vulnera ubera.md'), - 'lipsum/Isolated note': Path('lipsum/Isolated note.md'), - 'Causam mihi': Path('lipsum/Causam mihi.md'), - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, + "rel_filepath": { + "Sussudio": Path("Sussudio.md"), + "Isolated note": Path("Isolated note.md"), + "Brevissimus moenia": Path("lipsum/Brevissimus moenia.md"), + "Ne fuit": Path("lipsum/Ne fuit.md"), + "Alimenta": Path("lipsum/Alimenta.md"), + "Vulnera ubera": Path("lipsum/Vulnera ubera.md"), + "lipsum/Isolated note": Path("lipsum/Isolated note.md"), + "Causam mihi": Path("lipsum/Causam mihi.md"), + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, # abs_filepath would be here - 'note_exists': {'Sussudio': True, - 'Isolated note': True, - 'Brevissimus moenia': True, - 'Ne fuit': True, - 'Alimenta': True, - 'Vulnera ubera': True, - 'lipsum/Isolated note': True, - 'Causam mihi': True, - 'American Psycho (film)': False, - 'Tarpeia': False, - 'Caelum': False, - 'Vita': False, - 'Aras Teucras': False, - 'Manus': False, - 'Bacchus': False, - 'Amor': False, - 'Virtus': False, - 'Tydides': False, - 'Dives': False, - 'Aetna': False}, - 'n_backlinks': {'Sussudio': 0, - 'Isolated note': 0, - 'Brevissimus moenia': 1, - 'Ne fuit': 2, - 'Alimenta': 0, - 'Vulnera ubera': 0, - 'lipsum/Isolated note': 0, - 'Causam mihi': 1, - 'American Psycho (film)': 1, - 'Tarpeia': 3, - 'Caelum': 3, - 'Vita': 3, - 'Aras Teucras': 1, - 'Manus': 3, - 'Bacchus': 5, - 'Amor': 2, - 'Virtus': 1, - 'Tydides': 1, - 'Dives': 1, - 'Aetna': 1}, - 'n_wikilinks': {'Sussudio': 1.0, - 'Isolated note': 0.0, - 'Brevissimus moenia': 3.0, - 'Ne fuit': 6.0, - 'Alimenta': 12.0, - 'Vulnera ubera': 3.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 4.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, - 'n_tags': {'Sussudio': 5.0, - 'Isolated note': 0.0, - 'Brevissimus moenia': 0.0, - 'Ne fuit': 0.0, - 'Alimenta': 0.0, - 'Vulnera ubera': 0.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 0.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, - 'n_embedded_files': {'Isolated note': 0.0, - 'Sussudio': 2.0, - 'Brevissimus moenia': 0.0, - 'Ne fuit': 0.0, - 'Alimenta': 0.0, - 'Vulnera ubera': 0.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 0.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan} + "note_exists": { + "Sussudio": True, + "Isolated note": True, + "Brevissimus moenia": True, + "Ne fuit": True, + "Alimenta": True, + "Vulnera ubera": True, + "lipsum/Isolated note": True, + "Causam mihi": True, + "American Psycho (film)": False, + "Tarpeia": False, + "Caelum": False, + "Vita": False, + "Aras Teucras": False, + "Manus": False, + "Bacchus": False, + "Amor": False, + "Virtus": False, + "Tydides": False, + "Dives": False, + "Aetna": False, + }, + "n_backlinks": { + "Sussudio": 0, + "Isolated note": 0, + "Brevissimus moenia": 1, + "Ne fuit": 2, + "Alimenta": 0, + "Vulnera ubera": 0, + "lipsum/Isolated note": 0, + "Causam mihi": 1, + "American Psycho (film)": 1, + "Tarpeia": 3, + "Caelum": 3, + "Vita": 3, + "Aras Teucras": 1, + "Manus": 3, + "Bacchus": 5, + "Amor": 2, + "Virtus": 1, + "Tydides": 1, + "Dives": 1, + "Aetna": 1, + }, + "n_wikilinks": { + "Sussudio": 1.0, + "Isolated note": 0.0, + "Brevissimus moenia": 3.0, + "Ne fuit": 6.0, + "Alimenta": 12.0, + "Vulnera ubera": 3.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 4.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, + "n_tags": { + "Sussudio": 5.0, + "Isolated note": 0.0, + "Brevissimus moenia": 0.0, + "Ne fuit": 0.0, + "Alimenta": 0.0, + "Vulnera ubera": 0.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 0.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, + "n_embedded_files": { + "Isolated note": 0.0, + "Sussudio": 2.0, + "Brevissimus moenia": 0.0, + "Ne fuit": 0.0, + "Alimenta": 0.0, + "Vulnera ubera": 0.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 0.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, } @pytest.fixture def expected_media_file_metadata_dict(): return { - 'rel_filepath': {'1999.flac': np.nan, - 'Sussudio.mp3': np.nan}, + "rel_filepath": {"1999.flac": np.nan, "Sussudio.mp3": np.nan}, # abs_filepath would be here - 'file_exists': {'1999.flac': False, - 'Sussudio.mp3': False}, - 'n_backlinks': {'1999.flac': 1, - 'Sussudio.mp3': 1}, + "file_exists": {"1999.flac": False, "Sussudio.mp3": False}, + "n_backlinks": {"1999.flac": 1, "Sussudio.mp3": 1}, } @pytest.fixture def expected_embedded_files_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': ['Sussudio.mp3', '1999.flac'], - 'Brevissimus moenia': [], - 'Ne fuit': [], - 'Alimenta': [], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": ["Sussudio.mp3", "1999.flac"], + "Brevissimus moenia": [], + "Ne fuit": [], + "Alimenta": [], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture @@ -187,76 +197,76 @@ def actual_canvas_file_metadata_df(actual_connected_vault): def test_get_metadata_cols(actual_note_metadata_df): assert isinstance(actual_note_metadata_df, pd.DataFrame) - expected_cols = ['rel_filepath', 'abs_filepath', - 'note_exists', - 'n_backlinks', 'n_wikilinks', - 'n_tags', - 'n_embedded_files', - 'modified_time'] + expected_cols = [ + "rel_filepath", + "abs_filepath", + "note_exists", + "n_backlinks", + "n_wikilinks", + "n_tags", + "n_embedded_files", + "modified_time", + ] assert actual_note_metadata_df.columns.tolist() == expected_cols def test_get_metadata_dtypes(actual_note_metadata_df): - assert actual_note_metadata_df['rel_filepath'].dtype == 'object' - assert actual_note_metadata_df['abs_filepath'].dtype == 'object' - assert actual_note_metadata_df['note_exists'].dtype == 'bool' - assert actual_note_metadata_df['n_backlinks'].dtype == 'int' - assert actual_note_metadata_df['n_wikilinks'].dtype == 'float' - assert actual_note_metadata_df['n_tags'].dtype == 'float' - assert actual_note_metadata_df['n_embedded_files'].dtype == 'float' - assert actual_note_metadata_df['modified_time'].dtype == 'datetime64[ns]' + assert actual_note_metadata_df["rel_filepath"].dtype == "object" + assert actual_note_metadata_df["abs_filepath"].dtype == "object" + assert actual_note_metadata_df["note_exists"].dtype == "bool" + assert actual_note_metadata_df["n_backlinks"].dtype == "int" + assert actual_note_metadata_df["n_wikilinks"].dtype == "float" + assert actual_note_metadata_df["n_tags"].dtype == "float" + assert actual_note_metadata_df["n_embedded_files"].dtype == "float" + assert actual_note_metadata_df["modified_time"].dtype == "datetime64[ns]" -def test_get_metadata_backlinks(actual_note_metadata_df, - expected_note_metadata_dict): - TEST_COL = 'n_backlinks' +def test_get_metadata_backlinks(actual_note_metadata_df, expected_note_metadata_dict): + TEST_COL = "n_backlinks" actual_series = actual_note_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_note_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_note_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) def test_backlink_and_wikilink_totals_not_equal_for_test_vault(actual_note_metadata_df): # every wikilink is another note's backlink # INEQUALITY is expected when canvas files are INCLUDED in wikilinks list # for this vault - assert (actual_note_metadata_df['n_backlinks'].sum() - != actual_note_metadata_df['n_wikilinks'].sum()) + assert ( + actual_note_metadata_df["n_backlinks"].sum() + != actual_note_metadata_df["n_wikilinks"].sum() + ) def test_backlink_counts(actual_connected_vault): expected_bl_count_subset = { - 'Sussudio': {}, - 'Alimenta': {}, - 'Tarpeia': {'Brevissimus moenia': 1, - 'Alimenta': 1, - 'Vulnera ubera': 1}, - 'Ne fuit': {'Alimenta': 1, - 'Causam mihi': 1}, - 'Bacchus': {'Ne fuit': 1, - 'Alimenta': 4}, - '1999.flac': {'Sussudio': 1}, - 'Sussudio.mp3': {'Sussudio': 1} + "Sussudio": {}, + "Alimenta": {}, + "Tarpeia": {"Brevissimus moenia": 1, "Alimenta": 1, "Vulnera ubera": 1}, + "Ne fuit": {"Alimenta": 1, "Causam mihi": 1}, + "Bacchus": {"Ne fuit": 1, "Alimenta": 4}, + "1999.flac": {"Sussudio": 1}, + "Sussudio.mp3": {"Sussudio": 1}, } for k in list(expected_bl_count_subset.keys()): - assert (actual_connected_vault.get_backlink_counts(k) - == expected_bl_count_subset.get(k)) + assert actual_connected_vault.get_backlink_counts( + k + ) == expected_bl_count_subset.get(k) with pytest.raises(ValueError): actual_connected_vault.get_backlink_counts("Note that isn't in vault at all") def test_isolated_notes(actual_connected_vault): - expected_isol_notes = ['Isolated note', 'lipsum/Isolated note'] + expected_isol_notes = ["Isolated note", "lipsum/Isolated note"] assert isinstance(actual_connected_vault.isolated_notes, list) - assert (set(actual_connected_vault.isolated_notes) - == set(expected_isol_notes)) + assert set(actual_connected_vault.isolated_notes) == set(expected_isol_notes) # isolated notes can't have backlinks for n in actual_connected_vault.isolated_notes: @@ -270,12 +280,12 @@ def test_get_canvas_file_dicts_tuple(actual_connected_vault): # (linked_files_by_short_path, # non_linked_files_by_short_path, # nonexistent_files_by_short_path) - actual_tuple = (actual_connected_vault. - _get_canvas_file_dicts_tuple()) + actual_tuple = actual_connected_vault._get_canvas_file_dicts_tuple() expected_tuple = ( - {'Crazy wall 2.canvas': Path('Crazy wall 2.canvas')}, - {'Crazy wall.canvas': Path('Crazy wall.canvas')}, - {}) + {"Crazy wall 2.canvas": Path("Crazy wall 2.canvas")}, + {"Crazy wall.canvas": Path("Crazy wall.canvas")}, + {}, + ) assert actual_tuple == expected_tuple @@ -283,52 +293,54 @@ def test_get_media_file_dicts_tuple(actual_connected_vault): # (embedded_files_by_short_path, # non_embedded_files_by_short_path, # nonexistent_files_by_short_path) - actual_tuple = (actual_connected_vault. - _get_media_file_dicts_tuple()) - expected_tuple = ( - {}, - {}, - {'Sussudio.mp3': np.nan, '1999.flac': np.nan}) + actual_tuple = actual_connected_vault._get_media_file_dicts_tuple() + expected_tuple = ({}, {}, {"Sussudio.mp3": np.nan, "1999.flac": np.nan}) assert actual_tuple == expected_tuple -def test_nonexistent_canvas_files(actual_connected_vault, - actual_canvas_file_metadata_df): +def test_nonexistent_canvas_files( + actual_connected_vault, actual_canvas_file_metadata_df +): expected_non_e_files = [] assert isinstance(actual_connected_vault.nonexistent_canvas_files, list) - assert (set(actual_connected_vault.nonexistent_canvas_files) - == set(expected_non_e_files)) - assert (set(actual_canvas_file_metadata_df.loc[~actual_canvas_file_metadata_df['file_exists'], :] - .index.tolist()) - == set(expected_non_e_files)) + assert set(actual_connected_vault.nonexistent_canvas_files) == set( + expected_non_e_files + ) + assert set( + actual_canvas_file_metadata_df.loc[ + ~actual_canvas_file_metadata_df["file_exists"], : + ].index.tolist() + ) == set(expected_non_e_files) def test_nonexistent_media_files(actual_connected_vault, actual_media_file_metadata_df): - expected_non_e_files = ['1999.flac', 'Sussudio.mp3'] + expected_non_e_files = ["1999.flac", "Sussudio.mp3"] assert isinstance(actual_connected_vault.nonexistent_media_files, list) - assert (set(actual_connected_vault.nonexistent_media_files) - == set(expected_non_e_files)) - assert (set(actual_media_file_metadata_df.loc[~actual_media_file_metadata_df['file_exists'], :] - .index.tolist()) - == set(expected_non_e_files)) + assert set(actual_connected_vault.nonexistent_media_files) == set( + expected_non_e_files + ) + assert set( + actual_media_file_metadata_df.loc[ + ~actual_media_file_metadata_df["file_exists"], : + ].index.tolist() + ) == set(expected_non_e_files) def test_isolated_canvas_files(actual_connected_vault): - expected_isol_files = ['Crazy wall.canvas'] + expected_isol_files = ["Crazy wall.canvas"] assert isinstance(actual_connected_vault.isolated_canvas_files, list) - assert (set(actual_connected_vault.isolated_canvas_files) - == set(expected_isol_files)) + assert set(actual_connected_vault.isolated_canvas_files) == set(expected_isol_files) def test_n_backlinks_not_null_in_canvas_file_metadata(actual_connected_vault): df_canvas = actual_connected_vault.get_canvas_file_metadata() - assert df_canvas['n_backlinks'].isna().mean() == 0 + assert df_canvas["n_backlinks"].isna().mean() == 0 def test_all_file_metadata_df(actual_connected_vault): @@ -339,12 +351,12 @@ def test_all_file_metadata_df(actual_connected_vault): actual_canvas_df = actual_connected_vault.get_canvas_file_metadata() # check all dataframes concatenated successfully: - assert len(actual_all_df) == (len(actual_notes_df) - + len(actual_media_df) - + len(actual_canvas_df)) + assert len(actual_all_df) == ( + len(actual_notes_df) + len(actual_media_df) + len(actual_canvas_df) + ) # check that media files are included in graph under attachments=True, # with equality involving graph edges: - assert (actual_all_df['n_backlinks'].sum() - == (actual_all_df['n_wikilinks'].sum() - + actual_all_df['n_embedded_files'].sum())) + assert actual_all_df["n_backlinks"].sum() == ( + actual_all_df["n_wikilinks"].sum() + actual_all_df["n_embedded_files"].sum() + ) diff --git a/tests/test_api_vault_stub_connect_defaults_canvas.py b/tests/test_api_vault_stub_connect_defaults_canvas.py index cb6310a..007fcf8 100644 --- a/tests/test_api_vault_stub_connect_defaults_canvas.py +++ b/tests/test_api_vault_stub_connect_defaults_canvas.py @@ -1,7 +1,7 @@ -import pytest -import networkx as nx from pathlib import Path +import networkx as nx +import pytest from obsidiantools.api import Vault @@ -11,61 +11,62 @@ @pytest.fixture def expected_canvas_file_index(): - return {'Crazy wall.canvas': Path('Crazy wall.canvas'), - 'Crazy wall 2.canvas': Path('Crazy wall 2.canvas')} + return { + "Crazy wall.canvas": Path("Crazy wall.canvas"), + "Crazy wall 2.canvas": Path("Crazy wall 2.canvas"), + } @pytest.fixture def actual_connected_vault(): - return Vault(WKD / 'tests/vault-stub').connect() + return Vault(WKD / "tests/vault-stub").connect() -def test_canvas_file_index(actual_connected_vault, - expected_canvas_file_index): - assert (actual_connected_vault.canvas_file_index - == expected_canvas_file_index) +def test_canvas_file_index(actual_connected_vault, expected_canvas_file_index): + assert actual_connected_vault.canvas_file_index == expected_canvas_file_index def test_canvas_content_index(actual_connected_vault): - actual_crazy_wall_2_content = ( - actual_connected_vault.canvas_content_index - .get('Crazy wall 2.canvas')) - actual_crazy_wall_2_text = (actual_crazy_wall_2_content - .get('nodes')[0].get('text')) + actual_crazy_wall_2_content = actual_connected_vault.canvas_content_index.get( + "Crazy wall 2.canvas" + ) + actual_crazy_wall_2_text = actual_crazy_wall_2_content.get("nodes")[0].get("text") expected_crazy_wall_2_text = "Now we're getting meta..." assert actual_crazy_wall_2_text == expected_crazy_wall_2_text def test_canvas_graph_detail_index_graph(actual_connected_vault): actual_crazy_wall_graph_detail = ( - actual_connected_vault.canvas_graph_detail_index - .get('Crazy wall.canvas')) + actual_connected_vault.canvas_graph_detail_index.get("Crazy wall.canvas") + ) G, _, _ = actual_crazy_wall_graph_detail # check nodes in overall graph: - expected_nodes = ['0fb63a211244ab98', - '5b04fb9cabc4b282', - '8f032f9a663e27b5', - 'd3f112f83760095a', - 'c168506f5b075d91', - '9d13d42f967553bf', - '2919b72bf3df3791'] - actual_nodes = [i for i in G.nodes()] + expected_nodes = [ + "0fb63a211244ab98", + "5b04fb9cabc4b282", + "8f032f9a663e27b5", + "d3f112f83760095a", + "c168506f5b075d91", + "9d13d42f967553bf", + "2919b72bf3df3791", + ] + actual_nodes = list(G.nodes()) assert actual_nodes == expected_nodes # expect group node not in graph: - assert not set(['a10aaf054261706d']).issubset(set(actual_nodes)) + assert not {"a10aaf054261706d"}.issubset(set(actual_nodes)) # isolated nodes: - actual_isolated_nodes = [cv for cv in nx.isolates(G)] - expected_isolated_nodes = ['0fb63a211244ab98', '2919b72bf3df3791'] + actual_isolated_nodes = list(nx.isolates(G)) + expected_isolated_nodes = ["0fb63a211244ab98", "2919b72bf3df3791"] assert actual_isolated_nodes == expected_isolated_nodes # check main node's connections: actual_in_degree = {n[0]: n[1] for n in G.in_degree} actual_out_degree = {n[0]: n[1] for n in G.out_degree} - assert actual_in_degree.get('c168506f5b075d91') == 2 - assert actual_out_degree.get('c168506f5b075d91') == 1 + assert actual_in_degree.get("c168506f5b075d91") == 2 + assert actual_out_degree.get("c168506f5b075d91") == 1 # edge count: actual_n_edges = G.number_of_edges() @@ -74,29 +75,30 @@ def test_canvas_graph_detail_index_graph(actual_connected_vault): def test_canvas_graph_detail_index_graph_other_attributes(actual_connected_vault): actual_crazy_wall_graph_detail = ( - actual_connected_vault.canvas_graph_detail_index - .get('Crazy wall.canvas')) + actual_connected_vault.canvas_graph_detail_index.get("Crazy wall.canvas") + ) _, pos, edge_labels = actual_crazy_wall_graph_detail # check pos: - assert pos.get('2919b72bf3df3791') == (-1363, 812) + assert pos.get("2919b72bf3df3791") == (-1363, 812) actual_x_locs = {c: pos[0] for (c, pos) in pos.items()} - assert max(actual_x_locs, key=actual_x_locs.get) == 'c168506f5b075d91' - assert min(actual_x_locs, key=actual_x_locs.get) == '2919b72bf3df3791' + assert max(actual_x_locs, key=actual_x_locs.get) == "c168506f5b075d91" + assert min(actual_x_locs, key=actual_x_locs.get) == "2919b72bf3df3791" actual_y_locs = {c: pos[1] for (c, pos) in pos.items()} - assert max(actual_y_locs, key=actual_y_locs.get) == '0fb63a211244ab98' - assert min(actual_y_locs, key=actual_y_locs.get) == '5b04fb9cabc4b282' + assert max(actual_y_locs, key=actual_y_locs.get) == "0fb63a211244ab98" + assert min(actual_y_locs, key=actual_y_locs.get) == "5b04fb9cabc4b282" # check edge_labels: actual_non_blank_edge_labels = { - pair: label for pair, label in edge_labels.items() - if label != ''} + pair: label for pair, label in edge_labels.items() if label != "" + } expected_non_blank_edge_labels = { - ('d3f112f83760095a', 'c168506f5b075d91'): 'inspires?'} + ("d3f112f83760095a", "c168506f5b075d91"): "inspires?" + } assert actual_non_blank_edge_labels == expected_non_blank_edge_labels def test_n_backlinks_null_in_canvas_file_metadata(actual_connected_vault): df_canvas = actual_connected_vault.get_canvas_file_metadata() - assert df_canvas['n_backlinks'].isna().mean() == 1 + assert df_canvas["n_backlinks"].isna().mean() == 1 diff --git a/tests/test_api_vault_stub_connect_defaults_md.py b/tests/test_api_vault_stub_connect_defaults_md.py index 22b41d8..13fc057 100644 --- a/tests/test_api_vault_stub_connect_defaults_md.py +++ b/tests/test_api_vault_stub_connect_defaults_md.py @@ -1,13 +1,12 @@ -import pytest -import numpy as np -import pandas as pd from pathlib import Path -from pandas.testing import (assert_series_equal, - assert_frame_equal) +import numpy as np +import pandas as pd +import pytest +from pandas.testing import assert_frame_equal, assert_series_equal -from obsidiantools.api import Vault from obsidiantools._constants import METADATA_DF_COLS_GENERIC_TYPE +from obsidiantools.api import Vault # NOTE: run the tests from the project dir. WKD = Path().cwd() @@ -16,217 +15,249 @@ @pytest.fixture def expected_metadata_dict(): return { - 'rel_filepath': {'Sussudio': Path('Sussudio.md'), - 'Isolated note': Path('Isolated note.md'), - 'Brevissimus moenia': Path('lipsum/Brevissimus moenia.md'), - 'Ne fuit': Path('lipsum/Ne fuit.md'), - 'Alimenta': Path('lipsum/Alimenta.md'), - 'Vulnera ubera': Path('lipsum/Vulnera ubera.md'), - 'lipsum/Isolated note': Path('lipsum/Isolated note.md'), - 'Causam mihi': Path('lipsum/Causam mihi.md'), - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, + "rel_filepath": { + "Sussudio": Path("Sussudio.md"), + "Isolated note": Path("Isolated note.md"), + "Brevissimus moenia": Path("lipsum/Brevissimus moenia.md"), + "Ne fuit": Path("lipsum/Ne fuit.md"), + "Alimenta": Path("lipsum/Alimenta.md"), + "Vulnera ubera": Path("lipsum/Vulnera ubera.md"), + "lipsum/Isolated note": Path("lipsum/Isolated note.md"), + "Causam mihi": Path("lipsum/Causam mihi.md"), + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, # abs_filepath would be here - 'note_exists': {'Sussudio': True, - 'Isolated note': True, - 'Brevissimus moenia': True, - 'Ne fuit': True, - 'Alimenta': True, - 'Vulnera ubera': True, - 'lipsum/Isolated note': True, - 'Causam mihi': True, - 'American Psycho (film)': False, - 'Tarpeia': False, - 'Caelum': False, - 'Vita': False, - 'Aras Teucras': False, - 'Manus': False, - 'Bacchus': False, - 'Amor': False, - 'Virtus': False, - 'Tydides': False, - 'Dives': False, - 'Aetna': False}, - 'n_backlinks': {'Sussudio': 0, - 'Isolated note': 0, - 'Brevissimus moenia': 1, - 'Ne fuit': 2, - 'Alimenta': 0, - 'Vulnera ubera': 0, - 'lipsum/Isolated note': 0, - 'Causam mihi': 1, - 'American Psycho (film)': 1, - 'Tarpeia': 3, - 'Caelum': 3, - 'Vita': 3, - 'Aras Teucras': 1, - 'Manus': 3, - 'Bacchus': 5, - 'Amor': 2, - 'Virtus': 1, - 'Tydides': 1, - 'Dives': 1, - 'Aetna': 1}, - 'n_wikilinks': {'Sussudio': 1.0, - 'Isolated note': 0.0, - 'Brevissimus moenia': 3.0, - 'Ne fuit': 6.0, - 'Alimenta': 12.0, - 'Vulnera ubera': 3.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 4.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, - 'n_tags': {'Sussudio': 5.0, - 'Isolated note': 0.0, - 'Brevissimus moenia': 0.0, - 'Ne fuit': 0.0, - 'Alimenta': 0.0, - 'Vulnera ubera': 0.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 0.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan}, - 'n_embedded_files': {'Isolated note': 0.0, - 'Sussudio': 2.0, - 'Brevissimus moenia': 0.0, - 'Ne fuit': 0.0, - 'Alimenta': 0.0, - 'Vulnera ubera': 0.0, - 'lipsum/Isolated note': 0.0, - 'Causam mihi': 0.0, - 'American Psycho (film)': np.nan, - 'Tarpeia': np.nan, - 'Caelum': np.nan, - 'Vita': np.nan, - 'Aras Teucras': np.nan, - 'Manus': np.nan, - 'Bacchus': np.nan, - 'Amor': np.nan, - 'Virtus': np.nan, - 'Tydides': np.nan, - 'Dives': np.nan, - 'Aetna': np.nan} + "note_exists": { + "Sussudio": True, + "Isolated note": True, + "Brevissimus moenia": True, + "Ne fuit": True, + "Alimenta": True, + "Vulnera ubera": True, + "lipsum/Isolated note": True, + "Causam mihi": True, + "American Psycho (film)": False, + "Tarpeia": False, + "Caelum": False, + "Vita": False, + "Aras Teucras": False, + "Manus": False, + "Bacchus": False, + "Amor": False, + "Virtus": False, + "Tydides": False, + "Dives": False, + "Aetna": False, + }, + "n_backlinks": { + "Sussudio": 0, + "Isolated note": 0, + "Brevissimus moenia": 1, + "Ne fuit": 2, + "Alimenta": 0, + "Vulnera ubera": 0, + "lipsum/Isolated note": 0, + "Causam mihi": 1, + "American Psycho (film)": 1, + "Tarpeia": 3, + "Caelum": 3, + "Vita": 3, + "Aras Teucras": 1, + "Manus": 3, + "Bacchus": 5, + "Amor": 2, + "Virtus": 1, + "Tydides": 1, + "Dives": 1, + "Aetna": 1, + }, + "n_wikilinks": { + "Sussudio": 1.0, + "Isolated note": 0.0, + "Brevissimus moenia": 3.0, + "Ne fuit": 6.0, + "Alimenta": 12.0, + "Vulnera ubera": 3.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 4.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, + "n_tags": { + "Sussudio": 5.0, + "Isolated note": 0.0, + "Brevissimus moenia": 0.0, + "Ne fuit": 0.0, + "Alimenta": 0.0, + "Vulnera ubera": 0.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 0.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, + "n_embedded_files": { + "Isolated note": 0.0, + "Sussudio": 2.0, + "Brevissimus moenia": 0.0, + "Ne fuit": 0.0, + "Alimenta": 0.0, + "Vulnera ubera": 0.0, + "lipsum/Isolated note": 0.0, + "Causam mihi": 0.0, + "American Psycho (film)": np.nan, + "Tarpeia": np.nan, + "Caelum": np.nan, + "Vita": np.nan, + "Aras Teucras": np.nan, + "Manus": np.nan, + "Bacchus": np.nan, + "Amor": np.nan, + "Virtus": np.nan, + "Tydides": np.nan, + "Dives": np.nan, + "Aetna": np.nan, + }, } @pytest.fixture def expected_embedded_files_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': ['Sussudio.mp3', '1999.flac'], - 'Brevissimus moenia': [], - 'Ne fuit': [], - 'Alimenta': [], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": ["Sussudio.mp3", "1999.flac"], + "Brevissimus moenia": [], + "Ne fuit": [], + "Alimenta": [], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture def expected_front_matter_index(): - return {'Isolated note': {}, - 'lipsum/Isolated note': {}, - 'Sussudio': {'title': 'Sussudio', - 'artist': 'Phil Collins', - 'category': 'music', - 'year': 1985, - 'url': 'https://www.discogs.com/Phil-Collins-Sussudio/master/106239', - 'references': [[['American Psycho (film)']], 'Polka Party!'], - 'chart_peaks': [{'US': 1}, {'UK': 12}]}, - 'Brevissimus moenia': {}, - 'Ne fuit': {}, - 'Alimenta': {}, - 'Vulnera ubera': {}, - 'Causam mihi': {'title': 'Causam mihi', - 'author': 'Ovid', - 'category': 'literature', - 'year': 8, - 'language': 'la', - 'description': '\\{\\{description\\}\\}'}} + return { + "Isolated note": {}, + "lipsum/Isolated note": {}, + "Sussudio": { + "title": "Sussudio", + "artist": "Phil Collins", + "category": "music", + "year": 1985, + "url": "https://www.discogs.com/Phil-Collins-Sussudio/master/106239", + "references": [[["American Psycho (film)"]], "Polka Party!"], + "chart_peaks": [{"US": 1}, {"UK": 12}], + }, + "Brevissimus moenia": {}, + "Ne fuit": {}, + "Alimenta": {}, + "Vulnera ubera": {}, + "Causam mihi": { + "title": "Causam mihi", + "author": "Ovid", + "category": "literature", + "year": 8, + "language": "la", + "description": "\\{\\{description\\}\\}", + }, + } @pytest.fixture def expected_md_links_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': [], - 'Brevissimus moenia': ['http://www.alii.io/', - 'http://fronti.com/tumiseris.html'], - 'Ne fuit': ['http://vires.io/', - 'http://excoquitprotinus.net/quae.html', - 'http://medullis-me.net/novat', - 'http://sedibus.io/levemmonstra'], - 'Alimenta': ['http://fugitaer.net/dignus', - 'http://www.a-iuveni.com/', - 'http://cibos.net/venulus-redito.html', - 'http://et-pronus.com/', - 'http://iuppiter.net/'], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": [], + "Brevissimus moenia": [ + "http://www.alii.io/", + "http://fronti.com/tumiseris.html", + ], + "Ne fuit": [ + "http://vires.io/", + "http://excoquitprotinus.net/quae.html", + "http://medullis-me.net/novat", + "http://sedibus.io/levemmonstra", + ], + "Alimenta": [ + "http://fugitaer.net/dignus", + "http://www.a-iuveni.com/", + "http://cibos.net/venulus-redito.html", + "http://et-pronus.com/", + "http://iuppiter.net/", + ], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture def expected_tags_main_only_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': ['y1982', 'y_1982', 'y-1982', 'y1982', 'y2000'], - 'Brevissimus moenia': [], - 'Ne fuit': [], - 'Alimenta': [], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": ["y1982", "y_1982", "y-1982", "y1982", "y2000"], + "Brevissimus moenia": [], + "Ne fuit": [], + "Alimenta": [], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture def expected_math_index(): - return {'Isolated note': [], - 'lipsum/Isolated note': [], - 'Sussudio': [], - 'Brevissimus moenia': [], - 'Ne fuit': [], - 'Alimenta': [], - 'Vulnera ubera': [], - 'Causam mihi': []} + return { + "Isolated note": [], + "lipsum/Isolated note": [], + "Sussudio": [], + "Brevissimus moenia": [], + "Ne fuit": [], + "Alimenta": [], + "Vulnera ubera": [], + "Causam mihi": [], + } @pytest.fixture def actual_connected_vault(): - return Vault(WKD / 'tests/vault-stub').connect() + return Vault(WKD / "tests/vault-stub").connect() @pytest.fixture def actual_connected_vault_md_files_only(): - return Vault(WKD / 'tests/vault-stub/lipsum').connect() + return Vault(WKD / "tests/vault-stub/lipsum").connect() @pytest.fixture @@ -237,92 +268,88 @@ def actual_metadata_df(actual_connected_vault): def test_get_metadata_cols(actual_metadata_df): assert isinstance(actual_metadata_df, pd.DataFrame) - expected_cols = ['rel_filepath', 'abs_filepath', - 'note_exists', - 'n_backlinks', 'n_wikilinks', - 'n_tags', - 'n_embedded_files', - 'modified_time'] + expected_cols = [ + "rel_filepath", + "abs_filepath", + "note_exists", + "n_backlinks", + "n_wikilinks", + "n_tags", + "n_embedded_files", + "modified_time", + ] assert actual_metadata_df.columns.tolist() == expected_cols def test_get_metadata_dtypes(actual_metadata_df): - assert actual_metadata_df['rel_filepath'].dtype == 'object' - assert actual_metadata_df['abs_filepath'].dtype == 'object' - assert actual_metadata_df['note_exists'].dtype == 'bool' - assert actual_metadata_df['n_backlinks'].dtype == 'int' - assert actual_metadata_df['n_wikilinks'].dtype == 'float' - assert actual_metadata_df['n_tags'].dtype == 'float' - assert actual_metadata_df['n_embedded_files'].dtype == 'float' - assert actual_metadata_df['modified_time'].dtype == 'datetime64[ns]' + assert actual_metadata_df["rel_filepath"].dtype == "object" + assert actual_metadata_df["abs_filepath"].dtype == "object" + assert actual_metadata_df["note_exists"].dtype == "bool" + assert actual_metadata_df["n_backlinks"].dtype == "int" + assert actual_metadata_df["n_wikilinks"].dtype == "float" + assert actual_metadata_df["n_tags"].dtype == "float" + assert actual_metadata_df["n_embedded_files"].dtype == "float" + assert actual_metadata_df["modified_time"].dtype == "datetime64[ns]" -def test_get_metadata_rel_filepath(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'rel_filepath' +def test_get_metadata_rel_filepath(actual_metadata_df, expected_metadata_dict): + TEST_COL = "rel_filepath" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) -def test_get_metadata_note_exists(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'note_exists' +def test_get_metadata_note_exists(actual_metadata_df, expected_metadata_dict): + TEST_COL = "note_exists" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) -def test_get_metadata_wikilinks(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'n_wikilinks' +def test_get_metadata_wikilinks(actual_metadata_df, expected_metadata_dict): + TEST_COL = "n_wikilinks" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) -def test_get_metadata_backlinks(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'n_backlinks' +def test_get_metadata_backlinks(actual_metadata_df, expected_metadata_dict): + TEST_COL = "n_backlinks" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) -def test_get_metadata_tags(actual_metadata_df, - expected_metadata_dict): - TEST_COL = 'n_tags' +def test_get_metadata_tags(actual_metadata_df, expected_metadata_dict): + TEST_COL = "n_tags" actual_series = actual_metadata_df[TEST_COL] - expected_series = (pd.Series(expected_metadata_dict.get(TEST_COL), - name=TEST_COL) - .rename_axis('note')) - assert_series_equal(actual_series, expected_series, - check_like=True) + expected_series = pd.Series( + expected_metadata_dict.get(TEST_COL), name=TEST_COL + ).rename_axis("note") + assert_series_equal(actual_series, expected_series, check_like=True) def test_backlink_and_wikilink_totals_equal(actual_metadata_df): # every wikilink is another note's backlink # equality is expected when canvas files are excluded from wikilinks list # for ANY VAULT under the defaults - assert (actual_metadata_df['n_backlinks'].sum() - == actual_metadata_df['n_wikilinks'].sum()) + assert ( + actual_metadata_df["n_backlinks"].sum() + == actual_metadata_df["n_wikilinks"].sum() + ) def test_backlink_individual_notes(actual_connected_vault): @@ -331,10 +358,10 @@ def test_backlink_individual_notes(actual_connected_vault): assert isinstance(actual_bl_ix, dict) expected_bl_subset = { - 'Sussudio': [], - 'Alimenta': [], - 'Tarpeia': ['Brevissimus moenia', 'Alimenta', 'Vulnera ubera'], - 'Ne fuit': ['Alimenta', 'Causam mihi'] + "Sussudio": [], + "Alimenta": [], + "Tarpeia": ["Brevissimus moenia", "Alimenta", "Vulnera ubera"], + "Ne fuit": ["Alimenta", "Causam mihi"], } for k in list(expected_bl_subset.keys()): @@ -344,29 +371,25 @@ def test_backlink_individual_notes(actual_connected_vault): actual_connected_vault.get_backlinks("Note that isn't in vault at all") # check that every note is in the backlinks_index - graph_nodes = [n for n in actual_connected_vault.graph.nodes] - assert (len(actual_bl_ix) - == (actual_connected_vault.graph.number_of_nodes())) + graph_nodes = list(actual_connected_vault.graph.nodes) + assert len(actual_bl_ix) == (actual_connected_vault.graph.number_of_nodes()) for k in list(expected_bl_subset.keys()): assert k in graph_nodes def test_backlink_counts(actual_connected_vault): expected_bl_count_subset = { - 'Sussudio': {}, - 'Alimenta': {}, - 'Tarpeia': {'Brevissimus moenia': 1, - 'Alimenta': 1, - 'Vulnera ubera': 1}, - 'Ne fuit': {'Alimenta': 1, - 'Causam mihi': 1}, - 'Bacchus': {'Ne fuit': 1, - 'Alimenta': 4} + "Sussudio": {}, + "Alimenta": {}, + "Tarpeia": {"Brevissimus moenia": 1, "Alimenta": 1, "Vulnera ubera": 1}, + "Ne fuit": {"Alimenta": 1, "Causam mihi": 1}, + "Bacchus": {"Ne fuit": 1, "Alimenta": 4}, } for k in list(expected_bl_count_subset.keys()): - assert (actual_connected_vault.get_backlink_counts(k) - == expected_bl_count_subset.get(k)) + assert actual_connected_vault.get_backlink_counts( + k + ) == expected_bl_count_subset.get(k) with pytest.raises(ValueError): actual_connected_vault.get_backlink_counts("Note that isn't in vault at all") @@ -374,38 +397,36 @@ def test_backlink_counts(actual_connected_vault): def test_wikilink_counts(actual_connected_vault): expected_wl_count_subset = { - 'Sussudio': {'American Psycho (film)': 1}, - 'Isolated note': {}, - 'Vulnera ubera': {'Caelum': 1, - 'Tarpeia': 1, - 'Vita': 1}, - 'Ne fuit': {'Aras Teucras': 1, - 'Manus': 1, - 'Bacchus': 1, - 'Amor': 1, - 'Caelum': 1, - 'Causam mihi': 1}, - 'Causam mihi': {'Dives': 1, - 'Manus': 1, - 'Ne fuit': 1, - 'Aetna': 1}, - 'Brevissimus moenia': {'Tarpeia': 1, - 'Caelum': 1, - 'Vita': 1}, - 'Alimenta': {'Manus': 1, - 'Bacchus': 4, - 'Amor': 1, - 'Ne fuit': 1, - 'Virtus': 1, - 'Brevissimus moenia': 1, - 'Tarpeia': 1, - 'Tydides': 1, - 'Vita': 1} + "Sussudio": {"American Psycho (film)": 1}, + "Isolated note": {}, + "Vulnera ubera": {"Caelum": 1, "Tarpeia": 1, "Vita": 1}, + "Ne fuit": { + "Aras Teucras": 1, + "Manus": 1, + "Bacchus": 1, + "Amor": 1, + "Caelum": 1, + "Causam mihi": 1, + }, + "Causam mihi": {"Dives": 1, "Manus": 1, "Ne fuit": 1, "Aetna": 1}, + "Brevissimus moenia": {"Tarpeia": 1, "Caelum": 1, "Vita": 1}, + "Alimenta": { + "Manus": 1, + "Bacchus": 4, + "Amor": 1, + "Ne fuit": 1, + "Virtus": 1, + "Brevissimus moenia": 1, + "Tarpeia": 1, + "Tydides": 1, + "Vita": 1, + }, } for k in list(expected_wl_count_subset.keys()): - assert (actual_connected_vault.get_wikilink_counts(k) - == expected_wl_count_subset.get(k)) + assert actual_connected_vault.get_wikilink_counts( + k + ) == expected_wl_count_subset.get(k) with pytest.raises(ValueError): actual_connected_vault.get_wikilink_counts("Note that isn't in vault at all") @@ -418,29 +439,46 @@ def test_wikilink_individual_notes(actual_connected_vault): # these notes exist expected_wl_subset = { - 'Sussudio': ['American Psycho (film)'], - 'Alimenta': ['Manus', 'Bacchus', 'Amor', 'Ne fuit', 'Virtus', - 'Brevissimus moenia', 'Tarpeia', 'Tydides', 'Vita', - 'Bacchus', 'Bacchus', 'Bacchus'], - 'Ne fuit': ['Aras Teucras', 'Manus', 'Bacchus', - 'Amor', 'Caelum', 'Causam mihi'] + "Sussudio": ["American Psycho (film)"], + "Alimenta": [ + "Manus", + "Bacchus", + "Amor", + "Ne fuit", + "Virtus", + "Brevissimus moenia", + "Tarpeia", + "Tydides", + "Vita", + "Bacchus", + "Bacchus", + "Bacchus", + ], + "Ne fuit": [ + "Aras Teucras", + "Manus", + "Bacchus", + "Amor", + "Caelum", + "Causam mihi", + ], } - assert (actual_connected_vault.get_wikilinks('Alimenta') - == expected_wl_subset.get('Alimenta')) + assert actual_connected_vault.get_wikilinks("Alimenta") == expected_wl_subset.get( + "Alimenta" + ) for k in list(expected_wl_subset.keys()): # list - sequence the links appear in notes assert expected_wl_subset.get(k) == actual_wl_ix.get(k) with pytest.raises(ValueError): - actual_connected_vault.get_wikilinks('Tarpeia') + actual_connected_vault.get_wikilinks("Tarpeia") # check that every existing note (file) has wikilink info assert len(actual_wl_ix) == len(actual_connected_vault.md_file_index) for k in list(actual_wl_ix.keys()): - assert isinstance(actual_connected_vault.md_file_index.get(k), - Path) + assert isinstance(actual_connected_vault.md_file_index.get(k), Path) def test_unique_wikilinks(actual_connected_vault): @@ -450,39 +488,61 @@ def test_unique_wikilinks(actual_connected_vault): # these notes exist expected_u_wl_subset = { - 'Sussudio': ['American Psycho (film)'], - 'Alimenta': ['Manus', 'Bacchus', 'Amor', 'Ne fuit', 'Virtus', - 'Brevissimus moenia', 'Tarpeia', 'Tydides', 'Vita'], - 'Ne fuit': ['Aras Teucras', 'Manus', 'Bacchus', - 'Amor', 'Caelum', 'Causam mihi'] + "Sussudio": ["American Psycho (film)"], + "Alimenta": [ + "Manus", + "Bacchus", + "Amor", + "Ne fuit", + "Virtus", + "Brevissimus moenia", + "Tarpeia", + "Tydides", + "Vita", + ], + "Ne fuit": [ + "Aras Teucras", + "Manus", + "Bacchus", + "Amor", + "Caelum", + "Causam mihi", + ], } - assert (actual_u_wl_ix.get('Alimenta') - == expected_u_wl_subset.get('Alimenta')) + assert actual_u_wl_ix.get("Alimenta") == expected_u_wl_subset.get("Alimenta") def test_nonexistent_notes(actual_connected_vault, actual_metadata_df): - expected_non_e_notes = ['Tarpeia', 'Caelum', 'Vita', 'Aras Teucras', - 'Manus', 'Bacchus', 'Amor', 'Virtus', - 'Tydides', 'Dives', 'Aetna', - 'American Psycho (film)'] + expected_non_e_notes = [ + "Tarpeia", + "Caelum", + "Vita", + "Aras Teucras", + "Manus", + "Bacchus", + "Amor", + "Virtus", + "Tydides", + "Dives", + "Aetna", + "American Psycho (film)", + ] assert isinstance(actual_connected_vault.nonexistent_notes, list) - assert (set(actual_connected_vault.nonexistent_notes) - == set(expected_non_e_notes)) - assert (set(actual_metadata_df.loc[~actual_metadata_df['note_exists'], :] - .index.tolist()) - == set(expected_non_e_notes)) + assert set(actual_connected_vault.nonexistent_notes) == set(expected_non_e_notes) + assert set( + actual_metadata_df.loc[~actual_metadata_df["note_exists"], :].index.tolist() + ) == set(expected_non_e_notes) def test_isolated_notes(actual_connected_vault): - expected_isol_notes = ['Isolated note', 'lipsum/Isolated note'] + expected_isol_notes = ["Isolated note", "lipsum/Isolated note"] assert isinstance(actual_connected_vault.isolated_notes, list) - assert (set(actual_connected_vault.isolated_notes) - == set(expected_isol_notes)) + assert set(actual_connected_vault.isolated_notes) == set(expected_isol_notes) # isolated notes can't have backlinks for n in actual_connected_vault.isolated_notes: @@ -492,8 +552,7 @@ def test_isolated_notes(actual_connected_vault): assert actual_connected_vault.get_wikilinks(n) == [] -def test_front_matter_index( - actual_connected_vault, expected_front_matter_index): +def test_front_matter_index(actual_connected_vault, expected_front_matter_index): assert isinstance(actual_connected_vault.front_matter_index, dict) actual_front_matter_index = actual_connected_vault.front_matter_index @@ -501,27 +560,29 @@ def test_front_matter_index( def test_front_matter_sussudio(actual_connected_vault): - expected_fm = {'title': 'Sussudio', - 'artist': 'Phil Collins', - 'category': 'music', - 'year': 1985, - 'url': 'https://www.discogs.com/Phil-Collins-Sussudio/master/106239', - 'references': [[['American Psycho (film)']], 'Polka Party!'], - 'chart_peaks': [{'US': 1}, {'UK': 12}]} - - actual_fm = actual_connected_vault.get_front_matter('Sussudio') + expected_fm = { + "title": "Sussudio", + "artist": "Phil Collins", + "category": "music", + "year": 1985, + "url": "https://www.discogs.com/Phil-Collins-Sussudio/master/106239", + "references": [[["American Psycho (film)"]], "Polka Party!"], + "chart_peaks": [{"US": 1}, {"UK": 12}], + } + + actual_fm = actual_connected_vault.get_front_matter("Sussudio") assert actual_fm == expected_fm def test_front_matter_constructorerror(actual_connected_vault): - actual_fm = actual_connected_vault.get_front_matter('Causam mihi') - assert actual_fm['description'] == '\\{\\{description\\}\\}' + actual_fm = actual_connected_vault.get_front_matter("Causam mihi") + assert actual_fm["description"] == "\\{\\{description\\}\\}" def test_embedded_files_sussudio(actual_connected_vault): - expected_files = ['Sussudio.mp3', '1999.flac'] + expected_files = ["Sussudio.mp3", "1999.flac"] - actual_files = actual_connected_vault.get_embedded_files('Sussudio') + actual_files = actual_connected_vault.get_embedded_files("Sussudio") assert actual_files == expected_files @@ -532,77 +593,72 @@ def test_nodes_gte_files(actual_connected_vault): assert act_n_len >= act_f_len -def test_embedded_files_index( - actual_connected_vault, expected_embedded_files_index): +def test_embedded_files_index(actual_connected_vault, expected_embedded_files_index): actual_files_ix = actual_connected_vault.embedded_files_index assert actual_files_ix == expected_embedded_files_index -def test_math_index( - actual_connected_vault, expected_math_index): +def test_math_index(actual_connected_vault, expected_math_index): actual_math_index = actual_connected_vault.math_index assert actual_math_index == expected_math_index -def test_md_links_index( - actual_connected_vault, expected_md_links_index): +def test_md_links_index(actual_connected_vault, expected_md_links_index): actual_md_links_ix = actual_connected_vault.md_links_index assert actual_md_links_ix == expected_md_links_index -def test_tags_index( - actual_connected_vault, expected_tags_main_only_index): +def test_tags_index(actual_connected_vault, expected_tags_main_only_index): actual_tags_ix = actual_connected_vault.tags_index assert actual_tags_ix == expected_tags_main_only_index -def test_unique_md_links( - actual_connected_vault, expected_md_links_index): - actual_u_md_links_ix = (actual_connected_vault. - _unique_md_links_index) +def test_unique_md_links(actual_connected_vault, expected_md_links_index): + actual_u_md_links_ix = actual_connected_vault._unique_md_links_index # all notes in stub have unique md links: assert actual_u_md_links_ix == expected_md_links_index def test_md_links_individual_notes(actual_connected_vault): - actual_md_links = actual_connected_vault.get_md_links('Ne fuit') - expected_md_links = ['http://vires.io/', - 'http://excoquitprotinus.net/quae.html', - 'http://medullis-me.net/novat', - 'http://sedibus.io/levemmonstra'] + actual_md_links = actual_connected_vault.get_md_links("Ne fuit") + expected_md_links = [ + "http://vires.io/", + "http://excoquitprotinus.net/quae.html", + "http://medullis-me.net/novat", + "http://sedibus.io/levemmonstra", + ] assert actual_md_links == expected_md_links def test_tags_individual_notes(actual_connected_vault): - actual_md_links = actual_connected_vault.get_tags('Ne fuit') + actual_md_links = actual_connected_vault.get_tags("Ne fuit") expected_md_links = [] assert actual_md_links == expected_md_links def test_md_links_not_existing(actual_connected_vault): with pytest.raises(ValueError): - actual_connected_vault.get_md_links('Tarpeia') + actual_connected_vault.get_md_links("Tarpeia") def test_tags_not_existing(actual_connected_vault): with pytest.raises(ValueError): - actual_connected_vault.get_tags('Tarpeia') + actual_connected_vault.get_tags("Tarpeia") def test_front_matter_not_existing(actual_connected_vault): with pytest.raises(ValueError): - actual_connected_vault.get_front_matter('Tarpeia') + actual_connected_vault.get_front_matter("Tarpeia") def test_embedded_notes_not_existing(actual_connected_vault): with pytest.raises(ValueError): - actual_connected_vault.get_embedded_files('Tarpeia') + actual_connected_vault.get_embedded_files("Tarpeia") def test_media_file_metadata_df_empty(actual_connected_vault_md_files_only): # use the lipsum dir as the 'vault' dir (md only) - df_media = (actual_connected_vault_md_files_only - .get_media_file_metadata()) + df_media = actual_connected_vault_md_files_only.get_media_file_metadata() assert len(df_media) == 0 @@ -613,8 +669,7 @@ def test_media_file_metadata_df_empty(actual_connected_vault_md_files_only): def test_canvas_file_metadata_df_empty(actual_connected_vault_md_files_only): # use the lipsum dir as the 'vault' dir (md only) - df_media = (actual_connected_vault_md_files_only - .get_canvas_file_metadata()) + df_media = actual_connected_vault_md_files_only.get_canvas_file_metadata() assert len(df_media) == 0 @@ -631,16 +686,14 @@ def test_all_file_metadata_df(actual_connected_vault): # check that notes metadata was only used: assert_frame_equal( - actual_all_df.drop(columns=['graph_category']), - actual_note_df.rename(columns={'note_exists': 'file_exists'})) + actual_all_df.drop(columns=["graph_category"]), + actual_note_df.rename(columns={"note_exists": "file_exists"}), + ) # check that only notes are used for backlinks: - assert (actual_all_df['n_backlinks'].sum() - == (actual_all_df['n_wikilinks'].sum())) + assert actual_all_df["n_backlinks"].sum() == (actual_all_df["n_wikilinks"].sum()) -def test_internal_canvas_backlink_counts_func_errors( - actual_connected_vault): +def test_internal_canvas_backlink_counts_func_errors(actual_connected_vault): with pytest.raises(AttributeError): - (actual_connected_vault. - _get_backlink_counts_for_canvas_files_only()) + (actual_connected_vault._get_backlink_counts_for_canvas_files_only()) diff --git a/tests/test_api_vault_stub_gather.py b/tests/test_api_vault_stub_gather.py index 7adda27..1482c0c 100644 --- a/tests/test_api_vault_stub_gather.py +++ b/tests/test_api_vault_stub_gather.py @@ -1,6 +1,6 @@ -import pytest from pathlib import Path +import pytest from obsidiantools.api import Vault @@ -10,7 +10,7 @@ @pytest.fixture def actual_unconnected_vault(): - return Vault(WKD / 'tests/vault-stub') + return Vault(WKD / "tests/vault-stub") @pytest.fixture @@ -31,33 +31,31 @@ def test_vault_not_connected(actual_unconnected_vault): def test_vault_not_gathered(actual_unconnected_vault): with pytest.raises(AttributeError): - actual_unconnected_vault.get_source_text('Isolated note') + actual_unconnected_vault.get_source_text("Isolated note") with pytest.raises(AttributeError): - actual_unconnected_vault.get_readable_text('Isolated note') + actual_unconnected_vault.get_readable_text("Isolated note") def test_text_not_existing(actual_gathered_vault_defaults): assert actual_gathered_vault_defaults.is_gathered with pytest.raises(ValueError): - actual_gathered_vault_defaults.get_source_text('Tarpeia') + actual_gathered_vault_defaults.get_source_text("Tarpeia") with pytest.raises(ValueError): - actual_gathered_vault_defaults.get_readable_text('Tarpeia') + actual_gathered_vault_defaults.get_readable_text("Tarpeia") def test_source_text_existing_file(actual_gathered_vault_defaults): - actual_in_text = (actual_gathered_vault_defaults - .get_source_text('Isolated note')) - expected_start = '# Isolated note' - expected_end = 'an isolated note ~~an orphan~~.\n' + actual_in_text = actual_gathered_vault_defaults.get_source_text("Isolated note") + expected_start = "# Isolated note" + expected_end = "an isolated note ~~an orphan~~.\n" assert actual_in_text.startswith(expected_start) assert actual_in_text.endswith(expected_end) def test_readable_text_existing_file(actual_gathered_vault_defaults): - actual_in_text = (actual_gathered_vault_defaults - .get_readable_text('Sussudio')) - expected_start = '# Sussudio' - expected_end = '\\- #hash_char_not_tag\n' + actual_in_text = actual_gathered_vault_defaults.get_readable_text("Sussudio") + expected_start = "# Sussudio" + expected_end = "\\- #hash_char_not_tag\n" assert actual_in_text.startswith(expected_start) assert actual_in_text.endswith(expected_end) @@ -70,7 +68,7 @@ def test_isolated_note_md_text(actual_gathered_vault_defaults): assert actual_gathered_vault_defaults.is_gathered - actual_text = actual_gathered_vault_defaults.get_source_text('Isolated note') + actual_text = actual_gathered_vault_defaults.get_source_text("Isolated note") assert actual_text == expected_text @@ -107,5 +105,5 @@ def test_sussudio_readable_text(actual_gathered_vault_defaults): However these shouldn't be recognised as tags: \- (#y1985 ) \- #1985 \- American Psycho (film)#Patrick Bateman \- #hash_char_not_tag """ - actual_text = actual_gathered_vault_defaults.get_readable_text('Sussudio') + actual_text = actual_gathered_vault_defaults.get_readable_text("Sussudio") assert actual_text == expected_text diff --git a/tests/test_canvas_utils_fpath_funcs.py b/tests/test_canvas_utils_fpath_funcs.py index a674f99..f317217 100644 --- a/tests/test_canvas_utils_fpath_funcs.py +++ b/tests/test_canvas_utils_fpath_funcs.py @@ -1,14 +1,14 @@ from pathlib import Path -import pytest +import pytest -from obsidiantools.canvas_utils import (get_canvas_relpaths_from_dir) +from obsidiantools.canvas_utils import get_canvas_relpaths_from_dir @pytest.fixture def mocker_md_file(mocker): mocked_output = mocker.mock_open() - mocker.patch('builtins.open', mocked_output) + mocker.patch("builtins.open", mocked_output) return mocked_output @@ -19,4 +19,4 @@ def test_get_canvas_relpaths_from_dir(tmp_path): assert isinstance(actual_relpaths, list) for p in actual_relpaths: assert isinstance(p, Path) - assert p.suffix == 'canvas' + assert p.suffix == "canvas" diff --git a/tests/test_canvas_utils_vault_stub.py b/tests/test_canvas_utils_vault_stub.py index bb28b25..41d4238 100644 --- a/tests/test_canvas_utils_vault_stub.py +++ b/tests/test_canvas_utils_vault_stub.py @@ -1,39 +1,38 @@ -import pytest from pathlib import Path +import pytest from obsidiantools.canvas_utils import get_canvas_relpaths_matching_subdirs - # NOTE: run the tests from the project dir. WKD = Path().cwd() @pytest.fixture def actual_vault_path(): - return WKD / 'tests/vault-stub' + return WKD / "tests/vault-stub" def test_get_canvas_relpaths_matching_subdirs(actual_vault_path): actual_w_root = get_canvas_relpaths_matching_subdirs( - actual_vault_path, include_root=True) + actual_vault_path, include_root=True + ) # not including files directly in vault root: actual_wo_root = get_canvas_relpaths_matching_subdirs( - actual_vault_path, include_root=False) - expected_in_root = [Path('Crazy wall.canvas'), - Path('Crazy wall 2.canvas')] - assert (set(actual_w_root).difference(actual_wo_root) - == set(expected_in_root)) + actual_vault_path, include_root=False + ) + expected_in_root = [Path("Crazy wall.canvas"), Path("Crazy wall 2.canvas")] + assert set(actual_w_root).difference(actual_wo_root) == set(expected_in_root) # same result but via the other kwarg: actual_w_lipsum_only = get_canvas_relpaths_matching_subdirs( - actual_vault_path, include_subdirs=['lipsum']) - assert (set(actual_w_lipsum_only).difference(actual_wo_root) - == set(expected_in_root)) + actual_vault_path, include_subdirs=["lipsum"] + ) + assert set(actual_w_lipsum_only).difference(actual_wo_root) == set(expected_in_root) # both kwargs not default: actual_w_lipsum_only = get_canvas_relpaths_matching_subdirs( - actual_vault_path, include_subdirs=['lipsum'], include_root=False) - assert (set(actual_w_lipsum_only).difference(actual_wo_root) - == set()) + actual_vault_path, include_subdirs=["lipsum"], include_root=False + ) + assert set(actual_w_lipsum_only).difference(actual_wo_root) == set() diff --git a/tests/test_html_processing.py b/tests/test_html_processing.py index 4fec610..b15ffc4 100644 --- a/tests/test_html_processing.py +++ b/tests/test_html_processing.py @@ -1,8 +1,6 @@ from pathlib import Path -from obsidiantools.html_processing import (_remove_code, - _remove_del_text, - _remove_latex) +from obsidiantools.html_processing import _remove_code, _remove_del_text, _remove_latex from obsidiantools.md_utils import _get_html_from_md_file # NOTE: run the tests from the project dir. @@ -10,7 +8,7 @@ def test_remove_code(): - fpath = Path('.') / 'tests/general/wikilinks_exclude-code.md' + fpath = Path(".") / "tests/general/wikilinks_exclude-code.md" actual_html = _get_html_from_md_file(fpath) actual_proc_html = _remove_code(actual_html) @@ -24,7 +22,7 @@ def test_remove_code(): def test_remove_del_text(): - fpath = Path('.') / 'tests/general/readable-text_all-deleted.md' + fpath = Path(".") / "tests/general/readable-text_all-deleted.md" actual_html = _get_html_from_md_file(fpath) actual_proc_html = _remove_del_text(actual_html) @@ -35,7 +33,7 @@ def test_remove_del_text(): def test_remove_latex_in_note_with_highly_formatted_text(): - fpath = Path('.') / 'tests/general/latex.md' + fpath = Path(".") / "tests/general/latex.md" actual_html = _get_html_from_md_file(fpath) actual_proc_html = _remove_latex(actual_html) diff --git a/tests/test_md_utils.py b/tests/test_md_utils.py index b926080..c67f233 100644 --- a/tests/test_md_utils.py +++ b/tests/test_md_utils.py @@ -1,24 +1,27 @@ -import pytest from pathlib import Path -from obsidiantools.md_utils import (_get_all_wikilinks_from_source_text, - _get_all_embedded_files_from_source_text, - _get_unique_wikilinks_from_source_text, - _get_all_md_link_info_from_source_text, - _get_unique_md_links_from_source_text, - get_unique_md_links, - _get_html_from_md_file, - get_source_text_from_md_file, - _transform_md_file_string_for_tag_parsing, - get_wikilinks, - get_embedded_files, - get_front_matter, - get_tags, - _remove_wikilinks_from_source_text, - _replace_wikilinks_with_their_text, - _replace_md_links_with_their_text, - get_readable_text_from_md_file) -from obsidiantools.html_processing import (_get_all_latex_from_html_content) +import pytest + +from obsidiantools.html_processing import _get_all_latex_from_html_content +from obsidiantools.md_utils import ( + _get_all_embedded_files_from_source_text, + _get_all_md_link_info_from_source_text, + _get_all_wikilinks_from_source_text, + _get_html_from_md_file, + _get_unique_md_links_from_source_text, + _get_unique_wikilinks_from_source_text, + _remove_wikilinks_from_source_text, + _replace_md_links_with_their_text, + _replace_wikilinks_with_their_text, + _transform_md_file_string_for_tag_parsing, + get_embedded_files, + get_front_matter, + get_readable_text_from_md_file, + get_source_text_from_md_file, + get_tags, + get_unique_md_links, + get_wikilinks, +) @pytest.fixture @@ -71,78 +74,94 @@ def txt_md_links_stub(): @pytest.fixture def txt_sussudio_stub(): - text = _get_html_from_md_file('tests/vault-stub/Sussudio.md') + text = _get_html_from_md_file("tests/vault-stub/Sussudio.md") return text @pytest.fixture def txt_wikilink_extraction_stub(): - with open('tests/general/wikilinks_extraction.md') as f: + with open("tests/general/wikilinks_extraction.md") as f: in_str = f.read() return in_str @pytest.fixture def txt_md_link_extraction_stub(): - with open('tests/general/md-links_extraction.md') as f: + with open("tests/general/md-links_extraction.md") as f: in_str = f.read() return in_str def test_get_all_wikilinks_from_source_text(html_wikilinks_stub): actual_results = _get_all_wikilinks_from_source_text(html_wikilinks_stub) - expected_results = ['Shopping list', 'Bananas', 'Banana splits', - 'Apples', - 'Flour', 'Flower', - 'Bananas', - 'Durians', - 'Apples', 'Bananas', 'Protein shakes'] + expected_results = [ + "Shopping list", + "Bananas", + "Banana splits", + "Apples", + "Flour", + "Flower", + "Bananas", + "Durians", + "Apples", + "Bananas", + "Protein shakes", + ] assert actual_results == expected_results def test_get_all_wikilinks_from_source_text_keep_aliases(html_wikilinks_stub): actual_results = _get_all_wikilinks_from_source_text( - html_wikilinks_stub, remove_aliases=False) - expected_results = ['Shopping list | shopping list', - 'Bananas', 'Banana splits', - 'Apples', - 'Flour', 'Flower | flower', - 'Bananas | BANANAS', - 'Durians', - 'Apples|Freshly squeezed apple juice', - 'Bananas|Banana smoothie', - 'Protein shakes#Protein powder|Vanilla whey protein'] + html_wikilinks_stub, remove_aliases=False + ) + expected_results = [ + "Shopping list | shopping list", + "Bananas", + "Banana splits", + "Apples", + "Flour", + "Flower | flower", + "Bananas | BANANAS", + "Durians", + "Apples|Freshly squeezed apple juice", + "Bananas|Banana smoothie", + "Protein shakes#Protein powder|Vanilla whey protein", + ] assert actual_results == expected_results def test_get_all_embedded_files_from_source_text(html_wikilinks_stub): - actual_results = _get_all_embedded_files_from_source_text( - html_wikilinks_stub) - expected_results = ['Egg.jpg', 'Easter egg.png', 'Egg.jpg'] + actual_results = _get_all_embedded_files_from_source_text(html_wikilinks_stub) + expected_results = ["Egg.jpg", "Easter egg.png", "Egg.jpg"] assert actual_results == expected_results -def test_get_all_embedded_files_from_source_text_keep_aliases( - html_wikilinks_stub): +def test_get_all_embedded_files_from_source_text_keep_aliases(html_wikilinks_stub): actual_results = _get_all_embedded_files_from_source_text( - html_wikilinks_stub, remove_aliases=False) - expected_results = ['Egg.jpg', 'Easter egg.png', 'Egg.jpg | 125'] + html_wikilinks_stub, remove_aliases=False + ) + expected_results = ["Egg.jpg", "Easter egg.png", "Egg.jpg | 125"] assert actual_results == expected_results def test_get_unique_wikilinks_from_html_content(html_wikilinks_stub): actual_results = _get_unique_wikilinks_from_source_text( - html_wikilinks_stub, remove_aliases=True) - expected_results = ['Shopping list', - 'Bananas', 'Banana splits', - 'Apples', - 'Flour', 'Flower', - 'Durians', - 'Protein shakes'] + html_wikilinks_stub, remove_aliases=True + ) + expected_results = [ + "Shopping list", + "Bananas", + "Banana splits", + "Apples", + "Flour", + "Flower", + "Durians", + "Protein shakes", + ] assert actual_results == expected_results assert isinstance(expected_results, list) @@ -154,20 +173,27 @@ def test_get_unique_wikilinks_from_html_content_has_unique_links(html_wikilinks_ def test_get_all_md_link_info(txt_md_links_stub): - expected_links = [('The Times 03/Jan/2009 Chancellor on brink of second bailout for banks', - 'https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h'), - ("Chancellor Alistair Darling on brink of second bailout for banks", - 'https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h'), - ('ADA', 'https://cardano.org/') - ] + expected_links = [ + ( + "The Times 03/Jan/2009 Chancellor on brink of second bailout for banks", + "https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h", + ), + ( + "Chancellor Alistair Darling on brink of second bailout for banks", + "https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h", + ), + ("ADA", "https://cardano.org/"), + ] actual_links = _get_all_md_link_info_from_source_text(txt_md_links_stub) assert actual_links == expected_links def test_get_unique_md_links_has_order_preserved(txt_md_links_stub): - expected_links = ['https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h', - 'https://cardano.org/'] + expected_links = [ + "https://www.thetimes.co.uk/article/chancellor-alistair-darling-on-brink-of-second-bailout-for-banks-n9l382mn62h", + "https://cardano.org/", + ] actual_links = _get_unique_md_links_from_source_text(txt_md_links_stub) assert actual_links == expected_links @@ -180,39 +206,39 @@ def test_get_unique_md_links_has_unique_links(txt_md_links_stub): def test_pretend_wikilink_not_extracted_from_front_matter(txt_sussudio_stub): actual_links = _get_unique_wikilinks_from_source_text(txt_sussudio_stub) - assert not set(['Polka Party!']).issubset(set(actual_links)) + assert not {"Polka Party!"}.issubset(set(actual_links)) def test_sussudio_front_matter(): - expected_metadata = {'title': 'Sussudio', - 'artist': 'Phil Collins', - 'category': 'music', - 'year': 1985, - 'url': 'https://www.discogs.com/Phil-Collins-Sussudio/master/106239', - 'references': [[['American Psycho (film)']], 'Polka Party!'], - 'chart_peaks': [{'US': 1}, {'UK': 12}]} - actual_metadata = get_front_matter( - Path('.') / 'tests/vault-stub/Sussudio.md') + expected_metadata = { + "title": "Sussudio", + "artist": "Phil Collins", + "category": "music", + "year": 1985, + "url": "https://www.discogs.com/Phil-Collins-Sussudio/master/106239", + "references": [[["American Psycho (film)"]], "Polka Party!"], + "chart_peaks": [{"US": 1}, {"UK": 12}], + } + actual_metadata = get_front_matter(Path(".") / "tests/vault-stub/Sussudio.md") assert actual_metadata == expected_metadata def test_ne_fuit_front_matter(): expected_metadata = {} - actual_metadata = get_front_matter( - Path('.') / 'tests/vault-stub/lipsum/Ne fuit.md') + actual_metadata = get_front_matter(Path(".") / "tests/vault-stub/lipsum/Ne fuit.md") assert actual_metadata == expected_metadata def test_front_matter_only_parsing(): - fm_only_files = Path('.').glob('tests/general/frontmatter-only*.md') + fm_only_files = Path(".").glob("tests/general/frontmatter-only*.md") for f in fm_only_files: actual_txt = get_source_text_from_md_file(f) - expected_txt = '\n' + expected_txt = "\n" assert actual_txt == expected_txt def test_separators_not_front_matter_parsing(): - files = Path('.').glob('tests/general/not-frontmatter*.md') + files = Path(".").glob("tests/general/not-frontmatter*.md") for f in files: actual_output = get_front_matter(f) expected_output = {} @@ -220,7 +246,7 @@ def test_separators_not_front_matter_parsing(): def test_handle_invalid_front_matter(): - files = Path('.').glob('tests/general/invalid-frontmatter*.md') + files = Path(".").glob("tests/general/invalid-frontmatter*.md") for f in files: actual_output = get_front_matter(f) expected_output = {} @@ -228,10 +254,10 @@ def test_handle_invalid_front_matter(): def test_front_matter_parse_double_curly(): - fpath = Path('.') / 'tests/general/frontmatter_parse-double-curly.md' + fpath = Path(".") / "tests/general/frontmatter_parse-double-curly.md" actual_txt = get_source_text_from_md_file(fpath) - expected_txt = '\n' + expected_txt = "\n" assert actual_txt == expected_txt @@ -245,119 +271,124 @@ def test_hash_char_parsing_func(): def test_sussudio_tags_with_nesting_not_shown(): - actual_tags = get_tags( - Path('.') / 'tests/vault-stub/Sussudio.md') - expected_tags = ['y1982', 'y_1982', 'y-1982', - 'y1982', 'y2000'] + actual_tags = get_tags(Path(".") / "tests/vault-stub/Sussudio.md") + expected_tags = ["y1982", "y_1982", "y-1982", "y1982", "y2000"] assert actual_tags == expected_tags def test_sussudio_tags_with_nesting_shown(): - actual_tags = get_tags( - Path('.') / 'tests/vault-stub/Sussudio.md', show_nested=True) - expected_tags = ['y1982', 'y_1982', 'y-1982', - 'y1982/sep', 'y2000/party-over/oops/out-of-time'] + actual_tags = get_tags(Path(".") / "tests/vault-stub/Sussudio.md", show_nested=True) + expected_tags = [ + "y1982", + "y_1982", + "y-1982", + "y1982/sep", + "y2000/party-over/oops/out-of-time", + ] assert actual_tags == expected_tags def test_embedded_files_alias_scaling(): actual_embedded_images = get_embedded_files( - Path('.') / 'tests/general/embedded-images_in-table.md') - expected_embedded_images = ['test-image_1_before.png', - 'test-image_1_after.png', - 'test-image_2_before.png', - 'test-image_2_after.png'] + Path(".") / "tests/general/embedded-images_in-table.md" + ) + expected_embedded_images = [ + "test-image_1_before.png", + "test-image_1_after.png", + "test-image_2_before.png", + "test-image_2_after.png", + ] assert actual_embedded_images == expected_embedded_images def test_wikilinks_code_block(): - actual_links = get_wikilinks( - Path('.') / 'tests/general/wikilinks_exclude-code.md') + actual_links = get_wikilinks(Path(".") / "tests/general/wikilinks_exclude-code.md") expected_links = [] assert actual_links == expected_links def test_latex(): - html = _get_html_from_md_file(Path('.') / 'tests/general/latex.md') + html = _get_html_from_md_file(Path(".") / "tests/general/latex.md") actual_latex_list = _get_all_latex_from_html_content(html) - expected_latex_list = ['\\beta', '\\beta', - '\\hat{\\beta}_{GEE} \\xrightarrow{D} N(\\beta_{0}, \\Sigma(\\beta_{0}))', - '\\beta', - 'U_{GEE}(\\beta, \\alpha, \\phi) = \\sum_{i=1}^{n} D_{i}^T~V_{i}(\\alpha; \\phi)^{-1} (y_{i} - \\mu_{i}) = 0 \\tag{1} \\label{eq1}', - '\\eqref{eq1}'] + expected_latex_list = [ + "\\beta", + "\\beta", + "\\hat{\\beta}_{GEE} \\xrightarrow{D} N(\\beta_{0}, \\Sigma(\\beta_{0}))", + "\\beta", + "U_{GEE}(\\beta, \\alpha, \\phi) = \\sum_{i=1}^{n} D_{i}^T~V_{i}(\\alpha; \\phi)^{-1} (y_{i} - \\mu_{i}) = 0 \\tag{1} \\label{eq1}", + "\\eqref{eq1}", + ] assert actual_latex_list == expected_latex_list def test_remove_wikilinks(txt_wikilink_extraction_stub): - out_str = _remove_wikilinks_from_source_text( - txt_wikilink_extraction_stub) + out_str = _remove_wikilinks_from_source_text(txt_wikilink_extraction_stub) expected_str = "\n" * 6 assert out_str == expected_str def test_wikilinks_as_readable_text(txt_wikilink_extraction_stub): - out_str = _replace_wikilinks_with_their_text( - txt_wikilink_extraction_stub) + out_str = _replace_wikilinks_with_their_text(txt_wikilink_extraction_stub) expected_str = "\n".join(["A", "B", "see", "dee", "ee", "A"]) + "\n" assert out_str == expected_str def test_md_links_as_readable_text(txt_md_link_extraction_stub): - out_str = _replace_md_links_with_their_text( - txt_md_link_extraction_stub) + out_str = _replace_md_links_with_their_text(txt_md_link_extraction_stub) - expected_str = ( - """Obsidian.md homepage + expected_str = """Obsidian.md homepage Github homepage https://obsidian.md Github homepage -""") +""" assert out_str == expected_str def test_unique_md_links(): actual_links = get_unique_md_links( - Path('.') / 'tests/general/md-links_extraction.md') - expected_links = ['http://obsidian.md', 'https://github.com'] + Path(".") / "tests/general/md-links_extraction.md" + ) + expected_links = ["http://obsidian.md", "https://github.com"] assert actual_links == expected_links def test_readable_text_from_latex_md_stub_default_tags(): - actual_str = get_readable_text_from_md_file( - Path('.') / 'tests/general/latex.md') - expected_str = '# Note with LaTeX\n\n## GEE \n\nRegression coefficients estimated through GEE are asymptotically normal: \n\nThe underscore chars above need to be caught through MathJax - capture subscripts rather than emphasis in the parsing.\n\n## GEE estimation\n\nA few eqs more using deeper LaTeX functionality:\n\nEquations for GEE are solved for the regression parameters using: \n\nTaking the expectation of the equation system in ...\n' + actual_str = get_readable_text_from_md_file(Path(".") / "tests/general/latex.md") + expected_str = "# Note with LaTeX\n\n## GEE \n\nRegression coefficients estimated through GEE are asymptotically normal: \n\nThe underscore chars above need to be caught through MathJax - capture subscripts rather than emphasis in the parsing.\n\n## GEE estimation\n\nA few eqs more using deeper LaTeX functionality:\n\nEquations for GEE are solved for the regression parameters using: \n\nTaking the expectation of the equation system in ...\n" assert actual_str == expected_str def test_readable_text_from_latex_md_stub_allow_no_tags(): actual_str = get_readable_text_from_md_file( - Path('.') / 'tests/general/latex.md', tags=[]) - expected_str = 'Note with LaTeX GEE Regression coefficients estimated through GEE are asymptotically normal: The underscore chars above need to be caught through MathJax - capture subscripts rather than emphasis in the parsing. GEE estimation A few eqs more using deeper LaTeX functionality: Equations for GEE are solved for the regression parameters using: Taking the expectation of the equation system in ...\n' + Path(".") / "tests/general/latex.md", tags=[] + ) + expected_str = "Note with LaTeX GEE Regression coefficients estimated through GEE are asymptotically normal: The underscore chars above need to be caught through MathJax - capture subscripts rather than emphasis in the parsing. GEE estimation A few eqs more using deeper LaTeX functionality: Equations for GEE are solved for the regression parameters using: Taking the expectation of the equation system in ...\n" assert actual_str == expected_str def test_readable_text_strikethrough_is_deleted(): actual_str = get_readable_text_from_md_file( - Path('.') / 'tests/general/readable-text_all-deleted.md') - expected_str = '\n' + Path(".") / "tests/general/readable-text_all-deleted.md" + ) + expected_str = "\n" assert actual_str == expected_str def test_readable_text_embedded_files_are_removed(): actual_str = get_readable_text_from_md_file( - Path('.') / 'tests/general/embedded-files_in-body.md') - expected_str = '\n' + Path(".") / "tests/general/embedded-files_in-body.md" + ) + expected_str = "\n" assert actual_str == expected_str def test_source_text_has_text_after_problematic_latex(): - expected_str = ( - """# Generalised estimating equations + expected_str = """# Generalised estimating equations **Generalised estimating equations (GEE)** are ... @@ -378,10 +409,10 @@ def test_source_text_has_text_after_problematic_latex(): ### Another subheading Text that shouldn't disappear. -""") +""" actual_str = get_source_text_from_md_file( - Path('.') / 'tests/general/source-text_handle-latex.md', - remove_math=True) + Path(".") / "tests/general/source-text_handle-latex.md", remove_math=True + ) assert actual_str == expected_str diff --git a/tests/test_md_utils_fpath_funcs.py b/tests/test_md_utils_fpath_funcs.py index 9797b3d..7034a4a 100644 --- a/tests/test_md_utils_fpath_funcs.py +++ b/tests/test_md_utils_fpath_funcs.py @@ -1,18 +1,21 @@ from pathlib import Path + import pytest -from obsidiantools.md_utils import (_get_html_from_md_file, - get_source_text_from_md_file) -from obsidiantools.md_utils import (get_md_relpaths_from_dir, - get_md_links, - get_unique_wikilinks, - get_wikilinks) +from obsidiantools.md_utils import ( + _get_html_from_md_file, + get_md_links, + get_md_relpaths_from_dir, + get_source_text_from_md_file, + get_unique_wikilinks, + get_wikilinks, +) @pytest.fixture def mocker_md_file(mocker): mocked_output = mocker.mock_open() - mocker.patch('builtins.open', mocked_output) + mocker.patch("builtins.open", mocked_output) return mocked_output @@ -23,7 +26,7 @@ def test_get_md_relpaths_from_dir(tmp_path): assert isinstance(actual_relpaths, list) for p in actual_relpaths: assert isinstance(p, Path) - assert p.suffix == 'md' + assert p.suffix == "md" def test_get_html_from_md_file(mocker_md_file): diff --git a/tests/test_md_utils_vault_stub.py b/tests/test_md_utils_vault_stub.py index 0534d69..b8c8cf1 100644 --- a/tests/test_md_utils_vault_stub.py +++ b/tests/test_md_utils_vault_stub.py @@ -1,39 +1,38 @@ -import pytest from pathlib import Path +import pytest from obsidiantools.md_utils import get_md_relpaths_matching_subdirs - # NOTE: run the tests from the project dir. WKD = Path().cwd() @pytest.fixture def actual_vault_path(): - return WKD / 'tests/vault-stub' + return WKD / "tests/vault-stub" def test_get_md_relpaths_matching_subdirs(actual_vault_path): actual_w_root = get_md_relpaths_matching_subdirs( - actual_vault_path, include_root=True) + actual_vault_path, include_root=True + ) # not including files directly in vault root: actual_wo_root = get_md_relpaths_matching_subdirs( - actual_vault_path, include_root=False) - expected_in_root = [Path('Sussudio.md'), - Path('Isolated note.md')] - assert (set(actual_w_root).difference(actual_wo_root) - == set(expected_in_root)) + actual_vault_path, include_root=False + ) + expected_in_root = [Path("Sussudio.md"), Path("Isolated note.md")] + assert set(actual_w_root).difference(actual_wo_root) == set(expected_in_root) # same result but via the other kwarg: actual_w_lipsum_only = get_md_relpaths_matching_subdirs( - actual_vault_path, include_subdirs=['lipsum']) - assert (set(actual_w_lipsum_only).difference(actual_wo_root) - == set(expected_in_root)) + actual_vault_path, include_subdirs=["lipsum"] + ) + assert set(actual_w_lipsum_only).difference(actual_wo_root) == set(expected_in_root) # both kwargs not default: actual_w_lipsum_only = get_md_relpaths_matching_subdirs( - actual_vault_path, include_subdirs=['lipsum'], include_root=False) - assert (set(actual_w_lipsum_only).difference(actual_wo_root) - == set()) + actual_vault_path, include_subdirs=["lipsum"], include_root=False + ) + assert set(actual_w_lipsum_only).difference(actual_wo_root) == set() From 8b31f1961641bda160716bd0f44f6b7df0da0f89 Mon Sep 17 00:00:00 2001 From: JavierGOrdonnez Date: Mon, 9 Mar 2026 19:23:25 +0100 Subject: [PATCH 3/8] [FEAT] add uv-lock --- .gitignore | 1 + uv.lock | 1981 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 1982 insertions(+) create mode 100644 uv.lock diff --git a/.gitignore b/.gitignore index a34e460..e9fe51a 100644 --- a/.gitignore 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dict(zip(shortest_paths_arr, relpaths_list)) diff --git a/obsidiantools/html_processing.py b/obsidiantools/html_processing.py index a8e43b4..27b7ea3 100644 --- a/obsidiantools/html_processing.py +++ b/obsidiantools/html_processing.py @@ -1,3 +1,5 @@ +import re + import bleach from bs4 import BeautifulSoup from html2text import HTML2Text @@ -62,6 +64,8 @@ def _remove_latex(html: str) -> str: soup = BeautifulSoup(html, "lxml") soup = _remove_latex_via_soup(soup) html_str = str(soup) + # Strip leftover $ / $$ delimiters from pymdown-extensions arithmatex + html_str = re.sub(r"\${1,2}", "", html_str) return html_str diff --git a/obsidiantools/md_utils.py b/obsidiantools/md_utils.py index f74c48d..4f7f988 100644 --- a/obsidiantools/md_utils.py +++ b/obsidiantools/md_utils.py @@ -323,6 +323,8 @@ def get_source_text_from_html( if remove_math: soup = _remove_latex_via_soup(soup) new_str = str(soup) + # Strip leftover $ / $$ delimiters from pymdown-extensions arithmatex + new_str = re.sub(r"\${1,2}", "", new_str) return _get_plaintext_from_html(new_str) @@ -364,6 +366,8 @@ def _get_readable_text_from_html(html: str, *, tags: list[str] = None) -> str: soup = _remove_latex_via_soup(soup) soup = _remove_del_text_via_soup(soup) new_str = str(soup) + # Strip leftover $ / $$ delimiters from pymdown-extensions arithmatex + new_str = re.sub(r"\${1,2}", "", new_str) # -BLEACH- if tags is not None: new_str = _remove_main_formatting(new_str, tags=tags) From c0851e64928257146a32804c956069d3c5f42652 Mon Sep 17 00:00:00 2001 From: JavierGOrdonnez Date: Wed, 11 Mar 2026 08:52:37 +0100 Subject: [PATCH 5/8] [FEAT] add logging --- obsidiantools/__init__.py | 20 +++++++++++++++++++ obsidiantools/api.py | 42 ++++++++++++++++++++++++++++++++------- 2 files changed, 55 insertions(+), 7 deletions(-) diff --git a/obsidiantools/__init__.py b/obsidiantools/__init__.py index a00d166..9217570 100644 --- a/obsidiantools/__init__.py +++ b/obsidiantools/__init__.py @@ -1,5 +1,25 @@ +import logging + from . import api as api from . import canvas_utils as canvas_utils from . import html_processing as html_processing from . import md_utils as md_utils from . import media_utils as media_utils + + +def enable_debug(level: int = logging.DEBUG) -> None: + """Enable debug logging for obsidiantools. + + Usage: + import obsidiantools + obsidiantools.enable_debug() # DEBUG level + obsidiantools.enable_debug(logging.INFO) # INFO level only + """ + pkg_logger = logging.getLogger("obsidiantools") + pkg_logger.setLevel(level) + if not pkg_logger.handlers: + handler = logging.StreamHandler() + handler.setFormatter( + logging.Formatter("%(asctime)s [%(levelname)s] %(name)s: %(message)s") + ) + pkg_logger.addHandler(handler) diff --git a/obsidiantools/api.py b/obsidiantools/api.py index 31b51f1..5a0f800 100644 --- a/obsidiantools/api.py +++ b/obsidiantools/api.py @@ -1,3 +1,4 @@ +import logging import warnings from collections import Counter from itertools import chain @@ -7,6 +8,8 @@ import numpy as np import pandas as pd +logger = logging.getLogger(__name__) + from ._constants import METADATA_DF_COLS_GENERIC_TYPE from ._io import _get_shortest_path_by_filename @@ -158,6 +161,11 @@ def __init__( self._canvas_file_index = self._get_canvas_relpaths_by_name( include_subdirs=include_subdirs, include_root=include_root ) + logger.info( + "Found %d md files and %d canvas files", + len(self._md_file_index), + len(self._canvas_file_index), + ) self._is_connected = False self._is_gathered = False @@ -500,6 +508,11 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): """ if not self._is_connected: self._attachments = attachments + logger.info( + "Connecting vault (%d md files, attachments=%s)", + len(self._md_file_index), + attachments, + ) # md content: # index dicts, where k is a note name in the vault: @@ -514,16 +527,30 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): self._unique_wikilinks_index = {} # loop through md files: - for f, relpath in self._md_file_index.items(): - self._connect_update_based_on_new_relpath( - relpath, note=f, show_nested_tags=show_nested_tags - ) + n_md = len(self._md_file_index) + for i, (f, relpath) in enumerate(self._md_file_index.items(), 1): + logger.debug("connect: processing md file %d/%d: %s", i, n_md, relpath) + try: + self._connect_update_based_on_new_relpath( + relpath, note=f, show_nested_tags=show_nested_tags + ) + except Exception: + logger.error( + "connect: failed to process md file '%s'", + relpath, + exc_info=True, + ) + raise # canvas content: # loop through canvas files: self._canvas_content_index = {} self._canvas_graph_detail_index = {} - for f, relpath in self._canvas_file_index.items(): + n_canvas = len(self._canvas_file_index) + for i, (f, relpath) in enumerate(self._canvas_file_index.items(), 1): + logger.debug( + "connect: processing canvas file %d/%d: %s", i, n_canvas, relpath + ) content_c = get_canvas_content(self._dirpath / relpath) self._canvas_content_index[f] = content_c G_c, pos_c, edge_labels_c = get_canvas_graph_detail(content_c) @@ -534,6 +561,7 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): self._set_media_file_attrs() # graph setup: + logger.debug("connect: building graph") graph_data_dict = self.__get_graph_data_dict(attachments=attachments) G = nx.MultiDiGraph(graph_data_dict) self._graph = G @@ -1135,11 +1163,11 @@ def __get_relpaths_by_name(self, *, extension, **kwargs) -> dict[str, Path]: shortest_paths_arr = np.array(all_file_names_list, dtype=object) if extension == "md": shortest_paths_arr[dupe_names_ix] = np.array( - [str(fpath.with_suffix("")) for fpath in relpaths_list] + [fpath.with_suffix("").as_posix() for fpath in relpaths_list] )[dupe_names_ix] if extension == "canvas": shortest_paths_arr[dupe_names_ix] = np.array( - [str(fpath) for fpath in relpaths_list] + [fpath.as_posix() for fpath in relpaths_list] )[dupe_names_ix] return dict(zip(shortest_paths_arr, relpaths_list)) From e804f168fd07b76f1069229bd262494f58911afe Mon Sep 17 00:00:00 2001 From: JavierGOrdonnez Date: Wed, 11 Mar 2026 08:59:28 +0100 Subject: [PATCH 6/8] [FEAT] add skipping of malformed files --- obsidiantools/api.py | 74 +++++++++++++++++++++++++++++++++------ obsidiantools/md_utils.py | 23 ++++++++---- 2 files changed, 80 insertions(+), 17 deletions(-) diff --git a/obsidiantools/api.py b/obsidiantools/api.py index 5a0f800..21ab8d4 100644 --- a/obsidiantools/api.py +++ b/obsidiantools/api.py @@ -8,8 +8,6 @@ import numpy as np import pandas as pd -logger = logging.getLogger(__name__) - from ._constants import METADATA_DF_COLS_GENERIC_TYPE from ._io import _get_shortest_path_by_filename @@ -40,6 +38,8 @@ ) from .media_utils import _get_all_valid_media_file_relpaths +logger = logging.getLogger(__name__) + class Vault: def __init__( @@ -155,6 +155,13 @@ def __init__( self._dirpath = dirpath self._attachments = None # connect() + logger.info("Initialising vault from '%s'", dirpath) + logger.debug( + "Init options: include_subdirs=%s, include_root=%s", + include_subdirs, + include_root, + ) + self._md_file_index = self._get_md_relpaths_by_name( include_subdirs=include_subdirs, include_root=include_root ) @@ -528,6 +535,7 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): # loop through md files: n_md = len(self._md_file_index) + skipped_md = [] for i, (f, relpath) in enumerate(self._md_file_index.items(), 1): logger.debug("connect: processing md file %d/%d: %s", i, n_md, relpath) try: @@ -535,26 +543,35 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): relpath, note=f, show_nested_tags=show_nested_tags ) except Exception: - logger.error( - "connect: failed to process md file '%s'", + logger.warning( + "connect: skipping md file '%s' due to error", relpath, exc_info=True, ) - raise + skipped_md.append(relpath) # canvas content: # loop through canvas files: self._canvas_content_index = {} self._canvas_graph_detail_index = {} n_canvas = len(self._canvas_file_index) + skipped_canvas = [] for i, (f, relpath) in enumerate(self._canvas_file_index.items(), 1): logger.debug( "connect: processing canvas file %d/%d: %s", i, n_canvas, relpath ) - content_c = get_canvas_content(self._dirpath / relpath) - self._canvas_content_index[f] = content_c - G_c, pos_c, edge_labels_c = get_canvas_graph_detail(content_c) - self._canvas_graph_detail_index[f] = G_c, pos_c, edge_labels_c + try: + content_c = get_canvas_content(self._dirpath / relpath) + self._canvas_content_index[f] = content_c + G_c, pos_c, edge_labels_c = get_canvas_graph_detail(content_c) + self._canvas_graph_detail_index[f] = G_c, pos_c, edge_labels_c + except Exception: + logger.warning( + "connect: skipping canvas file '%s' due to error", + relpath, + exc_info=True, + ) + skipped_canvas.append(relpath) # set these up before graph is created: self._set_canvas_file_attrs() @@ -574,6 +591,22 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): self._set_media_file_attrs() self._is_connected = True + n_skipped = len(skipped_md) + len(skipped_canvas) + if n_skipped: + logger.warning( + "Vault connected with %d skipped file(s) (%d md, %d canvas): %s", + n_skipped, + len(skipped_md), + len(skipped_canvas), + [str(p) for p in skipped_md + skipped_canvas], + ) + logger.info( + "Vault connected: %d nodes, %d edges in graph", + G.number_of_nodes(), + G.number_of_edges(), + ) + else: + logger.debug("connect: vault already connected, skipping") return self # fluent @@ -864,9 +897,28 @@ def gather(self, *, tags: list[str] = None): will remove all header formatting (e.g. '#', '##' chars) and produces a one-line string. """ - for f, relpath in self._md_file_index.items(): - self._gather_update_based_on_new_relpath(relpath, note=f, tags=tags) + logger.info("Gathering text from %d md files", len(self._md_file_index)) + n_md = len(self._md_file_index) + skipped = [] + for i, (f, relpath) in enumerate(self._md_file_index.items(), 1): + logger.debug("gather: processing file %d/%d: %s", i, n_md, relpath) + try: + self._gather_update_based_on_new_relpath(relpath, note=f, tags=tags) + except Exception: + logger.warning( + "gather: skipping file '%s' due to error", + relpath, + exc_info=True, + ) + skipped.append(relpath) self._is_gathered = True + if skipped: + logger.warning( + "Vault gathered with %d skipped file(s): %s", + len(skipped), + [str(p) for p in skipped], + ) + logger.info("Vault gathered successfully") return self # fluent diff --git a/obsidiantools/md_utils.py b/obsidiantools/md_utils.py index 4f7f988..1409f39 100644 --- a/obsidiantools/md_utils.py +++ b/obsidiantools/md_utils.py @@ -1,3 +1,4 @@ +import logging import re from pathlib import Path @@ -25,6 +26,8 @@ _remove_main_formatting, ) +logger = logging.getLogger(__name__) + def get_md_relpaths_from_dir(dir_path: Path) -> list[Path]: """Get list of relative paths for markdown files in a given directory, @@ -263,17 +266,25 @@ def _get_md_front_matter_and_content( return frontmatter.parse(file_string) # for invalid YAML, return the whole file as content: except yaml.scanner.ScannerError as e: - print(f"Front matter not populated for {filepath.name}: {repr(e)}") + logger.debug("Front matter not populated for %s: %r", filepath.name, e) return {}, file_string except yaml.parser.ParserError as e: - print(f"Front matter not populated for {filepath.name}: {repr(e)}") + logger.debug("Front matter not populated for %s: %r", filepath.name, e) return {}, file_string # handle template {{}} chars in front matter: except yaml.constructor.ConstructorError: - file_string_esc = file_string.translate( - str.maketrans({"{": r"\{", "}": r"\}"}) - ) - return frontmatter.parse(file_string_esc) + try: + file_string_esc = file_string.translate( + str.maketrans({"{": r"\{", "}": r"\}"}) + ) + return frontmatter.parse(file_string_esc) + except Exception as e: + logger.debug( + "Front matter not populated for %s after escaping: %r", + filepath.name, + e, + ) + return {}, file_string # any others: except Exception: return {}, file_string From c87e4e4456292c6fd8e6a8ec8ea62a9b5a7f4feb Mon Sep 17 00:00:00 2001 From: JavierGOrdonnez Date: Wed, 11 Mar 2026 10:04:23 +0100 Subject: [PATCH 7/8] [FEAT] introduce parallel loading --- obsidiantools/api.py | 224 +++++++++++++++++------- test_quick.py | 46 +++++ tests/test_api_vault_stub_parallel.py | 238 ++++++++++++++++++++++++++ 3 files changed, 446 insertions(+), 62 deletions(-) create mode 100644 test_quick.py create mode 100644 tests/test_api_vault_stub_parallel.py diff --git a/obsidiantools/api.py b/obsidiantools/api.py index 21ab8d4..e709e24 100644 --- a/obsidiantools/api.py +++ b/obsidiantools/api.py @@ -1,6 +1,7 @@ import logging import warnings from collections import Counter +from concurrent.futures import ThreadPoolExecutor, as_completed from itertools import chain from pathlib import Path @@ -491,7 +492,13 @@ def canvas_graph_detail_index( ]: self._canvas_graph_detail_index = value - def connect(self, *, show_nested_tags: bool = False, attachments=False): + def connect( + self, + *, + show_nested_tags: bool = False, + attachments=False, + workers: int = None, + ): """connect your notes together by representing the vault as a Networkx graph object, G. @@ -512,13 +519,18 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): To include media files in the graph, set this option to True. This will lead to the inclusion of media files' in the backlinks_index. + workers (int, optional): number of threads to use for parallel + file processing. Defaults to None (sequential processing). + Set to a positive integer to enable threading, e.g. + ``workers=os.cpu_count()``. """ if not self._is_connected: self._attachments = attachments logger.info( - "Connecting vault (%d md files, attachments=%s)", + "Connecting vault (%d md files, attachments=%s, workers=%s)", len(self._md_file_index), attachments, + workers, ) # md content: @@ -536,19 +548,49 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): # loop through md files: n_md = len(self._md_file_index) skipped_md = [] - for i, (f, relpath) in enumerate(self._md_file_index.items(), 1): - logger.debug("connect: processing md file %d/%d: %s", i, n_md, relpath) - try: - self._connect_update_based_on_new_relpath( - relpath, note=f, show_nested_tags=show_nested_tags - ) - except Exception: - logger.warning( - "connect: skipping md file '%s' due to error", - relpath, - exc_info=True, + + if workers and workers > 1: + # parallel processing via thread pool: + with ThreadPoolExecutor(max_workers=workers) as executor: + futures = { + executor.submit( + self._connect_process_md_file, + relpath, + note=f, + show_nested_tags=show_nested_tags, + ): (f, relpath) + for f, relpath in self._md_file_index.items() + } + for future in as_completed(futures): + f, relpath = futures[future] + try: + result = future.result() + self._connect_merge_result(result) + except Exception: + logger.warning( + "connect: skipping md file '%s' due to error", + relpath, + exc_info=True, + ) + skipped_md.append(relpath) + else: + # sequential processing (default): + for i, (f, relpath) in enumerate(self._md_file_index.items(), 1): + logger.debug( + "connect: processing md file %d/%d: %s", i, n_md, relpath ) - skipped_md.append(relpath) + try: + result = self._connect_process_md_file( + relpath, note=f, show_nested_tags=show_nested_tags + ) + self._connect_merge_result(result) + except Exception: + logger.warning( + "connect: skipping md file '%s' due to error", + relpath, + exc_info=True, + ) + skipped_md.append(relpath) # canvas content: # loop through canvas files: @@ -610,11 +652,13 @@ def connect(self, *, show_nested_tags: bool = False, attachments=False): return self # fluent - def _connect_update_based_on_new_relpath( + def _connect_process_md_file( self, relpath: Path, *, note: str, show_nested_tags: bool - ): - """Individual file read & associated attrs update for the - connect method.""" + ) -> dict: + """Process a single md file for the connect method. + + Returns a dict of extracted data (pure computation, no mutation). + """ exclude_canvas = not self._attachments # MAIN file read: @@ -624,30 +668,37 @@ def _connect_update_based_on_new_relpath( html = _get_html_from_md_content(content) src_txt = get_source_text_from_html(html, remove_code=True) - # info from core text: - self._md_links_index[note] = _get_md_links_from_source_text(src_txt) - self._unique_md_links_index[note] = _get_unique_md_links_from_source_text( - src_txt - ) - self._embedded_files_index[note] = ( - _get_all_embedded_files_from_source_text(src_txt, remove_aliases=True) - # (aliases are redundant for connect method) - ) - self._wikilinks_index[note] = _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=True, exclude_canvas=exclude_canvas - ) - self._unique_wikilinks_index[note] = _get_unique_wikilinks_from_source_text( - src_txt, remove_aliases=True, exclude_canvas=exclude_canvas - ) - # info from html: - self._math_index[note] = _get_all_latex_from_html_content(html) - # split out front matter: - self._front_matter_index[note] = front_matter - - # MORE file reads needed for extra info: - self._tags_index[note] = get_tags( - self._dirpath / relpath, show_nested=show_nested_tags - ) + return { + "note": note, + "md_links": _get_md_links_from_source_text(src_txt), + "unique_md_links": _get_unique_md_links_from_source_text(src_txt), + "embedded_files": _get_all_embedded_files_from_source_text( + src_txt, remove_aliases=True + ), + "wikilinks": _get_all_wikilinks_from_source_text( + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ), + "unique_wikilinks": _get_unique_wikilinks_from_source_text( + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ), + "math": _get_all_latex_from_html_content(html), + "front_matter": front_matter, + "tags": get_tags( + self._dirpath / relpath, show_nested=show_nested_tags + ), + } + + def _connect_merge_result(self, result: dict): + """Merge a single file's processed result into the indexes.""" + note = result["note"] + self._md_links_index[note] = result["md_links"] + self._unique_md_links_index[note] = result["unique_md_links"] + self._embedded_files_index[note] = result["embedded_files"] + self._wikilinks_index[note] = result["wikilinks"] + self._unique_wikilinks_index[note] = result["unique_wikilinks"] + self._math_index[note] = result["math"] + self._front_matter_index[note] = result["front_matter"] + self._tags_index[note] = result["tags"] def _set_media_file_attrs(self): ( @@ -875,7 +926,7 @@ def _set_graph_related_attributes(self): self._nonexistent_notes = self._get_nonexistent_notes() self._isolated_notes = self._get_isolated_notes(graph=self._graph) - def gather(self, *, tags: list[str] = None): + def gather(self, *, tags: list[str] = None, workers: int = None): """gather the content of your notes so that all the plaintext is stored in one place for easy access. @@ -896,21 +947,60 @@ def gather(self, *, tags: list[str] = None): their formatting in the final text. For example, tags=[] will remove all header formatting (e.g. '#', '##' chars) and produces a one-line string. + workers (int, optional): number of threads to use for parallel + file processing. Defaults to None (sequential processing). + Set to a positive integer to enable threading, e.g. + ``workers=os.cpu_count()``. """ - logger.info("Gathering text from %d md files", len(self._md_file_index)) + logger.info( + "Gathering text from %d md files (workers=%s)", + len(self._md_file_index), + workers, + ) n_md = len(self._md_file_index) skipped = [] - for i, (f, relpath) in enumerate(self._md_file_index.items(), 1): - logger.debug("gather: processing file %d/%d: %s", i, n_md, relpath) - try: - self._gather_update_based_on_new_relpath(relpath, note=f, tags=tags) - except Exception: - logger.warning( - "gather: skipping file '%s' due to error", - relpath, - exc_info=True, - ) - skipped.append(relpath) + + if workers and workers > 1: + # parallel processing via thread pool: + with ThreadPoolExecutor(max_workers=workers) as executor: + futures = { + executor.submit( + self._gather_process_md_file, + relpath, + note=f, + tags=tags, + ): (f, relpath) + for f, relpath in self._md_file_index.items() + } + for future in as_completed(futures): + f, relpath = futures[future] + try: + result = future.result() + self._gather_merge_result(result) + except Exception: + logger.warning( + "gather: skipping file '%s' due to error", + relpath, + exc_info=True, + ) + skipped.append(relpath) + else: + # sequential processing (default): + for i, (f, relpath) in enumerate(self._md_file_index.items(), 1): + logger.debug("gather: processing file %d/%d: %s", i, n_md, relpath) + try: + result = self._gather_process_md_file( + relpath, note=f, tags=tags + ) + self._gather_merge_result(result) + except Exception: + logger.warning( + "gather: skipping file '%s' due to error", + relpath, + exc_info=True, + ) + skipped.append(relpath) + self._is_gathered = True if skipped: logger.warning( @@ -922,20 +1012,30 @@ def gather(self, *, tags: list[str] = None): return self # fluent - def _gather_update_based_on_new_relpath( + def _gather_process_md_file( self, relpath: Path, *, note: str, tags: list[str] - ): - """Individual file read & associated attrs update for the - gather method.""" + ) -> dict: + """Process a single md file for the gather method. + + Returns a dict of extracted data (pure computation, no mutation). + """ # MAIN file read: _, content = _get_md_front_matter_and_content(self._dirpath / relpath) html = _get_html_from_md_content(content) # (also remove LaTeX for source text:) src_txt = get_source_text_from_html(html, remove_code=True, remove_math=True) - # 'source' text will not remove any content, but 'readable' will: - self._source_text_index[note] = src_txt - self._readable_text_index[note] = _get_readable_text_from_html(html, tags=tags) + return { + "note": note, + "source_text": src_txt, + "readable_text": _get_readable_text_from_html(html, tags=tags), + } + + def _gather_merge_result(self, result: dict): + """Merge a single file's processed result into the indexes.""" + note = result["note"] + self._source_text_index[note] = result["source_text"] + self._readable_text_index[note] = result["readable_text"] def get_backlinks(self, note_name: str) -> list[str]: """Get backlinks for a note (given its name). diff --git a/test_quick.py b/test_quick.py new file mode 100644 index 0000000..1f14704 --- /dev/null +++ b/test_quick.py @@ -0,0 +1,46 @@ +#!/usr/bin/env python3 +"""Quick test to verify parallel tests work.""" +import time +from pathlib import Path +from obsidiantools.api import Vault + +WKD = Path().cwd() +VAULT_STUB = WKD / "tests/vault-stub" + +print("Testing sequential connection...") +start = time.time() +v_seq = Vault(VAULT_STUB).connect() +seq_connect_time = time.time() - start +print(f" Sequential connect: {seq_connect_time:.3f}s") +print(f" Graph nodes: {len(v_seq.graph.nodes)}") +print(f" Graph edges: {len(v_seq.graph.edges)}") + +start = time.time() +v_seq = v_seq.gather() +seq_gather_time = time.time() - start +print(f" Sequential gather: {seq_gather_time:.3f}s") +print(f" Source text files: {len(v_seq.source_text_index)}") + +print("\nTesting parallel connection with 4 workers...") +start = time.time() +v_par = Vault(VAULT_STUB).connect(workers=4) +par_connect_time = time.time() - start +print(f" Parallel connect: {par_connect_time:.3f}s") +print(f" Graph nodes: {len(v_par.graph.nodes)}") +print(f" Graph edges: {len(v_par.graph.edges)}") + +start = time.time() +v_par = v_par.gather(workers=4) +par_gather_time = time.time() - start +print(f" Parallel gather: {par_gather_time:.3f}s") +print(f" Source text files: {len(v_par.source_text_index)}") + +print("\nVerifying equivalence...") +print(f" Graph nodes match: {set(v_seq.graph.nodes) == set(v_par.graph.nodes)}") +print(f" Graph edges match: {set(v_seq.graph.edges) == set(v_par.graph.edges)}") +print(f" Wikilinks match: {v_seq.wikilinks_index == v_par.wikilinks_index}") +print(f" Source text match: {v_seq.source_text_index == v_par.source_text_index}") + +print("\nTiming comparison:") +print(f" Connect speedup: {seq_connect_time / par_connect_time:.2f}x") +print(f" Gather speedup: {seq_gather_time / par_gather_time:.2f}x") diff --git a/tests/test_api_vault_stub_parallel.py b/tests/test_api_vault_stub_parallel.py new file mode 100644 index 0000000..ae9f44a --- /dev/null +++ b/tests/test_api_vault_stub_parallel.py @@ -0,0 +1,238 @@ +"""Tests for parallel (threaded) execution of connect() and gather(). + +Verifies that using workers > 1 produces identical results to the +default sequential path, and that edge cases around the workers param +behave correctly. +""" + +from pathlib import Path + +import pytest + +from obsidiantools.api import Vault + +# NOTE: run the tests from the project dir. +WKD = Path().cwd() +VAULT_STUB = WKD / "tests/vault-stub" +WORKERS = 4 + + +# --- fixtures: sequential (reference) --- + + +@pytest.fixture +def vault_sequential(): + """Vault connected and gathered sequentially (the reference).""" + return Vault(VAULT_STUB).connect().gather() + + +# --- fixtures: parallel --- + + +@pytest.fixture +def vault_parallel(): + """Vault connected and gathered with threads.""" + return Vault(VAULT_STUB).connect(workers=WORKERS).gather(workers=WORKERS) + + +# --- connect(): parallel vs sequential equivalence --- + + +class TestConnectParallel: + """Verify that connect(workers=N) produces the same indexes as + the sequential default.""" + + def test_graph_nodes_match(self, vault_sequential, vault_parallel): + assert set(vault_sequential.graph.nodes) == set(vault_parallel.graph.nodes) + + def test_graph_edges_match(self, vault_sequential, vault_parallel): + assert set(vault_sequential.graph.edges) == set(vault_parallel.graph.edges) + + def test_wikilinks_index_match(self, vault_sequential, vault_parallel): + assert vault_sequential.wikilinks_index == vault_parallel.wikilinks_index + + def test_unique_wikilinks_index_match(self, vault_sequential, vault_parallel): + assert ( + vault_sequential.unique_wikilinks_index + == vault_parallel.unique_wikilinks_index + ) + + def test_md_links_index_match(self, vault_sequential, vault_parallel): + assert vault_sequential.md_links_index == vault_parallel.md_links_index + + def test_embedded_files_index_match(self, vault_sequential, vault_parallel): + assert ( + vault_sequential.embedded_files_index + == vault_parallel.embedded_files_index + ) + + def test_tags_index_match(self, vault_sequential, vault_parallel): + assert vault_sequential.tags_index == vault_parallel.tags_index + + def test_math_index_match(self, vault_sequential, vault_parallel): + assert vault_sequential.math_index == vault_parallel.math_index + + def test_front_matter_index_match(self, vault_sequential, vault_parallel): + assert ( + vault_sequential.front_matter_index == vault_parallel.front_matter_index + ) + + def test_backlinks_index_match(self, vault_sequential, vault_parallel): + # backlinks_index values are lists; order may differ with threading + # so we compare as sets + seq_backlinks = { + k: set(v) for k, v in vault_sequential.backlinks_index.items() + } + par_backlinks = { + k: set(v) for k, v in vault_parallel.backlinks_index.items() + } + assert seq_backlinks == par_backlinks + + def test_nonexistent_notes_match(self, vault_sequential, vault_parallel): + assert set(vault_sequential.nonexistent_notes) == set( + vault_parallel.nonexistent_notes + ) + + def test_isolated_notes_match(self, vault_sequential, vault_parallel): + assert set(vault_sequential.isolated_notes) == set( + vault_parallel.isolated_notes + ) + + def test_is_connected_flag(self, vault_parallel): + assert vault_parallel.is_connected + + +# --- gather(): parallel vs sequential equivalence --- + + +class TestGatherParallel: + """Verify that gather(workers=N) produces the same text indexes as + the sequential default.""" + + def test_source_text_index_match(self, vault_sequential, vault_parallel): + assert vault_sequential.source_text_index == vault_parallel.source_text_index + + def test_readable_text_index_match(self, vault_sequential, vault_parallel): + assert ( + vault_sequential.readable_text_index + == vault_parallel.readable_text_index + ) + + def test_is_gathered_flag(self, vault_parallel): + assert vault_parallel.is_gathered + + def test_all_files_in_source_text_index(self, vault_parallel): + assert set(vault_parallel.md_file_index.keys()) == set( + vault_parallel.source_text_index.keys() + ) + + def test_all_files_in_readable_text_index(self, vault_parallel): + assert set(vault_parallel.md_file_index.keys()) == set( + vault_parallel.readable_text_index.keys() + ) + + +# --- metadata equivalence --- + + +class TestMetadataParallel: + """Verify that the note metadata DataFrame is identical regardless + of sequential vs parallel processing.""" + + def test_metadata_df_match(self, vault_sequential, vault_parallel): + df_seq = vault_sequential.get_note_metadata() + df_par = vault_parallel.get_note_metadata() + # sort by index so order doesn't matter + df_seq = df_seq.sort_index() + df_par = df_par.sort_index() + assert df_seq.equals(df_par) + + +# --- workers edge cases --- + + +class TestWorkersEdgeCases: + """Verify that unusual values for workers behave correctly.""" + + def test_workers_none_is_sequential(self, vault_sequential): + """workers=None should behave identically to default.""" + v = Vault(VAULT_STUB).connect(workers=None).gather(workers=None) + assert v.wikilinks_index == vault_sequential.wikilinks_index + assert v.source_text_index == vault_sequential.source_text_index + + def test_workers_one_is_sequential(self, vault_sequential): + """workers=1 should use the sequential path.""" + v = Vault(VAULT_STUB).connect(workers=1).gather(workers=1) + assert v.wikilinks_index == vault_sequential.wikilinks_index + assert v.source_text_index == vault_sequential.source_text_index + + def test_workers_zero_is_sequential(self, vault_sequential): + """workers=0 (falsy) should fall back to sequential.""" + v = Vault(VAULT_STUB).connect(workers=0).gather(workers=0) + assert v.wikilinks_index == vault_sequential.wikilinks_index + assert v.source_text_index == vault_sequential.source_text_index + + def test_workers_large_number(self, vault_sequential): + """workers much larger than file count should still work.""" + v = Vault(VAULT_STUB).connect(workers=100).gather(workers=100) + assert v.wikilinks_index == vault_sequential.wikilinks_index + assert v.source_text_index == vault_sequential.source_text_index + + +# --- connect with options + parallel --- + + +class TestConnectOptionsParallel: + """Verify that connect() options interact correctly with workers.""" + + def test_show_nested_tags_parallel(self): + v_seq = Vault(VAULT_STUB).connect(show_nested_tags=True) + v_par = Vault(VAULT_STUB).connect(show_nested_tags=True, workers=WORKERS) + assert v_seq.tags_index == v_par.tags_index + + def test_attachments_true_parallel(self): + v_seq = Vault(VAULT_STUB).connect(attachments=True) + v_par = Vault(VAULT_STUB).connect(attachments=True, workers=WORKERS) + assert v_seq.wikilinks_index == v_par.wikilinks_index + assert set(v_seq.graph.nodes) == set(v_par.graph.nodes) + assert set(v_seq.graph.edges) == set(v_par.graph.edges) + + +# --- idempotency: calling connect/gather twice --- + + +class TestIdempotencyParallel: + """Calling connect() or gather() twice should not change results.""" + + def test_double_connect_parallel(self): + v = Vault(VAULT_STUB).connect(workers=WORKERS) + nodes_before = set(v.graph.nodes) + edges_before = set(v.graph.edges) + v.connect(workers=WORKERS) # second call should be a no-op + assert set(v.graph.nodes) == nodes_before + assert set(v.graph.edges) == edges_before + + def test_gather_after_parallel_connect(self): + """gather() sequentially after parallel connect() should work.""" + v = Vault(VAULT_STUB).connect(workers=WORKERS).gather() + assert v.is_gathered + assert set(v.md_file_index.keys()) == set(v.source_text_index.keys()) + + +# --- thread safety: run connect multiple times concurrently on +# separate Vault instances to check for shared-state leaks --- + + +class TestThreadSafety: + """Smoke test that multiple Vault instances processed in parallel + don't interfere with each other.""" + + def test_independent_vaults_parallel(self): + """Create two independent vaults with parallel workers and + verify they both produce correct, identical results.""" + v1 = Vault(VAULT_STUB).connect(workers=WORKERS).gather(workers=WORKERS) + v2 = Vault(VAULT_STUB).connect(workers=WORKERS).gather(workers=WORKERS) + + assert v1.wikilinks_index == v2.wikilinks_index + assert v1.source_text_index == v2.source_text_index + assert set(v1.graph.nodes) == set(v2.graph.nodes) From 6bdbd9622d1f14736682bb4fa3b69d9d806de212 Mon Sep 17 00:00:00 2001 From: Javier Garcia Ordonez Date: Wed, 11 Mar 2026 19:34:25 +0100 Subject: [PATCH 8/8] [FEAT] switch to ProcessPool; add support for .env vault directory --- README.md | 28 +++- obsidiantools/api.py | 184 +++++++++++++++----------- parallelism_benchmark.py | 58 ++++++++ pyproject.toml | 1 + test_quick.py | 46 ------- tests/test_api_vault_stub_parallel.py | 41 ++++-- uv.lock | 44 ++++++ 7 files changed, 261 insertions(+), 141 deletions(-) create mode 100644 parallelism_benchmark.py delete mode 100644 test_quick.py diff --git a/README.md b/README.md index c3e275f..08468fc 100644 --- a/README.md +++ b/README.md @@ -7,11 +7,37 @@ It's incredibly easy to explore structured data on your vault through this fluent interface. This is all the code you need to generate a `vault` object that stores all the data: ```python +from pathlib import Path import obsidiantools.api as otools -vault = otools.Vault().connect().gather() +vault = otools.Vault(Path()).connect().gather() ``` +You can store your vault path in a `.env` file (ignored by git) so you don't have to retype it: + +``` +# .env +VAULT_DIR=C:\Users\me\My Vault +``` + +```python +import os +from pathlib import Path +from dotenv import load_dotenv +import obsidiantools.api as otools + +load_dotenv() +vault = otools.Vault(Path(os.environ["VAULT_DIR"])).connect().gather() +``` + +To speed up processing on large vaults, enable parallel loading with the `workers` parameter: + +```python +vault = otools.Vault(Path(os.environ["VAULT_DIR"]), workers=8).connect().gather() +``` + +The `workers` value set at initialisation is used by both `connect()` and `gather()`. You can override it per-call, e.g. `.connect(workers=4).gather(workers=2)`. + These are the basics of the method calls: - `connect()`: connect your notes together in a graph structure and get metadata on links (e.g. wikilinks, backlinks, etc.) There ais the option to support the inclusion of 'attachment' files in the graph. - `gather()`: gather the plaintext content from your notes in one place. This includes the 'source text' that represent how your notes are written. There are arguments to support what text you want to remove, e.g. remove code. diff --git a/obsidiantools/api.py b/obsidiantools/api.py index e709e24..eca4073 100644 --- a/obsidiantools/api.py +++ b/obsidiantools/api.py @@ -1,7 +1,9 @@ import logging +import os +import sys import warnings from collections import Counter -from concurrent.futures import ThreadPoolExecutor, as_completed +from concurrent.futures import ProcessPoolExecutor, as_completed from itertools import chain from pathlib import Path @@ -41,14 +43,72 @@ logger = logging.getLogger(__name__) +# Windows caps ProcessPoolExecutor at 61 workers. +_MAX_WORKERS = 61 if sys.platform == "win32" else os.cpu_count() or 1 + + +def _cap_workers(workers: int) -> int: + """Cap workers to the platform limit.""" + return min(workers, _MAX_WORKERS) + + +def _process_md_file_for_connect( + dirpath: Path, + relpath: Path, + note: str, + show_nested_tags: bool, + exclude_canvas: bool, +) -> dict: + """Process a single md file for connect (pure, picklable).""" + front_matter, content = _get_md_front_matter_and_content(dirpath / relpath) + html = _get_html_from_md_content(content) + src_txt = get_source_text_from_html(html, remove_code=True) + + return { + "note": note, + "md_links": _get_md_links_from_source_text(src_txt), + "unique_md_links": _get_unique_md_links_from_source_text(src_txt), + "embedded_files": _get_all_embedded_files_from_source_text( + src_txt, remove_aliases=True + ), + "wikilinks": _get_all_wikilinks_from_source_text( + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ), + "unique_wikilinks": _get_unique_wikilinks_from_source_text( + src_txt, remove_aliases=True, exclude_canvas=exclude_canvas + ), + "math": _get_all_latex_from_html_content(html), + "front_matter": front_matter, + "tags": get_tags(dirpath / relpath, show_nested=show_nested_tags), + } + + +def _process_md_file_for_gather( + dirpath: Path, + relpath: Path, + note: str, + tags: list[str], +) -> dict: + """Process a single md file for gather (pure, picklable).""" + _, content = _get_md_front_matter_and_content(dirpath / relpath) + html = _get_html_from_md_content(content) + src_txt = get_source_text_from_html(html, remove_code=True, remove_math=True) + + return { + "note": note, + "source_text": src_txt, + "readable_text": _get_readable_text_from_html(html, tags=tags), + } + class Vault: def __init__( self, dirpath: Path, *, - include_subdirs: list[str] = None, + include_subdirs: list[str] | None = None, include_root: bool = True, + workers: int | None = None, ): """A Vault object lets you dig into your Obsidian vault, by giving you a toolkit for analysing its contents. Specify a dirpath to @@ -87,6 +147,12 @@ def __init__( Defaults to None. include_root (bool, optional): include files that are directly in the dir_path (root dir). Defaults to True. + workers (int, optional): default number of threads to use for + parallel file processing in connect() and gather(). + Defaults to None (sequential processing). Set to a + positive integer to enable threading, e.g. + ``workers=os.cpu_count()``. Can be overridden per-call + by passing workers to connect() or gather() directly. -- METHODS -- Methods for setup: @@ -154,6 +220,7 @@ def __init__( # args: self._dirpath = dirpath + self._workers = workers self._attachments = None # connect() logger.info("Initialising vault from '%s'", dirpath) @@ -484,9 +551,7 @@ def canvas_graph_detail_index( return self._canvas_graph_detail_index @canvas_graph_detail_index.setter - def canvas_graph_detail_index( - self, value - ) -> dict[ + def canvas_graph_detail_index(self, value) -> dict[ str, tuple[nx.MultiDiGraph, dict[str, tuple[int, int]], dict[tuple[str, str], str]], ]: @@ -520,12 +585,13 @@ def connect( This will lead to the inclusion of media files' in the backlinks_index. workers (int, optional): number of threads to use for parallel - file processing. Defaults to None (sequential processing). - Set to a positive integer to enable threading, e.g. - ``workers=os.cpu_count()``. + file processing. Defaults to None, which uses the value + set at Vault initialisation. Set to a positive integer + to override, e.g. ``workers=os.cpu_count()``. """ if not self._is_connected: self._attachments = attachments + workers = workers if workers is not None else self._workers logger.info( "Connecting vault (%d md files, attachments=%s, workers=%s)", len(self._md_file_index), @@ -549,15 +615,19 @@ def connect( n_md = len(self._md_file_index) skipped_md = [] + exclude_canvas = not self._attachments + if workers and workers > 1: - # parallel processing via thread pool: - with ThreadPoolExecutor(max_workers=workers) as executor: + # parallel processing via process pool: + with ProcessPoolExecutor(max_workers=_cap_workers(workers)) as executor: futures = { executor.submit( - self._connect_process_md_file, + _process_md_file_for_connect, + self._dirpath, relpath, - note=f, - show_nested_tags=show_nested_tags, + f, + show_nested_tags, + exclude_canvas, ): (f, relpath) for f, relpath in self._md_file_index.items() } @@ -580,8 +650,12 @@ def connect( "connect: processing md file %d/%d: %s", i, n_md, relpath ) try: - result = self._connect_process_md_file( - relpath, note=f, show_nested_tags=show_nested_tags + result = _process_md_file_for_connect( + self._dirpath, + relpath, + f, + show_nested_tags, + exclude_canvas, ) self._connect_merge_result(result) except Exception: @@ -652,42 +726,6 @@ def connect( return self # fluent - def _connect_process_md_file( - self, relpath: Path, *, note: str, show_nested_tags: bool - ) -> dict: - """Process a single md file for the connect method. - - Returns a dict of extracted data (pure computation, no mutation). - """ - exclude_canvas = not self._attachments - - # MAIN file read: - front_matter, content = _get_md_front_matter_and_content( - self._dirpath / relpath - ) - html = _get_html_from_md_content(content) - src_txt = get_source_text_from_html(html, remove_code=True) - - return { - "note": note, - "md_links": _get_md_links_from_source_text(src_txt), - "unique_md_links": _get_unique_md_links_from_source_text(src_txt), - "embedded_files": _get_all_embedded_files_from_source_text( - src_txt, remove_aliases=True - ), - "wikilinks": _get_all_wikilinks_from_source_text( - src_txt, remove_aliases=True, exclude_canvas=exclude_canvas - ), - "unique_wikilinks": _get_unique_wikilinks_from_source_text( - src_txt, remove_aliases=True, exclude_canvas=exclude_canvas - ), - "math": _get_all_latex_from_html_content(html), - "front_matter": front_matter, - "tags": get_tags( - self._dirpath / relpath, show_nested=show_nested_tags - ), - } - def _connect_merge_result(self, result: dict): """Merge a single file's processed result into the indexes.""" note = result["note"] @@ -948,10 +986,11 @@ def gather(self, *, tags: list[str] = None, workers: int = None): will remove all header formatting (e.g. '#', '##' chars) and produces a one-line string. workers (int, optional): number of threads to use for parallel - file processing. Defaults to None (sequential processing). - Set to a positive integer to enable threading, e.g. - ``workers=os.cpu_count()``. + file processing. Defaults to None, which uses the value + set at Vault initialisation. Set to a positive integer + to override, e.g. ``workers=os.cpu_count()``. """ + workers = workers if workers is not None else self._workers logger.info( "Gathering text from %d md files (workers=%s)", len(self._md_file_index), @@ -961,14 +1000,15 @@ def gather(self, *, tags: list[str] = None, workers: int = None): skipped = [] if workers and workers > 1: - # parallel processing via thread pool: - with ThreadPoolExecutor(max_workers=workers) as executor: + # parallel processing via process pool: + with ProcessPoolExecutor(max_workers=_cap_workers(workers)) as executor: futures = { executor.submit( - self._gather_process_md_file, + _process_md_file_for_gather, + self._dirpath, relpath, - note=f, - tags=tags, + f, + tags, ): (f, relpath) for f, relpath in self._md_file_index.items() } @@ -989,8 +1029,11 @@ def gather(self, *, tags: list[str] = None, workers: int = None): for i, (f, relpath) in enumerate(self._md_file_index.items(), 1): logger.debug("gather: processing file %d/%d: %s", i, n_md, relpath) try: - result = self._gather_process_md_file( - relpath, note=f, tags=tags + result = _process_md_file_for_gather( + self._dirpath, + relpath, + f, + tags, ) self._gather_merge_result(result) except Exception: @@ -1012,25 +1055,6 @@ def gather(self, *, tags: list[str] = None, workers: int = None): return self # fluent - def _gather_process_md_file( - self, relpath: Path, *, note: str, tags: list[str] - ) -> dict: - """Process a single md file for the gather method. - - Returns a dict of extracted data (pure computation, no mutation). - """ - # MAIN file read: - _, content = _get_md_front_matter_and_content(self._dirpath / relpath) - html = _get_html_from_md_content(content) - # (also remove LaTeX for source text:) - src_txt = get_source_text_from_html(html, remove_code=True, remove_math=True) - - return { - "note": note, - "source_text": src_txt, - "readable_text": _get_readable_text_from_html(html, tags=tags), - } - def _gather_merge_result(self, result: dict): """Merge a single file's processed result into the indexes.""" note = result["note"] diff --git a/parallelism_benchmark.py b/parallelism_benchmark.py new file mode 100644 index 0000000..7169b80 --- /dev/null +++ b/parallelism_benchmark.py @@ -0,0 +1,58 @@ +#!/usr/bin/env python3 +"""Quick test to verify parallel tests work.""" +import os +import time +from pathlib import Path + +from dotenv import load_dotenv + +from obsidiantools.api import Vault + +load_dotenv() + +VAULT_DIR = Path(os.environ["VAULT_DIR"]) +N_WORKERS = 8 + + +def main(): + print("Testing sequential connection...") + start = time.time() + v_seq = Vault(VAULT_DIR).connect() + seq_connect_time = time.time() - start + print(f" Sequential connect: {seq_connect_time:.3f}s") + print(f" Graph nodes: {len(v_seq.graph.nodes)}") + print(f" Graph edges: {len(v_seq.graph.edges)}") + + start = time.time() + v_seq = v_seq.gather() + seq_gather_time = time.time() - start + print(f" Sequential gather: {seq_gather_time:.3f}s") + print(f" Source text files: {len(v_seq.source_text_index)}") + + print(f"\nTesting parallel connection with {N_WORKERS} workers...") + start = time.time() + v_par = Vault(VAULT_DIR, workers=N_WORKERS).connect() + par_connect_time = time.time() - start + print(f" Parallel connect: {par_connect_time:.3f}s") + print(f" Graph nodes: {len(v_par.graph.nodes)}") + print(f" Graph edges: {len(v_par.graph.edges)}") + + start = time.time() + v_par = v_par.gather() + par_gather_time = time.time() - start + print(f" Parallel gather: {par_gather_time:.3f}s") + print(f" Source text files: {len(v_par.source_text_index)}") + + print("\nVerifying equivalence...") + print(f" Graph nodes match: {set(v_seq.graph.nodes) == set(v_par.graph.nodes)}") + print(f" Graph edges match: {set(v_seq.graph.edges) == set(v_par.graph.edges)}") + print(f" Wikilinks match: {v_seq.wikilinks_index == v_par.wikilinks_index}") + print(f" Source text match: {v_seq.source_text_index == v_par.source_text_index}") + + print("\nTiming comparison:") + print(f" Connect speedup: {seq_connect_time / par_connect_time:.2f}x") + print(f" Gather speedup: {seq_gather_time / par_gather_time:.2f}x") + + +if __name__ == "__main__": + main() diff --git a/pyproject.toml b/pyproject.toml index 20ea001..1a2d7b5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,6 +45,7 @@ dependencies = [ "beautifulsoup4", "bleach", "lxml", + "dotenv>=0.9.9", ] [project.urls] diff --git a/test_quick.py b/test_quick.py deleted file mode 100644 index 1f14704..0000000 --- a/test_quick.py +++ /dev/null @@ -1,46 +0,0 @@ -#!/usr/bin/env python3 -"""Quick test to verify parallel tests work.""" -import time -from pathlib import Path -from obsidiantools.api import Vault - -WKD = Path().cwd() -VAULT_STUB = WKD / "tests/vault-stub" - -print("Testing sequential connection...") -start = time.time() -v_seq = Vault(VAULT_STUB).connect() -seq_connect_time = time.time() - start -print(f" Sequential connect: {seq_connect_time:.3f}s") -print(f" Graph nodes: {len(v_seq.graph.nodes)}") -print(f" Graph edges: {len(v_seq.graph.edges)}") - -start = time.time() -v_seq = v_seq.gather() -seq_gather_time = time.time() - start -print(f" Sequential gather: {seq_gather_time:.3f}s") -print(f" Source text files: {len(v_seq.source_text_index)}") - -print("\nTesting parallel connection with 4 workers...") -start = time.time() -v_par = Vault(VAULT_STUB).connect(workers=4) -par_connect_time = time.time() - start -print(f" Parallel connect: {par_connect_time:.3f}s") -print(f" Graph nodes: {len(v_par.graph.nodes)}") -print(f" Graph edges: {len(v_par.graph.edges)}") - -start = time.time() -v_par = v_par.gather(workers=4) -par_gather_time = time.time() - start -print(f" Parallel gather: {par_gather_time:.3f}s") -print(f" Source text files: {len(v_par.source_text_index)}") - -print("\nVerifying equivalence...") -print(f" Graph nodes match: {set(v_seq.graph.nodes) == set(v_par.graph.nodes)}") -print(f" Graph edges match: {set(v_seq.graph.edges) == set(v_par.graph.edges)}") -print(f" Wikilinks match: {v_seq.wikilinks_index == v_par.wikilinks_index}") -print(f" Source text match: {v_seq.source_text_index == v_par.source_text_index}") - -print("\nTiming comparison:") -print(f" Connect speedup: {seq_connect_time / par_connect_time:.2f}x") -print(f" Gather speedup: {seq_gather_time / par_gather_time:.2f}x") diff --git a/tests/test_api_vault_stub_parallel.py b/tests/test_api_vault_stub_parallel.py index ae9f44a..0bfc913 100644 --- a/tests/test_api_vault_stub_parallel.py +++ b/tests/test_api_vault_stub_parallel.py @@ -31,8 +31,8 @@ def vault_sequential(): @pytest.fixture def vault_parallel(): - """Vault connected and gathered with threads.""" - return Vault(VAULT_STUB).connect(workers=WORKERS).gather(workers=WORKERS) + """Vault connected and gathered with threads (workers set at init).""" + return Vault(VAULT_STUB, workers=WORKERS).connect().gather() # --- connect(): parallel vs sequential equivalence --- @@ -156,25 +156,38 @@ class TestWorkersEdgeCases: def test_workers_none_is_sequential(self, vault_sequential): """workers=None should behave identically to default.""" - v = Vault(VAULT_STUB).connect(workers=None).gather(workers=None) + v = Vault(VAULT_STUB, workers=None).connect().gather() assert v.wikilinks_index == vault_sequential.wikilinks_index assert v.source_text_index == vault_sequential.source_text_index def test_workers_one_is_sequential(self, vault_sequential): """workers=1 should use the sequential path.""" - v = Vault(VAULT_STUB).connect(workers=1).gather(workers=1) + v = Vault(VAULT_STUB, workers=1).connect().gather() assert v.wikilinks_index == vault_sequential.wikilinks_index assert v.source_text_index == vault_sequential.source_text_index def test_workers_zero_is_sequential(self, vault_sequential): """workers=0 (falsy) should fall back to sequential.""" - v = Vault(VAULT_STUB).connect(workers=0).gather(workers=0) + v = Vault(VAULT_STUB, workers=0).connect().gather() assert v.wikilinks_index == vault_sequential.wikilinks_index assert v.source_text_index == vault_sequential.source_text_index def test_workers_large_number(self, vault_sequential): - """workers much larger than file count should still work.""" - v = Vault(VAULT_STUB).connect(workers=100).gather(workers=100) + """workers much larger than file count should still work + (capped internally to platform limit).""" + v = Vault(VAULT_STUB, workers=200).connect().gather() + assert v.wikilinks_index == vault_sequential.wikilinks_index + assert v.source_text_index == vault_sequential.source_text_index + + def test_method_workers_overrides_init(self, vault_sequential): + """workers passed to connect/gather should override the init value.""" + v = Vault(VAULT_STUB, workers=1).connect(workers=WORKERS).gather(workers=WORKERS) + assert v.wikilinks_index == vault_sequential.wikilinks_index + assert v.source_text_index == vault_sequential.source_text_index + + def test_init_workers_used_when_method_omitted(self, vault_sequential): + """When no workers passed to methods, init value should be used.""" + v = Vault(VAULT_STUB, workers=WORKERS).connect().gather() assert v.wikilinks_index == vault_sequential.wikilinks_index assert v.source_text_index == vault_sequential.source_text_index @@ -187,12 +200,12 @@ class TestConnectOptionsParallel: def test_show_nested_tags_parallel(self): v_seq = Vault(VAULT_STUB).connect(show_nested_tags=True) - v_par = Vault(VAULT_STUB).connect(show_nested_tags=True, workers=WORKERS) + v_par = Vault(VAULT_STUB, workers=WORKERS).connect(show_nested_tags=True) assert v_seq.tags_index == v_par.tags_index def test_attachments_true_parallel(self): v_seq = Vault(VAULT_STUB).connect(attachments=True) - v_par = Vault(VAULT_STUB).connect(attachments=True, workers=WORKERS) + v_par = Vault(VAULT_STUB, workers=WORKERS).connect(attachments=True) assert v_seq.wikilinks_index == v_par.wikilinks_index assert set(v_seq.graph.nodes) == set(v_par.graph.nodes) assert set(v_seq.graph.edges) == set(v_par.graph.edges) @@ -205,16 +218,16 @@ class TestIdempotencyParallel: """Calling connect() or gather() twice should not change results.""" def test_double_connect_parallel(self): - v = Vault(VAULT_STUB).connect(workers=WORKERS) + v = Vault(VAULT_STUB, workers=WORKERS).connect() nodes_before = set(v.graph.nodes) edges_before = set(v.graph.edges) - v.connect(workers=WORKERS) # second call should be a no-op + v.connect() # second call should be a no-op assert set(v.graph.nodes) == nodes_before assert set(v.graph.edges) == edges_before def test_gather_after_parallel_connect(self): """gather() sequentially after parallel connect() should work.""" - v = Vault(VAULT_STUB).connect(workers=WORKERS).gather() + v = Vault(VAULT_STUB, workers=WORKERS).connect().gather(workers=1) assert v.is_gathered assert set(v.md_file_index.keys()) == set(v.source_text_index.keys()) @@ -230,8 +243,8 @@ class TestThreadSafety: def test_independent_vaults_parallel(self): """Create two independent vaults with parallel workers and verify they both produce correct, identical results.""" - v1 = Vault(VAULT_STUB).connect(workers=WORKERS).gather(workers=WORKERS) - v2 = Vault(VAULT_STUB).connect(workers=WORKERS).gather(workers=WORKERS) + v1 = Vault(VAULT_STUB, workers=WORKERS).connect().gather() + v2 = Vault(VAULT_STUB, workers=WORKERS).connect().gather() assert v1.wikilinks_index == v2.wikilinks_index assert v1.source_text_index == v2.source_text_index diff --git a/uv.lock b/uv.lock index 9c51131..942e217 100644 --- a/uv.lock +++ b/uv.lock @@ -559,6 +559,18 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/02/10/5da547df7a391dcde17f59520a231527b8571e6f46fc8efb02ccb370ab12/docutils-0.22.4-py3-none-any.whl", hash = "sha256:d0013f540772d1420576855455d050a2180186c91c15779301ac2ccb3eeb68de", size = 633196, upload-time = "2025-12-18T19:00:18.077Z" }, ] +[[package]] +name = "dotenv" +version = "0.9.9" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "python-dotenv", version = "1.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, + { name = "python-dotenv", version = "1.2.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, +] +wheels = [ + { url = "https://files.pythonhosted.org/packages/b2/b7/545d2c10c1fc15e48653c91efde329a790f2eecfbbf2bd16003b5db2bab0/dotenv-0.9.9-py2.py3-none-any.whl", hash = "sha256:29cf74a087b31dafdb5a446b6d7e11cbce8ed2741540e2339c69fbef92c94ce9", size = 1892, upload-time = "2025-02-19T22:15:01.647Z" }, +] + [[package]] name = "exceptiongroup" version = "1.3.1" @@ -1224,6 +1236,7 @@ dependencies = [ { name = "beautifulsoup4" }, { name = "bleach", version = "6.2.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "bleach", version = "6.3.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, + { name = "dotenv" }, { 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