Enhance OMV tests and update README with examples

.gitignore

@@ -127,3 +127,6 @@ __pycache__
 /src/worm2d/neuromlLocal/testc302SigSim/*.dat
 /src/worm2d/neuromlLocal/testc302SigSim/testc302NervousSystem
 /src/worm2d/neuromlLocal/testc302SigSim/report.txt
+/synchere.sh
+/wheelhouse
+/tests/test_files/test_py_cpp

README.md

@@ -1,4 +1,54 @@
 # Worm2D
-Simulator of 2D worm body models
 
-Work in progress. Latest verison of this code can be found here: https://github.com/openworm/CE_locomotion/tree/test_stable
+Worm2D is a neuromechanical simulator of *C. elegans* locomotion. This is an initiative of the [OpenWorm project](https://www.openworm.org). It is based on earlier work on development of 2D worm neuromechanical models of Netta Cohen and team, as well as Dr. Eduardo J. Izquiredo, Dr. Erick Olivares and Prof. Randall Beer (See [HISTORY.md](HISTORY.md)).
+
+Worm2D is a hybrid C++/Python package: C++ binaries implement the physics, nervous system, and evolutionary search, while Python handles configuration, binary dispatch, and post-run analysis/plotting. 
+
+
+## Build & Install
+
+The package uses [scikit-build-core](https://scikit-build-core.readthedocs.io/) with CMake. nlohmann-json is bundled as a header at `src/cpp/nlohmann/json.hpp` — no system package needed.
+
+Install in editable mode (builds C++ and installs Python package):
+
+```bash
+pip install -e .[all]
+```
+
+The `[all]` extra pulls in `[neuroml]` (pyNeuroML, NEURON<9.0) and `[dev]` (ruff, pytest, ipywidgets, OSBModelValidation, modelspec).
+
+## Running Tests
+
+Quick test (runs after `pip install -e .`):
+
+```bash
+python tests/test.py # runs a single optimisation run & saves output to exampleRun folder, see below
+```
+
+![Example](exampleRun/ExampleActivity.png)
+
+
+Full test suite (cleans prior run folders, then runs all model variants and OMV tests):
+
+```bash
+./test_all.sh        # full
+./test_all.sh -q     # quick (skips OMV and most model-specific tests)
+```
+
+Individual test scripts in `tests/` and `src/worm2d/` follow the naming pattern `test<ModelVariant>.py`. Run any directly:
+
+```bash
+cd tests
+python testW2DCE.py
+```
+
+
+## CLI
+
+After install, the `worm2d` command is available:
+
+```bash
+worm2d -f <outputFolder> [-E] [-O <modelName>] [-T <modelFolder>] [...]
+```
+
+Key flags: `-E` / `--doEvol` runs the evolutionary search; `-f` specifies the output folder (required); `-O` sets the model name when using the `Worm2D` binary family.

test_all.sh

@@ -72,5 +72,10 @@ if [ "$quick_test" == 0 ]; then
 
 
     omv test -V .test.example.omt #Izq original test.example.mep
+    omv test -V .test.W2DCEa.omt #main_osc.cpp test.example.mep
+    omv test -V .test.W2DCEanm.omt #main_osc.cpp test.W2DCEanm.mep, as W2DCEa but origMusc=False
+    omv test -V .test.W2DCEanm2.omt ${OMV_ARGS}
+    omv test -V .test.W2DCE.omt
+    omv test -V .test.W2DCEs.omt
 
 fi

tests/.test.W2DCE.mep

@@ -0,0 +1,12 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test:
+        expected:
+            spike times: [0.405, 8.555]
+    Test2:
+        expected:
+            spike times: [0.405, 8.655]
+    Test3:
+        expected:
+            spike times: [0.455, 8.655]

tests/.test.W2DCE.omt

@@ -0,0 +1,18 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: testW2DCE.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.W2DCE.mep
+experiments:
+  Test:
+    observables:
+      spike times:
+        file: 
+          path: ../exampleRunW2DCE/act.dat
+          columns: [0,3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 2
+        tolerance: 0

tests/.test.W2DCEa.omt

@@ -0,0 +1,18 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: testW2DCEa.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.example.mep
+experiments:
+  Test:
+    observables:
+      spike times:
+        file: 
+          path: ../testruns/exW2DCEa/act.dat
+          columns: [0,3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 2
+        tolerance: 0

tests/.test.W2DCEanm.mep

@@ -0,0 +1,6 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test:
+        expected:
+            spike times: [0.405, 5.955, 11.155, 16.155, 21.105, 26.105]

tests/.test.W2DCEanm.omt

@@ -0,0 +1,18 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: testW2DCEanm.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.W2DCEanm.mep
+experiments:
+  Test:
+    observables:
+      spike times:
+        file: 
+          path: ../testruns/exW2DCEanm/act.dat
+          columns: [0,3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 2
+        tolerance: 0

tests/.test.W2DCEanm2.mep

@@ -0,0 +1,9 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test:
+        expected:
+            spike times: [8.21, 11.56, 14.96, 18.36, 21.76, 25.16, 28.61, 32.01]
+    Test2:
+        expected:
+            spike times: [9.06, 13.01, 16.96, 20.91, 24.86, 28.81]

tests/.test.W2DCEanm2.omt

@@ -0,0 +1,29 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: testW2DCEanm2.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.W2DCEanm2.mep
+experiments:
+  Test:
+    observables:
+      spike times:
+        file: 
+          path: ../testruns/exW2DCEanm2/act.dat
+          columns: [0,3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 2
+        tolerance: 0
+  Test2:
+    observables:
+      spike times:
+        file: 
+          path: ../testruns/exW2DCEanm2_1/act.dat
+          columns: [0,3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 2
+        tolerance: 0

tests/.test.W2DCEs.mep

@@ -0,0 +1,6 @@
+system: Testing activity of some neurons
+
+experiments:
+    Test:
+        expected:
+            spike times: [0.555, 2.305]

tests/.test.W2DCEs.omt

@@ -0,0 +1,18 @@
+# Framework for running automated tests on Open Source Brain
+# See https://github.com/OpenSourceBrain/osb-model-validation for more details
+
+target: testW2DCEs.py
+engine: Brian2  # This installs Brian2, but all we really need is a Python environment to run the script in
+mep: .test.W2DCEs.mep
+experiments:
+  Test:
+    observables:
+      spike times:
+        file: 
+          path: ../testruns/exW2DCEs/act.dat
+          columns: [0,3]
+          scaling: [1, 1]
+        spike detection: 
+          method: threshold
+          threshold: 2
+        tolerance: 0

tests/testW2DCE.py

@@ -0,0 +1,27 @@
+from worm2d import run
+
+run(
+    simduration=20,
+    simtransient=0,
+    popSize=96,
+    RandSeed=1233,
+    maxGens=10,
+    modelName="W2DCE",
+    modelFolder="Worm2D",
+    # inputFolderName="exampleRunW2Dosc_t1",
+    outputFolderName="../exampleRunW2DCE",
+    # outputFolderName="exampleRunW2Dosc_t1_nml",
+    doEvol=True,
+    overwrite=True,
+    checkPointInterval=5,
+    reRand=True,
+    doPlotEvol=True,
+    doNML=False,
+    # doCPT=True,
+    evo_type="EvoCE",
+    AvgSpeed=0.0001,
+    # SRType = "SR_TRANS_STRETCH"
+    doTestRun=True,
+    doOrigMuscInput=True,
+    SRZeroGainsType=1,
+)

tests/testW2DCEa.py

@@ -0,0 +1,23 @@
+from worm2d import run
+
+run(
+    simduration=30,
+    simtransient=0,
+    popSize=96,
+    RandSeed=1233,
+    modelName="W2DCE",
+    modelFolder="Worm2D",
+    outputFolderName="../testruns/exW2DCEa",
+    doEvol=True,
+    overwrite=True,
+    checkPointInterval=5,
+    doOrigMuscInput=True,
+    evo_type="EvoCE",
+    doTestRun=False,
+    SRZeroGainsType=1,
+    doReverse=0,
+    fitType=0,
+    AvgSpeed=0.0001,
+    inputInd=2,
+    debug=False,
+)

tests/testW2DCEanm.py

@@ -0,0 +1,23 @@
+from worm2d import run
+
+run(
+    simduration=30,
+    simtransient=0,
+    popSize=96,
+    RandSeed=1233,
+    modelName="W2DCE",
+    modelFolder="Worm2D",
+    outputFolderName="../testruns/exW2DCEanm",
+    doEvol=True,
+    overwrite=True,
+    checkPointInterval=5,
+    doOrigMuscInput=False,
+    evo_type="EvoCE",
+    doTestRun=False,
+    SRZeroGainsType=1,
+    doReverse=0,
+    fitType=0,
+    AvgSpeed=0.0001,
+    inputInd=2,
+    debug=False,
+)

tests/testW2DCEanm2.py

@@ -0,0 +1,48 @@
+from worm2d import run
+from worm2d.helper_funcs import get_worm_json, write_worm_json, delete_directory
+
+outputFolderName = "../testruns/exW2DCEanm2"
+outputFolderName_2 = "../testruns/exW2DCEanm2_1"
+origFolderName = "../testruns/exW2DCEanm"
+
+
+# x = 0.1
+delete_directory(outputFolderName_2)
+delete_directory(outputFolderName)
+json_data = get_worm_json(origFolderName)
+# json_data['evolvable_ranges']['evotag_2']["active"] = False
+write_worm_json(outputFolderName, json_data)
+
+args = dict(
+    modelFolder="Worm2D",  # folder containing the compiled C++ binary code
+    modelName="W2DSR",  # rerun using the generic json loaded model
+    maxGens=5,  # number of generations to run
+    popSize=10,
+    doEvol=True,
+    # inputFolderName=origFolderName,  # input folder
+    # outputFolderName=outputFolderName,  # output folder
+    overwrite=True,  # allow overwrite of output folder
+    # randInitState=True, #use fixed initial conditions from JSON file
+    # doTestRun=True, #run a single simple simulation
+    reRand=True,
+    RandSeed=900351,
+)
+
+args["outputFolderName"] = outputFolderName
+run(**args)
+
+
+json_data = get_worm_json(origFolderName)
+json_data["evolvable_ranges"]["ns_cells_bias_0"]["active"] = False
+json_data["evolvable_ranges"]["ns_chemcons_1"]["active"] = False
+json_data["evolvable_ranges"]["DA_0_1_tau"] = {
+    "active": True,
+    "lower_limit": 0.1,
+    "upper_limit": 2.5,
+    "name": "DA_tau",
+}
+json_data["nervous_system"]["cells"]["DA_0"]["tau"]["evotag"] = "DA_0_1_tau"
+json_data["nervous_system"]["cells"]["DA_1"]["tau"]["evotag"] = "DA_0_1_tau"
+write_worm_json(outputFolderName_2, json_data)
+args["outputFolderName"] = outputFolderName_2
+run(**args)  #

tests/testW2DCEs.py

@@ -0,0 +1,25 @@
+from worm2d import run
+
+run(
+    simduration=20,
+    simtransient=0,
+    popSize=96,
+    RandSeed=1233,
+    maxGens=5,
+    modelName="W2DCE",
+    modelFolder="Worm2D",
+    outputFolderName="../testruns/exW2DCEs",
+    doEvol=True,
+    overwrite=True,
+    checkPointInterval=5,
+    reRand=True,
+    doPlotEvol=True,
+    doNML=False,
+    # doCPT=True,
+    evo_type="EvoCE",
+    AvgSpeed=0.0001,
+    # SRType = "SR_TRANS_STRETCH"
+    doTestRun=True,
+    doOrigMuscInput=True,
+    SRZeroGainsType=1,
+)