worm2d 0.2.8__tar.gz

worm2d-0.2.8/.github/workflows/ci-make.yml

@@ -0,0 +1,87 @@
+name: C/C++ CI
+
+on:
+  push:
+    branches: [ "main", "development", "experimental", "test*", "feat*", "bug*" ]
+  pull_request:
+    branches: [ "main", "development", "experimental", "test*", "feat*", "bug*" ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        runs-on: [ubuntu-22.04, ubuntu-latest, macos-latest, macos-14 ]
+        python-version: [ "3.10", "3.12" ] # Note: 3.14 causes issues with Neuron 8.2.7
+
+    steps:
+    - uses: actions/checkout@v6
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version:  ${{ matrix.python-version }}
+
+    - name: C++ info
+      run: g++ -v
+
+    - name: Install graphviz
+      uses: ts-graphviz/setup-graphviz@v2
+      with:
+        # Skip to run brew update command on macOS.
+        macos-skip-brew-update: 'true' # default false
+
+    - name: Install dependencies (Ubuntu)
+      run: sudo apt-get install -y tree graphviz openjdk-11-jdk cmake
+      if: ${{ contains(matrix.runs-on, 'ubuntu') }}
+
+    - name: Install dependencies (macOS)
+      run: brew install tree cmake
+      if: ${{ contains(matrix.runs-on, 'macos') }}
+
+    - name: Build and install worm2d package (with C++ binaries)
+      env:
+        CMAKE_BUILD_PARALLEL_LEVEL: 4
+      run: |
+      
+        pip install setuptools==80 # needed for Neuron on py >=3.12
+
+        pip install -e .[dev] -v
+
+    - name: Run C++ unit tests
+      run: |
+        cmake -B build -DCMAKE_BUILD_TYPE=Release
+        cmake --build build --target worm2d_tests worm2d_tests2
+        ./build/tests
+
+    - name: Test C++/Python interactions
+      run: |
+        cd tests/test_files
+        ./test.sh
+        cd modelspec_api
+        ./test.sh
+
+    - name: Test Python command line script
+      run: |
+        python -m worm2d.run_main -R 1233 -p 6 --doEvol --outputFolderName exampleRun2  # Note: small population of 6 for quick runtime
+
+    - name: Test using test_all.sh
+      run: |
+        pip list
+
+        pip install scikit_build_core # Needed for building C++ extensions with scikit-build &  --no-build-isolation
+
+        export NEURON_HOME=$pythonLocation
+        env
+
+        ./test_all.sh 
+
+
+
+    - name: list generated files
+      run: |
+          ls -alth
+          tree
+          pip list

worm2d-0.2.8/.github/workflows/python-publish.yml

@@ -0,0 +1,90 @@
+name: Upload Python Package
+
+on:
+  push:
+  release:
+    types: [published]
+
+jobs:
+  build_wheels:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v7
+
+    - name: Build wheels
+      uses: pypa/cibuildwheel@v4.1.0
+      env:
+        CIBW_BUILD: cp39-* cp310-* cp311-* cp312-* cp313-*
+        CIBW_ARCHS_LINUX: x86_64
+        CIBW_BEFORE_ALL_LINUX: |
+          set -e
+          if command -v dnf >/dev/null 2>&1; then
+            dnf install -y cmake python3-devel
+            dnf install -y java-11-openjdk-devel graphviz tree || true
+          elif command -v yum >/dev/null 2>&1; then
+            yum install -y cmake python3-devel
+            yum install -y java-11-openjdk-devel graphviz tree || true
+          elif command -v apt-get >/dev/null 2>&1; then
+            apt-get update && apt-get install -y cmake python3-dev
+            apt-get install -y openjdk-11-jdk graphviz tree || true
+          elif command -v apk >/dev/null 2>&1; then
+            apk add --no-cache cmake python3-dev
+            apk add --no-cache openjdk11 graphviz tree || true
+          else
+            echo "No supported package manager found!" >&2
+            exit 1
+          fi
+
+        CIBW_BEFORE_BUILD_LINUX: |
+          set -e
+          python -m pip install --upgrade pip setuptools wheel cmake
+
+    - uses: actions/upload-artifact@v7
+      with:
+        name: wheels
+        path: ./wheelhouse/*.whl
+
+  build_sdist:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v7
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+
+    - name: Install system dependencies (Ubuntu)
+      run: sudo apt-get install -y tree graphviz openjdk-11-jdk cmake
+
+    - name: Build sdist
+      run: python -m build --sdist
+
+    - uses: actions/upload-artifact@v7
+      with:
+        name: sdist
+        path: dist/*.tar.gz
+
+  publish:
+    if: github.event_name == 'release'
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+    - uses: actions/download-artifact@v8
+      with:
+        pattern: "*"
+        path: dist/
+        merge-multiple: true
+
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

worm2d-0.2.8/.gitignore

@@ -0,0 +1,129 @@
+*.o
+/build/
+/dist/
+/src/worm2d/bin/
+*.egg-info/
+/main
+/act.dat
+/best.gen.dat
+/body.dat
+/curv.dat
+/fitness.dat
+/phenotype.dat
+/seed.dat
+/__pycache__
+/testExample
+/nv.dat
+/nv2.dat
+/phenotype2.dat
+/w_verb.dat
+/test_output/*.dat
+/neuromlLocal/*.dat
+/neuromlLocal/report.txt
+/test_files/test_py_cpp
+/neuromlLocal/__pycache__
+/neuromlLocal/*.mod
+/neuromlLocal/arm64
+*_nrn.py
+/neuromlLocal/*.gv
+/neuromlLocal/Worm2DNet.gv.png
+/neuromlLocal/x86_64
+/neuromlLocal/testc302NervousSystem
+/arm64
+/x86_64
+/report.txt
+/exampleRun_nml
+/*.dat
+/exampleRun2
+/neuromlLocal/testc302SigSim/*.dat
+/neuromlLocal/testc302SigSim/arm64
+/neuromlLocal/testc302SigSim/x86_64
+/neuromlLocal/testc302SigSim/report.txt
+/neuromlLocal/testc302SigSim/testc302NervousSystem
+/RoyalSociety2018/*.dat
+/RoyalSociety2018/main
+/Worm2D/main
+/network2021/main
+/experiments/izq_runs_nets/*/*.gv
+/experiments/izq_runs_nets/*/*.pdf
+/experiments/izq_runs_nets_nml/*/*.gv
+/experiments/izq_runs_nets_nml/*/*.pdf
+/*/*.gv
+/*/*.pdf
+.DS_Store
+/CE_orientation/main
+/Worm2D/main_osc
+/checkoutexp.sh
+/.ipynb_checkpoints
+/RoyalSociety2018/testRS18/ExampleActivity.png
+/RoyalSociety2018/testRS18/Motion.png
+/RoyalSociety2018/testRS18/Orient.png
+/RoyalSociety2018/testRS18/act.dat
+/RoyalSociety2018/testRS18/best.gen.dat
+/RoyalSociety2018/testRS18/body.dat
+/RoyalSociety2018/testRS18/body_mm.dat
+/RoyalSociety2018/testRS18/curv.dat
+/RoyalSociety2018/testRS18/curv_t.dat
+/RoyalSociety2018/testRS18/fitness.dat
+/RoyalSociety2018/testRS18/output.wcon
+/RoyalSociety2018/testRS18/params.dat
+/RoyalSociety2018/testRS18/seed.dat
+/RoyalSociety2018/testRS18/speed.dat
+/RoyalSociety2018/testRS18/worm_data.json
+/experiments/izq_runs*
+
+/ex*/Orient.png
+/ex*/*.dat
+/ex*/*.json
+/ex*/*.cpt
+/ex*/Evo*.png
+/ex*/Fit*.png
+/ex*/LEM*.png
+/ex*/Motion.png
+/ex*/beha*.png
+/ex*/Worm*.png
+/ex*/*.mod
+/ex*/*.nml
+/ex*/*.xml
+/ex*/*.wcon
+
+
+/experiments/*/*.dat
+/experiments/*/*.json
+/experiments/*/*.mod
+/experiments/*/*.nml
+/experiments/*/*.xml
+/experiments/*/Fit*.png
+/experiments/*/Mot*.png
+/experiments/*/Or*.png
+/experiments/*/Ev*.png
+/experiments/*/LE*.png
+/experiments/*/Wo*.png
+/experiments/*/*.cpt
+/experiments/*/*.gv
+/experiments/*/beha*
+/experiments/*/*.wcon
+
+/testruns/*/*.dat
+/testruns/*/*.json
+/testruns/*/Ev*.png
+/testruns/*/Fit*.png
+/testruns/*/Mot*.png
+/testruns/*/Or*.png
+/testruns/*/Wor*.png
+/testruns/*/LE*.png
+/testruns/*/beh*.*
+/testruns/*/*.mod
+/testruns/*/*.*ml
+/testruns/*/*.gv
+/testruns/*/*.cpt
+/testruns/*/*.wcon
+/RoyalSociety2018/testRS18_2
+/docs
+/notebooks
+__pycache__
+/src/worm2d/neuromlLocal/testc302SigSim/arm64
+/src/worm2d/neuromlLocal/testc302SigSim/x86_64
+/src/worm2d/neuromlLocal/testc302SigSim/*.dat
+/src/worm2d/neuromlLocal/testc302SigSim/testc302NervousSystem
+/src/worm2d/neuromlLocal/testc302SigSim/report.txt

worm2d-0.2.8/CMakeLists.txt

@@ -0,0 +1,317 @@
+cmake_minimum_required(VERSION 3.17)
+project(worm2d CXX)
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# ---------------------------------------------------------------------------
+# Extract package version from pyproject.toml so W2D_VERSION stays in sync
+# ---------------------------------------------------------------------------
+file(READ "${CMAKE_SOURCE_DIR}/pyproject.toml" _PYPROJECT_CONTENTS)
+string(REGEX MATCH "version = \"([0-9]+\\.[0-9]+\\.[0-9]+)\"" _ "${_PYPROJECT_CONTENTS}")
+if(CMAKE_MATCH_1)
+    set(W2D_VERSION_STR "v${CMAKE_MATCH_1}")
+else()
+    set(W2D_VERSION_STR "v0.0.0")
+    message(WARNING "[worm2d] Could not extract version from pyproject.toml; defaulting to v0.0.0")
+endif()
+message(STATUS "[worm2d] Package version: ${W2D_VERSION_STR}")
+add_compile_definitions(W2D_VERSION_FROM_CMAKE="${W2D_VERSION_STR}")
+
+# ---------------------------------------------------------------------------
+# Find Python (for embedding)
+# ---------------------------------------------------------------------------
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module)
+
+# ---------------------------------------------------------------------------
+# Python embedding support (optional — manylinux containers have no libpython)
+# When OFF, the NeuroML/doNML mode is unavailable but all other functionality
+# builds and runs normally.
+# ---------------------------------------------------------------------------
+option(PYTHON_EMBEDDING "Build C++ executables with Python embedding (required for doNML/NeuroML mode)" ON)
+
+if(PYTHON_EMBEDDING)
+    find_package(Python3 OPTIONAL_COMPONENTS Development.Embed)
+    if(Python3_Development.Embed_FOUND)
+        message(STATUS "[worm2d] Python embedding: enabled")
+    else()
+        message(WARNING "[worm2d] Python3 Development.Embed not found — disabling Python embedding (doNML mode unavailable)")
+        set(PYTHON_EMBEDDING OFF)
+    endif()
+endif()
+
+if(NOT PYTHON_EMBEDDING)
+    message(STATUS "[worm2d] Python embedding: disabled")
+    add_compile_definitions(WORM2D_NO_PYTHON_EMBEDDING)
+endif()
+
+# ---------------------------------------------------------------------------
+# Derive a reliable Python library directory for rpath embedding.
+# FindPython3 may leave Python3_LIBRARY_DIRS empty in conda/venv environments;
+# fall back to extracting the directory from the full library path or the
+# interpreter location so that @rpath/libpython resolves at runtime on macOS.
+# ---------------------------------------------------------------------------
+if(PYTHON_EMBEDDING)
+    if(Python3_LIBRARY_DIRS)
+        set(PYTHON_LIB_RPATH ${Python3_LIBRARY_DIRS})
+    elseif(Python3_LIBRARIES)
+        list(GET Python3_LIBRARIES 0 _py_first_lib)
+        get_filename_component(PYTHON_LIB_RPATH "${_py_first_lib}" DIRECTORY)
+    else()
+        get_filename_component(_py_bin_dir "${Python3_EXECUTABLE}" DIRECTORY)
+        get_filename_component(PYTHON_LIB_RPATH "${_py_bin_dir}/../lib" ABSOLUTE)
+    endif()
+    message(STATUS "[worm2d] Python library rpath: ${PYTHON_LIB_RPATH}")
+else()
+    set(PYTHON_LIB_RPATH "")
+endif()
+
+# ---------------------------------------------------------------------------
+# nlohmann_json — bundled header-only library
+# ---------------------------------------------------------------------------
+set(NLOHMANN_JSON_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/src/cpp")
+
+# ---------------------------------------------------------------------------
+# Common compiler flags
+# ---------------------------------------------------------------------------
+add_compile_options(-O3 -flto)
+
+# ---------------------------------------------------------------------------
+# Shared include directories used by multiple targets
+# ---------------------------------------------------------------------------
+set(CPP_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp)
+
+# ---------------------------------------------------------------------------
+# Helper macro: build a binary and install it into worm2d/bin/<subdir>
+# ---------------------------------------------------------------------------
+macro(add_worm_binary TARGET_NAME SUBDIR)
+    # Remaining args are source files
+    set(SRCS ${ARGN})
+    if("${SUBDIR}" STREQUAL "")
+        set(_w2d_bin_path "bin/main")
+    else()
+        set(_w2d_bin_path "bin/${SUBDIR}/main")
+    endif()
+    message(STATUS "[worm2d] Configuring C++ binary: ${_w2d_bin_path}")
+    add_executable(${TARGET_NAME} ${SRCS})
+    # Ninja uses a flat build dir — give each target its own subdir to avoid
+    # "multiple rules generate main" when several targets share OUTPUT_NAME main.
+    if("${SUBDIR}" STREQUAL "")
+        set_target_properties(${TARGET_NAME} PROPERTIES
+            RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+    else()
+        set_target_properties(${TARGET_NAME} PROPERTIES
+            RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/${SUBDIR})
+    endif()
+    add_custom_command(TARGET ${TARGET_NAME} PRE_LINK
+        COMMAND ${CMAKE_COMMAND} -E echo "[worm2d] Linking ${_w2d_bin_path} ..."
+        VERBATIM
+    )
+    target_compile_options(${TARGET_NAME} PRIVATE -fPIE)
+    target_include_directories(${TARGET_NAME} PRIVATE
+        ${CPP_DIR}
+        ${CPP_DIR}/Worm2D
+        ${Python3_INCLUDE_DIRS}
+        ${NLOHMANN_JSON_INCLUDE_DIR}
+        /opt/homebrew/include
+    )
+    if(PYTHON_EMBEDDING)
+        target_link_libraries(${TARGET_NAME} PRIVATE
+            Python3::Python
+            Threads::Threads
+            ${CMAKE_DL_LIBS}
+        )
+        # Use CMake's INSTALL_RPATH so the rpath survives install_name_tool rewriting
+        # at install time (raw -Wl,-rpath linker flags are stripped by CMake on macOS).
+        if(APPLE)
+            set_target_properties(${TARGET_NAME} PROPERTIES
+                INSTALL_RPATH "@loader_path;${PYTHON_LIB_RPATH}"
+                BUILD_WITH_INSTALL_RPATH TRUE
+            )
+        else()
+            set_target_properties(${TARGET_NAME} PROPERTIES
+                INSTALL_RPATH "${PYTHON_LIB_RPATH}"
+                BUILD_WITH_INSTALL_RPATH TRUE
+            )
+        endif()
+        target_link_directories(${TARGET_NAME} PRIVATE
+            /opt/homebrew/lib
+            ${PYTHON_LIB_RPATH}
+        )
+    else()
+        target_link_libraries(${TARGET_NAME} PRIVATE
+            Threads::Threads
+            ${CMAKE_DL_LIBS}
+        )
+        target_link_directories(${TARGET_NAME} PRIVATE
+            /opt/homebrew/lib
+        )
+    endif()
+    install(TARGETS ${TARGET_NAME}
+        RUNTIME DESTINATION worm2d/bin/${SUBDIR}
+    )
+endmacro()
+
+find_package(Threads REQUIRED)
+
+# ---------------------------------------------------------------------------
+# Core shared sources (used by both main and Worm2D targets)
+# ---------------------------------------------------------------------------
+set(CORE_SRCS
+    ${CPP_DIR}/Worm.cpp
+    ${CPP_DIR}/WormBody.cpp
+    ${CPP_DIR}/NervousSystem.cpp
+    ${CPP_DIR}/StretchReceptor.cpp
+    ${CPP_DIR}/Muscles.cpp
+    ${CPP_DIR}/TSearch.cpp
+    ${CPP_DIR}/random.cpp
+    ${CPP_DIR}/argUtils.cpp
+    ${CPP_DIR}/jsonUtils.cpp
+    ${CPP_DIR}/utils.cpp
+    ${CPP_DIR}/neuromlLocal/c302NervousSystem.cpp
+    ${CPP_DIR}/neuromlLocal/c302ForW2D.cpp
+    ${CPP_DIR}/neuromlLocal/owSignalSimulatorForWorm2D.cpp
+    ${CPP_DIR}/neuromlLocal/owSignalSimulator.cpp
+)
+
+# ---------------------------------------------------------------------------
+# Top-level main binary  →  worm2d/bin/main
+# ---------------------------------------------------------------------------
+add_worm_binary(worm2d_main ""
+    ${CPP_DIR}/main.cpp
+    ${CORE_SRCS}
+)
+set_target_properties(worm2d_main PROPERTIES OUTPUT_NAME main)
+
+# ---------------------------------------------------------------------------
+# C++ unit tests  (built separately, not installed)
+# ---------------------------------------------------------------------------
+add_executable(worm2d_tests
+    ${CPP_DIR}/tests.cpp
+    ${CPP_DIR}/NervousSystem.cpp
+    ${CPP_DIR}/random.cpp
+)
+target_include_directories(worm2d_tests PRIVATE ${CPP_DIR})
+target_link_libraries(worm2d_tests PRIVATE Threads::Threads)
+set_target_properties(worm2d_tests PROPERTIES OUTPUT_NAME tests)
+
+add_executable(worm2d_tests2
+    ${CPP_DIR}/tests2.cpp
+    ${CPP_DIR}/NervousSystem.cpp
+    ${CPP_DIR}/random.cpp
+    ${CPP_DIR}/jsonUtils.cpp
+    ${CPP_DIR}/argUtils.cpp
+)
+target_include_directories(worm2d_tests2 PRIVATE
+    ${CPP_DIR}
+    ${Python3_INCLUDE_DIRS}
+    ${NLOHMANN_JSON_INCLUDE_DIR}
+    /opt/homebrew/include
+)
+target_link_libraries(worm2d_tests2 PRIVATE Threads::Threads ${CMAKE_DL_LIBS})
+target_link_directories(worm2d_tests2 PRIVATE /opt/homebrew/lib)
+set_target_properties(worm2d_tests2 PROPERTIES OUTPUT_NAME tests2)
+
+# ---------------------------------------------------------------------------
+# Worm2D shared sources
+# ---------------------------------------------------------------------------
+set(W2D_COMMON_SRCS
+    ${CPP_DIR}/Worm2D/Evolvable.cpp
+    ${CPP_DIR}/Worm2D/WormAgent.cpp
+    ${CPP_DIR}/Worm2D/Worm2DSR.cpp
+    ${CPP_DIR}/Worm2D/Simulation.cpp
+    ${CPP_DIR}/Worm2D/Worm2D21.cpp
+    ${CPP_DIR}/Worm2D/Worm2DCE.cpp
+    ${CPP_DIR}/Worm2D/WormRS18.cpp
+    ${CPP_DIR}/Worm2D/Worm21.cpp
+    ${CPP_DIR}/Worm2D/Segment21.cpp
+    ${CPP_DIR}/Worm2D/Worm2D.cpp
+    ${CPP_DIR}/Worm2D/Evolution21.cpp
+    ${CPP_DIR}/Worm2D/Evolution.cpp
+    ${CPP_DIR}/Worm2D/EvolutionCE.cpp
+    ${CPP_DIR}/Worm2D/EvolutionRS18.cpp
+    ${CPP_DIR}/Worm2D/StretchReceptor18.cpp
+    ${CPP_DIR}/Worm2D/StretchReceptorCE.cpp
+    ${CPP_DIR}/Worm2D/StretchReceptor.cpp
+    ${CPP_DIR}/Worm2D/TSearchCO.cpp
+    ${CPP_DIR}/Worm2D/NSToMuscles.cpp
+    ${CPP_DIR}/Worm2D/EvolutionCO.cpp
+    ${CPP_DIR}/Worm2D/Worm2Dmods.cpp
+    ${CPP_DIR}/Worm2D/jsonUtils.cpp
+    # shared core files referenced by Worm2D
+    ${CPP_DIR}/WormBody.cpp
+    ${CPP_DIR}/NervousSystem.cpp
+    ${CPP_DIR}/Muscles.cpp
+    ${CPP_DIR}/TSearch.cpp
+    ${CPP_DIR}/random.cpp
+    ${CPP_DIR}/utils.cpp
+    ${CPP_DIR}/neuromlLocal/c302ForW2D.cpp
+    ${CPP_DIR}/neuromlLocal/owSignalSimulatorForWorm2D.cpp
+    ${CPP_DIR}/neuromlLocal/owSignalSimulator.cpp
+)
+
+# Worm2D/main  →  worm2d/bin/Worm2D/main
+add_worm_binary(worm2d_w2d_main "Worm2D"
+    ${CPP_DIR}/Worm2D/main.cpp
+    ${W2D_COMMON_SRCS}
+)
+set_target_properties(worm2d_w2d_main PROPERTIES OUTPUT_NAME main)
+
+# Worm2D/main_osc  →  worm2d/bin/Worm2D/main_osc
+add_worm_binary(worm2d_main_osc "Worm2D"
+    ${CPP_DIR}/Worm2D/main_osc.cpp
+    ${W2D_COMMON_SRCS}
+)
+set_target_properties(worm2d_main_osc PROPERTIES OUTPUT_NAME main_osc)
+
+# ---------------------------------------------------------------------------
+# RoyalSociety2018/main  →  worm2d/bin/RoyalSociety2018/main
+# ---------------------------------------------------------------------------
+set(RS18_DIR ${CPP_DIR}/RoyalSociety2018)
+add_worm_binary(worm2d_rs18 "RoyalSociety2018"
+    ${RS18_DIR}/main.cpp
+    ${RS18_DIR}/Worm.cpp
+    ${RS18_DIR}/WormBody.cpp
+    ${RS18_DIR}/NervousSystem.cpp
+    ${RS18_DIR}/StretchReceptor.cpp
+    ${RS18_DIR}/Muscles.cpp
+    ${RS18_DIR}/TSearch.cpp
+    ${RS18_DIR}/random.cpp
+    ${RS18_DIR}/jsonUtils.cpp
+    ${CPP_DIR}/argUtils.cpp
+)
+target_include_directories(worm2d_rs18 BEFORE PRIVATE ${RS18_DIR})
+set_target_properties(worm2d_rs18 PROPERTIES OUTPUT_NAME main)
+
+# ---------------------------------------------------------------------------
+# network2021/main  →  worm2d/bin/network2021/main
+# ---------------------------------------------------------------------------
+set(NET21_DIR ${CPP_DIR}/network2021)
+add_worm_binary(worm2d_net21 "network2021"
+    ${NET21_DIR}/main.cpp
+    ${NET21_DIR}/Worm.cpp
+    ${NET21_DIR}/WormBody.cpp
+    ${NET21_DIR}/NervousSystem.cpp
+    ${NET21_DIR}/Segment.cpp
+    ${NET21_DIR}/Muscles.cpp
+    ${NET21_DIR}/TSearch.cpp
+    ${NET21_DIR}/random.cpp
+    ${CPP_DIR}/argUtils.cpp
+)
+target_include_directories(worm2d_net21 BEFORE PRIVATE ${NET21_DIR})
+set_target_properties(worm2d_net21 PROPERTIES OUTPUT_NAME main)
+
+# ---------------------------------------------------------------------------
+# CE_orientation/main  →  worm2d/bin/CE_orientation/main
+# ---------------------------------------------------------------------------
+set(CEO_DIR ${CPP_DIR}/CE_orientation)
+add_worm_binary(worm2d_ceo "CE_orientation"
+    ${CEO_DIR}/main.cpp
+    ${CEO_DIR}/CTRNN.cpp
+    ${CEO_DIR}/WormAgent.cpp
+    ${CEO_DIR}/TSearch.cpp
+    ${CEO_DIR}/random.cpp
+    ${CPP_DIR}/argUtils.cpp
+)
+target_include_directories(worm2d_ceo BEFORE PRIVATE ${CEO_DIR})
+set_target_properties(worm2d_ceo PROPERTIES OUTPUT_NAME main)

worm2d-0.2.8/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 OpenWorm
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

worm2d-0.2.8/PKG-INFO

@@ -0,0 +1,22 @@
+Metadata-Version: 2.2
+Name: worm2d
+Version: 0.2.8
+Summary: Neuromechanical model of C. elegans locomotion
+Requires-Python: >=3.10
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: scipy
+Provides-Extra: neuroml
+Requires-Dist: pyNeuroML; extra == "neuroml"
+Requires-Dist: NEURON<9.0; extra == "neuroml"
+Provides-Extra: dev
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ipywidgets; extra == "dev"
+Requires-Dist: OSBModelValidation; extra == "dev"
+Requires-Dist: pyNeuroML; extra == "dev"
+Requires-Dist: modelspec; extra == "dev"
+Provides-Extra: all
+Requires-Dist: worm2d[neuroml]; extra == "all"
+Requires-Dist: worm2d[dev]; extra == "all"
+

worm2d-0.2.8/README.md

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+# 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