From 7156ba7902285ff371f5d52b7cd272127e8be987 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 10 Nov 2026 14:33:05 +0000 Subject: [PATCH 1/3] Revise README with project status and links Updated README to reflect current project status and provide a link to the latest work. --- README.md | 53 +---------------------------------------------------- 1 file changed, 1 insertion(+), 52 deletions(-) diff --git a/README.md b/README.md index b747da1..8147f26 100644 --- a/README.md +++ b/README.md @@ -1,56 +1,5 @@ # Worm2D -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.py`. Run any directly: - -```bash -cd tests -python testW2DCE.py -``` - - -## CLI - -After install, the `worm2d` command is available: - -```bash -worm2d -f [-E] [-O ] [-T ] [...] -``` - -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. +Work in progress, see https://github.com/openworm/CE_locomotion/tree/test_package for latest. From f47a84f7159b45510eadfd589949940e63be730e Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 10 Nov 2026 14:34:19 +0000 Subject: [PATCH 2/3] Update CI matrix to remove macOS 14 Removed macOS 14 from the CI matrix to simplify testing environments. --- .github/workflows/ci-make.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-make.yml b/.github/workflows/ci-make.yml index e403864..d10ab3a 100644 --- a/.github/workflows/ci-make.yml +++ b/.github/workflows/ci-make.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - runs-on: [ubuntu-22.04, ubuntu-latest, macos-latest, macos-14 ] + runs-on: [ubuntu-22.04, ubuntu-latest, macos-latest ] python-version: [ "3.10", "3.12" ] # Note: 3.14 causes issues with Neuron 8.2.7 steps: From bcd3dcca0a515edc3aa139e956a51d30202837a0 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 10 Nov 2026 17:35:56 +0000 Subject: [PATCH 3/3] Update CI matrix to exclude 'ubuntu-latest' Removed 'ubuntu-latest' from the CI matrix for compatibility. --- .github/workflows/ci-make.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-make.yml b/.github/workflows/ci-make.yml index d10ab3a..d66580a 100644 --- a/.github/workflows/ci-make.yml +++ b/.github/workflows/ci-make.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - runs-on: [ubuntu-22.04, ubuntu-latest, macos-latest ] + runs-on: [ubuntu-22.04, macos-latest ] python-version: [ "3.10", "3.12" ] # Note: 3.14 causes issues with Neuron 8.2.7 steps: