diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d67b6b9..d925b09 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,3 +1,6 @@ +default_language_version: + python: python3.10 + files: simularium_readdy_models repos: diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d772be4..e24bbc1 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -27,15 +27,15 @@ Ready to contribute? Here's how to set up `simularium_readdy_models` for local d Windows: `scoop install just` or `choco install just` MacOS: `brew install just` -4. Install the project in editable mode. (It is also recommended to work in a virtualenv or anaconda environment): +4. Install the project in editable mode in an anaconda environment: ```bash - cd simularium_readdy_models/ + cd readdy-models/ + conda env create -f environment.yml + conda activate readdy_models just install ``` - If this doesn't work try: `pip install -e '.[lint,test,docs,dev]'`. - 5. Create a branch for local development: ```bash diff --git a/README.md b/README.md index 0f35d76..b2b416d 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,14 @@ See [examples/README.md](examples/README.md) to run example actin, microtubules, **Stable Release:** `pip install simularium_readdy_models`
**Development Head:** `pip install git+https://github.com/simularium/simularium_readdy_models.git`
-**Local Editable Install** `pip install -e .[dev]` (or `pip install -e .\[dev\]` on mac) from repo root directory + +### Development Install with `conda`: + +(`conda` is currently required to install `readdy`.) + +1. Create a virtual environment with conda-specific dependencies: `conda env create -f environment.yml` +2. Activate the environment: `conda activate readdy_models` +3. Install remaining dependencies: `just install` ## Documentation diff --git a/environment.yml b/environment.yml index 2cbb7f6..10467d7 100644 --- a/environment.yml +++ b/environment.yml @@ -1,6 +1,4 @@ -name: anaconda-client-env -channels: - - conda-forge +name: readdy_models dependencies: - - readdy==2.0.9 - - numpy>=1.20 + - python=3.10 + - conda-forge::readdy diff --git a/pyproject.toml b/pyproject.toml index de4a182..6e619df 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,10 +28,10 @@ classifiers = [ ] dynamic = ["version"] dependencies = [ - "numpy>=1.16", - "scipy>=1.5.2", - "pandas>=1.0", - "simulariumio", + "numpy", + "scipy", + "pandas", + "simulariumio>=1.11.0", "subcell_pipeline @ git+https://github.com/simularium/subcell-pipeline.git", ]