test and update install and build documentation

.pre-commit-config.yaml

@@ -1,3 +1,6 @@
+default_language_version:
+    python: python3.10
+
 files: simularium_readdy_models
 repos:
 

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

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`<br>
 **Development Head:** `pip install git+https://github.com/simularium/simularium_readdy_models.git`<br>
-**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

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

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",
 ]