Merge pull request #287 from CCPBioSim/284-feature-add-automated-conda-upload

Add automated Conda publishing to release workflow

Author: harryswift01

.github/workflows/release.yaml

@@ -146,3 +146,46 @@ jobs:
       env:
         FLIT_USERNAME: __token__
         FLIT_PASSWORD:  ${{ secrets.PYPI_API_TOKEN }}
+
+  conda:
+    name: publish conda to anaconda.org
+    needs: [tag, release]
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: main
+
+      - name: Set version in conda recipe
+        run: |
+          sed -i -E "s/^{% set version = \".*\" %}$/{% set version = \"${{ github.event.inputs.version }}\" %}/" conda-recipe/meta.yaml
+
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Miniforge3
+          python-version: "3.12"
+          auto-activate-base: false
+
+      - name: Install build tools
+        shell: bash -l {0}
+        run: |
+          conda install -y conda-build anaconda-client
+          conda config --add channels conda-forge
+          conda config --set channel_priority strict
+          conda config --set anaconda_upload no
+
+      - name: Build package
+        shell: bash -l {0}
+        run: |
+          conda build conda-recipe
+
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          PKG_PATH=$(conda build conda-recipe --output)
+          anaconda -t "$ANACONDA_API_TOKEN" upload "$PKG_PATH" --user CCPBioSim --force

.pre-commit-config.yaml

@@ -12,6 +12,7 @@ repos:
       - id: check-added-large-files
       - id: check-merge-conflict
       - id: check-yaml
+        exclude: ^conda-recipe/meta\.yaml$
       - id: check-toml
       - id: check-case-conflict
       - id: check-ast

README.md

@@ -13,8 +13,8 @@ CodeEntropy
 CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
 
 <p align="center">
-    <img src="docs/images/biosim-codeentropy_logo_light.png#gh-light-mode-only" alt="CodeEntropy logo" width="300"/>
-    <img src="docs/images/biosim-codeentropy_logo_dark.png#gh-dark-mode-only" alt="CodeEntropy logo" width="300"/>
+    <img src="docs/_static/logos/biosim-codeentropy_logo_light.png#gh-light-mode-only" alt="CodeEntropy logo" width="300"/>
+    <img src="docs/_static/logos/biosim-codeentropy_logo_dark.png#gh-dark-mode-only" alt="CodeEntropy logo" width="300"/>
 </p>
 
 See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information.

conda-recipe/meta.yaml

@@ -0,0 +1,47 @@
+{% set name = "CodeEntropy" %}
+{% set version = "0.0.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  path: ..
+
+build:
+  noarch: python
+  script: python -m pip install . -vv --no-deps
+  entry_points:
+    - CodeEntropy=CodeEntropy.cli:main
+
+requirements:
+  host:
+    - python >=3.12
+    - pip
+    - flit-core >=3.4,<4
+  run:
+    - python >=3.11
+    - numpy >=2.3,<3.0
+    - mdanalysis >=2.10,<3.0
+    - pandas >=3.0,<3.1
+    - psutil >=7.1,<8.0
+    - pyyaml >=6.0,<7.0
+    - python-json-logger >=4.0,<5.0
+    - rich >=14.2,<15.0
+    - art >=6.5,<7.0
+    - networkx >=3.6,<3.7
+    - matplotlib >=3.10,<3.11
+    - waterentropy >=2,<2.1
+    - requests >=2.32,<3.0
+
+test:
+  imports:
+    - CodeEntropy
+  commands:
+    - CodeEntropy --help
+
+about:
+  home: https://ccpbiosim.github.io/CodeEntropy/
+  license: MIT
+  license_file: LICENSE
+  summary: "Entropy analysis tools for macromolecular systems and MD simulation"

docs/developer_guide.rst

@@ -9,12 +9,19 @@ the continuous integration workflows.
 Getting Started for Developers
 ------------------------------
 
-Create a virtual environment::
+Create a development environment using either venv or Conda.
+
+Using venv::
 
     python -m venv codeentropy-dev
     source codeentropy-dev/bin/activate  # Linux/macOS
     codeentropy-dev\Scripts\activate     # Windows
 
+Using Conda::
+
+    conda create -n codeentropy-dev python=3.14
+    conda activate codeentropy-dev
+
 Clone the repository::
 
     git clone https://github.com/CCPBioSim/CodeEntropy.git

docs/getting_started.rst

@@ -23,13 +23,37 @@ Requirements
 Installation
 ------------
 
-To install the released version:
+CodeEntropy can be installed using either pip or Conda.
+
+Install with pip
+^^^^^^^^^^^^^^^^
+
+To install the released version from PyPI:
 
 .. code-block:: bash
 
    pip install CodeEntropy
 
 
+Install with Conda
+^^^^^^^^^^^^^^^^^^
+
+CodeEntropy is also available via the CCPBioSim Anaconda channel.
+
+Create a dedicated environment:
+
+.. code-block:: bash
+
+   conda create -n codeentropy python=3.14
+   conda activate codeentropy
+
+Install CodeEntropy:
+
+.. code-block:: bash
+
+   conda install -c conda-forge -c CCPBioSim CodeEntropy
+
+
 Input Files
 -----------
 

pyproject.toml

@@ -35,7 +35,7 @@ classifiers = [
     "Development Status :: 5 - Production/Stable"
 ]
 keywords = ["entropy", "macromolecular systems", "MD simulation"]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 dependencies = [
     "numpy>=2.3,<3.0",
     "mdanalysis>=2.10,<3.0",