From 19ce7ccf4da0117bacfbd793797ced0f29452cab Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Feb 2026 11:36:28 +0000 Subject: [PATCH 1/5] change CodeEntropy name within `conda-recipe/meta.yaml` to `codeentropy` --- conda-recipe/meta.yaml | 2 +- docs/getting_started.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index f87d610..8398f48 100644 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -1,4 +1,4 @@ -{% set name = "CodeEntropy" %} +{% set name = "codeentropy" %} {% set version = "0.0.0" %} package: diff --git a/docs/getting_started.rst b/docs/getting_started.rst index 51f7b20..ff3cdba 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -51,7 +51,7 @@ Install CodeEntropy: .. code-block:: bash - conda install -c conda-forge -c CCPBioSim CodeEntropy + conda install -c conda-forge -c CCPBioSim codeentropy Input Files From 43a6c9d668b7ee33f4de824dc8c686cfea20a148 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Feb 2026 13:56:32 +0000 Subject: [PATCH 2/5] update `conda-recipe/meta.yaml` to use lower case and fix dependencies --- conda-recipe/meta.yaml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 8398f48..2caa806 100644 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -10,7 +10,9 @@ source: build: noarch: python - script: python -m pip install . -vv --no-deps + script: | + python -m pip install . -vv --no-deps + PIP_NO_INDEX=0 python -m pip install -vv --index-url https://pypi.org/simple waterEntropy entry_points: - CodeEntropy=CodeEntropy.cli:main @@ -20,19 +22,21 @@ requirements: - pip - flit-core >=3.4,<4 run: - - python >=3.11 + - python >=3.12 - 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 + - python-json-logger >=2.0,<3.0 - rich >=14.2,<15.0 - - art >=6.5,<7.0 + - python-art >=6.5,<7.0 - networkx >=3.6,<3.7 - matplotlib >=3.10,<3.11 - - waterentropy >=2,<2.1 - requests >=2.32,<3.0 + - dask >=2026.1.2,<2026.2.0 + - distributed >=2026.1.2,<2026.2.0 + - dask-jobqueue >=0.9,<0.10 test: imports: From 52e79e02d2d05fbb64500af2dd327736c7123e01 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Feb 2026 14:42:35 +0000 Subject: [PATCH 3/5] include Anaconda.org GitHub badges within `README.md` --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index db32d17..c55871d 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,7 @@ CodeEntropy | **Documentation** | [![Weekly Docs](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-docs.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-docs.yaml) [![Docs - Status](https://app.readthedocs.org/projects/codeentropy/badge/?version=latest)](https://codeentropy.readthedocs.io/en/latest/?badge=latest) | | **Citation** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17570721.svg)](https://doi.org/10.5281/zenodo.17570721) | | **PyPI** | ![PyPI - Status](https://img.shields.io/pypi/status/codeentropy?logo=pypi&logoColor=white) ![PyPI - Version](https://img.shields.io/pypi/v/codeentropy?logo=pypi&logoColor=white) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/CodeEntropy) ![PyPI - Total Downloads](https://img.shields.io/pepy/dt/codeentropy?logo=pypi&logoColor=white&color=blue) ![PyPI - Monthly Downloads](https://img.shields.io/pypi/dm/CodeEntropy?logo=pypi&logoColor=white&color=blue) | +| **Anaconda** | [![Anaconda.org](https://anaconda.org/CCPBioSim/codeentropy/badges/version.svg)](https://anaconda.org/CCPBioSim/codeentropy/) [![Last Updated](https://anaconda.org/CCPBioSim/codeentropy/badges/latest_release_date.svg)](https://anaconda.org/CCPBioSim/codeentropy) [![Platforms](https://anaconda.org/CCPBioSim/codeentropy/badges/platforms.svg)](https://anaconda.org/CCPBioSim/codeentropy) [![License](https://anaconda.org/CCPBioSim/codeentropy/badges/license.svg)](https://anaconda.org/CCPBioSim/codeentropy) [![Downloads](https://anaconda.org/CCPBioSim/codeentropy/badges/downloads.svg)](https://anaconda.org/CCPBioSim/codeentropy)| | **Quality** | [![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/CodeEntropy/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/CodeEntropy?branch=main) | 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. From 3b7f5254d1f041b055d8bf205b1e5462b2de3997 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Feb 2026 14:47:52 +0000 Subject: [PATCH 4/5] ci: build and publish CodeEntropy conda package to CCPBioSim channel --- .github/workflows/release.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index b2d803e..79a838a 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -180,13 +180,18 @@ jobs: - name: Build package shell: bash -l {0} + env: + PIP_NO_INDEX: "0" run: | + PKG_PATH=$(conda build conda-recipe --output) + echo "PKG_PATH=$PKG_PATH" >> $GITHUB_ENV conda build conda-recipe + test -f "$PKG_PATH" + echo "Built: $PKG_PATH" - 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 From 30d93c5bb2085b99ee3430514bcb897b6009142e Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 27 Feb 2026 16:07:29 +0000 Subject: [PATCH 5/5] ci(conda): configure conda-forge-only build and clean release workflow --- .github/workflows/release.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index 79a838a..df65713 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -163,19 +163,20 @@ jobs: sed -i "s/^{% set version = \".*\" %}$/{% set version = \"${{ github.event.inputs.version }}\" %}/" conda-recipe/meta.yaml grep '{% set version' conda-recipe/meta.yaml - - name: Setup Conda + - name: Setup Conda (conda-forge only) uses: conda-incubator/setup-miniconda@v3 with: miniforge-variant: Miniforge3 python-version: "3.12" - auto-activate-base: false + auto-activate: false + conda-remove-defaults: true + channels: conda-forge + channel-priority: strict - 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 @@ -184,7 +185,7 @@ jobs: PIP_NO_INDEX: "0" run: | PKG_PATH=$(conda build conda-recipe --output) - echo "PKG_PATH=$PKG_PATH" >> $GITHUB_ENV + echo "PKG_PATH=$PKG_PATH" >> "$GITHUB_ENV" conda build conda-recipe test -f "$PKG_PATH" echo "Built: $PKG_PATH"