CI: move PyPI deps installation to conda

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.0
+current_version = 3.0.1
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved

.github/actions/install-python-and-package/action.yml

@@ -26,70 +26,43 @@ runs:
       uses: styfle/[email protected]
       with:
         access_token: ${{ github.token }}
+
     - uses: actions/checkout@v3
-    - name: Setup conda
-      uses: s-weigand/setup-conda@v1
+
+    - name: Setup miniconda
+      uses: conda-incubator/setup-miniconda@v2
       with:
-        update-conda: true
+        auto-update-conda: true
+        miniforge-variant: Mambaforge
+        channels: conda-forge
         python-version: ${{ inputs.python-version }}
-        conda-channels: pytorch, pyg, bioconda, defaults, sbl, conda-forge
+        activate-environment: deeprank2
+        environment-file: env/deeprank2.yml
+        use-mamba: true
+
     - run: |
         conda --version
         conda env list
-      shell: bash {0}
+      shell: bash -l {0}
+
     - name: Python info
-      shell: bash -e {0}
+      shell: bash -l {0}
       run: |
         which python3
         python3 --version
-    - name: Install dependencies on Linux
-      shell: bash {0}
-      env:
-        CMAKE_INSTALL_PREFIX: .local
-      if: runner.os == 'Linux'
-      run: |
-        # Install deeprank2 conda dependencies
-        ## DSSP
-        conda install -c sbl dssp>=4.2.2.1
-        ## MSMS
-        conda install -c bioconda msms>=2.6.1
-        ## PyTorch, PyG, PyG adds
-        ### Installing for CPU only on the CI
-        conda install pytorch=2.1.1 torchvision=0.16.1 torchaudio=2.1.1 cpuonly=2.0.* -c pytorch
-        conda install pyg=2.4.0 -c pyg
-        pip install torch_scatter==2.1.2 torch_sparse==0.6.18 torch_cluster==1.6.3 torch_spline_conv==1.2.2 -f https://data.pyg.org/whl/torch-2.1.0+cpu.html
-    - name: Install dependencies on MacOS
-      shell: bash {0}
-      env:
-        CMAKE_INSTALL_PREFIX: .local
-      if: runner.os == 'macOS'
-      run: |
-        # Install dependencies not handled by setuptools
-        ## DSSP
-        conda install -c sbl dssp>=4.2.2.1
-        ## MSMS
-        cd /tmp/
-        wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL2.6.1/msms_i86Linux2_2.6.1.tar.gz
-        sudo mkdir /usr/local/lib/msms
-        cd /usr/local/lib/msms
-        sudo tar zxvf /tmp/msms_i86Linux2_2.6.1.tar.gz
-        sudo ln -s /usr/local/lib/msms/msms.i86Linux2.2.6.1 /usr/local/bin/msms
-        sudo ln -s /usr/local/lib/msms/pdb_to_xyzr* /usr/local/bin
-        ## PyTorch, PyG, PyG adds
-        ### Installing for CPU only on the CI
-        conda install pytorch torchvision torchaudio cpuonly -c pytorch
-        pip install torch_geometric
-        pip install torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-$(python3 -c "import torch; print(torch.__version__)")+cpu.html
-        # PyTables via conda only for MacOS
-        conda install pytables
+
     - name: Install the GitHub repository version of the package
-      shell: bash {0}
+      shell: bash -l {0}
       if: ${{ inputs.pkg-installation-type == 'repository' }}
-      run: pip install .'[${{ inputs.extras-require }}]'
-    - name: Install the latest released version of the package
-      shell: bash {0}
+      run: |
+        conda activate deeprank2
+        pip install .'[${{ inputs.extras-require }}]'
+
+    - name: Install the latest released PyPI version of the package
+      shell: bash -l {0}
       if: ${{ inputs.pkg-installation-type == 'latest' }}
       run: |
+        conda activate deeprank2
         pip install pytest
         rm -r deeprank2
         pip install deeprank2

.github/workflows/build-repo.yml

@@ -39,14 +39,22 @@ jobs:
         os: ["ubuntu-latest"]
         python-version: ["3.10"] # ["3.10", "3.11"]
 
+    # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
+    defaults:
+      run:
+        shell: bash -l {0}
+
     steps:
       - uses: actions/checkout@v3
+
       - uses: ./.github/actions/install-python-and-package
         with:
           python-version: ${{ matrix.python-version }}
           extras-require: test, publishing
           pkg-installation-type: "repository"
+
       - name: Run unit tests
         run: pytest -v
+
       - name: Verify that we can build the package
         run: python3 -m build

.github/workflows/coveralls.yml

@@ -39,6 +39,11 @@ jobs:
         os: ["ubuntu-latest"]
         python-version: ["3.10"]
 
+    # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
+    defaults:
+      run:
+        shell: bash -l {0}
+
     steps:
       - uses: actions/checkout@v3
       - uses: ./.github/actions/install-python-and-package

.github/workflows/linting.yml

@@ -39,6 +39,11 @@ jobs:
         os: ["ubuntu-latest"]
         python-version: ["3.10"]
 
+    # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
+    defaults:
+      run:
+        shell: bash -l {0}
+
     steps:
       - uses: actions/checkout@v3
       - uses: ./.github/actions/install-python-and-package

.zenodo.json

@@ -1,42 +1,42 @@
 {
   "creators": [
     {
-      "affiliation": "Netherlands eScience Center, Amsterdam, NL",
+      "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands",
       "name": "Giulia Crocioni",
       "orcid": "0000-0002-0823-0121"
     },
     {
-      "affiliation": "Netherlands eScience Center, Amsterdam, NL",
+      "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands",
       "name": "Dani L. Bodor",
       "orcid": "0000-0003-2109-2349"
     },
     {
-      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL",
+      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands",
       "name": "Coos Baakman",
       "orcid": "0000-0003-4317-1566"
     },
     {
-      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL",
+      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands",
       "name": "Farzaneh M. Parizi",
       "orcid": "0000-0003-4230-7492"
     },
     {
-      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL",
+      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands",
       "name": "Daniel T. Rademaker",
       "orcid": "0000-0003-1959-1317"
     },
     {
-      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL",
+      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands",
       "name": "Gayatri Ramakrishnan",
       "orcid": "0000-0001-8203-2783"
     },
     {
-      "affiliation": "Netherlands eScience Center, Amsterdam, NL",
+      "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands",
       "name": "Sven van der Burg",
       "orcid": "0000-0003-1250-6968"
     },
     {
-      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL",
+      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands",
       "name": "Dario F. Marzella",
       "orcid": "0000-0002-0043-3055"
     },
@@ -45,7 +45,7 @@
       "orcid": "0000-0002-9113-0622"
     },
     {
-      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL",
+      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands",
       "name": "Li C. Xue",
       "orcid": "0000-0002-2613-538X"
     }

CITATION.cff

@@ -12,44 +12,44 @@ authors:
   - given-names: Giulia
     family-names: Crocioni
     email: [email protected]
-    affiliation: Netherlands eScience Center, Amsterdam, NL
+    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
     orcid: "https://orcid.org/0000-0002-0823-0121"
   - given-names: Dani L.
     family-names: Bodor
     email: [email protected]
-    affiliation: Netherlands eScience Center, Amsterdam, NL
+    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
     orcid: "https://orcid.org/0000-0003-2109-2349"
   - given-names: Coos
     family-names: Baakman
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0003-4317-1566"
   - given-names: Farzaneh Meimandi
     family-names: Parizi
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0003-4230-7492"
   - given-names: Daniel-T.
     family-names: Rademaker
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0003-1959-1317"
   - given-names: Gayatri
     family-names: Ramakrishnan
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0001-8203-2783"
   - given-names: Sven A.
     family-names: van der Burg
-    affiliation: Netherlands eScience Center, Amsterdam, NL
+    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
     orcid: "https://orcid.org/0000-0003-1250-6968"
   - given-names: Dario F.
     family-names: Marzella
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0002-0043-3055"
   - given-names: João M.C.
     family-names: Teixeira
     affiliation: Independent Researcher
     orcid: "https://orcid.org/0000-0002-9113-0622"
   - given-names: Li C.
     family-names: Xue
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0002-2613-538X"
 abstract: >-
   DeepRank2 is an open-source deep learning
@@ -68,5 +68,5 @@ keywords:
   - DeepRank
 license: Apache-2.0
 commit: 4e8823758ba03f824b4281f5689cb6a335ab2f6c
-version: "3.0.0"
-date-released: "2024-01-25"
+version: "3.0.1"
+date-released: "2024-02-22"

CONTRIBUTING.rst

@@ -37,8 +37,8 @@ You want to make some kind of change to the code base
 #. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions `here <https://help.github.com/articles/configuring-a-remote-for-a-fork/>`__ and `here <https://help.github.com/articles/syncing-a-fork/>`__);
 #. make sure the existing tests still work by running ``python setup.py test``;
 #. add your own tests (if necessary);
-#. ensure the code is correctly linted (`ruff .`) and formatted (`ruff format .`);
-#. see our `developer's readme <README.dev.md>`` for detailed information on our style conventions, etc.;
+#. ensure the code is correctly linted (``ruff .``) and formatted (``ruff format .``);
+#. see our `developer's readme <README.dev.md>`_ for detailed information on our style conventions, etc.;
 #. update or expand the documentation;
 #. `push <http://rogerdudler.github.io/git-guide/>`_ your feature branch to (your fork of) the DeepRank2 repository on GitHub;
 #. create the pull request, e.g. following the instructions `here <https://help.github.com/articles/creating-a-pull-request/>`__.

Dockerfile

@@ -3,26 +3,26 @@ FROM --platform=linux/x86_64 condaforge/miniforge3:23.3.1-1
 
 # Add files
 ADD ./tutorials /home/deeprank2/tutorials
-ADD ./env/environment.yml /home/deeprank2
-ADD ./env/requirements.txt /home/deeprank2
+ADD ./env/deeprank2-docker.yml /home/deeprank2
+ADD ./env/requirements-docker.txt /home/deeprank2
 
-# Install
 RUN \
-  apt update -y &&
-  apt install unzip -y &&
+  # Install dependencies and package
+  apt update -y && \
+  apt install unzip -y && \
   ## GCC
-  apt install -y gcc &&
-  ## Conda and pip deps
-  mamba env create -f /home/deeprank2/environment.yml &&
-  ## Get the data for running the tutorials
-  if [ -d "/home/deeprank2/tutorials/data_raw" ]; then rm -Rf /home/deeprank2/tutorials/data_raw; fi &&
-  if [ -d "/home/deeprank2/tutorials/data_processed" ]; then rm -Rf /home/deeprank2/tutorials/data_processed; fi &&
-  wget https://zenodo.org/records/8349335/files/data_raw.zip &&
-  unzip data_raw.zip -d data_raw &&
+  apt install -y gcc && \
+  ## Create the environment and install the dependencies
+  mamba env create -f /home/deeprank2/deeprank2-docker.yml && \
+  ## Activate the environment automatically when entering the container
+  echo "source activate deeprank2" >~/.bashrc && \
+  # Get the data for running the tutorials
+  if [ -d "/home/deeprank2/tutorials/data_raw" ]; then rm -Rf /home/deeprank2/tutorials/data_raw; fi && \
+  if [ -d "/home/deeprank2/tutorials/data_processed" ]; then rm -Rf /home/deeprank2/tutorials/data_processed; fi && \
+  wget https://zenodo.org/records/8349335/files/data_raw.zip && \
+  unzip data_raw.zip -d data_raw && \
   mv data_raw /home/deeprank2/tutorials
 
-# Activate the environment
-RUN echo "source activate deeprank2" >~/.bashrc
 ENV PATH /opt/conda/envs/deeprank2/bin:$PATH
 
 # Define working directory

README.dev.md

@@ -79,7 +79,7 @@ During the development cycle, three main supporting branches are used:
 
 ## Making a release
 
-1. Branch from `dev` and prepare the branch for the release (e.g., removing the unnecessary dev files such as the current one, fix minor bugs if necessary).
+1. Branch from `dev` and prepare the branch for the release (e.g., removing the unnecessary dev files, fix minor bugs if necessary).
 2. [Bump the version](https://github.com/DeepRank/deeprank2/blob/dev/README.dev.md#versioning).
 3. Verify that the information in `CITATION.cff` is correct (update the release date), and that `.zenodo.json` contains equivalent data.
 4. Merge the release branch into `main` (and `dev`), and [run the tests](https://github.com/DeepRank/deeprank2/blob/dev/README.dev.md#running-the-tests).