release: 3.0.2 patch

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.1
+current_version = 3.0.2
 
 [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
@@ -15,3 +15,7 @@ replace = version = "{new_version}"
 [bumpversion:file:CITATION.cff]
 search = version: "{current_version}"
 replace = version: "{new_version}"
+
+[bumpversion:file:requirements-docker.txt]
+search = deeprank2==current_version
+replace = deeprank2==new_version

.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

@@ -39,11 +39,18 @@ 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
         with:
           python-version: ${{ matrix.python-version }}
           extras-require: test
       - name: Check style against standards using ruff
-        run: ruff .
+        run: |
+          ruff check
+          ruff format --check

.github/workflows/notebooks.yml

@@ -0,0 +1,62 @@
+name: notebooks
+
+on:
+  push:
+    paths-ignore:
+      # specific folder locations
+      - ".vscode/**"
+      - "docs/**"
+      # filetypes
+      - "**.md"
+      - "**.rst"
+      - "**.cff"
+      - "**.png"
+    branches:
+      - main
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths-ignore:
+      # specific folder locations
+      - ".vscode/**"
+      - "docs/**"
+      # filetypes
+      - "**.md"
+      - "**.rst"
+      - "**.cff"
+      - "**.png"
+
+jobs:
+  build:
+    if: github.event.pull_request.draft == false
+    name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        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, notebooks
+          pkg-installation-type: "repository"
+
+      - name: Download the data for the tutorials
+        shell: bash -l {0}
+        run: |
+          wget https://zenodo.org/records/8349335/files/data_raw.zip
+          unzip data_raw.zip -d data_raw
+          mv data_raw tutorials
+
+      - name: Run tutorial notebooks
+        run: pytest --nbmake tutorials

.vscode/settings.json

@@ -17,6 +17,10 @@
   },
   "notebook.diff.ignoreMetadata": true,
 
+  // Pytest
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true,
+
   // Format all files on save
   "editor.formatOnSave": true,
   "editor.defaultFormatter": "esbenp.prettier-vscode",

CITATION.cff

@@ -1,45 +1,5 @@
 cff-version: "1.2.0"
 authors:
-- family-names: Crocioni
-  given-names: Giulia
-  orcid: "https://orcid.org/0000-0002-0823-0121"
-- family-names: Bodor
-  given-names: Dani L.
-  orcid: "https://orcid.org/0000-0003-2109-2349"
-- family-names: Baakman
-  given-names: Coos
-  orcid: "https://orcid.org/0000-0003-4317-1566"
-- family-names: Parizi
-  given-names: Farzaneh M.
-  orcid: "https://orcid.org/0000-0003-4230-7492"
-- family-names: Rademaker
-  given-names: Daniel-T.
-  orcid: "https://orcid.org/0000-0003-1959-1317"
-- family-names: Ramakrishnan
-  given-names: Gayatri
-  orcid: "https://orcid.org/0000-0001-8203-2783"
-- family-names: Burg
-  given-names: Sven A.
-  name-particle: van der
-  orcid: "https://orcid.org/0000-0003-1250-6968"
-- family-names: Marzella
-  given-names: Dario F.
-  orcid: "https://orcid.org/0000-0002-0043-3055"
-- family-names: Teixeira
-  given-names: João M. C.
-  orcid: "https://orcid.org/0000-0002-9113-0622"
-- family-names: Xue
-  given-names: Li C.
-  orcid: "https://orcid.org/0000-0002-2613-538X"
-contact:
-- family-names: Crocioni
-  given-names: Giulia
-  orcid: "https://orcid.org/0000-0002-0823-0121"
-doi: 10.5281/zenodo.10566809
-message: If you use this software, please cite our article in the
-  Journal of Open Source Software.
-preferred-citation:
-  authors:
   - family-names: Crocioni
     given-names: Giulia
     orcid: "https://orcid.org/0000-0002-0823-0121"
@@ -71,6 +31,46 @@ preferred-citation:
   - family-names: Xue
     given-names: Li C.
     orcid: "https://orcid.org/0000-0002-2613-538X"
+contact:
+  - family-names: Crocioni
+    given-names: Giulia
+    orcid: "https://orcid.org/0000-0002-0823-0121"
+doi: 10.5281/zenodo.10566809
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+    - family-names: Crocioni
+      given-names: Giulia
+      orcid: "https://orcid.org/0000-0002-0823-0121"
+    - family-names: Bodor
+      given-names: Dani L.
+      orcid: "https://orcid.org/0000-0003-2109-2349"
+    - family-names: Baakman
+      given-names: Coos
+      orcid: "https://orcid.org/0000-0003-4317-1566"
+    - family-names: Parizi
+      given-names: Farzaneh M.
+      orcid: "https://orcid.org/0000-0003-4230-7492"
+    - family-names: Rademaker
+      given-names: Daniel-T.
+      orcid: "https://orcid.org/0000-0003-1959-1317"
+    - family-names: Ramakrishnan
+      given-names: Gayatri
+      orcid: "https://orcid.org/0000-0001-8203-2783"
+    - family-names: Burg
+      given-names: Sven A.
+      name-particle: van der
+      orcid: "https://orcid.org/0000-0003-1250-6968"
+    - family-names: Marzella
+      given-names: Dario F.
+      orcid: "https://orcid.org/0000-0002-0043-3055"
+    - family-names: Teixeira
+      given-names: João M. C.
+      orcid: "https://orcid.org/0000-0002-9113-0622"
+    - family-names: Xue
+      given-names: Li C.
+      orcid: "https://orcid.org/0000-0002-2613-538X"
   date-published: 2024-02-27
   doi: 10.21105/joss.05983
   issn: 2475-9066
@@ -86,3 +86,4 @@ preferred-citation:
   volume: 9
 title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep
   Learning"
+version: "3.0.2"

CONTRIBUTING.rst

@@ -37,7 +37,7 @@ 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 .``);
+#. ensure the code is correctly linted (``ruff check.``) 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;

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

@@ -48,7 +48,7 @@ We use [ruff](https://docs.astral.sh/ruff/) for linting, sorting imports and for
 
 If you are using VS code, please install and activate the [Ruff extension](https://marketplace.visualstudio.com/items?itemName=charliermarsh.ruff) to automatically format and check linting.
 
-Otherwise, please ensure check both linting (`ruff fix .`) and formatting (`ruff format .`) before requesting a review.
+Otherwise, please ensure check both linting (`ruff check .`) and formatting (`ruff format .`) before requesting a review.
 
 We use [prettier](https://prettier.io/) for formatting most other files. If you are editing or adding non-python files and using VS code, the [Prettier extension](https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode) can be installed to auto-format these files as well.