Merge pull request #562 from DeepRank/557_release_dev_3.0.0_gcroci2

release: merge dev with main for release 3.0.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.1.2
+current_version = 3.0.0
 
 [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/ISSUE_TEMPLATE/bug_report.md

@@ -1,29 +1,29 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-title: 'Bug: <please fill here>'
-labels: 'bug'
-assignees: ''
-
+title: "Bug: <please fill here>"
+labels: "bug"
+assignees: ""
 ---
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **Environment:**
+
 - OS system:
 - Version:
-- Branch commit ID: 
+- Branch commit ID:
 - Inputs:
 
 **To Reproduce**
 Steps/commands/screenshots to reproduce the behaviour:
- 
- 1.  
- 
- 2.
- 
- 3. 
+
+1.
+
+2.
+
+3.
 
 **Expected Results**
 A clear and concise description of what you expected to happen.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,10 +1,9 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
-title: 'Add/edit'
-labels: 'feature'
-assignees: ''
-
+title: "Add/edit"
+labels: "feature"
+assignees: ""
 ---
 
 **Is your feature request related to a problem? Please describe.**
@@ -20,7 +19,8 @@ A clear and concise description of any alternative solutions or features you've
 Add any other context or screenshots about the feature request here.
 
 **Checks for the developer**
-After having implemented the request, please remember to: 
+After having implemented the request, please remember to:
+
 - [ ] Add all the necessary tests. Make sure that the parameter functionality is well tested, from all points of views.
 - [ ] Add the proper documentation to the source code (docstrings).
 - [ ] Add the proper documentation to the readme. Examples about how using the new feature should be clear and easy to follow.

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

@@ -3,7 +3,6 @@ name: "Install Python and DeepRank2"
 description: "Installs Python, updates pip and installs DeepRank2 together with its dependencies."
 
 inputs:
-
   python-version:
     required: false
     description: "The Python version to use. Specify major and minor version, e.g. '3.10'."
@@ -14,23 +13,29 @@ inputs:
     description: "The extras dependencies packages to be installed, for instance 'dev' or 'dev,publishing,notebooks'."
     default: "test"
 
-runs:
+  pkg-installation-type:
+    required: false
+    description: "The package installation type to install, the latest released version on PyPI ('latest') or the GitHub repository one ('repository')."
+    default: "repository"
 
+runs:
   using: "composite"
 
   steps:
     - name: Cancel Previous Runs and Set up Python
       uses: styfle/[email protected]
       with:
-          access_token: ${{ github.token }}
+        access_token: ${{ github.token }}
     - uses: actions/checkout@v3
     - name: Setup conda
       uses: s-weigand/setup-conda@v1
       with:
         update-conda: true
         python-version: ${{ inputs.python-version }}
-        conda-channels: anaconda
-    - run: conda --version
+        conda-channels: pytorch, pyg, bioconda, defaults, sbl, conda-forge
+    - run: |
+        conda --version
+        conda env list
       shell: bash {0}
     - name: Python info
       shell: bash -e {0}
@@ -43,44 +48,25 @@ runs:
         CMAKE_INSTALL_PREFIX: .local
       if: runner.os == 'Linux'
       run: |
-        # Install dependencies not handled by setuptools 
+        # Install deeprank2 conda dependencies
         ## DSSP
-        sudo apt-get install -y dssp
+        conda install -c sbl dssp>=4.2.2.1
         ## MSMS
-        conda install -c bioconda msms
+        conda install -c bioconda msms>=2.6.1
         ## PyTorch, PyG, PyG adds
         ### Installing for CPU only on the CI
-        conda install pytorch torchvision torchaudio cpuonly -c pytorch
-        conda install pyg -c pyg
-        pip install torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-$(python3 -c "import torch; print(torch.__version__)")+cpu.html
+        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 
+        # Install dependencies not handled by setuptools
         ## DSSP
-        git clone https://github.com/PDB-REDO/libcifpp.git --recurse-submodules
-        cd libcifpp
-        cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local -DCMAKE_BUILD_TYPE=Release
-        cmake --build build
-        cmake --install build
-        #######
-        git clone https://github.com/mhekkel/libmcfp.git
-        cd libmcfp
-        mkdir build
-        cd build
-        cmake ..
-        cmake --build .
-        cmake --install .
-        #######
-        git clone https://github.com/PDB-REDO/dssp.git
-        cd dssp
-        mkdir build
-        cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
-        cmake --build build
-        cmake --install build
+        conda install -c sbl dssp>=4.2.2.1
         ## MSMS
         cd /tmp/
         wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL2.6.1/msms_i86Linux2_2.6.1.tar.gz
@@ -96,6 +82,14 @@ runs:
         pip install torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-$(python3 -c "import torch; print(torch.__version__)")+cpu.html
         # PyTables via conda only for MacOS
         conda install pytables
-    - name: Install the package
+    - name: Install the GitHub repository version of the package
       shell: bash {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}
+      if: ${{ inputs.pkg-installation-type == 'latest' }}
+      run: |
+        pip install pytest
+        rm -r deeprank2
+        pip install deeprank2

.github/workflows/build-latest-release.yml

@@ -0,0 +1,28 @@
+name: build (latest release)
+
+# Only trigger, when the release workflow succeeded
+on:
+  workflow_run:
+    workflows: ["Build and upload to PyPI"]
+    types:
+      - completed
+
+jobs:
+  build:
+    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"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/install-python-and-package
+        with:
+          python-version: ${{ matrix.python-version }}
+          pkg-installation-type: "latest"
+      - name: Run unit tests
+        run: pytest -v

.github/workflows/build.yml → .github/workflows/build-repo.yml

@@ -1,4 +1,4 @@
-name: build
+name: build (repository package)
 
 on:
   push:
@@ -36,15 +36,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11']
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"] # ["3.10", "3.11"]
 
     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

.github/workflows/cffconvert.yml

@@ -16,4 +16,4 @@ jobs:
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/[email protected]
         with:
-          args: "--validate"
+          args: "--validate"

.github/workflows/coveralls.yml

@@ -37,7 +37,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ['3.10']
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v3
@@ -46,7 +46,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           extras-require: test
       - name: Run unit tests with coverage
-        run: pytest --cov --cov-append --cov-report xml --cov-report term --cov-report html
+        run: pytest --cov --cov-append --cov-report xml --cov-fail-under=80 --cov-report term --cov-report html
       - name: Coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.github_token }}

.github/workflows/draft-pdf.yml

@@ -23,4 +23,4 @@ jobs:
           # This is the output path where Pandoc will write the compiled
           # PDF. Note, this should be the same directory as the input
           # paper.md
-          path: paper/paper.pdf
+          path: paper/paper.pdf

.github/workflows/fair-software.yml

@@ -5,7 +5,7 @@ on:
     branches:
       - main
   pull_request:
-      types: [opened, synchronize, reopened, ready_for_review]
+    types: [opened, synchronize, reopened, ready_for_review]
 
 jobs:
   verify:

.github/workflows/linting.yml

@@ -37,13 +37,13 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ['3.10']
+        python-version: ["3.10"]
 
     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 prospector
-        run: prospector --die-on-tool-error
+      - name: Check style against standards using ruff
+        run: ruff .

.github/workflows/markdown-link-check.yml

@@ -3,7 +3,7 @@ name: markdown-link-check
 on:
   push:
     branches:
-    - main
+      - main
     paths:
       # filetypes
       - "**.md"
@@ -25,7 +25,7 @@ jobs:
     name: Check markdown links
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
-      with:
-        config-file: '.github/workflows/markdown-link-check.yml'
+      - uses: actions/checkout@v3
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          config-file: ".github/workflows/markdown-link-check.yml"

.github/workflows/release.yml

@@ -14,15 +14,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.10']
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v3
       - uses: ./.github/actions/install-python-and-package
         with:
           python-version: ${{ matrix.python-version }}
           extras-require: publishing
+          pkg-installation-type: "repository"
       - name: Build wheel and source distribution
         run: python -m build
       - uses: actions/upload-artifact@v3

.github/workflows/stale_issue_pr.yml

@@ -21,4 +21,4 @@ jobs:
           days-before-pr-close: -1
           stale-pr-message: "This PR is stale because it has been open for 14 days with no activity."
           close-pr-message: "This PR was closed because it has been inactive for 7 days since being marked as stale."
-          exempt-issue-labels: 'blocked'
+          exempt-issue-labels: "blocked"

.readthedocs.yaml

@@ -12,4 +12,4 @@ sphinx:
 # Explicitly set the version of Python and its requirements
 python:
   install:
-    - requirements: docs/requirements.txt
+    - requirements: docs/requirements.txt