CI: fewer actions

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

@@ -41,27 +41,34 @@ runs:
     - run: which python
       shell: bash {0}
 
-    - name: Upgrade pip and install dependencies
+    - name: Install non pip items
+      shell: bash {0}
+      run: |
+        # Safest way to install PyTorch and PyTorch Geometric is through conda
+        conda install pytorch==2.0.0 torchvision=0.15.0 torchaudio=2.0.0 cpuonly -c pytorch
+        conda install pyg -c pyg
+        # Install dssp
+        sudo apt-get install -y dssp
+
+    - uses: actions/cache@v3
+      id: cache-python-env
+      with:
+        path: ${{ env.pythonLocation }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+
+    - name: Upgrade pip, install dependencies and package
+      if: steps.cache-python-env.outputs.cache-hit != 'true'
       shell: bash {0}
       env:
         CMAKE_INSTALL_PREFIX: .local
+        CONDA_PREFIX: /usr/share/miniconda
       run: |
         python3 -m pip install --upgrade pip setuptools wheel
-        # Install dssp
-        sudo apt-get install -y dssp
         # Only way to install msms is through conda
         conda install -c bioconda msms
-        # Safest way to install PyTorch and PyTorch Geometric is through conda
-        conda install pytorch==2.0.0 torchvision=0.15.0 torchaudio=2.0.0 cpuonly -c pytorch
-        conda install pyg -c pyg
         # Install optional pyg dependencies
         python3 -m pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-$(python3 -c "import torch; print(torch.__version__)")+cpu.html
+        # install the package
+        python3 -m pip install .[${{ inputs.extras-require }}]        
         # In the future, release h5xplorer on PyPI
         pip install git+https://github.com/DeepRank/h5xplorer.git@master
-
-    - name: Install the package
-      shell: bash {0}
-      run: python3 -m pip install .[${{ inputs.extras-require }}]
-      env:
-        CONDA_PREFIX: /usr/share/miniconda
-

.github/workflows/build.yml

@@ -1,17 +1,35 @@
 name: build
 
 on:
-  # Trigger analysis when pushing in main or pull requests, and when creating
-  # a pull request. 
   push:
+    # paths-ignore:
+    #   - "**.md"
+    #   - "**.rst"
+    #   - "**.ipynb"
+    paths:
+      - "deeprankcore/**"
+      - "tests/**"
+      - ".github/workflows/build.yml"
+      - ".github/actions/install-python-and-package/action.yml"
+      - "setup.cfg"
     branches:
       - main
   pull_request:
-      types: [opened, synchronize, reopened]
-
+      types: [opened, synchronize, reopened, ready_for_review]
+    # paths-ignore:
+    #   - "**.md"
+    #   - "**.rst"
+    #   - "**.ipynb"
+    # paths:
+    #   - "deeprankcore/**"
+    #   - "tests/**"
+    #   - ".github/workflows/build.yml"
+    #   - ".github/actions/install-python-and-package/action.yml"
+    #   - "setup.cfg"
 
 jobs:
   build:
+    if: github.event.pull_request.draft == false
     name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
 

.github/workflows/coveralls.yml

@@ -2,20 +2,37 @@ name: coveralls
 
 on:
   push:
+    paths-ignore:
+      - "**.md"
+      - "**.rst"
+      - "**.ipynb"
+    paths:
+      - "deeprankcore/**"
+      - "tests/**"
+      - ".github/workflows/linting.yml"
     branches:
-    - main
+      - main
   pull_request:
-    types: [opened, synchronize, reopened]
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths-ignore:
+      - "**.md"
+      - "**.rst"
+      - "**.ipynb"
+    paths:
+      - "deeprankcore/**"
+      - "tests/**"
+      - ".github/workflows/linting.yml"
 
 jobs:
   build:
+    if: github.event.pull_request.draft == false
     name: Coveralls
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest']
+        os: ["ubuntu-latest"]
         python-version: [3.9]
 
     steps:
@@ -26,6 +43,6 @@ jobs:
       - name: Coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.github_token }}
-          COVERALLS_FLAG_NAME: python-${{ matrix.version }}
+          COVERALLS_FLAG_NAME: python-${{ matrix.os }}
         run: |
           coveralls --service=github

.github/workflows/fair-software.yml

@@ -5,10 +5,11 @@ on:
     branches:
       - main
   pull_request:
-      types: [opened, synchronize, reopened]
+      types: [opened, synchronize, reopened, ready_for_review]
 
 jobs:
   verify:
+    if: github.event.pull_request.draft == false
     name: "fair-software"
     runs-on: ubuntu-latest
     steps:

.github/workflows/linting.yml

@@ -2,20 +2,37 @@ name: linting
 
 on:
   push:
+    paths-ignore:
+      - "**.md"
+      - "**.rst"
+      - "**.ipynb"
+    paths:
+      - "deeprankcore/**"
+      - "tests/**"
+      - ".github/workflows/linting.yml"
     branches:
-    - main
+      - main
   pull_request:
-    types: [opened, synchronize, reopened]
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths-ignore:
+      - "**.md"
+      - "**.rst"
+      - "**.ipynb"
+    paths:
+      - "deeprankcore/**"
+      - "tests/**"
+      - ".github/workflows/linting.yml"
 
 jobs:
   build:
+    if: github.event.pull_request.draft == false
     name: Linting build
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest']
+        os: ["ubuntu-latest"]
         python-version: [3.9]
 
     steps:

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

@@ -4,13 +4,20 @@ on:
   push:
     branches:
     - main
+    paths:
+      - "**.md"
+      - "**.rst"
+      - ".github/workflows/markdown-link-check.yml"
   pull_request:
-    branches:
-    - main
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths:
+      - "**.md"
+      - "**.rst"
+      - ".github/workflows/markdown-link-check.yml"
 
 jobs:
-
   markdown-link-check:
+    if: github.event.pull_request.draft == false
     name: Check markdown links
     runs-on: ubuntu-latest
     steps:

setup.cfg

@@ -40,7 +40,6 @@ install_requires =
     numpy >= 1.21.5
     scipy >= 1.8.0
     h5py >= 3.6.0
-    h5xplorer
     networkx >= 2.6.3
     matplotlib >= 3.5.1
     pdb2sql >= 0.5.1