Merge pull request #9 from CDDLeiden/dev

Create v3.0.0 Release

.github/setup.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+RUNNER_OS=$1
+env=$2
+
+# Set up Clustal Omega and MAFFT
+export HOME_DIR=$PWD
+if [ "$RUNNER_OS" = "macOS" ]; then
+wget http://www.clustal.org/omega/clustal-omega-1.2.3-macosx -O clustalo && chmod +x clustalo
+brew install mafft && unset MAFFT_BINARIES
+echo "$HOME_DIR" >> $GITHUB_PATH # make clustalo available in the next steps
+elif [ "$RUNNER_OS" = "Linux" ]; then
+wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
+wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
+echo "MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/" >> $GITHUB_ENV
+echo "$HOME_DIR/mafft-linux64/mafftdir/bin/" >> $GITHUB_PATH
+echo "$HOME_DIR" >> $GITHUB_PATH # make clustalo available in the next steps
+elif [ "$RUNNER_OS" = "Windows" ]; then
+choco install clustal-omega mafft
+echo "::add-path::$env:ProgramFiles\Clustal Omega"
+echo "::add-path::$env:ProgramFiles\MAFFT"
+fi
+
+# Set up Python environment
+python -m pip install --upgrade pip
+python -m pip install ".[full]"  --upgrade --upgrade-strategy eager
+python -m pip install pytest
+python -m pip install jupyterlab

.github/workflows/dev_ci.yml

@@ -0,0 +1,70 @@
+name: Multi-OS Complete Test
+
+on:
+  push:
+    branches:
+      - dev
+      - main
+  pull_request:
+    branches:
+      - dev
+      - main
+
+env:
+  QSPPRED_TEST_EXTRAS: true
+  QSPRPRED_VERBOSE_LOGGING: true
+
+jobs:
+  tests-all:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 120
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ] # FIXME: add macos-latest and windows-latest (removed for now due to limited debugging options)
+        python-version: [ '3.10' ]
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set Up Dependencies
+        run: |
+          python -m pip cache purge
+          source .github/setup.sh ${{ runner.os }} $env
+
+      - name: Check Environment Info
+        run: |
+          echo "Clustal Omega version: $(clustalo --version)"
+          echo "MAFFT version: $(mafft --version)"
+          python -m pip freeze
+          python -c "print('Python version: ' + '$(python --version)')"
+          python -c "import platform; print('System info: ', platform.system(), platform.release())"
+          python -c "import qsprpred; print('QSPRpred version:', qsprpred.__version__)"
+
+      - name: Run pytest
+        run: cd testing/test_pytest && ./run.sh
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v4
+        if: success() || failure() # always run even if the previous step fails
+        with:
+          report_paths: 'testing/test_pytest/test_report.xml'
+
+      - name: Test CLI
+        run: cd testing/test_cli && ./run.sh
+
+      - name: Test Consistency
+        run: cd testing/test_consistency && ./run.sh
+
+      - name: Test Tutorials
+        run: cd testing/test_tutorial && ./run.sh

.github/workflows/docs_ci.yml

@@ -0,0 +1,46 @@
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches:
+      - dev
+      - main
+
+env:
+  CI_COMMIT_AUTHOR: ${{ github.event.head_commit.author.name }}
+  CI_COMMIT_EMAIL: ${{ github.event.head_commit.author.email }}
+
+jobs:
+  docs-build-and-deploy:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Cache Python Environment
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
+
+      - name: Set Up Dependencies
+        run: |
+          source .github/setup.sh ${{ runner.os }} $env
+          python -m pip install -r docs/requirements.txt
+
+      - name: Build and Deploy Documentation
+        run: |
+          git config --global user.name "${{ env.CI_COMMIT_AUTHOR }}"
+          git config --global user.email "${{ env.CI_COMMIT_EMAIL }}"
+          cd docs && ./make.sh && REPO_URL=https://${{ github.actor }}:${{ github.token }}@github.com/${{ github.repository }}.git ./upload.sh

.github/workflows/pre_merge_ci.yml

@@ -0,0 +1,67 @@
+name: Python3.10 CI with Basic Tests
+
+on:
+  push:
+    branches:
+      - '**' # all branches
+      - '!dev' # except dev
+      - '!main' # except main
+      - '!gh_pages' # except gh_pages
+
+env:
+  QSPPRED_TEST_EXTRAS: false
+  QSPRPRED_VERBOSE_LOGGING: true
+
+jobs:
+  tests-basic:
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Cache Python Environment
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
+      #          restore-keys: |
+      #            ${{ runner.os }}-pip-
+
+      - name: Set Up Dependencies
+        run: |
+          source .github/setup.sh ${{ runner.os }} $env
+
+      - name: Check Environment Info
+        run: |
+          echo "Clustal Omega version: $(clustalo --version)"
+          echo "MAFFT version: $(mafft --version)"
+          python -m pip freeze
+          python -c "print('Python version: ' + '$(python --version)')"
+          python -c "import platform; print('System info: ', platform.system(), platform.release())"
+          python -c "import qsprpred; print('QSPRpred version:', qsprpred.__version__)"
+
+      - name: Run pytest
+        run: cd testing/test_pytest && ./run.sh
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v4
+        if: success() || failure() # always run even if the previous step fails
+        with:
+          report_paths: 'testing/test_pytest/test_report.xml'
+
+      - name: Test CLI
+        run: cd testing/test_cli && ./run.sh
+
+      - name: Test Consistency
+        run: cd testing/test_consistency && ./run.sh

.gitignore

@@ -1,5 +1,6 @@
 ### QSPRpred Specific
 /.*
+!.github
 !.gitignore
 !.gitlab-ci.yml
 !.pre-commit-config.yaml
@@ -11,9 +12,13 @@
 *.gzip
 *.tar.gz
 *.out
-/**/test_files/generated/
 /**/tutorial/test_files/
 /**/tutorial/cli_tutorial/
+/**/tutorials/tutorial_data/papyrus/
+/**/tutorials/tutorial_data/A2A_LIGANDS.tsv
+/**/tutorials/tutorial_data/AR_LIGANDS.tsv
+/**/tutorials/tutorial_data/AR_LIGANDS_pivot.tsv
+/**/tutorials/tutorial_output
 
 ### Python template
 # Byte-compiled / optimized / DLL files

.gitlab-ci.yml

@@ -1,33 +1,31 @@
 # This workflow will install Python dependencies, run tests, and write documentation
 
 variables:
-   GIT_STRATEGY: clone # clone entire repo instead of reusing workspace
-   GIT_DEPTH: "0" # avoid shallow clone to give sonar all the info it needs
+  GIT_STRATEGY: clone # clone entire repo instead of reusing workspace
+  GIT_DEPTH: "0" # avoid shallow clone to give sonar all the info it needs
 
 stages:
-   - test
-   - deploy
+  - test
+  - deploy
 
 # Install python dependencies and run python tests with pytest and the CLI test script
 .test:
-   stage: test
-   before_script:
-      - python --version  # For debugging python version
-      - wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
-      - wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
-      - export PATH=$PATH:$PWD/mafft-linux64/mafftdir/bin/:$PWD
-      - export MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/
-      - clustalo --version  # For debugging clustalo version
-      - mafft --version  # For debugging mafft version
-      - python -m pip install ".[full]" --no-cache-dir
-      - python -c "import qsprpred; print(qsprpred.__version__)" # For debugging package version
-      - python -m pip install pytest
-      - python -m pip install jupyterlab
-      - python -m pip freeze # For debugging environment
-   script:
-      - pytest qsprpred
-      - cd clitest && ./run.sh
-      - cd ../tutorial && ./run_all.sh
+  stage: test
+  before_script:
+    - python --version  # For debugging python version
+    - wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
+    - wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
+    - export PATH=$PATH:$PWD/mafft-linux64/mafftdir/bin/:$PWD
+    - export MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/
+    - clustalo --version  # For debugging clustalo version
+    - mafft --version  # For debugging mafft version
+    - pip install ".[full]" --no-cache-dir
+    - python -c "import qsprpred; print(qsprpred.__version__)" # For debugging package version
+    - pip install pytest
+    - pip install jupyterlab
+    - pip freeze # For debugging environment
+  script:
+    - cd testing && QSPPRED_TEST_SPLIT_UNITS=true QSPRPRED_VERBOSE_LOGGING=true ./run.sh
 
 # # Run tests on Python version 11 (linux image)
 # test:python3.11:
@@ -36,21 +34,5 @@ stages:
 
 # Run tests on Python version 10 (linux image)
 test:python3.10:
-   extends: .test
-   image: python:3.10
-
-# Write documentation on main branch
-pages:
-   stage: deploy
-   image: python:3.10
-   before_script:
-      - python -m pip install -U sphinx
-      - python -m pip install sphinx-rtd-theme
-   script:
-      - mkdir public
-      - sphinx-build -b html ./docs public
-   artifacts:
-      paths:
-      - public
-   only:
-      - main
+  extends: .test
+  image: python:3.10