Merge branch 'release/v0.10.0'

Author: mdbenito

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.2
+current_version = 0.10.0
 commit = False
 tag = False
 allow_dirty = False

.gitattributes

@@ -2,3 +2,4 @@ notebooks/*.ipynb -linguist-detectable
 *.png filter=lfs diff=lfs merge=lfs -text
 *.svg filter=lfs diff=lfs merge=lfs -text
 logo.svg -filter=lfs -diff=lfs -merge=lfs text
+*.pkl filter=lfs diff=lfs merge=lfs -text

.github/workflows/cleanup-caches.yaml

@@ -0,0 +1,27 @@
+name: Delete caches for a PR after merging
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Cleanup
+        run: |
+          echo "Fetching list of cache keys for PR..."
+          cacheKeysForPR=$(gh cache list --ref $BRANCH --limit 100 --json id --jq '.[].id')
+
+          ## Setting this to not fail the workflow while deleting cache keys.
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh cache delete $cacheKey
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+          BRANCH: refs/pull/${{ github.event.pull_request.number }}/merge

.github/workflows/main.yaml

@@ -22,21 +22,21 @@ env:
 jobs:
   code-quality:
     name: Lint code and check type hints
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v4
-    - name: Setup Python 3.8
+    - name: Setup Python 3.9
       uses: ./.github/actions/python
       with:
-        python_version: 3.8
+        python_version: 3.9
     - uses: actions/cache@v4
       with:
         path: ~/.cache/pre-commit
         key: pre-commit-${{ env.pythonLocation }}-${{ hashFiles('.pre-commit-config.yaml') }}
     - name: Lint Code
       run: |
         pre-commit run --all --show-diff-on-failure
-        python build_scripts/run_pylint.py | (pylint-json2html -f jsonextended -o pylint.html)
+        ruff check src/ --fix
       shell: bash
     - name: Generate mypy cache key
       id: generate-mypy-cache-key
@@ -52,16 +52,16 @@ jobs:
 
   docs:
     name: Build Docs
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         lfs: true
-    - name: Setup Python 3.8
+    - name: Setup Python 3.9
       uses: ./.github/actions/python
       with:
-        python_version: 3.8
+        python_version: 3.9
     - name: Install Pandoc
       uses: r-lib/actions/setup-pandoc@v2
       with:
@@ -73,10 +73,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11"]
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
         group_number: [1, 2, 3, 4]
     name: Run Tests - Python ${{ matrix.python_version }} - Group ${{ matrix.group_number }}
     uses: ./.github/workflows/run-tests-workflow.yaml
+    secrets: inherit
     with:
       split_size: 4
       group_number: ${{ matrix.group_number }}
@@ -87,7 +88,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ["3.8", "3.9", "3.10", "3.11"]
+        python_version: ["3.9", "3.10", "3.11", "3.12"]
         group_number: [1, 2, 3, 4]
     name: Run Notebook tests -  Python ${{ matrix.python_version }} - Group ${{ matrix.group_number }}
     uses: ./.github/workflows/run-notebook-tests-workflow.yaml
@@ -97,41 +98,79 @@ jobs:
       group_number: ${{ matrix.group_number }}
     needs: [code-quality]
 
-  push-docs-and-release-testpypi:
-    name: Push Docs and maybe release Package to TestPyPI
-    runs-on: ubuntu-latest
+  legacy-tests:
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: [ "3.11" ]
+        group_number: [ 1, 2, 3, 4 ]
+    name: Run Legacy tests -  Python ${{ matrix.python_version }} - Group ${{ matrix.group_number }}
+    uses: ./.github/workflows/run-legacy-tests-workflow.yaml
+    with:
+      python_version: ${{ matrix.python_version }}
+      split_size: 4
+      group_number: ${{ matrix.group_number }}
+    needs: [ code-quality ]
+
+  publish-docs:
+    name: Publish documentation
+    runs-on: ubuntu-22.04
     needs: [docs, group-tests, notebook-tests]
-    if: ${{ github.ref == 'refs/heads/develop' }}
+    if: ${{ github.ref == 'refs/heads/develop' && github.event_name != 'pull_request'  }}
     concurrency:
-      group: publish
+      group: publish-docs
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
           lfs: true
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: ./.github/actions/python
         with:
-          python_version: 3.8
+          python_version: 3.9
       - name: Install Pandoc
         uses: r-lib/actions/setup-pandoc@v2
         with:
           pandoc-version: ${{ env.PANDOC_VERSION }}
-      - name: Deploy Docs
+      - name: Deploy docs
         uses: ./.github/actions/deploy-docs
         with:
           version: devel
           alias: develop
           title: Development
           email: ${{ env.GITHUB_BOT_EMAIL }}
           username: ${{ env.GITHUB_BOT_USERNAME }}
-      - name: Build and publish to TestPyPI
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
+
+
+  publish-testpypi:
+    name: Publish package to TestPyPI
+    runs-on: ubuntu-22.04
+    needs: [group-tests, notebook-tests]
+    if: ${{ github.ref == 'refs/heads/develop' && github.event_name != 'pull_request' }}
+    concurrency:
+      group: publish-testpypi
+    permissions:
+      id-token: write
+    environment:
+      name: testpypi
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          lfs: true
+      - name: Setup Python 3.9
+        uses: ./.github/actions/python
+        with:
+          python_version: 3.9
+      - name: Bump version and build package
         run: |
           set -x
           export BUILD_NUMBER=$GITHUB_RUN_NUMBER
           bump2version --no-tag --no-commit --verbose --serialize '{major}.{minor}.{patch}.{release}{$BUILD_NUMBER}' boguspart
           python setup.py sdist bdist_wheel
-          twine upload -r testpypi --verbose --non-interactive dist/*
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          print-hash: true
+          verbose: true

.github/workflows/publish.yaml

@@ -22,7 +22,7 @@ env:
 
 jobs:
   publish:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     concurrency:
       group: publish
     steps:
@@ -44,10 +44,10 @@ jobs:
         run: |
           echo "Running action locally. Failing"
           exit -1
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: ./.github/actions/python
         with:
-          python_version: 3.8
+          python_version: 3.9
       - name: Get Current Version
         run: |
           export CURRENT_VERSION=$(python setup.py --version --quiet | awk -F. '{print $1"."$2"."$3}')

.github/workflows/run-legacy-tests-workflow.yaml

@@ -0,0 +1,54 @@
+name: Run Legacy Tests
+
+on:
+  workflow_call:
+    inputs:
+      split_size:
+        description: "Determines the number of groups into which the tests should be split"
+        type: string
+        default: 4
+      group_number:
+        description: "Determines which which group of tests to run. Can be 1, 2, ..., split_size"
+        type: string
+        required: true
+      python_version:
+        description: "Determines which Python version to use"
+        type: string
+        required: true
+
+
+env:
+  PY_COLORS: 1
+
+jobs:
+  run-legacy-tests:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          large-packages: false
+          docker-images: false
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Python ${{ inputs.python_version }}
+        uses: ./.github/actions/python
+        with:
+          python_version: ${{ inputs.python_version }}
+      - name: Cache Tox Directory for Tests
+        uses: actions/cache@v4
+        with:
+          key: tox-${{ runner.os }}-${{ github.ref }}-${{ hashFiles('tox.ini', 'requirements.txt') }}-${{ inputs.python_version }}
+          path: .tox
+      - name: Set up memcached
+        uses: niden/actions-memcached@v7
+      - name: Test Group ${{ inputs.group_number }}
+        run: tox -e legacy-tests -- --slow-tests --splits ${{ inputs.split_size }} --group ${{ inputs.group_number }}
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          env_vars: OS,PYTHON
+          verbose: false

.github/workflows/run-notebook-tests-workflow.yaml

@@ -21,11 +21,17 @@ env:
 
 jobs:
   run-tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
+    - name: Free Disk Space (Ubuntu)
+      uses: jlumbroso/free-disk-space@main
+      with:
+        large-packages: true
+        docker-images: false
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
+        lfs: true
     - name: Setup Python ${{ inputs.python_version }}
       uses: ./.github/actions/python
       with:

.github/workflows/run-tests-workflow.yaml

@@ -22,7 +22,7 @@ env:
 
 jobs:
   run-tests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - name: Free Disk Space (Ubuntu)
       uses: jlumbroso/free-disk-space@main

.github/workflows/stale.yaml

@@ -5,7 +5,7 @@ on:
 
 jobs:
   stale:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/stale@v9
         with:

.gitignore

@@ -141,6 +141,7 @@ pylint.html
 runs/
 data/models/
 *.pkl
+!data/*.pkl
 
 # Docs
 docs_build