Merge branch 'main' into dependabot/github_actions/docker/build-push-…

…action-6.3.0

.github/workflows/code_checks.yml

@@ -33,7 +33,7 @@ jobs:
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-      - uses: actions/setup-python@v5.1.0
+      - uses: actions/setup-python@v5.1.1
         with:
           python-version: '3.10'
           cache: 'poetry'

.github/workflows/docs.yml

@@ -2,82 +2,64 @@ name: docs
 
 on:
   pull_request:
-    branches:
-      - main
-    paths:
-      - .pre-commit-config.yaml
-      - .github/workflows/docs.yml
-      - '**.py'
-      - '**.ipynb'
-      - '**.html'
-      - '**.jinja'
-      - '**.js'
-      - poetry.lock
-      - pyproject.toml
-      - '**.rst'
-      - '**.md'
-      - docs/cyclops-webpage
+    branches: [main]
     types: [opened, synchronize, closed]
-  push:
-    branches:
-      - main
-    paths:
-      - .pre-commit-config.yaml
-      - .github/workflows/docs.yml
-      - '**.py'
-      - '**.ipynb'
-      - '**.html'
-      - '**.jinja'
-      - '**.js'
-      - poetry.lock
-      - pyproject.toml
-      - '**.rst'
-      - '**.md'
-      - docs/cyclops-webpage
 
 jobs:
   build:
-    if: github.event_name == 'push' || (github.event_name == 'pull_request' && (github.event.action == 'opened' || github.event.action == 'synchronize' || (github.event.action == 'closed' && github.event.pull_request.merged == true)))
-    runs-on: ubuntu-latest
+    runs-on: ${{ (github.event_name == 'pull_request' && github.event.pull_request.merged == true && contains(github.event.pull_request.labels.*.name, 'release')) && fromJSON('["self-hosted", "db", "cyclops"]') || 'ubuntu-latest' }}
     steps:
       - uses: actions/checkout@v4.1.7
         with:
           submodules: 'true'
+          fetch-depth: 0
+
       - name: Install poetry
         run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/setup-python@v5.1.0
+
+      - uses: actions/setup-python@v5.1.1
         with:
           python-version: '3.10'
           cache: 'poetry'
-      - name: Install dependencies, build docs without running notebooks
+
+      - name: Install dependencies
         run: |
-          python3 -m pip install --upgrade pip && python3 -m pip install poetry
           poetry env use '3.10'
-          source $(poetry env info --path)/bin/activate
           poetry install --with docs,test --all-extras
 
-          # Install Pandoc
-          PANDOC_VERSION="2.19"
-          curl -sLo- "https://github.com/jgm/pandoc/releases/download/${PANDOC_VERSION}/pandoc-${PANDOC_VERSION}-linux-amd64.tar.gz" | tar xzf - --strip-components 2 -C /usr/local/bin --exclude="share"
-
+      - name: Build docs
+        run: |
+          source $(poetry env info --path)/bin/activate
           cd docs
           rm -rf source/reference/api/_autosummary
-          make html
+          if [[ "${{ github.event_name == 'pull_request' && github.event.pull_request.merged == true && contains(github.event.pull_request.labels.*.name, 'release') }}" == "true" ]]; then
+            make html-with-notebooks
+          else
+            make html
+          fi
+
       - name: Set up Node.js
-        uses: actions/setup-node@v4.0.2
+        uses: actions/setup-node@v4.0.3
         with:
           node-version: 18
           cache: yarn
           cache-dependency-path: '**/yarn.lock'
+
       - name: Build webpage
         run: |
           cd docs/cyclops-webpage
           yarn install --frozen-lockfile
           yarn build
           cp -r ../build/html build/api
+
+      - name: Create .nojekyll file
+        run: touch ./docs/cyclops-webpage/build/.nojekyll
+
       - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v4.0.0
+        uses: peaceiris/actions-gh-pages@v4
+        if: github.event_name == 'pull_request' && github.event.pull_request.merged == true && contains(github.event.pull_request.labels.*.name, 'release')
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_branch: github_pages
-          publish_dir: docs/cyclops-webpage/build
+          publish_dir: ./docs/cyclops-webpage/build
+          force_orphan: true

.github/workflows/integration_tests.yml

@@ -43,7 +43,7 @@ jobs:
       - uses: actions/checkout@v4.1.7
       - name: Install poetry
         run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/setup-python@v5.1.0
+      - uses: actions/setup-python@v5.1.1
         with:
           python-version: '3.10'
           cache: 'poetry'

.github/workflows/package.yml

@@ -29,7 +29,7 @@ jobs:
       - uses: actions/checkout@v4.1.7
       - name: Install pip
         run: python3 -m pip install --upgrade pip
-      - uses: actions/setup-python@v5.1.0
+      - uses: actions/setup-python@v5.1.1
         with:
           python-version: '3.10'
       - name: Install package and test import

.github/workflows/publish.yml

@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v4.1.7
       - name: Install poetry
         run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/setup-python@v5.1.0
+      - uses: actions/setup-python@v5.1.1
         with:
           python-version: '3.10'
       - name: Build package

.github/workflows/unit_tests.yml

@@ -33,7 +33,7 @@ jobs:
       - uses: actions/checkout@v4.1.7
       - name: Install dependencies, run unit tests and coverage report
         run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/setup-python@v5.1.0
+      - uses: actions/setup-python@v5.1.1
         with:
           python-version: '3.10'
           cache: 'poetry'

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     - id: check-toml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.4.10'
+    rev: 'v0.5.2'
     hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
@@ -25,7 +25,7 @@ repos:
       types_or: [python, jupyter]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.10.1
     hooks:
     - id: mypy
       entry: python3 -m mypy --config-file pyproject.toml

cyclops/data/clean.py

@@ -131,7 +131,7 @@ def normalize_events(
     data = data.infer_objects()
     data[event_name_col] = normalize_names(data[event_name_col])
 
-    if event_value_col and data[event_value_col].dtypes == object:
+    if event_value_col and data[event_value_col].dtypes == object:  # noqa: E721
         data[event_value_col] = normalize_values(data[event_value_col])
         log_df_counts(data, event_name_col, "Normalized values...", columns=True)
 

cyclops/data/slicer.py

@@ -923,7 +923,7 @@ def is_datetime(
             return False
     if isinstance(value, (list, np.ndarray)):
         return all((is_datetime(v) for v in value))
-    if isinstance(value, (datetime.datetime, np.datetime64)):
+    if isinstance(value, (datetime.datetime, np.datetime64)):  # noqa: SIM103
         return True
 
     return False

cyclops/evaluate/metrics/average_precision.py

@@ -131,9 +131,13 @@ def __new__(  # type: ignore # mypy expects a subclass of AveragePrecision
                 pos_label=pos_label,
             )
         if task == "multiclass":
-            NotImplementedError("Multiclass average precision is not implemented.")
+            raise NotImplementedError(
+                "Multiclass average precision is not implemented."
+            )
         if task == "multilabel":
-            NotImplementedError("Multilabel average precision is not implemented.")
+            raise NotImplementedError(
+                "Multilabel average precision is not implemented."
+            )
 
         raise ValueError(
             "Expected argument `task` to be either 'binary', 'multiclass' or "

cyclops/evaluate/metrics/functional/average_precision.py

@@ -159,9 +159,9 @@ def average_precision(
     if task == "binary":
         return binary_average_precision(target, preds, thresholds, pos_label)
     if task == "multiclass":
-        NotImplementedError("Multiclass average precision is not implemented.")
+        raise NotImplementedError("Multiclass average precision is not implemented.")
     if task == "multilabel":
-        NotImplementedError("Multilabel average precision is not implemented.")
+        raise NotImplementedError("Multilabel average precision is not implemented.")
 
     raise ValueError(
         "Expected argument `task` to be either 'binary', 'multiclass' or "