Merge branch 'main' into links-testing-docs

.github/workflows/ci.yml

@@ -12,40 +12,46 @@ jobs:
     name: Formatting and static analysis
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
-      - uses: actions/setup-python@v3
-        with:
-          python-version: 3.8
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r requirements/ci.txt
       - run: tox -e static
-      - uses: stefanzweifel/git-auto-commit-action@v4
+      - uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: Apply automatic formatting
 
+  type-checking:
+    name: Type checking
+    needs: formatting
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install -r requirements/ci.txt
+      - run: tox -e mypy
+
   tests:
     name: Tests ${{ matrix.os }} ${{ matrix.tox }}
     needs: formatting
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         include:
-          - {python: '3.11', os: ubuntu-22.04, tox: pydantic1-full}
+          - {python: '3.12', os: ubuntu-22.04, tox: py312-full}
           - {python: '3.11', os: ubuntu-22.04, tox: py311-full}
           - {python: '3.10', os: ubuntu-22.04, tox: py310-full}
           - {python: '3.9', os: ubuntu-22.04, tox: py39-full}
-          - {python: '3.8', os: ubuntu-22.04, tox: py38-full}
-          - {python: '3.8', os: macos-12, tox: py38}
-          - {python: '3.8', os: windows-2022, tox: py38}
+          - {python: '3.9', os: macos-12, tox: py39}
+          - {python: '3.9', os: windows-2022, tox: py39}
     steps:
       - run: sudo apt install --yes docker-compose
         if: ${{ contains(matrix.variant.os, 'ubuntu') }}
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
       - run: python -m pip install --upgrade pip

.github/workflows/codeql-analysis.yml

@@ -18,13 +18,13 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: python
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/docs.yml

@@ -21,19 +21,19 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - run: sudo apt install --yes pandoc
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r requirements/ci.txt
       - run: tox -e docs
       - run: touch html/.nojekyll
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: documentation
           path: html/
-      - uses: JamesIves/github-pages-deploy-action@v4.4.3
+      - uses: JamesIves/github-pages-deploy-action@v4.5.0
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

.github/workflows/release.yml

@@ -6,26 +6,35 @@ on:
   workflow_dispatch:
 
 jobs:
+  check_release:
+    name: Check if package can be released
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install -r requirements/ci.txt
+      - run: tox -e check-release
+        if: github.event_name == 'release' && github.event.action == 'published'
+
   build_wheels:
     name: Wheels
     runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # history required so setuptools_scm can determine version
 
-      - uses: actions/setup-python@v3
-        with:
-          python-version: 3.8
+      - uses: actions/setup-python@v5
       - run: python -m pip install --upgrade pip
       - run: python -m pip install -r requirements/wheels.txt
 
       - name: Build wheels
         run: python -m build
 
       - name: Upload wheels
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist
@@ -40,8 +49,8 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-      - uses: actions/download-artifact@v2
-      - uses: pypa/gh-action-pypi-publish@v1.8.10
+      - uses: actions/download-artifact@v4
+      - uses: pypa/gh-action-pypi-publish@v1.8.14
 
   docs:
     needs: upload_packages

.pre-commit-config.yaml

@@ -1,33 +1,33 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
     - id: check-added-large-files
     - id: check-json
+    - id: check-merge-conflict
     - id: check-toml
     - id: check-yaml
     - id: detect-private-key
     - id: end-of-file-fixer
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]
-- repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 23.9.1
-  hooks:
-    - id: black
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.6.0
+  rev: 0.7.1
   hooks:
     - id: nbstripout
       types: ["jupyter"]
       args: ["--drop-empty-cells",
              "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'"]
-- repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: 'v0.0.291'
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.3.7
   hooks:
+    - id: ruff-format
+      types_or: [ python, pyi ]
     - id: ruff
-      args: ["--fix"]
+      args: [--fix, --exit-non-zero-on-fix]
+      types_or: [ python, pyi, jupyter ]
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.5
+  rev: v2.2.6
   hooks:
     - id: codespell
       additional_dependencies:

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-jan-lukas.wynen@ess.eu.
+jan-lukas.wynen[at]ess.eu.
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

SECURITY.md

@@ -6,13 +6,12 @@ Only the latest version is supported.
 
 ## Reporting a Vulnerability
 
-If you believe you have found a security vulnerability in Scitacean, please report it to us through coordinated disclosure.
-
-**Please do not report security vulnerabilities through public GitHub issues, discussions, or pull requests.**
-
-Instead, please send an email to jan-lukas.wynen[@]ess.eu
+If you believe you have found a security vulnerability in Scitacean, please
+- ✅ report it to us by creating a [security advisory](https://github.com/SciCatProject/scitacean/security/advisories/new).
+- ❌ do not report security vulnerabilities through public GitHub issues, discussions, or pull requests, etc.
 
 Please include as much information as you can to help us better understand and resolve the issue.
+We work on fixing the issues [privately](https://docs.github.com/en/code-security/security-advisories/working-with-repository-security-advisories/collaborating-in-a-temporary-private-fork-to-resolve-a-repository-security-vulnerability).
 
 ## Disclosure