Merge pull request #264 from daisybio/development

v1.4.0

Author: JudithBernett

.github/labels.yml

@@ -67,3 +67,6 @@
 - name: skip-changelog
   description: Changes that should be omitted from the release notes
   color: "#ededed"
+- name: DEPENDABOT
+  description: Pull requests created by Dependabot
+  color: "#ff00b3"

.github/workflows/build_package.yml

@@ -12,11 +12,11 @@ jobs:
         python: ["3.11", "3.12", "3.13"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         name: Check out source-code repository
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python }}
 

.github/workflows/labeler.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Run Labeler
         uses: crazy-max/[email protected]

.github/workflows/publish-docker.yml

@@ -26,7 +26,7 @@ jobs:
     steps:
       # Necessary for buildx
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup QEMU
         uses: docker/setup-qemu-action@v3

.github/workflows/publish_docs.yml

@@ -7,11 +7,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         name: Check out source-code repository
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 

.github/workflows/python-package.yml

@@ -19,10 +19,10 @@ jobs:
 
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/python-publish.yml

@@ -20,9 +20,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.x"
       - name: Install dependencies
@@ -32,7 +32,7 @@ jobs:
       - name: Build package
         run: python -m build
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/run_tests.yml

@@ -13,7 +13,7 @@ jobs:
     name: ${{ matrix.session }} ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         include:
           - { python-version: "3.13", os: ubuntu-latest, session: "pre-commit" }
@@ -28,10 +28,10 @@ jobs:
 
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -64,7 +64,7 @@ jobs:
           print("::set-output name=result::{}".format(result))
 
       - name: Restore pre-commit cache
-        uses: actions/cache@v4.2.3
+        uses: actions/cache@v4.3.0
         if: matrix.session == 'pre-commit'
         with:
           path: ~/.cache/pre-commit
@@ -73,19 +73,20 @@ jobs:
             ${{ steps.pre-commit-cache.outputs.result }}-
 
       - name: Run Nox
-        run: nox --force-color --python=${{ matrix.python-version }}
+        run: |
+          nox --force-color --python=${{ matrix.python-version }}
 
       - name: Upload coverage data
         if: always() && matrix.session == 'tests' && matrix.os == 'ubuntu-latest'
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: coverage-data
           path: ".coverage.*"
           include-hidden-files: "true"
 
       - name: Upload documentation
         if: matrix.session == 'docs-build'
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: docs
           path: docs/_build
@@ -95,12 +96,12 @@ jobs:
     needs: tests
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.12
+          python-version: 3.13
 
       - name: Install Poetry
         run: |
@@ -116,7 +117,7 @@ jobs:
           nox --version
 
       - name: Download coverage data
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: coverage-data
 
@@ -127,6 +128,6 @@ jobs:
         run: nox --force-color --session=coverage -- xml -i
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v5.4.3
+        uses: codecov/codecov-action@v5.5.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/safety_scan.yml

@@ -9,6 +9,7 @@ data/TOYv1
 data/TOYv2
 data/CTRPv1
 data/CTRPv2
+data/meta
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -171,3 +172,4 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 /data/GDSC/
+.Rproj.user