Merge branch 'main' of github.com:daisybio/drevalpy

Author: JudithBernett

.gitattributes

@@ -0,0 +1 @@
+* text=auto

.github/workflows/build_package.yml

@@ -22,7 +22,8 @@ jobs:
 
       - name: Install Poetry
         run: |
-          pip install poetry
+          pipx install poetry
+          pipx inject poetry poetry-plugin-export
           poetry --version
 
       - name: Build package

.github/workflows/labeler.yml

@@ -13,6 +13,6 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Run Labeler
-        uses: crazy-max/ghaction-github-labeler@v5.1.0
+        uses: crazy-max/ghaction-github-labeler@v5.3.0
         with:
           skip-delete: true

.github/workflows/publish-docker.yml

@@ -2,9 +2,6 @@ name: Create and publish a Docker image
 
 # Configures this workflow to run every time a release is published
 on:
-  push:
-    branches:
-      - main
   release:
     types: [published]
 

.github/workflows/publish_docs.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.13"
 
       - name: Install pip
         run: |

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
       - name: Check out the repository

.github/workflows/python-publish.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Build package
         run: python -m build
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70
+        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/run_tests.yml

@@ -16,14 +16,12 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { python-version: "3.11", os: ubuntu-latest, session: "pre-commit" }
-          - { python-version: "3.11", os: ubuntu-latest, session: "safety" }
-          - { python-version: "3.11", os: ubuntu-latest, session: "mypy" }
-          - { python-version: "3.11", os: ubuntu-latest, session: "tests" }
-          - { python-version: "3.11", os: windows-latest, session: "tests" }
-          - { python-version: "3.11", os: ubuntu-latest, session: "typeguard" }
-          - { python-version: "3.11", os: ubuntu-latest, session: "xdoctest" }
-          - { python-version: "3.11", os: ubuntu-latest, session: "docs-build" }
+          - { python-version: "3.12", os: ubuntu-latest, session: "pre-commit" }
+          - { python-version: "3.12", os: ubuntu-latest, session: "mypy" }
+          - { python-version: "3.12", os: ubuntu-latest, session: "tests" }
+          - { python-version: "3.12", os: windows-latest, session: "typeguard" }
+          - { python-version: "3.12", os: ubuntu-latest, session: "xdoctest" }
+          - { python-version: "3.12", os: ubuntu-latest, session: "docs-build" }
 
     env:
       NOXSESSION: ${{ matrix.session }}
@@ -66,7 +64,7 @@ jobs:
           print("::set-output name=result::{}".format(result))
 
       - name: Restore pre-commit cache
-        uses: actions/[email protected].0
+        uses: actions/[email protected].3
         if: matrix.session == 'pre-commit'
         with:
           path: ~/.cache/pre-commit
@@ -99,10 +97,10 @@ jobs:
       - name: Check out the repository
         uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install Poetry
         run: |
@@ -129,6 +127,6 @@ jobs:
         run: nox --force-color --session=coverage -- xml -i
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v5.1.1
+        uses: codecov/codecov-action@v5.4.3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/safety_scan.yml

@@ -0,0 +1,15 @@
+name: Safety Action
+
+on:
+  push: # Run on every push to any branch
+  pull_request: # Run on new pull requests
+
+jobs:
+  security:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@main
+      - name: Run Safety CLI to check for vulnerabilities
+        uses: pyupio/safety-action@v1
+        with:
+          api-key: ${{ secrets.SAFETY_API_KEY }}

.gitignore

@@ -5,7 +5,10 @@ data/mapping
 data/GDSC1
 data/GDSC2
 data/CCLE
-data/Toy_Data
+data/TOYv1
+data/TOYv2
+data/CTRPv1
+data/CTRPv2
 
 # Byte-compiled / optimized / DLL files
 __pycache__/