Pain

.gitattributes

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

.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/pull_request_template.md

@@ -1,22 +1,49 @@
 <!-- Many thanks for contributing to this project! -->
 
-**PR Checklist**
+# PR Checklist for all PRs
 
 <!-- Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). -->
 
 - [ ] This comment contains a description of changes (with reason)
 - [ ] Referenced issue is linked
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] Documentation in `docs` is updated
-
-**Description of changes**
-
-<!-- Please state what you've changed and how it might affect the user. -->
-
-**Technical details**
-
-<!-- Please state any technical details such as limitations, reasons for additional dependencies, benchmarks etc. here. -->
-
-**Additional context**
-
-<!-- Add any other context or screenshots here. -->
+- [ ] Documentation in `docs` is updated. If you've created a new file, add it to the API documentation pages.
+
+<!-- Only applies to PRs for a new version release, delete the lines that don't apply -->
+
+### Changes
+
+### Bug fixes
+
+### New features
+
+### Maintenance
+
+## Version release checklist
+
+- [ ] Update the version in pyproject.toml
+- [ ] Update version/release in docs/conf.py
+- [ ] Run ‚poetry update‘ to get the latest package versions. This will update the poetry.lock file
+- [ ] Run ‚poetry export --without-hashes --without development -f requirements.txt -o requirements.txt‘ to update the requirements.txt file
+- [ ] (If one of the sphinx packages has been updated, you also need to update docs/requirements.txt)
+- [ ] (If poetry itself was updated, update that in the Dockerfile and installation.rst)
+- [ ] If you updated the python version:
+  - [ ] Update the Dockerfile so that it always runs on the latest python version. Watch out: the ‚builder‘ is the full python, the ‚runtime‘ is a slim python build.
+  - [ ] Update the python version in .github/workflows/: run_tests.yml, build_package.yml, publish_docs.yml, python-package.yml
+  - [ ] Update the python version in noxfile.py
+  - [ ] Update the documentation: contributing.rst, installation.rst
+
+Then,
+
+1. Open a PR from development to main with these changes.
+2. Wait for a review and merge.
+3. Create a new release on GitHub with the version number. Update the release notes with the changes made in this version.
+4. If the Docker github action fails (e.g., no space left on device), you can do it manually:
+   - Enable Docker buildx locally. If you don't have a builder that supports multi-arch, create one:
+   ```{bash}
+   docker buildx ls
+   docker buildx create --use --name multiarch-builder
+   docker buildx inspect --bootstrap
+   ```
+   - Login to ghcr `docker login --username <GitHub-Username> --password <personal-access-token> ghcr.io`
+   - Build the multi-platform image, insert the correct version `docker buildx build --platform linux/amd64,linux/arm64 -t ghcr.io/daisybio/drevalpy:v<INSERT-VERSION> -t ghcr.io/daisybio/drevalpy:latest --push .`

.github/workflows/build_package.yml

@@ -9,14 +9,14 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python: ["3.11", "3.12"]
+        python: ["3.11", "3.12", "3.13"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         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@v6
 
       - 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@v6
 
       - name: Setup QEMU
         uses: docker/setup-qemu-action@v3

.github/workflows/publish_docs.yml

@@ -7,13 +7,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         name: Check out source-code repository
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pip
         run: |

.github/workflows/python-package.yml

@@ -15,14 +15,14 @@ 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
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - 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@v6
       - 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

@@ -13,25 +13,25 @@ jobs:
     name: ${{ matrix.session }} ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         include:
-          - { python-version: "3.12", 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" }
+          - { python-version: "3.13", os: ubuntu-latest, session: "pre-commit" }
+          - { python-version: "3.13", os: ubuntu-latest, session: "mypy" }
+          - { python-version: "3.13", os: ubuntu-latest, session: "tests" }
+          - { python-version: "3.13", os: windows-latest, session: "typeguard" }
+          - { python-version: "3.13", os: ubuntu-latest, session: "xdoctest" }
+          - { python-version: "3.13", os: ubuntu-latest, session: "docs-build" }
 
     env:
       NOXSESSION: ${{ matrix.session }}
 
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - 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@v5.0.2
         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@v6
         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@v6
         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@v6
 
-      - 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@v7
         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@v5.5.2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -1,14 +1,11 @@
 # Data
-data/cell_line_input
-data/response_output
-data/mapping
-data/GDSC1
-data/GDSC2
-data/CCLE
-data/TOYv1
-data/TOYv2
-data/CTRPv1
-data/CTRPv2
+data/
+
+# Results directory is created when running the demo notebook
+results/
+
+# Wandb directory is created when running the benchmark with wandb
+wandb/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -171,3 +168,4 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 /data/GDSC/
+.Rproj.user

.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
       - id: check-added-large-files
         name: Check for added large files
         entry: check-added-large-files
+        exclude: ^dreval_demo\.ipynb$
         language: system
       - id: check-toml
         name: Check Toml
@@ -35,26 +36,20 @@ repos:
         types: [python]
         require_serial: true
         args:
-          - --ignore=D212,W503,C901,N803,N806
+          - --ignore=D212,W503,C901,N803,N806,S615,S403,S301
       - id: pyupgrade
         name: pyupgrade
         description: Automatically upgrade syntax for newer versions.
         entry: pyupgrade
         language: system
         types: [python]
         args: [--py39-plus, --keep-runtime-typing]
-      - id: trailing-whitespace
-        name: Trim Trailing Whitespace
-        entry: trailing-whitespace-fixer
-        language: system
-        types: [text]
-        stages: [pre-commit, pre-push, manual]
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v2.5.1
     hooks:
       - id: prettier
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 6.0.1
     hooks:
       - id: isort
         name: isort (python)
@@ -64,3 +59,7 @@ repos:
       - id: isort
         name: isort (pyi)
         types: [pyi]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace

Dockerfile

@@ -2,9 +2,9 @@
 # https://medium.com/@albertazzir/blazing-fast-python-docker-builds-with-poetry-a78a66f5aed0
 
 # The builder image, used to build the virtual environment
-FROM python:3.11-buster AS builder
+FROM python:3.13-bookworm AS builder
 
-RUN pip install poetry==2.0.0
+RUN pip install poetry==2.3.2
 
 # POETRY_CACHE_DIR: When removing the cache folder, make sure this is done in the same RUN command. If it’s done in a
 # separate RUN command, the cache will still be part of the previous Docker layer (the one containing poetry install )
@@ -25,26 +25,24 @@ RUN touch README.md
 RUN poetry install --without development --no-root && rm -rf $POETRY_CACHE_DIR
 
 # The runtime image, used to run the code
-FROM python:3.11-slim-buster AS runtime
+FROM python:3.13-slim-bookworm AS runtime
 
 LABEL image.author.name="Judith Bernett"
 LABEL image.author.email="[email protected]"
 
 # Copy installed dependencies from the builder image
-COPY --from=builder /usr/local/lib/python3.11/site-packages /usr/local/lib/python3.11/site-packages
+COPY --from=builder /usr/local/lib/python3.13/site-packages /usr/local/lib/python3.13/site-packages
 COPY --from=builder /usr/local/bin /usr/local/bin
 
 # Copy all relevant code
 
 COPY drevalpy ./drevalpy
-COPY create_report.py ./
 COPY README.md ./
-COPY run_suite.py ./
 COPY pyproject.toml ./
 COPY poetry.lock ./
 
 # Install drevalpy
 RUN pip install .
 
 # Nextflow needs the command ps to be available
-RUN apt-get update && apt-get install -y procps && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y procps unzip && rm -rf /var/lib/apt/lists/*