use poe

Author: quentinblampey

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
 
   tests:
     needs: [pre-commit]
-    name: "pytest"
+    name: "pytest with uv"
     runs-on: ubuntu-latest
 
     strategy:
@@ -43,8 +43,27 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
+  test_pip_install:
+    needs: [pre-commit]
+    name: "pytest with pip install"
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install sopa with pip
+        run: pip install -e . && pip install pytest-cov poethepoet
+
+      - name: Run short tests
+        run: poe test_no_multimodal
+
   deploy-docs:
-    needs: [tests]
+    needs: [tests, test_pip_install]
     if: contains(github.ref, 'tags')
     name: "Deploy documentation"
     runs-on: ubuntu-latest
@@ -58,7 +77,7 @@ jobs:
         run: uv run mkdocs gh-deploy --force
 
   pypi-release:
-    needs: [tests]
+    needs: [tests, test_pip_install]
     if: contains(github.ref, 'tags')
     name: "PyPI release"
     runs-on: ubuntu-latest

CONTRIBUTING.md

@@ -64,13 +64,8 @@ When create a pull request, tests are run automatically. But you can also run th
 To check the coverage of the tests:
 
 ```sh
-uv run coverage run -m pytest
+uv run poe test
 
-# option 1: show the report in the console
-uv run coverage report
-
-# option 2: generate and open a html report
-uv run coverage html
 open htmlcov/index.html
 ```
 
@@ -81,5 +76,5 @@ You can update the documentation in the `./docs` directory. Refer to the [mkdocs
 To serve the documentation locally:
 
 ```sh
-uv run mkdocs serve
+uv run poe docs
 ```

pyproject.toml

@@ -46,6 +46,7 @@ dev = [
   "mkdocs-jupyter>=0.21.0",
   "mkdocstrings>=0.19.0",
   "mkdocstrings-python>=0.7.1",
+  "poethepoet>=0.38.0",
 ]
 
 [project.urls]
@@ -76,6 +77,12 @@ ignore_missing_imports = true
 testpaths = ["tests"]
 python_files = "test_*.py"
 
+[tool.poe.tasks]
+docs = "mkdocs serve"
+pre-commit = "pre-commit run --all-files"
+test = "pytest --cov --cov-config=pyproject.toml --cov-report=html --disable-warnings"
+test_no_multimodal = "pytest -m 'not multimodal' --cov --cov-config=pyproject.toml --cov-report=html --disable-warnings"
+
 [tool.ruff]
 target-version = "py39"
 line-length = 120

tests/test_he.py

@@ -1,12 +1,14 @@
 import numpy as np
 import pytest
-import sopa
-import torch
 
 import novae
 
 
+@pytest.mark.multimodal
 def test_he_embeddings():
+    import sopa
+    import torch
+
     sdata1 = sopa.io.toy_dataset(as_output=True, genes=50)
     sdata2 = sopa.io.toy_dataset(as_output=True, genes=50)