Merge pull request #240 from Aarhus-Psychiatry-Research/martbern/smoo…

…ther_devops

Smoother devops

.github/workflows/pre-commit.yml

@@ -15,4 +15,6 @@ jobs:
     - uses: actions/setup-python@v4
       with:
         python-version: 3.9
-    - uses: pre-commit/[email protected]
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: "--hook-stage manual --all-files"

.pre-commit-config.yaml

@@ -1,4 +1,5 @@
-default_stages: [commit, push]
+default_stages: [push, manual]
+default_install_hook_types: [pre-push, pre-commit] # Using the "manual" stage for github actions
 
 repos:
   - repo: https://github.com/PyCQA/autoflake
@@ -12,7 +13,7 @@ repos:
     hooks:
       - id: isort
         name: isort (python)
-        args: ["--profile", "black", "--filter-files", "--skip __init__.py"]
+        args: ["--profile", "black"]
 
   - repo: https://github.com/asottile/add-trailing-comma
     rev: v2.2.3
@@ -56,7 +57,7 @@ repos:
         entry: check-yaml
         language: python
         types: [yaml]
-        
+
   - repo: https://github.com/pycqa/pylint
     rev: v2.15.2
     hooks:
@@ -67,5 +68,15 @@ repos:
             "-rn", # Only display messages
             "-sn", # Don't display the score
             "--disable=R,import-error" # Refactors are not important enough to block a commit. 
-            # Unused-imports aren't testable by the github action, so don't test that here.
-          ]
+            # Unused-imports aren't testable by the github action without installing the whole project, so don't test that here.
+          ]
+
+  - repo: local
+    hooks:
+    -   id: pytest
+        name: Run integration tests before push
+        entry: .venv/bin/pytest -m pre_push_test
+        language: script
+        stages: [push]
+        pass_filenames: false
+        always_run: true

pyproject.toml

@@ -71,6 +71,11 @@ good-names = "df,p,f,d,e,n,k,i,v,y_,X,y"
 disable = "too-many-lines,line-too-long,missing-raises-doc,no-self-argument,unused-wildcard-import,wildcard-import,no-else-return,too-many-arguments,redefined-outer-name,c-extension-no-member,wrong-import-order,import-outside-toplevel"
 extension-pkg-allow-list = "wandb"
 
+[tool.pytest.ini_options]
+markers = [
+    "pre_push_test: Tests run on push. Should be as minimal as possible to maintain fast push speeds.",
+]
+
 [tool.isort]
 known_third_party = ["wandb"]
 

tests/test_train_model.py

@@ -18,6 +18,20 @@ def test_main(model_name):
         main(cfg)
 
 
+@pytest.mark.pre_push_test
+def test_integration_test():
+    """test main using the logistic model.
+
+    Used for quickly testing functions before a push.
+    """
+    with initialize(version_base=None, config_path="../src/psycopt2d/config/"):
+        cfg = compose(
+            config_name="integration_testing.yaml",
+            overrides=["+model=logistic-regression"],
+        )
+        main(cfg)
+
+
 def test_crossvalidation():
     """Test crossvalidation."""
     with initialize(version_base=None, config_path="../src/psycopt2d/config/"):