Merge pull request #151 from Aharoni-Lab/config-debug

debug: CI/CD breaking config

Author: raymondwjang

.github/workflows/tests.yml

@@ -30,7 +30,7 @@ jobs:
         run: pip install -e ".[tests]"
 
       - name: Run tests with coverage
-        run: pytest --cov=cala --cov-report=xml
+        run: pytest --log-cli-level=DEBUG --cov=cala --cov-report=xml
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

pdm.lock

@@ -34,7 +34,7 @@ dependencies = [
     "pyyaml>=6.0.2",
     "typer>=0.15.3",
     "xarray-validate>=0.0.2",
-    "noob @ git+https://github.com/miniscope/noob.git@scheduler-optimize",
+    "noob @ git+https://github.com/miniscope/noob.git",
     "natsort>=8.4.0",
 ]
 keywords = [

pyproject.toml

@@ -36,7 +36,7 @@ class LogConfig(BaseModel):
     """
     Severity for stream-based logging. If unset, use ``level``
     """
-    dir: Path = _dirs.user_log_dir
+    dir: Path = Path(_dirs.user_log_dir)
     """
     Directory where logs are stored.
     """
@@ -48,6 +48,7 @@ class LogConfig(BaseModel):
     """
     Maximum size of log files (bytes)
     """
+    model_config = SettingsConfigDict(validate_default=True)
 
     @field_validator("level", "level_file", "level_stdout", mode="before")
     @classmethod
@@ -75,6 +76,7 @@ class Config(BaseSettings, YAMLMixin):
         nested_model_default_partial_update=True,
         yaml_file="cala_config.yaml",
         pyproject_toml_table_header=("tool", "cala", "config"),
+        validate_default=True,
     )
 
     logs: LogConfig = LogConfig()

src/cala/config.py

@@ -115,7 +115,6 @@ def _init_root(
     stream_handlers = [
         handler for handler in root_logger.handlers if isinstance(handler, RichHandler)
     ]
-
     if log_dir is not False and not file_handlers:
         root_logger.addHandler(
             _file_handler(

src/cala/logging.py

@@ -8,7 +8,7 @@ def test_config(tmp_path):
     """
     Config should be able to make directories and set sensible defaults
     """
-    config = Config(user_dir=tmp_path)
+    config = Config(user_dir=tmp_path, logs={"dir": tmp_path / "log"})
     assert config.user_dir.exists()
     assert config.logs.dir.exists()