fixed bugs

Author: Prokash21

scripts/build_features.py

@@ -15,8 +15,8 @@
 if str(SRC_PATH) not in sys.path:
     sys.path.insert(0, str(SRC_PATH))
 
-from patchseq_pipeline.config import load_config
-from patchseq_pipeline.data.preprocess import preprocess_pipeline
+# Local imports that require the repository `src/` on sys.path are imported inside
+# the CLI function to keep top-level imports tidy and satisfy linters.
 
 logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
 
@@ -26,13 +26,17 @@
 @app.command()
 def run(
     config_path: Path = typer.Option(
-        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."
+        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."  # noqa: B008
     ),
     output_path: Optional[Path] = typer.Option(
-        None, "--output", "-o", help="Override destination for processed AnnData."
+        None, "--output", "-o", help="Override destination for processed AnnData."  # noqa: B008
     ),
 ) -> None:
     """Execute preprocessing using the configuration file."""
+    # Import project package here to avoid module-level imports after code (E402)
+    from patchseq_pipeline.config import load_config
+    from patchseq_pipeline.data.preprocess import preprocess_pipeline
+
     config = load_config(config_path)
     output = output_path or Path(config["paths"]["processed_dir"]) / "patchseq_processed.h5ad"
     preprocess_pipeline(

scripts/checksums.py

@@ -15,8 +15,8 @@
 if str(SRC_PATH) not in sys.path:
     sys.path.insert(0, str(SRC_PATH))
 
-from patchseq_pipeline.config import load_config
-from patchseq_pipeline.utils.checksums import digest_map
+# Project imports are performed inside the CLI handler to avoid module-level
+# imports after executable code (which triggers E402 in linters).
 
 logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
 
@@ -36,21 +36,25 @@ def _collect_files(config: Dict) -> Dict[str, Path]:
 @app.command()
 def run(
     config_path: Path = typer.Option(
-        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."
+        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."  # noqa: B008
     ),
     output_file: Path = typer.Option(
-        None,
+        None,  # noqa: B008
         "--output",
         "-o",
         help="Destination for checksum file (defaults to data/raw/checksums.sha256).",
     ),
     verify: bool = typer.Option(
-        False,
+        False,  # noqa: B008
         "--verify",
         help="Verify computed digests against values in config.download.checksums.",
     ),
 ) -> None:
     """Compute SHA256 digests and optionally verify against expected values."""
+    # Local project imports to satisfy linters (E402)
+    from patchseq_pipeline.config import load_config
+    from patchseq_pipeline.utils.checksums import digest_map
+
     config = load_config(config_path)
     files = _collect_files(config)
     missing = [name for name, path in files.items() if not path.exists()]

scripts/download_data.py

@@ -14,12 +14,8 @@
 if str(SRC_PATH) not in sys.path:
     sys.path.insert(0, str(SRC_PATH))
 
-from patchseq_pipeline.config import load_config
-from patchseq_pipeline.data.download import (
-    download_ephys_features,
-    download_metadata,
-    download_transcriptomics,
-)
+# Project imports are deferred into the CLI handler to avoid module-level
+# imports after executable code (E402 lint violations).
 
 logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
 
@@ -29,21 +25,29 @@
 @app.command()
 def run(
     config_path: Path = typer.Option(
-        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."
+        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."  # noqa: B008
     ),
     manifest_path: Path = typer.Option(
-        None,
+        None,  # noqa: B008
         "--manifest",
         "-m",
         help="Optional override for AllenSDK manifest path (defaults to config.paths.manifest).",
     ),
     force: bool = typer.Option(
-        False,
+        False,  # noqa: B008
         "--force",
         help="Re-download files even if they already exist.",
     ),
 ) -> None:
     """Download the Patch-seq assets defined in the configuration file."""
+    # Local project imports to satisfy linters (E402)
+    from patchseq_pipeline.config import load_config
+    from patchseq_pipeline.data.download import (
+        download_ephys_features,
+        download_metadata,
+        download_transcriptomics,
+    )
+
     config = load_config(config_path)
     paths = config["paths"]
     manifest = manifest_path or Path(paths["manifest"])

scripts/generate_figures.py

@@ -14,9 +14,7 @@
 if str(SRC_PATH) not in sys.path:
     sys.path.insert(0, str(SRC_PATH))
 
-from patchseq_pipeline.analysis.feature_selection import summarize_feature_importance
-from patchseq_pipeline.config import load_config
-from patchseq_pipeline.viz.figures import generate_all_figures
+# Project imports deferred into the CLI handler to avoid E402.
 
 logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
 
@@ -26,28 +24,33 @@
 @app.command()
 def run(
     config_path: Path = typer.Option(
-        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."
+        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."  # noqa: B008
     ),
     processed_path: Path = typer.Option(
-        Path("data/processed/patchseq_processed.h5ad"),
+        Path("data/processed/patchseq_processed.h5ad"),  # noqa: B008
         "--processed",
         "-p",
         help="Processed AnnData file.",
     ),
     models_dir: Path = typer.Option(
-        Path("results/models"),
+        Path("results/models"),  # noqa: B008
         "--models-dir",
         "-m",
         help="Directory containing trained models.",
     ),
     output_dir: Path = typer.Option(
-        Path("results/figures"),
+        Path("results/figures"),  # noqa: B008
         "--output-dir",
         "-o",
         help="Destination directory for figures.",
     ),
 ) -> None:
     """Generate all figures and save them to the configured output directory."""
+    # Local imports to avoid module-level imports after top-level code
+    from patchseq_pipeline.analysis.feature_selection import summarize_feature_importance
+    from patchseq_pipeline.config import load_config
+    from patchseq_pipeline.viz.figures import generate_all_figures
+
     config = load_config(config_path)
     config["figures"]["output_dir"] = str(output_dir)
     summary_csv = summarize_feature_importance(models_dir, config, output_dir)

scripts/train_model.py

@@ -15,8 +15,7 @@
 if str(SRC_PATH) not in sys.path:
     sys.path.insert(0, str(SRC_PATH))
 
-from patchseq_pipeline.config import ensure_output_dir, load_config
-from patchseq_pipeline.models.multimodal import train_elastic_net
+# Project imports deferred into the CLI handler to avoid E402.
 
 logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
 
@@ -26,19 +25,23 @@
 @app.command()
 def run(
     config_path: Path = typer.Option(
-        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."
+        Path("config/config.yaml"), "--config", "-c", help="Path to config YAML."  # noqa: B008
     ),
     input_path: Path = typer.Option(
-        Path("data/processed/patchseq_processed.h5ad"),
+        Path("data/processed/patchseq_processed.h5ad"),  # noqa: B008
         "--input",
         "-i",
         help="Processed AnnData file.",
     ),
     output_dir: Path = typer.Option(
-        Path("results/models"), "--output-dir", "-o", help="Directory for trained models."
+        Path("results/models"), "--output-dir", "-o", help="Directory for trained models."  # noqa: B008
     ),
 ) -> None:
     """Train ElasticNet models for each electrophysiology target."""
+    # Local imports to avoid module-level imports after top-level code
+    from patchseq_pipeline.config import ensure_output_dir, load_config
+    from patchseq_pipeline.models.multimodal import train_elastic_net
+
     config = load_config(config_path)
     ensure_output_dir(config)
     adata = anndata.read_h5ad(input_path)

src/patchseq_pipeline/__init__.py

@@ -1,6 +1,6 @@
 """PatchSeq-Epilepsy pipeline package."""
 
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import PackageNotFoundError, version
 
 try:
     __version__ = version("patchseq-epilepsy")