Add codespell and ruff (#32)

* Create codespell.yml

* Create ruff.yml

* Allow ruff workflow to run on command

* Fix spelling, exclude lockin

* Fix some lint errors

.github/workflows/codespell.yml

@@ -0,0 +1,14 @@
+name: Codespell
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/ruff.yml

@@ -0,0 +1,13 @@
+name: Ruff
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Run ruff
+        uses: astral-sh/ruff-action@v3

notebook/read_phot_box_files.ipynb

@@ -721,7 +721,7 @@
     "print(sig2)\n",
     "print(OG_signals['sig2'])\n",
     "\n",
-    "# print(f\"Lenth of visits: {len(visits)}\")\n",
+    "# print(f\"Length of visits: {len(visits)}\")\n",
     "# print(visits)\n",
     "\n",
     "import matplotlib.pyplot as plt\n",

pyproject.toml

@@ -81,7 +81,7 @@ exclude = [
 
 [tool.codespell]
 skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs"
-ignore-words-list = "datas,assertIn"
+ignore-words-list = "datas,assertIn,lockin"
 
 [tool.coverage.run]
 branch = true
@@ -99,7 +99,7 @@ preview = true
 exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb"
 
 [tool.ruff]
-lint.select = ["E", "F", "T100", "T201", "T203"]
+lint.select = ["E", "F", "T100", "T203"]
 exclude = [
   ".git",
   ".tox",

src/jdb_to_nwb/__init__.py

@@ -1 +1,5 @@
 from ._version import __version__
+
+__all__ = [
+    "__version__",
+]

src/jdb_to_nwb/convert.py

@@ -58,7 +58,7 @@ def create_nwbs(
     # reset the session start time to the earliest of the data streams
     nwbfile.fields["session_start_time"] = datetime.now(tz.tzlocal())
 
-    print(f"Writing file, including iterative read from raw ephys data...")
+    print("Writing file, including iterative read from raw ephys data...")
 
     with NWBHDF5IO(output_nwb_file_path, mode="w") as io:
         io.write(nwbfile)

src/jdb_to_nwb/convert_behavior.py

@@ -22,8 +22,8 @@ def load_maze_configurations(maze_configuration_file_path: Path):
                 maze = set(map(int, line.strip().split(",")))
                 maze_sequence.append(maze)
             return maze_sequence
-    except:
-        warnings.warn(f"Could not load maze configurations from {maze_configuration_file_path}")
+    except Exception as e:
+        warnings.warn(f"Could not load maze configurations from {maze_configuration_file_path}: {e}")
         return []
 
 

src/jdb_to_nwb/convert_photometry.py

@@ -308,7 +308,7 @@ def airPLS(data, lambda_=1e8, max_iterations=50):
     """
 
     num_data_points = data.shape[0]
-    weights = np.ones(num_data_points)  # Set the intial weights to 1 to treat all points equally
+    weights = np.ones(num_data_points)  # Set the initial weights to 1 to treat all points equally
 
     # Loop runs up to 'max_iterations' times to adjust the weights and fit the baseline
     for i in range(1, max_iterations + 1):

src/jdb_to_nwb/convert_raw_ephys.py

@@ -156,7 +156,7 @@ def add_electrode_data(
     ).all(), "First column is not the same as the second column."
     electrode_data.drop(columns=["Channel Number"], inplace=True)
 
-    # Get electrode coordinates as a (2, 256) arrray
+    # Get electrode coordinates as a (2, 256) array
     # The first column is the relative x coordinate, and the second column is the relative y coordinate
     channel_geometry = get_electrode_coords() # formerly pd.read_csv(channel_geometry_file_path, header=None)
 

tests/test_convert_behavior.py

@@ -27,7 +27,7 @@ def test_convert_behavior():
     assert photometry_start_in_arduino_time == 55520059.6736
 
     # Note that we do not run validation tests on the trial- and block-level data (e.g. trials/blocks are
-    # enumerated corrrectly, block metadata is valid, number of trials per block adds to the
+    # enumerated correctly, block metadata is valid, number of trials per block adds to the
     # total number of trials, block start/end times are aligned to trial start/end times)
     # because these checks are already run by validate_trial_and_block_data every time add_behavior is run
 

tests/test_convert_photometry.py

@@ -110,7 +110,8 @@ def test_add_photometry_from_signals_mat():
 
     # Check that the lengths match
     assert len(green_z_scored_dFF) == len(green_z_scored_dFF_reference), (
-        f"Data length mismatch: z_scored_green_dFF has {len(green_z_scored_dFF)} points, " f"but the reference signal has {len(green_z_scored_dFF_reference)} points."
+        f"Data length mismatch: z_scored_green_dFF has {len(green_z_scored_dFF)} points, "
+        f"but the reference signal has {len(green_z_scored_dFF_reference)} points."
     )
 
     # Check that the z-scored green dF/F signal in the nwbfile matches the reference green signal (within a tolerance)
@@ -119,7 +120,7 @@ def test_add_photometry_from_signals_mat():
         green_z_scored_dFF_reference,
         atol=0.005,
         rtol=0.05,
-        err_msg=f"Data mismatch between nwbfile z_scored_green_dFF and reference data",
+        err_msg="Data mismatch between nwbfile z_scored_green_dFF and reference data",
     )
 
 
@@ -204,7 +205,7 @@ def test_add_photometry_from_pyphotometry():
 
     This version of the test uses the ppd file from pyPhotometry to add photometry signals to the NWB.
     
-    TODO: Implement this test once adding photometry via ppd file is inplemented!!
+    TODO: Implement this test once adding photometry via ppd file is implemented!!
     """
 
     # Create a test metadata dictionary with pyPhotometry data