Small fixes and adjust pre-commit (#22)

* isolated change

* update pre-commit

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* adjust settings

* remove codespell action

* remove codecov secret

* fix some ruff requirements (#23)

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/testing.yml

@@ -1,9 +1,6 @@
 name: Full Tests
 on:
   workflow_call:
-    secrets:
-      CODECOV_TOKEN:
-        required: true
 
 jobs:
   run:

.pre-commit-config.yaml

@@ -3,15 +3,24 @@ repos:
     rev: v4.6.0
     hooks:
     -   id: check-yaml
-    -   id: check-toml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
-    -   id: check-added-large-files
+
 -   repo: https://github.com/psf/black
     rev: 24.4.2
     hooks:
     -   id: black
--   repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
-    hooks:
-    -   id: isort
+        exclude: ^docs/
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.2
+  hooks:
+  - id: ruff
+    args: [ --fix ]
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.3.0
+  hooks:
+  - id: codespell
+    additional_dependencies:
+    - tomli

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 61.0"]
+requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
@@ -23,8 +23,7 @@ keywords = ["leifer", "C elegans", "NWB", "conversion", "open data", "microscopy
 
 classifiers = [
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: BSD License",
     "Intended Audience :: Developers",
     "Operating System :: Microsoft :: Windows",
@@ -42,7 +41,7 @@ dependencies = [
 
 [tool.black]
 line-length = 120
-target-version = ["py310", "py311"]
+target-version = ["py312"]
 include = '\.pyi?$'
 extend-exclude = '''
 /(
@@ -61,7 +60,18 @@ extend-exclude = '''
 )/
 '''
 
-[tool.isort]
-profile = "black"
-reverse_relative = true
-known_first_party = ["leifer_lab_to_nwb"]
+[tool.ruff]
+exclude = [
+  "*/__init__.py"
+]
+
+[tool.ruff.lint.isort]
+relative-imports-order = "closest-to-furthest"
+known-first-party = ["leifer_lab_to_nwb"]
+
+
+
+[tool.codespell]
+skip = '.git*,*.pdf,*.css'
+check-hidden = true
+ignore-words-list = 'assertin'  # Should be able to remove on next codespell release

src/leifer_lab_to_nwb/randi_nature_2023/_randi_nature_2023_converter.py

@@ -1,5 +1,4 @@
 import copy
-from typing import Union
 
 import ndx_multichannel_volume
 import neuroconv

src/leifer_lab_to_nwb/randi_nature_2023/convert_session.py

@@ -4,8 +4,6 @@
 import pathlib
 import warnings
 
-import pandas
-import pynwb
 from dateutil import tz
 
 from leifer_lab_to_nwb.randi_nature_2023 import RandiNature2023Converter

src/leifer_lab_to_nwb/randi_nature_2023/interfaces/_extra_ophys_metadata.py

@@ -28,8 +28,8 @@ def __init__(self, *, pumpprobe_folder_path: str | pathlib.Path) -> None:
 
     def add_to_nwbfile(self, nwbfile: pynwb.NWBFile, metadata: dict):
         # Plane depths
-        volt_per_um = 0.125  # Hardcoded value by the lab
-        depth_in_um_per_pixel = 0.42  # Hardcoded value by the lab
+        # volt_per_um = 0.125  # Hardcoded value by the lab
+        # depth_in_um_per_pixel = 0.42  # Hardcoded value by the lab
 
         # zScan contents
 
@@ -73,18 +73,18 @@ def add_to_nwbfile(self, nwbfile: pynwb.NWBFile, metadata: dict):
         # TODO: could include as a simple TimeSeries with same timestamps as volumetric photon series but values 1, -1
 
         # Extra frameSynchronous information
-        frame_sync_to_nwb_names = {
-            "Piezo position (V)": "piezo_position_in_volume",
-            "Piezo direction (+-1)": "piezo_direction",
-            "Ludl X": "ludl_x",
-            "Ludl Y": "ludl_y",
-        }
-        frame_sync_scanning_column_descriptions = {
-            "piezo_position_in_volume": "",
-            "piezo_direction": "",
-            "ludl_x": "",
-            "ludl_y": "",
-        }
+        # frame_sync_to_nwb_names = {
+        #     "Piezo position (V)": "piezo_position_in_volume",
+        #     "Piezo direction (+-1)": "piezo_direction",
+        #     "Ludl X": "ludl_x",
+        #     "Ludl Y": "ludl_y",
+        # }
+        # frame_sync_scanning_column_descriptions = {
+        #     "piezo_position_in_volume": "",
+        #     "piezo_direction": "",
+        #     "ludl_x": "",
+        #     "ludl_y": "",
+        # }
 
         # TODO: unpack frameSync content, likely as several TimeSeries with same timestamps as volumetric photon series
         # Will require some reshaping into the volumes since these are flattened frames

src/leifer_lab_to_nwb/randi_nature_2023/interfaces/_neuropal_imaging_interface.py

@@ -1,12 +1,9 @@
 import json
 import pathlib
-import shutil
-from typing import Literal
 
 import ndx_microscopy
 import neuroconv
 import numpy
-import pandas
 import pynwb
 
 

src/leifer_lab_to_nwb/randi_nature_2023/interfaces/_optogenetic_stimulation.py

@@ -1,7 +1,6 @@
 import pathlib
 from typing import Union
 
-import ndx_microscopy
 import ndx_patterned_ogen
 import neuroconv
 import numpy

src/leifer_lab_to_nwb/randi_nature_2023/interfaces/_pump_probe_imaging_interface.py

@@ -1,5 +1,4 @@
 import pathlib
-import shutil
 from typing import Literal
 
 import ndx_microscopy

src/leifer_lab_to_nwb/randi_nature_2023/test_all_interfaces.py

@@ -10,20 +10,11 @@
 import pathlib
 import warnings
 
-import pandas
 import pynwb
 from dateutil import tz
 from pynwb.testing.mock.file import mock_NWBFile
 
 from leifer_lab_to_nwb.randi_nature_2023 import RandiNature2023Converter
-from leifer_lab_to_nwb.randi_nature_2023.interfaces import (
-    ExtraOphysMetadataInterface,
-    NeuroPALImagingInterface,
-    NeuroPALSegmentationInterface,
-    OptogeneticStimulationInterface,
-    PumpProbeImagingInterface,
-    PumpProbeSegmentationInterface,
-)
 
 # Define base folder of source data
 # Change these as needed on new systems