setting up CI for the repo (#33)

* making test_plots.py independent from ONE

* removing outdated examples

* analysis folder added to gitignore

* more ruffing

* CI adjust

* CI adjust 2

* CI adjust 3

* fixing requirements to include develop branch of ibllib and iblrig

* and now correctly formatted

* adding data from kcenia, changing stimOn_times key. Very unclear why as of now

* removed python 3.11

* fix test plots import base tests

* CI for unit tests

* ruff

---------

Co-authored-by: owinter <olivier.winter@hotmail.fr>

.github/workflows/python-package.yaml → .github/workflows/run_tests.yaml

@@ -22,17 +22,19 @@ jobs:
         name: ruff format
         with:
           args: 'format --check'
-  build:
-    runs-on: ubuntu-latest
+  tests:
+    name: unit tests (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on:  ${{ matrix.os }}
     strategy:
       fail-fast: false
+      max-parallel: 6
       matrix:
-        python-version: ["3.10"]
-
+        os: ["ubuntu-latest", "windows-latest", "macos-latest"]
+        python-version: ["3.10", "3.12"]
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install deps

.gitignore

@@ -162,4 +162,5 @@ cython_debug/
 #.idea/
 
 # local scripts
-src/local
+src/local
+src/analysis

requirements.txt

@@ -1,6 +1,6 @@
-ibllib
+ibllib @ git+https://github.com/int-brain-lab/ibllib@develop
 numpy
 matplotlib
 pytest
 scipy
-pandera
+pandera

src/gui/rawdata_visualizer.py

@@ -1,30 +1,23 @@
 import sys
-import pandas as pd
-import matplotlib.pyplot as plt
 from PyQt5.QtWidgets import (
     QApplication,
     QWidget,
     QVBoxLayout,
     QHBoxLayout,
     QPushButton,
     QFileDialog,
-    QTableWidget,
-    QTableWidgetItem,
     QComboBox,
     QGridLayout,
     QLineEdit,
 )
-from PyQt5.QtCore import Qt
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt5 import NavigationToolbar2QT as NavigationToolbar
-from pydantic.v1 import NoneStr
 
 from iblphotometry.io import from_raw_neurophotometrics
 import iblphotometry.plots as plots
 
 import iblphotometry.preprocessing as ffpr
 import numpy as np
-from matplotlib.colorbar import Colorbar
 
 
 class DataFrameVisualizerApp(QWidget):

src/iblphotometry/loaders.py

@@ -12,15 +12,15 @@ def __init__(self, one, verbose=False):
         self.one = one
         self.verbose = verbose
 
-    def load_photometry_data(self, eid=None, pid=None, rename=True) -> nap.TsdFrame:
+    def load_photometry_data(self, eid=None, pid=None, rename=True) -> pd.DataFrame:
         if pid is not None:
             raise NotImplementedError
             # return self._load_data_from_pid(pid)
 
         if eid is not None:
             return self._load_data_from_eid(eid, rename=rename)
 
-    def _load_data_from_eid(self, eid, rename=True) -> nap.TsdFrame:
+    def _load_data_from_eid(self, eid, rename=True) -> pd.DataFrame:
         raw_photometry_df = self.one.load_dataset(eid, 'photometry.signal.pqt')
         locations_df = self.one.load_dataset(eid, 'photometryROI.locations.pqt')
         read_config = dict(

src/iblphotometry/pipelines.py

@@ -2,11 +2,8 @@
 
 import numpy as np
 import pandas as pd
-from iblphotometry.helpers import z, filt
 
 # from ibldsp.utils import WindowGenerator
-from iblphotometry import sliding_operations
-from iblphotometry import bleach_corrections
 from iblphotometry.outlier_detection import remove_spikes
 from iblphotometry.bleach_corrections import lowpass_bleachcorrect, isosbestic_correct
 from iblphotometry.sliding_operations import sliding_mad
@@ -15,7 +12,6 @@
 from iblphotometry.helpers import zscore
 
 import logging
-from copy import copy
 
 logger = logging.getLogger()
 

src/iblphotometry/plots.py

@@ -17,7 +17,7 @@
 
 PSTH_EVENTS = {
     'feedback_times': 'Feedback',
-    'stimOnTrigger_times': 'Stim on',
+    'stimOn_times': 'Stim on',
     'firstMovement_times': 'First move',
 }
 
@@ -209,7 +209,7 @@ def plot_trialsort_psth(self):
         fig.tight_layout()
         return fig, axs
 
-    def plot_processed_trialtick(self, event_key='stimOnTrigger_times'):
+    def plot_processed_trialtick(self, event_key='stimOn_times'):
         fig, ax = plt.subplots(1, 1)
         plt.figure(figsize=(10, 6))
         events = self.trials[event_key]

src/iblphotometry_tests/base_tests.py

@@ -17,6 +17,8 @@ def get_fixtures() -> dict:
         / session_folder
         / Path('raw_photometry_data/_neurophotometrics_fpData.raw.pqt'),
         'raw_neurophotometrics_csv': data_folder / 'raw_photometry.csv',
+        'raw_kcenia_pqt': data_folder / 'raw_photometry.pqt',
+        'trials_table_kcenia_pqt': data_folder / '_ibl_trials.table.pqt',
         'trials_table_pqt': data_folder / session_folder / 'alf/_ibl_trials.table.pqt',
     }
 

src/iblphotometry_tests/test_loaders.py

@@ -1,4 +1,3 @@
-import unittest
 import iblphotometry.io as fio
 import numpy as np
 from iblphotometry_tests.base_tests import PhotometryDataTestCase

src/iblphotometry_tests/test_metrics.py

@@ -1,4 +1,3 @@
-import unittest
 import iblphotometry.io as fio
 import iblphotometry.metrics as metrics
 import pandas as pd

src/iblphotometry_tests/test_pipelines.py

@@ -1,4 +1,3 @@
-import unittest
 from pathlib import Path
 import iblphotometry.io as fio
 from iblphotometry.pipelines import (