Update Dev Branch with the latest changes from main (#157)

Author: pauladkisson

.github/actions/load-data/action.yml

@@ -0,0 +1,33 @@
+name: 'Prepare Datasets'
+description: 'Restores data from caches or downloads it from Google Drive.'
+inputs:
+  rclone-config:
+    description: 'Rclone configuration'
+    required: true
+runs:
+  using: 'composite'
+  steps:
+    - name: Setup Rclone
+      uses: AnimMouse/setup-rclone@v1
+      with:
+        rclone_config: ${{ inputs.rclone-config }}
+
+    - name: Get dataset version hash
+      shell: bash
+      run: |
+        HASH=$(rclone lsl remote:"SampleData" --drive-shared-with-me)
+        echo "DATASET_HASH=$HASH" >> $GITHUB_OUTPUT
+
+    - name: Cache datasets
+      uses: actions/cache@v4
+      id: cache-datasets
+      with:
+        path: ./testing_data
+        key: ephys-datasets-${{ steps.ephys.outputs.DATASET_HASH }}
+        enableCrossOsArchive: true
+
+    - if: ${{ steps.cache-datasets.outputs.cache-hit != 'true' }}
+      name: Download datasets from Google Drive
+      shell: bash
+      run: |
+        rclone copy remote:"SampleData" ./testing_data --drive-shared-with-me

.github/workflows/pr-tests.yml

@@ -0,0 +1,13 @@
+name: PR Tests
+
+on:
+  pull_request:
+    types: [synchronize, opened, reopened, ready_for_review]
+    # Synchronize, open and reopened are the default types for pull request
+    # We add ready_for_review to trigger the check for changelog and full tests when ready for review is clicked
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true

.github/workflows/run-tests.yml

@@ -0,0 +1,14 @@
+name: Run Tests
+
+on:
+  workflow_call:
+    inputs:
+      python-versions:
+        description: 'List of Python versions to use in matrix, as JSON string'
+        required: true
+        type: string
+      os-versions:
+        description: 'List of OS versions to use in matrix, as JSON string'
+        required: true
+        type: string
+  workflow_dispatch:

src/guppy/computePsth.py

@@ -58,6 +58,8 @@ def writeToFile(value: str):
 # function to read hdf5 file
 def read_hdf5(event, filepath, key):
 	if event:
+		event = event.replace("\\","_")
+		event = event.replace("/","_")
 		op = os.path.join(filepath, event+'.hdf5')
 	else:
 		op = filepath
@@ -72,6 +74,8 @@ def read_hdf5(event, filepath, key):
 
 # function to write hdf5 file
 def write_hdf5(data, event, filepath, key):
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
 	op = os.path.join(filepath, event+'.hdf5')
 
 	# if file does not exist create a new file
@@ -120,6 +124,8 @@ def create_csv_area_peak(filepath, arr, name, index=[]):
 
 # function to create dataframe for each event PSTH and save it to h5 file
 def create_Df(filepath, event, name, psth, columns=[]):
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
 	if name:
 		op = os.path.join(filepath, event+'_{}.h5'.format(name))
 	else:
@@ -162,6 +168,8 @@ def create_Df(filepath, event, name, psth, columns=[]):
 
 # function to read h5 file and make a dataframe from it
 def read_Df(filepath, event, name):
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
 	if name:
 		op = os.path.join(filepath, event+'_{}.h5'.format(name))
 	else:
@@ -222,6 +230,9 @@ def helper_psth(z_score, event, filepath,
 				bin_psth_trials, use_time_or_trials,
 				baselineStart, baselineEnd, 
 				naming, just_use_signal):
+	
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
 
 	sampling_rate = read_hdf5('timeCorrection_'+naming, filepath, 'sampling_rate')[0]
 
@@ -351,6 +362,9 @@ def helper_psth(z_score, event, filepath,
 # function to create PSTH for each event using function helper_psth and save the PSTH to h5 file
 def storenamePsth(filepath, event, inputParameters):
 
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
+
 	selectForComputePsth = inputParameters['selectForComputePsth']
 	bin_psth_trials = inputParameters['bin_psth_trials']
 	use_time_or_trials = inputParameters['use_time_or_trials']
@@ -440,6 +454,9 @@ def helperPSTHPeakAndArea(psth_mean, timestamps, sampling_rate, peak_startPoint,
 
 # function to compute PSTH peak and area using the function helperPSTHPeakAndArea save the values to h5 and csv files.
 def findPSTHPeakAndArea(filepath, event, inputParameters):
+	
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
 
 	#sampling_rate = read_hdf5(storesList[0,0], filepath, 'sampling_rate')
 	peak_startPoint = inputParameters['peak_startPoint']
@@ -512,6 +529,9 @@ def psth_shape_check(psth):
 # function to compute average of group of recordings
 def averageForGroup(folderNames, event, inputParameters):
 
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
+
 	print("Averaging group of data...")
 	insertLog("Averaging group of data", logging.DEBUG)
 	path = []

src/guppy/preprocess.py

@@ -204,6 +204,8 @@ def read_hdf5(event, filepath, key):
 
 # function to write hdf5 file
 def write_hdf5(data, event, filepath, key):
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
 	op = os.path.join(filepath, event+'.hdf5')
 
 	# if file does not exist create a new file

src/guppy/visualizePlot.py

@@ -65,6 +65,8 @@ def insertLog(text, level):
 
 # read h5 file as a dataframe
 def read_Df(filepath, event, name):
+	event = event.replace("\\","_")
+	event = event.replace("/","_")
 	if name:
 		op = os.path.join(filepath, event+'_{}.h5'.format(name))
 	else:
@@ -649,6 +651,11 @@ def heatmap(self):
 
 # function to combine all the output folders together and preprocess them to use them in helper_plots function
 def createPlots(filepath, event, inputParameters):
+
+	for i in range(len(event)):
+		event[i] = event[i].replace("\\","_")
+		event[i] = event[i].replace("/","_")
+
 	average = inputParameters['visualizeAverageResults']
 	visualize_zscore_or_dff = inputParameters['visualize_zscore_or_dff']