Codespell: config, action (to detect), and fix typos found

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git
+# puls - used all around
+ignore-words-list = puls

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1

bidsphysio.base/tests/test_bidsphysio.py

@@ -68,7 +68,7 @@ def test_calculate_timing(
     """
     Test for calculate_timing
     It checks that it gives an error when it is supposed to, and it returns the
-    correct timing when the neccessary parameters are present
+    correct timing when the necessary parameters are present
     """
 
     # 1) Try with a PhysioSignal without sampling rate:

bidsphysio.edf2bids/bidsphysio/edf2bids/edf2bidsphysio.py

@@ -1,7 +1,7 @@
 """
 Purpose
 ----
-Read eye tracking data from an SR Reasearch .edf file and return a
+Read eye tracking data from an SR Research .edf file and return a
 BIDS physiology recording object and as BIDS events object.
 It uses "pyedfread" to read the EDF file.
 
@@ -208,7 +208,7 @@ def edfevents2bids(physio_edf):
         EventIdentifiers.append(sm)
 
     # Read the EDF data into three pandas dataframes including the messages
-    # TODO: delete the unecessary columns?
+    # TODO: delete the unnecessary columns?
     all_messages = pd.DataFrame()
     for tm in EventIdentifiers:
         samples, events, messages = edf.pread(physio_edf, trial_marker = tm)

bidsphysio.physio2bids/tests/test_physio2bidsphysio.py

@@ -61,7 +61,7 @@ def test_main(
 ):
     """
     Tests for "main"
-    Just check the arguments, etc. We test the call to the differnt XXX2bids functions in a
+    Just check the arguments, etc. We test the call to the different XXX2bids functions in a
     separated test module
     """
 

bidsphysio.pmu2bids/bidsphysio/pmu2bids/pmu2bidsphysio.py

@@ -295,7 +295,7 @@ def readVE11Cpmu(physio_file, forceRead=False):
             # (continue reading the file)
 
 
-    # The third and fouth groups we ignore, and the fifth gives us the physio signal itself.
+    # The third and fourth groups we ignore, and the fifth gives us the physio signal itself.
     raw_signal = s[4].split(' ')
 
     physio_signal = parserawPMUsignal(raw_signal)

bidsphysio.pmu2bids/tests/test_pmu2bidsphysio.py

@@ -125,7 +125,7 @@ def test_parserawPMUsignal(capfd):
 def test_getPMUtiming():
     """
     Tests for getPMUtiming
-    We only care about the lines that contain te MPCUTime and MDHTime
+    We only care about the lines that contain MPCUTime and MDHTime
     """
 
     # 1) If the keywords are missing, the outputs should be 0

bidsphysio.session/bidsphysio/session/session2bids.py

@@ -194,7 +194,7 @@ def synchronize_onsets(phys_df, scan_df):
 
 def plot_sync(scan_df, physio_df):
     """
-    Plot unsynchronized and synchonized scan and physio onsets and durations.
+    Plot unsynchronized and synchronized scan and physio onsets and durations.
     """
 
     # You need a scan_df already synchronized (so it has the 'phys_onset':