diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..faf34d0 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,4 @@ +[codespell] +skip = .git +# puls - used all around +ignore-words-list = puls diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..5768d7c --- /dev/null +++ b/.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 diff --git a/bidsphysio.base/tests/test_bidsphysio.py b/bidsphysio.base/tests/test_bidsphysio.py index 58a1c3c..300f1ca 100644 --- a/bidsphysio.base/tests/test_bidsphysio.py +++ b/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: diff --git a/bidsphysio.edf2bids/bidsphysio/edf2bids/edf2bidsphysio.py b/bidsphysio.edf2bids/bidsphysio/edf2bids/edf2bidsphysio.py index ef190a6..a1ffc7d 100644 --- a/bidsphysio.edf2bids/bidsphysio/edf2bids/edf2bidsphysio.py +++ b/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) diff --git a/bidsphysio.physio2bids/tests/test_physio2bidsphysio.py b/bidsphysio.physio2bids/tests/test_physio2bidsphysio.py index e3d0d76..5f5fb15 100644 --- a/bidsphysio.physio2bids/tests/test_physio2bidsphysio.py +++ b/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 """ diff --git a/bidsphysio.pmu2bids/bidsphysio/pmu2bids/pmu2bidsphysio.py b/bidsphysio.pmu2bids/bidsphysio/pmu2bids/pmu2bidsphysio.py index 79b08ec..001f055 100644 --- a/bidsphysio.pmu2bids/bidsphysio/pmu2bids/pmu2bidsphysio.py +++ b/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) diff --git a/bidsphysio.pmu2bids/tests/test_pmu2bidsphysio.py b/bidsphysio.pmu2bids/tests/test_pmu2bidsphysio.py index a3e5d6d..09e1f28 100644 --- a/bidsphysio.pmu2bids/tests/test_pmu2bidsphysio.py +++ b/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 diff --git a/bidsphysio.session/bidsphysio/session/session2bids.py b/bidsphysio.session/bidsphysio/session/session2bids.py index 19e8b95..ca7dcdc 100644 --- a/bidsphysio.session/bidsphysio/session/session2bids.py +++ b/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':