From fdb7c71e7899480a1ae9fbb1fc46d2237b178ff7 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 17 Feb 2023 08:58:35 -0500 Subject: [PATCH 1/4] fix the typo (remove te which was intended to be the I guess) --- bidsphysio.pmu2bids/tests/test_pmu2bidsphysio.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From f2456dcb30dd53a578c7043f1437bb1dba9059a4 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 17 Feb 2023 08:59:08 -0500 Subject: [PATCH 2/4] rudimentary .codespellrc --- .codespellrc | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 .codespellrc 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 From e36e813af0bc2c066c0e14e1b52c177bff7cd87d Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 17 Feb 2023 09:00:10 -0500 Subject: [PATCH 3/4] codespell workflow --- .github/workflows/codespell.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .github/workflows/codespell.yml 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 From 731f3fb4da8077401eddc38e8721994b087190e6 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 17 Feb 2023 09:00:18 -0500 Subject: [PATCH 4/4] [DATALAD RUNCMD] Run codespell throughout fixing 1 typo === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- bidsphysio.base/tests/test_bidsphysio.py | 2 +- bidsphysio.edf2bids/bidsphysio/edf2bids/edf2bidsphysio.py | 4 ++-- bidsphysio.physio2bids/tests/test_physio2bidsphysio.py | 2 +- bidsphysio.pmu2bids/bidsphysio/pmu2bids/pmu2bidsphysio.py | 2 +- bidsphysio.session/bidsphysio/session/session2bids.py | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) 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.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':