From eb050bdf6d18ff01f19c86d05052681ec23507e5 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 7 Aug 2023 11:38:28 -0400 Subject: [PATCH 1/5] [DATALAD RUNCMD] Text files which are not scripts must not be executable === Do not change lines below === { "chain": [], "cmd": "find -type f -perm /+x | xargs grep -L \"^#!/\" | xargs chmod a-x", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- pynacollada/position_tracking/1819-211231_1.h5 | Bin 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 pynacollada/position_tracking/1819-211231_1.h5 diff --git a/pynacollada/position_tracking/1819-211231_1.h5 b/pynacollada/position_tracking/1819-211231_1.h5 old mode 100755 new mode 100644 From 39140358404201a668668ee3862e2157d953bc18 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 7 Aug 2023 11:38:42 -0400 Subject: [PATCH 2/5] Add github action to codespell main on push and PRs --- .github/workflows/codespell.yml | 22 ++++++++++++++++++++++ 1 file changed, 22 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..3ebbf55 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,22 @@ +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: read + +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@v2 From 0a6413f2774bb3b9747ad348c631c83dae9ab77e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 7 Aug 2023 11:38:42 -0400 Subject: [PATCH 3/5] Add rudimentary codespell config --- .codespellrc | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 .codespellrc diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..da3c057 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,4 @@ +[codespell] +skip = .git,*.pdf,*.svg +# +# ignore-words-list = From 8e221b18de1c802b00d89b302e857df6378bf06e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 7 Aug 2023 11:39:54 -0400 Subject: [PATCH 4/5] Skip images in notebooks and ADN abbreviation --- .codespellrc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.codespellrc b/.codespellrc index da3c057..1ffebb2 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,4 +1,4 @@ [codespell] skip = .git,*.pdf,*.svg -# -# ignore-words-list = +ignore-regex = ^\s*"image/\S+": ".* +ignore-words-list = adn From 8918d58f7e639c25b52464491e689a399a080415 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 7 Aug 2023 11:39:59 -0400 Subject: [PATCH 5/5] [DATALAD RUNCMD] run codespell throughout === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- .../Pynapple Paper Figures/Siegle 2021/Siegle_dataset.ipynb | 2 +- pynacollada/eeg_processing/Tutorial_ripple_detection.ipynb | 2 +- pynacollada/eeg_processing/eeg_processing.py | 6 +++--- pynacollada/neural_tuning/neural_tuning.py | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pynacollada/Pynapple Paper Figures/Siegle 2021/Siegle_dataset.ipynb b/pynacollada/Pynapple Paper Figures/Siegle 2021/Siegle_dataset.ipynb index 289a2e7..07dfd36 100644 --- a/pynacollada/Pynapple Paper Figures/Siegle 2021/Siegle_dataset.ipynb +++ b/pynacollada/Pynapple Paper Figures/Siegle 2021/Siegle_dataset.ipynb @@ -41,7 +41,7 @@ "source": [ "The __EcephysProjectCache__ object of the AllenSDK delivers the data to you as ready-to-analyze Python objects. It automatically keeps track of which files are stored locally, and will download additional files as needed.\n", "\n", - "The next bit involves dowloading the data onto your local machine. This section is adapted from here, where you can find a more detailed account of how to use data from the Allen Institute.\n", + "The next bit involves downloading the data onto your local machine. This section is adapted from here, where you can find a more detailed account of how to use data from the Allen Institute.\n", "\n", "Before downloading the data, you must decide where the manifest.json file lives. This file serves as the map that guides the EcephysProjectCache object to the file locations.\n", "\n", diff --git a/pynacollada/eeg_processing/Tutorial_ripple_detection.ipynb b/pynacollada/eeg_processing/Tutorial_ripple_detection.ipynb index 2995889..910d83d 100644 --- a/pynacollada/eeg_processing/Tutorial_ripple_detection.ipynb +++ b/pynacollada/eeg_processing/Tutorial_ripple_detection.ipynb @@ -176,7 +176,7 @@ "id": "82b21ea7", "metadata": {}, "source": [ - "Second step is to look at the enveloppe of the filtered signal." + "Second step is to look at the envelope of the filtered signal." ] }, { diff --git a/pynacollada/eeg_processing/eeg_processing.py b/pynacollada/eeg_processing/eeg_processing.py index 4965ad0..a640314 100644 --- a/pynacollada/eeg_processing/eeg_processing.py +++ b/pynacollada/eeg_processing/eeg_processing.py @@ -64,7 +64,7 @@ def bandpass_filter(data, lowcut, highcut, fs, order=4): time_units='s') else: - raise RuntimeError("Unknow format. Should be Tsd/TsdFrame") + raise RuntimeError("Unknown format. Should be Tsd/TsdFrame") def detect_oscillatory_events(lfp, epoch, freq_band, thres_band, duration_band, min_inter_duration, wsize=51): """ @@ -85,7 +85,7 @@ def detect_oscillatory_events(lfp, epoch, freq_band, thres_band, duration_band, min_inter_duration : float The minimum duration between two events otherwise they are merged (in seconds) wsize : int, optional - The size of the window for digitial filtering + The size of the window for digital filtering Returns ------- @@ -145,7 +145,7 @@ def detect_oscillatory_events(lfp, epoch, freq_band, thres_band, duration_band, # def getPeaksandTroughs(lfp, min_points): # """ -# At 250Hz (1250/5), 2 troughs cannont be closer than 20 (min_points) points (if theta reaches 12Hz); +# At 250Hz (1250/5), 2 troughs cannot be closer than 20 (min_points) points (if theta reaches 12Hz); # """ # import scipy.signal # if isinstance(lfp, nap.time_series.Tsd): diff --git a/pynacollada/neural_tuning/neural_tuning.py b/pynacollada/neural_tuning/neural_tuning.py index ed2c11b..ba8a0ed 100644 --- a/pynacollada/neural_tuning/neural_tuning.py +++ b/pynacollada/neural_tuning/neural_tuning.py @@ -183,7 +183,7 @@ def centerTuningCurves(tcurve): # copied to neural_tuning def offsetTuningCurves(tcurve, diffs): """ - offseting tuning curves synced by diff + offsetting tuning curves synced by diff """ new_tcurve = [] for p in tcurve.columns: