From 5dd53dc882db622fb8b1816f45957a859303a96f Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 18 Mar 2024 14:26:50 -0400 Subject: [PATCH] Make codespell great again! (#269) Co-authored-by: Ben Dichter Co-authored-by: Ryan Ly --- .codespellrc | 4 ++-- .github/workflows/codespell.yml | 4 ++-- Cosyne_2023/caiman_demo.ipynb | 4 ++-- Cosyne_2023/pynwb_read_demo.ipynb | 2 +- Cosyne_2023/tutorials/advanced_asset_search.ipynb | 2 +- Cosyne_2023/tutorials/spikeinterface_tutorial.ipynb | 4 ++-- HCK15_2023_Janelia/README.md | 2 +- linkml_neurodata_hackashop_2024/README.md | 2 +- 8 files changed, 12 insertions(+), 12 deletions(-) diff --git a/.codespellrc b/.codespellrc index 0fd2b6a4a..9335485fd 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,6 +1,6 @@ [codespell] -skip = .git,*.pdf,*.svg,*_201[789]*,*_2020* +skip = .git,*.pdf,*.svg,*_201[789]*,*_202[012]* # embedded in ipynb images -ignore-regex = '^\s*"image/\S+": ".*' +ignore-regex = (^\s*"image/\S+": "|.*_json = {).* # # ignore-words-list = diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml index 7373affc3..3ebbf5504 100644 --- a/.github/workflows/codespell.yml +++ b/.github/workflows/codespell.yml @@ -3,9 +3,9 @@ name: Codespell on: push: - branches: [master] + branches: [main] pull_request: - branches: [master] + branches: [main] permissions: contents: read diff --git a/Cosyne_2023/caiman_demo.ipynb b/Cosyne_2023/caiman_demo.ipynb index 92e6b4fe3..b9f215d70 100644 --- a/Cosyne_2023/caiman_demo.ipynb +++ b/Cosyne_2023/caiman_demo.ipynb @@ -508,7 +508,7 @@ "max_shifts = [int(a/b) for a, b in zip(max_shift_um, dxy)]\n", "# start a new patch for pw-rigid motion correction every x pixels\n", "strides = tuple([int(a/b) for a, b in zip(patch_motion_um, dxy)])\n", - "# overlap between pathes (size of patch in pixels: strides+overlaps)\n", + "# overlap between paths (size of patch in pixels: strides+overlaps)\n", "overlaps = (24, 24)\n", "# maximum deviation allowed for patch with respect to rigid shifts\n", "max_deviation_rigid = 3\n", @@ -523,7 +523,7 @@ "gSig = [4, 4] # expected half size of neurons in pixels\n", "method_init = 'greedy_roi' # initialization method (if analyzing dendritic data using 'sparse_nmf')\n", "ssub = 2 # spatial subsampling during initialization\n", - "tsub = 2 # temporal subsampling during intialization\n", + "tsub = 2 # temporal subsampling during initialization\n", "\n", "# parameters for component evaluation\n", "min_SNR = 2.0 # signal to noise ratio for accepting a component\n", diff --git a/Cosyne_2023/pynwb_read_demo.ipynb b/Cosyne_2023/pynwb_read_demo.ipynb index 968919fa0..95f65c4d3 100644 --- a/Cosyne_2023/pynwb_read_demo.ipynb +++ b/Cosyne_2023/pynwb_read_demo.ipynb @@ -143,7 +143,7 @@ " ImagingPlane \n", " }\n", " institution: ETH Zurich\n", - " lab: Bio Engineering Laboratory (BEL) - Department of Bio Systems Science and Engineeering (D-BSSE)\n", + " lab: Bio Engineering Laboratory (BEL) - Department of Bio Systems Science and Engineering (D-BSSE)\n", " processing: {\n", " ophys \n", " }\n", diff --git a/Cosyne_2023/tutorials/advanced_asset_search.ipynb b/Cosyne_2023/tutorials/advanced_asset_search.ipynb index 5c118d1f7..22668136f 100644 --- a/Cosyne_2023/tutorials/advanced_asset_search.ipynb +++ b/Cosyne_2023/tutorials/advanced_asset_search.ipynb @@ -209,7 +209,7 @@ "outputs": [], "source": [ "from warnings import simplefilter\n", - "simplefilter(\"ignore\") # Supress namespace warnings from reading older NWB files\n", + "simplefilter(\"ignore\") # Suppress namespace warnings from reading older NWB files\n", "\n", "from nwbinspector.tools import get_s3_urls_and_dandi_paths\n", "from pynwb import NWBHDF5IO" diff --git a/Cosyne_2023/tutorials/spikeinterface_tutorial.ipynb b/Cosyne_2023/tutorials/spikeinterface_tutorial.ipynb index a8e9abc56..ca27d49cd 100644 --- a/Cosyne_2023/tutorials/spikeinterface_tutorial.ipynb +++ b/Cosyne_2023/tutorials/spikeinterface_tutorial.ipynb @@ -654,7 +654,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "**NOTE:** Internally the properties is jus a dictionary attached to the recording that is accessible as `_properties`" + "**NOTE:** Internally the properties is just a dictionary attached to the recording that is accessible as `_properties`" ] }, { @@ -1809,7 +1809,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Postprocessing spike sorting results ranges from computing additional information, such as spike amplitudes and Principal Component Analisys (PCA) scores, to computing features of the extracellular waveforms, similarity between templates and crosscorrelograms. All of this is possible with the `postprocessing` module." + "Postprocessing spike sorting results ranges from computing additional information, such as spike amplitudes and Principal Component Analysis (PCA) scores, to computing features of the extracellular waveforms, similarity between templates and crosscorrelograms. All of this is possible with the `postprocessing` module." ] }, { diff --git a/HCK15_2023_Janelia/README.md b/HCK15_2023_Janelia/README.md index 968abfa07..44b7b5a2d 100644 --- a/HCK15_2023_Janelia/README.md +++ b/HCK15_2023_Janelia/README.md @@ -33,7 +33,7 @@ The final report for the 2023 NWB User Days and Developer Days is now available ## Registration -Registration is now closed. If you would like to be added, please contact the organizers and we may be able to accomodate your request. +Registration is now closed. If you would like to be added, please contact the organizers and we may be able to accommodate your request. ## Logistics diff --git a/linkml_neurodata_hackashop_2024/README.md b/linkml_neurodata_hackashop_2024/README.md index c7eac4004..cba9f5ee6 100644 --- a/linkml_neurodata_hackashop_2024/README.md +++ b/linkml_neurodata_hackashop_2024/README.md @@ -33,7 +33,7 @@ The objective of the event is to bring the neurophysiology data and standards de ### Directions - **ICSI (Main Event):** ICSI is located in Downtown Berkeley across from the Downtown Berkeley BART station (on the second floor above the CHASE bank), with convenient access to hotels, restaurants, and transit. BART will conveniently get you from the airport to ICSI: - **From San Francisco International Airport** Depending on the time you can either take: 1) the Richmond (red) train directly to the Downtown Berkeley station, or 2) the Antioch (yellow) train to 19th Street Oakland and transfer to the Richmond (orange) line (across the platform) to Downtown Berkeley. Transfer time with BART is ~54min. - - **From Oakland International Airport** Take the BART conector train from the Airport to the Oakland Coliseum station and transfer to the Richmond (orange) train to Downtown Berkeley BART station. + - **From Oakland International Airport** Take the BART connector train from the Airport to the Oakland Coliseum station and transfer to the Richmond (orange) train to Downtown Berkeley BART station. - [BART online schedule](https://www.bart.gov/planner) - [GoogleMap](https://www.google.com/maps/place/International+Computer+Science+Institute/@37.8700159,-122.2695811,18z/data=!3m2!4b1!5s0x80857e9eacbaf82b:0x71414272a685c989!4m6!3m5!1s0x80857e99566a4815:0x9226568954e914ed!8m2!3d37.8700159!4d-122.2685444!16s%2Fg%2F1vb9d8mq?entry=ttu) - **LBNL (Bonus Hacking Days):** Building 59 (Shyh Wang Hall) is located on the Lawrence Berkeley National Laboratory campus. See the [static](https://www2.lbl.gov/Workplace/lab-site-map.html) and