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codespell: tuneup of config and some new typos detected fixes #1334

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merged 2 commits into from
Oct 16, 2023

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@@ -3,7 +3,7 @@
"schemaKey": "Dandiset",
"schemaVersion": "0.4.0",
"name": "A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task",
"description": "A challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy re-use of this hard-to-obtain data for both teaching and research on the mechanisms of human memory.",
"description": "A challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy reuse of this hard-to-obtain data for both teaching and research on the mechanisms of human memory.",
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image

although may be we should just ignore such files too

@yarikoptic
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type checking issues is most likely unrelated and due to newer versions of requests or smth like that
typing: aiohttp==3.8.6,aiosignal==1.3.1,anys==0.3.0,appdirs==1.4.4,arrow==1.3.0,asciitree==0.3.3,async-timeout==4.0.3,attrs==23.1.0,bidsschematools==0.7.2,blessed==1.20.0,boto3==1.28.63,botocore==1.31.63,certifi==2023.7.22,cffi==1.16.0,charset-normalizer==3.3.0,ci-info==0.3.0,citeproc-py==0.6.0,click==8.1.7,click-didyoumean==0.3.0,coverage==7.3.2,cryptography==41.0.4,dandi @ file:///home/runner/work/dandi-cli/dandi-cli/.tox/.tmp/package/1/dandi-0.56.2%2B2.g58b61f7.tar.gz#sha256=de62a81650d229567edca201ff48e7a50cea1177498a9ca16ffda494081951a0,dandischema==0.8.4,dnspython==2.4.2,duecredit==0.9.2,email-validator==2.0.0.post2,etelemetry==0.3.1,exceptiongroup==1.1.3,fasteners==0.19,fqdn==1.5.1,frozenlist==1.4.0,fscacher==0.4.0,fsspec==2023.9.2,h5py==3.10.0,hdmf==3.10.0,humanize==4.8.0,idna==3.4,importlib-metadata==6.8.0,importlib-resources==6.1.0,iniconfig==2.0.0,interleave==0.2.1,isodate==0.6.1,isoduration==20.11.0,jaraco.classes==3.3.0,jeepney==0.8.0,jmespath==1.0.1,joblib==1.3.2,jsonpointer==2.4,jsonschema==4.19.1,jsonschema-specifications==2023.7.1,keyring==24.2.0,keyrings.alt==5.0.0,lxml==4.9.3,more-itertools==10.1.0,multidict==6.0.4,mypy==1.6.0,mypy-extensions==1.0.0,natsort==8.4.0,numcodecs==0.12.0,numpy==1.24.4,nwbinspector==0.4.30,opencv-python==4.8.1.78,packaging==23.2,pandas==2.0.3,pip==23.2.1,pkgutil_resolve_name==1.3.10,pluggy==1.3.0,pycparser==2.21,pycryptodomex==3.19.0,pydantic==1.10.13,pynwb==2.5.0,pyout==0.7.3,pytest==7.4.2,pytest-cov==4.1.0,pytest-mock==3.11.1,pytest-rerunfailures==12.0,python-dateutil==2.8.2,pytz==2023.3.post1,PyYAML==6.0.1,referencing==0.30.2,requests==2.31.0,responses==0.23.3,rfc3339-validator==0.1.4,rfc3987==1.3.8,rpds-py==0.10.6,ruamel.yaml==0.17.35,ruamel.yaml.clib==0.2.8,s3fs==0.4.2,s3transfer==0.7.0,scipy==1.10.1,SecretStorage==3.3.3,semantic-version==2.10.0,setuptools==68.2.0,six==1.16.0,tenacity==8.2.3,tomli==2.0.1,tqdm==4.66.1,types-appdirs==1.4.3.5,types-python-dateutil==2.8.19.14,types-PyYAML==6.0.12.12,types-requests==2.31.0.9,typing_extensions==4.8.0,tzdata==2023.3,uri-template==1.3.0,urllib3==1.26.17,vcrpy==5.1.0,wcwidth==0.2.8,webcolors==1.13,wheel==0.41.2,wrapt==1.15.0,yarl==1.9.2,zarr==2.16.1,zarr-checksum==0.2.9,zipp==3.17.0
typing: commands[0]> mypy dandi
dandi/dandiapi.py:[25](https://github.com/dandi/dandi-cli/actions/runs/6534602041/job/17742171073?pr=1334#step:5:26)1: error: Item "None" of "Optional[Response]" has no
attribute "status_code"  [union-attr]
                        e.response.status_code,
                        ^~~~~~~~~~~~~~~~~~~~~~
dandi/dandiapi.py:254: error: Item "None" of "Optional[Response]" has no
attribute "text"  [union-attr]
                        e.response.text,
                        ^~~~~~~~~~~~~~~
dandi/files/bases.py:365: error: Item "None" of "Optional[Response]" has no
attribute "status_code"  [union-attr]
                if e.response.status_code == 409:
                   ^~~~~~~~~~~~~~~~~~~~~~
dandi/files/bases.py:367: error: Item "None" of "Optional[Response]" has no
attribute "headers"  [union-attr]
                    blob_id = e.response.headers["Location"]
                              ^~~~~~~~~~~~~~~~~~
dandi/files/zarr.py:302: error: Item "None" of "Optional[Response]" has no
attribute "text"  [union-attr]
                    if "Zarr already exists" in e.response.text:
                                                ^~~~~~~~~~~~~~~
dandi/dandiarchive.py:168: error: Item "None" of "Optional[Response]" has no
attribute "status_code"  [union-attr]
                    if e.response.status_code == 401 and authenticate is n...
                       ^~~~~~~~~~~~~~~~~~~~~~
dandi/dandiarchive.py:[29](https://github.com/dandi/dandi-cli/actions/runs/6534602041/job/17742171073?pr=1334#step:5:30)6: error: Item "None" of "Optional[Response]" has no
attribute "status_code"  [union-attr]
                    if e.response.status_code == 401 and authenticate is n...
                       ^~~~~~~~~~~~~~~~~~~~~~
dandi/download.py:703: error: Item "None" of "Optional[Response]" has no
attribute "status_code"  [union-attr]
                if attempt >= 2 or exc.response.status_code not in (
                                   ^~~~~~~~~~~~~~~~~~~~~~~~
Found 8 errors in 5 files (checked 78 source files)

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codecov bot commented Oct 16, 2023

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (0c1d4a0) 88.81% compared to head (58b61f7) 88.78%.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1334      +/-   ##
==========================================
- Coverage   88.81%   88.78%   -0.03%     
==========================================
  Files          76       76              
  Lines       10216    10216              
==========================================
- Hits         9073     9070       -3     
- Misses       1143     1146       +3     
Flag Coverage Δ
unittests 88.78% <ø> (-0.03%) ⬇️

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see 7 files with indirect coverage changes

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@yarikoptic yarikoptic added the internal Changes only affect the internal API label Oct 16, 2023
@yarikoptic yarikoptic merged commit a0199fc into master Oct 16, 2023
20 of 25 checks passed
@yarikoptic yarikoptic deleted the bf-codespell branch October 16, 2023 17:59
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github-actions bot commented Nov 1, 2023

🚀 PR was released in 0.57.0 🚀

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