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Update the docs #236

Merged
merged 47 commits into from
Oct 11, 2024
Merged

Update the docs #236

merged 47 commits into from
Oct 11, 2024

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robomics
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Closes #213.

@robomics robomics added the documentation Improvements or additions to documentation label Aug 27, 2024
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codecov bot commented Aug 28, 2024 •
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Codecov Report

Attention: Patch coverage is 97.82609% with 1 line in your changes missing coverage. Please review.

Project coverage is 79.28%. Comparing base (dfd3db3) to head (ff71292).
Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/hictk/validate/validate.cpp 80.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #236      +/-   ##
==========================================
- Coverage   79.33%   79.28%   -0.05%     
==========================================
  Files         173      173              
  Lines       17000    17003       +3     
  Branches     2309     2309              
==========================================
- Hits        13487    13481       -6     
- Misses       2510     2514       +4     
- Partials     1003     1008       +5
Flag Coverage Δ
[tests integration](https://app.codecov.io/gh/paulsengroup/hictk/pull/236/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=paulsengroup) 69.73% <97.82%> (-0.04%)
[tests unittests](https://app.codecov.io/gh/paulsengroup/hictk/pull/236/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=paulsengroup) 77.38% <ø> (+0.04%)

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@robomics
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Double-check API docs.

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TODO: mention compression formats supported by hitck load

@robomics robomics marked this pull request as ready for review October 10, 2024 14:03
@robomics robomics merged commit a905013 into main Oct 11, 2024
126 checks passed
@robomics robomics deleted the docs/update branch October 11, 2024 09:20
robomics added a commit that referenced this pull request Oct 11, 2024
@robomics
Update the docs (#236)
062d2de 
* Update docstrings

* Update the README

* Update CLI reference

* Update requirements.txt for the docs

* Update test dataset download instructions

* Add docs for hictk metadata

* Update CLI reference

* Update docs for C++ API

* Update docs and tutorials for hictk

* hictk load: document supported compression algorithms

* Update docs for To*Matrix transformers

* Update CITATION.cff and add workflow to lint CITATION.cff

* Rewrite generate_cli_reference script in python

* Fix incorrect display of std::uint8_t default values in the CLI help message

* Remove unnecessary extension from docs/conf.py

* Switch to using build.commands in .readthedocs.yaml in preparation for RTD Addons

* Check for broken links when building the docs

* Add script to automate updating doc links in index.rst

* Update links to the doc in the readme
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[docs] improve docs for hictk metadata
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