-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* 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 [no ci]
- Loading branch information
Showing
44 changed files
with
1,143 additions
and
725 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| # Copyright (C) 2024 Roberto Rossini <[email protected]> | ||
| # SPDX-License-Identifier: MIT | ||
|
|
||
| name: Lint CITATION.cff | ||
|
|
||
| on: | ||
| push: | ||
| branches: [main] | ||
| paths: | ||
| - ".github/workflows/lint-cff.yml" | ||
| - "CITATION.cff" | ||
|
|
||
| pull_request: | ||
| paths: | ||
| - ".github/workflows/lint-cff.yml" | ||
| - "CITATION.cff" | ||
|
|
||
| # https://stackoverflow.com/a/72408109 | ||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| defaults: | ||
| run: | ||
| shell: bash | ||
|
|
||
| jobs: | ||
| lint-cff: | ||
| runs-on: ubuntu-latest | ||
| name: Lint CITATION.cff | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| sparse-checkout: CITATION.cff | ||
| sparse-checkout-cone-mode: false | ||
|
|
||
| - name: Generate DESCRIPTION file | ||
| run: | | ||
| cat << EOF > DESCRIPTION | ||
| Package: hictk | ||
| Title: What the Package Does (One Line, Title Case) | ||
| Version: 0.0.0.9000 | ||
| Authors@R: | ||
| person("First", "Last", , "[email protected]", role = c("aut", "cre")) | ||
| Description: What the package does (one paragraph). | ||
| License: MIT | ||
| Encoding: UTF-8 | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.3.2 | ||
| Imports: | ||
| cffr | ||
| EOF | ||
| - name: Setup R | ||
| uses: r-lib/actions/setup-r@v2 | ||
|
|
||
| - name: Add requirements | ||
| uses: r-lib/actions/setup-r-dependencies@v2 | ||
|
|
||
| - name: Lint CITATION.cff | ||
| run: Rscript -e 'cffr::cff_validate("CITATION.cff")' |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -15,8 +15,19 @@ abstract: 'Blazing fast toolkit to work with .hic and .cool files.' | |
| doi: '10.5281/zenodo.8214220' | ||
| url: 'https://github.com/paulsengroup/hictk' | ||
| repository-code: 'https://github.com/paulsengroup/hictk' | ||
| repository-artifact: 'https://github.com/paulsengroup/hictk/pkgs/container/hictk' | ||
| type: software | ||
| license: MIT | ||
| keywords: | ||
| - bioinformatics | ||
| - cxx | ||
| - conversion | ||
| - cooler | ||
| - cli-application | ||
| - hic | ||
| - cxx17 | ||
| - cxx-library | ||
| - hictk | ||
| preferred-citation: | ||
| type: article | ||
| authors: | ||
|
|
@@ -30,10 +41,22 @@ preferred-citation: | |
| orcid: 'https://orcid.org/0000-0002-7918-5495' | ||
| email: [email protected] | ||
| affiliation: 'Department of Biosciences, University of Oslo' | ||
| doi: '10.1101/2023.11.26.568707' | ||
| url: 'https://doi.org/10.1101/2023.11.26.568707' | ||
| journal: 'Cold Spring Harbor Laboratory' | ||
| year: 2023 | ||
| month: 11 | ||
| doi: '10.1093/bioinformatics/btae408' | ||
| url: 'https://academic.oup.com/bioinformatics/article/40/7/btae408/7698028' | ||
| journal: 'Bioinformatics' | ||
| year: 2024 | ||
| month: 06 | ||
| title: 'hictk: blazing fast toolkit to work with .hic and .cool files' | ||
| abstract: 'We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.' | ||
| abstract: > | ||
| Hi-C is gaining prominence as a method for mapping genome organization. | ||
| With declining sequencing costs and a growing demand for higher-resolution data, efficient tools for processing Hi-C datasets at different resolutions are crucial. | ||
| Over the past decade, the .hic and Cooler file formats have become the de-facto standard to store interaction matrices produced by Hi-C experiments in binary format. | ||
| Interoperability issues make it unnecessarily difficult to convert between the two formats and to develop applications that can process each format natively. | ||
| We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. | ||
| The toolkit is written in C++ and consists of a C++ library with Python and R bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. | ||
| We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication. | ||
| The hictk library, Python bindings and CLI tools are released under the MIT license as a multi-platform application available at github.com/paulsengroup/hictk. | ||
| Pre-built binaries for Linux and macOS are available on bioconda. | ||
| Python bindings for hictk are available on GitHub at github.com/paulsengroup/hictkpy, while R bindings are available on GitHub at github.com/paulsengroup/hictkR. | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.