diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ffc9365..5132930 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -3,8 +3,7 @@ name: CI on: push: branches: [ main ] - tags: - - "v*" # Tag events matching v*, i.e. v1.0, v20.15.10 + pull_request: branches: [ main ] diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 3357c73..41e608d 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -1,7 +1,8 @@ name: Publish Python Package to PyPI on: - workflow_call: + release: + types: [published] workflow_dispatch: jobs: diff --git a/CHANGES.md b/CHANGES.md index 28cee6a..984157f 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,8 +1,18 @@ # Release notes -## [Upcoming release](https://github.com/open2c/bioframe/compare/v0.6.2...HEAD) +## [Upcoming release](https://github.com/open2c/bioframe/compare/v0.6.3...HEAD) + +## [v0.6.3](https://github.com/open2c/bioframe/compare/v0.6.2...v0.6.3) +Date 2024-03-11 + +Fixes: +* Prevent dropout from `closest` in some cases of left intervals with no neighbors by @agalitsyna in https://github.com/open2c/bioframe/pull/185 +* Fix overlap returning float indexes causing failing tests (numpy v1.22.4, pandas v1.5.2) by @agalitsyna in https://github.com/open2c/bioframe/pull/185 + +**Full Changelog**: https://github.com/open2c/bioframe/compare/v0.6.2...v0.6.3 ## [v0.6.2](https://github.com/open2c/bioframe/compare/v0.6.1...v0.6.2) +Date 2024-02-08 Changes: * cols and df_view_col passed to downstream functions by @smitkadvani in https://github.com/open2c/bioframe/pull/182 diff --git a/CITATION.cff b/CITATION.cff index 8bd7133..c7153f0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -46,12 +46,15 @@ identifiers: description: Zenodo - type: doi value: 10.1101/2022.02.16.480748 - description: bioRxiv + description: bioRxiv preprint + - type: doi + value: 10.1093/bioinformatics/btae088 + description: Publication preferred-citation: type: article title: "Bioframe: Operations on Genomic Intervals in Pandas Dataframes" authors: - - given-names: Open2C + - family-names: Open2C - given-names: Nezar family-names: Abdennur orcid: 'https://orcid.org/0000-0001-5814-0864' @@ -60,9 +63,11 @@ preferred-citation: orcid: "https://orcid.org/0000-0001-5905-6517" - given-names: Ilya family-names: Flyamer + name-suffix: M orcid: "https://orcid.org/0000-0002-4892-4208" - given-names: Aleksandra family-names: Galitsyna + name-suffix: A orcid: "https://orcid.org/0000-0001-8969-5694" - given-names: Anton family-names: Goloborodko @@ -73,6 +78,7 @@ preferred-citation: - given-names: Sergey family-names: Venev orcid: "https://orcid.org/0000-0002-1507-7460" - journal: bioRxiv - year: 2022 - doi: "10.1101/2022.02.16.480748" + journal: Bioinformatics + year: 2024 + url: "https://doi.org/10.1093/bioinformatics/btae088" + doi: "10.1093/bioinformatics/btae088" diff --git a/README.md b/README.md index b2f6bfa..b44aa40 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ ![CI](https://github.com/open2c/bioframe/actions/workflows/ci.yml/badge.svg) [![Docs status](https://readthedocs.org/projects/bioframe/badge/)](https://bioframe.readthedocs.io/en/latest/) -[![Preprint](https://img.shields.io/badge/DOI-10.1101%2F2022.02.16.480748-blue)](https://doi.org/10.1101/2022.02.16.480748) +[![Paper](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtae088-blue)](https://doi.org/10.1093/bioinformatics/btae088) [![Zenodo](https://zenodo.org/badge/69901992.svg)](https://zenodo.org/badge/latestdoi/69901992) [![Slack](https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack)](https://bit.ly/open2c-slack) [![NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://www.numfocus.org) @@ -97,11 +97,11 @@ See this [jupyter notebook](https://github.com/open2c/bioframe/tree/master/docs/ If you use ***bioframe*** in your work, please cite: ```bibtex -@article{bioframe_2022, -author = {Open2C and Abdennur, Nezar and Fudenberg, Geoffrey and Flyamer, Ilya and Galitsyna, Aleksandra and Goloborodko, Anton and Imakaev, Maxim and Venev, Sergey}, -doi = {10.1101/2022.02.16.480748}, -journal = {bioRxiv}, +@article{bioframe_2024, +author = {Open2C and Abdennur, Nezar and Fudenberg, Geoffrey and Flyamer, Ilya M and Galitsyna, Aleksandra A and Goloborodko, Anton and Imakaev, Maxim and Venev, Sergey}, +doi = {10.1093/bioinformatics/btae088}, +journal = {Bioinformatics}, title = {{Bioframe: Operations on Genomic Intervals in Pandas Dataframes}}, -year = {2022} +year = {2024} } ``` diff --git a/bioframe/_version.py b/bioframe/_version.py index 22049ab..63af887 100644 --- a/bioframe/_version.py +++ b/bioframe/_version.py @@ -1 +1 @@ -__version__ = "0.6.2" +__version__ = "0.6.3"