Merge branch 'main' of https://github.com/open2c/bioframe into main

.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 ]
 

.github/workflows/publish.yml

@@ -1,7 +1,8 @@
 name: Publish Python Package to PyPI
 
 on:
-  workflow_call:
+  release:
+    types: [published]
   workflow_dispatch:
 
 jobs:

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

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"

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}
 }
 ```

bioframe/_version.py

@@ -1 +1 @@
-__version__ = "0.6.2"
+__version__ = "0.6.3"