Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / pyranges/pyranges issues and pull requests

#390 - Add explicit setuptools dependency

Pull Request - State: open - Opened by tomwardio 10 days ago - 1 comment

#389 - fix bug in join.py when left join.

Pull Request - State: open - Opened by y9c 3 months ago - 2 comments

#387 - Add importable constants for Chromosome, Start, End, etc.

Issue - State: closed - Opened by dvmcconnell 5 months ago - 2 comments

#386 - `np.bool` error in gr.head()

Issue - State: open - Opened by davidhbrann 5 months ago

#385 - `join` method exits unexpectedly

Issue - State: closed - Opened by WhenMelancholy 6 months ago - 4 comments

#384 - Update README.md

Pull Request - State: closed - Opened by yfarjoun 6 months ago - 1 comment

#383 - Fixed warnings

Pull Request - State: closed - Opened by marco-mariotti 6 months ago

#382 - Bump version only

Pull Request - State: closed - Opened by endrebak 6 months ago

#381 - Bump version

Pull Request - State: closed - Opened by endrebak 6 months ago

#380 - SyntaxError: invalid syntax for L131 in names.py

Issue - State: closed - Opened by simonharnqvist 7 months ago - 12 comments

#379 - Open file fix

Pull Request - State: closed - Opened by endrebak 7 months ago

#377 - ResourceWarning: files opened in readers.read_bed are never closed

Issue - State: closed - Opened by Isy89 8 months ago - 3 comments

#374 - Unexpected behaviour with strandedness of pyranges object

Issue - State: open - Opened by kkuret 10 months ago - 8 comments
Labels: bug

#373 - Bump jinja2 from 3.1.2 to 3.1.3 in /docs

Pull Request - State: open - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#371 - pyranges.cluster() Exception: Starts/Ends not int64 or int32: int64

Issue - State: closed - Opened by mvolar 11 months ago - 9 comments

#370 - PyRanges.intersect - "invert=True" kwarg behavior

Issue - State: open - Opened by vincentczhou 12 months ago - 1 comment

#369 - Del

Pull Request - State: closed - Opened by endrebak 12 months ago

#368 - COC

Pull Request - State: closed - Opened by endrebak 12 months ago

#367 - Coc

Pull Request - State: closed - Opened by endrebak 12 months ago

#366 - pr.get_sequence may not be working?

Issue - State: closed - Opened by brian-arnold 12 months ago - 4 comments

#362 - ModuleNotFoundError: No module named 'pyfaidx'

Issue - State: closed - Opened by brian-arnold about 1 year ago - 2 comments

#361 - count_overlaps causes overflow errors when number of reads are large

Issue - State: open - Opened by leetaiyi about 1 year ago - 1 comment

#359 - Bump urllib3 from 2.0.6 to 2.0.7 in /docs

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#358 - Minor doc edits

Pull Request - State: closed - Opened by marco-mariotti about 1 year ago

#356 - subtract does not respect strandedness default

Issue - State: open - Opened by michaelJwilson about 1 year ago

#355 - Return overlap between PyRanges objects, keeping columns from both?

Issue - State: closed - Opened by BeyondTheProof about 1 year ago - 6 comments
Labels: cookbook

#354 - Option to automatically rename reserved GTF columns in `read_gtf`

Pull Request - State: closed - Opened by fairliereese about 1 year ago

#353 - Stable non-conflicting interface: v.1.0.0

Issue - State: closed - Opened by marco-mariotti about 1 year ago - 2 comments
Labels: enhancement

#352 - Bump urllib3 from 2.0.5 to 2.0.6 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#351 - Additional how-to-pages

Issue - State: closed - Opened by marco-mariotti about 1 year ago - 1 comment
Labels: enhancement

#350 - RTD bugfix

Pull Request - State: closed - Opened by marco-mariotti about 1 year ago

#349 - pandas futurewarning in init.py

Issue - State: closed - Opened by Jeltje about 1 year ago - 2 comments

#347 - New documentation

Pull Request - State: closed - Opened by marco-mariotti about 1 year ago

#344 - 342 2

Pull Request - State: closed - Opened by endrebak over 1 year ago

#343 - 0.0.128 Fix left join category error #342

Pull Request - State: closed - Opened by endrebak over 1 year ago

#342 - left join broken with ValueError and TypeError

Issue - State: closed - Opened by hardingnj over 1 year ago - 22 comments

#341 - Duplicated reserved GTF columns with certain attribute tags in `write_gtf`

Issue - State: closed - Opened by fairliereese over 1 year ago - 4 comments

#340 - Add types

Pull Request - State: open - Opened by endrebak over 1 year ago

#339 - Fix tostring2

Pull Request - State: closed - Opened by endrebak over 1 year ago

#338 - Write developer docs?

Issue - State: closed - Opened by endrebak over 1 year ago - 1 comment
Labels: enhancement

#337 - Require fewer property tests on github actions

Pull Request - State: closed - Opened by endrebak over 1 year ago

#336 - Add property tests

Pull Request - State: closed - Opened by endrebak over 1 year ago

#335 - Update run_hypothesis_tests.yml

Pull Request - State: closed - Opened by endrebak over 1 year ago

#334 - Update run_hypothesis_tests.yml

Pull Request - State: closed - Opened by endrebak over 1 year ago

#333 - hi

Pull Request - State: closed - Opened by endrebak over 1 year ago

#332 - Code coverage badge for README.md

Issue - State: open - Opened by endrebak over 1 year ago
Labels: enhancement, good first issue

#331 - hia

Pull Request - State: closed - Opened by endrebak over 1 year ago

#330 - hi

Pull Request - State: closed - Opened by endrebak over 1 year ago

#329 - ho

Pull Request - State: closed - Opened by endrebak over 1 year ago

#328 - hi

Pull Request - State: closed - Opened by endrebak over 1 year ago

#324 - bedtools fixed so we can test jaccard properly

Issue - State: open - Opened by endrebak over 1 year ago
Labels: good first issue

#323 - Use Jupyterbook instead of bookdown?

Issue - State: closed - Opened by endrebak over 1 year ago - 2 comments

#322 - Make example data its own package?

Issue - State: open - Opened by endrebak over 1 year ago - 1 comment
Labels: enhancement, good first issue

#319 - Preserve order aallahyar

Pull Request - State: closed - Opened by endrebak over 1 year ago

#318 - book: index and tutorial

Pull Request - State: closed - Opened by marco-mariotti over 1 year ago

#317 - Low efficiency on transcriptomes or fragmented genomes

Issue - State: closed - Opened by marco-mariotti over 1 year ago - 4 comments
Labels: enhancement

#316 - Add methods to reverse complement and translate nucleotides

Issue - State: closed - Opened by marco-mariotti over 1 year ago - 1 comment
Labels: enhancement

#315 - Mapping between coordinates systems

Issue - State: open - Opened by marco-mariotti over 1 year ago - 2 comments
Labels: enhancement

#314 - Add slack argument to overlap, intersect, set_intersect, set_union

Issue - State: open - Opened by marco-mariotti over 1 year ago - 1 comment
Labels: enhancement

#313 - Streamline README.md

Issue - State: closed - Opened by marco-mariotti over 1 year ago - 3 comments
Labels: enhancement

#312 - Improve API documentation

Issue - State: open - Opened by marco-mariotti over 1 year ago
Labels: enhancement

#311 - Documentation is unaccessible

Issue - State: closed - Opened by DongzeHE over 1 year ago - 4 comments

#310 - Add a tox file to ease testing and linting

Issue - State: closed - Opened by endrebak over 1 year ago - 2 comments
Labels: enhancement

#309 - Add typing with mypy.

Issue - State: open - Opened by endrebak over 1 year ago - 2 comments
Labels: enhancement

#308 - Set up github actions for testing, linting, type-checking etc. that are run in a pre-commit

Issue - State: closed - Opened by endrebak over 1 year ago - 5 comments
Labels: enhancement

#307 - Cannot convert non-finite values (NA or inf) to integer

Issue - State: closed - Opened by seven1112233 over 1 year ago - 10 comments

#306 - Remove CPU-flag?

Issue - State: open - Opened by endrebak over 1 year ago

#305 - Implement correct but slow gtf/gff-reader to be used as backup.

Issue - State: open - Opened by endrebak over 1 year ago - 1 comment

#304 - added a `preserve_order` flag to `pr.join()`

Pull Request - State: closed - Opened by aallahyar over 1 year ago - 5 comments

#303 - Row-order after df1.join(df2, how="right")

Issue - State: closed - Opened by aallahyar over 1 year ago - 3 comments

#302 - Remove support for int32 chromosome starts/ends?

Issue - State: open - Opened by endrebak over 1 year ago - 5 comments

#301 - Cython wants us to stop executing setup.py

Issue - State: closed - Opened by endrebak over 1 year ago - 2 comments
Labels: enhancement

#300 - 0.0.121

Pull Request - State: closed - Opened by endrebak over 1 year ago

#299 - Incompatibility with pandas 2.0

Issue - State: closed - Opened by rob-p over 1 year ago - 2 comments

#298 - Overlap function met error using multi-cpus

Issue - State: open - Opened by ttbond over 1 year ago - 2 comments

#297 - fixed empty attribute bug in read_gtf when duplicate_attr=True

Pull Request - State: closed - Opened by fairliereese over 1 year ago - 4 comments

#296 - Inconsistent handling of bookended intervals

Issue - State: open - Opened by marco-mariotti over 1 year ago - 3 comments

#295 - Improve genome bounds

Pull Request - State: closed - Opened by marco-mariotti over 1 year ago - 1 comment

#294 - Bug fix on subsequence and spliced_subsequence

Pull Request - State: closed - Opened by marco-mariotti over 1 year ago

#293 - subsequence has inconsistent behavior with strand argument

Issue - State: closed - Opened by marco-mariotti over 1 year ago - 2 comments

#292 - Cannot read GTF: expected 2 values got 1

Issue - State: open - Opened by almart7 almost 2 years ago - 3 comments

#291 - Boolean columns in original data frame in join

Issue - State: closed - Opened by LudvigOlsen almost 2 years ago - 3 comments

#290 - Docstring update

Pull Request - State: closed - Opened by marco-mariotti almost 2 years ago

#289 - overlap() return an empty object

Issue - State: closed - Opened by axol0tl almost 2 years ago - 2 comments

#288 - [Feature request] Incorporate inplace parameter in drop() method

Issue - State: closed - Opened by maxtico almost 2 years ago - 1 comment

#287 - NumPy `bool` attribute error

Issue - State: closed - Opened by lbarbon almost 2 years ago - 2 comments

#286 - Feature request: wrap panda dataframe methods

Issue - State: closed - Opened by marco-mariotti almost 2 years ago - 3 comments
Labels: enhancement

#285 - Ranges disappear when get out of bounds on the 5' end in spliced_subsequence

Issue - State: closed - Opened by JoanPAAL almost 2 years ago - 2 comments

#284 - Fix FutureWarning

Pull Request - State: closed - Opened by y9c almost 2 years ago - 1 comment

#283 - pyranges could not be installed on Python 3.11 due to pyrle dependency failed.

Issue - State: closed - Opened by y9c almost 2 years ago - 9 comments

#282 - nearest and k_nearest not reporting ties

Issue - State: open - Opened by ASintsova about 2 years ago - 1 comment