Ecosyste.ms: Issues

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GitHub / biocommons/bioutils issues and pull requests

#70 - test: ignore existing NCBI_API_KEY env var

Pull Request - State: open - Opened by jsstevenson 3 months ago

#69 - Stop pinning urllib3 (only done for testing dep)

Pull Request - State: open - Opened by DavidCain 3 months ago - 1 comment

#68 - Update python-package.yml

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

#66 - chore: add git ignore revs file

Pull Request - State: closed - Opened by jsstevenson 5 months ago

#65 - style: format with Ruff

Pull Request - State: closed - Opened by jsstevenson 6 months ago - 3 comments

#64 - build: update supported python versions to 3.10-3.12

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

#63 - chore: use correct license classifier

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

#62 - fix: use importlib.metadata instead of pkg_resources

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

#61 - chore: remove __future__ imports

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

#60 - refactor: use importlib instead of pkg_resources

Pull Request - State: closed - Opened by jsstevenson 6 months ago - 3 comments

#59 - chore: remove whitespace

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

#58 - Fix `anchor` -> `anchor_length` in `normalize()` docs

Pull Request - State: closed - Opened by mihaitodor 10 months ago

#57 - This PR fixes the broken make develop.

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

#56 - build broken

Issue - State: closed - Opened by andreasprlic 12 months ago - 2 comments
Labels: stale, closed-by-stale

#55 - adding vertebrate mitochondrial translate table

Pull Request - State: closed - Opened by veenarajaraman about 1 year ago - 3 comments
Labels: enhancement, help wanted

#54 - Add GRCh38p13 and GRCh38p14

Issue - State: closed - Opened by davmlaw over 1 year ago - 1 comment

#53 - feat: #45: update assemblies and add T2T-CHM13v2.0

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

#52 - adopt conventional commits and semantic release

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

#51 - 50 synchronize biocommonsexample with bioutils

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

#50 - synchronize biocommons.example with bioutils

Issue - State: closed - Opened by reece over 1 year ago

#49 - Make tests run by specifying urllib3 version

Pull Request - State: closed - Opened by theferrit32 over 1 year ago

#48 - Rewrite trim_left and trim_right for linear performance.

Pull Request - State: closed - Opened by theferrit32 over 1 year ago - 2 comments

#47 - bioutils.normalize.normalize performance degrades for large sequences

Issue - State: closed - Opened by theferrit32 over 1 year ago - 3 comments

#46 - Tests do not run when package is freshly installed

Issue - State: closed - Opened by theferrit32 over 1 year ago - 3 comments

#45 - Add T2T-CHM13v2.0

Issue - State: closed - Opened by davmlaw over 1 year ago

#44 - Independent control of trimming and shuffling in `normalize()`

Pull Request - State: closed - Opened by gomoto over 2 years ago

#43 - Create python-package.yml

Pull Request - State: closed - Opened by reece over 2 years ago

#42 - release latest main branch

Issue - State: closed - Opened by andreasprlic over 2 years ago - 2 comments

#41 - Handle Ensembl transcript versions

Pull Request - State: closed - Opened by davmlaw over 2 years ago - 3 comments

#40 - seqfetcher doesn't support Ensembl transcript versions

Issue - State: closed - Opened by davmlaw over 2 years ago - 1 comment

#39 - 38 fix testing warnings

Pull Request - State: closed - Opened by reece over 2 years ago

#38 - Fix testing warnings

Issue - State: closed - Opened by reece over 2 years ago

#37 - fix #36 by adding a new translation table ...

Pull Request - State: closed - Opened by andreasprlic over 2 years ago - 6 comments

#36 - Add support for selenoproteins

Issue - State: closed - Opened by andreasprlic over 2 years ago

#35 - (PTC-W0019) Consider using literal syntax to create the data structure

Issue - State: closed - Opened by reece over 3 years ago - 1 comment
Labels: wontfix

#34 - (PYL-W0102) Dangerous default argument

Issue - State: closed - Opened by reece over 3 years ago - 1 comment
Labels: wontfix

#33 - fix: don't retry on invalid input with ncbi

Pull Request - State: closed - Opened by pjcoenen over 3 years ago - 4 comments

#32 - issue 31: improve support for degenerate codons

Pull Request - State: closed - Opened by kyuhas over 3 years ago - 2 comments

#31 - Improve support for degenerate codons

Issue - State: closed - Opened by reece over 3 years ago - 1 comment

#30 - support translation of ambiguity codes

Pull Request - State: closed - Opened by kyuhas over 3 years ago - 4 comments

#29 - Support degenerate codons in translate table

Issue - State: closed - Opened by reece over 4 years ago - 1 comment

#28 - passable docstrings

Pull Request - State: closed - Opened by trentwatt over 5 years ago - 5 comments

#27 - more docstrings

Pull Request - State: closed - Opened by trentwatt over 5 years ago

#26 - wheel build fails

Issue - State: closed - Opened by marty-brandon-nih over 5 years ago - 2 comments

#25 - #22: merge into master

Pull Request - State: closed - Opened by reece over 5 years ago

#24 - revert `vmc_digest` back to `truncated_digest`

Issue - State: closed - Opened by reece over 5 years ago - 6 comments
Labels: wontfix

#23 - Add pypi project description

Issue - State: closed - Opened by reece over 5 years ago - 3 comments
Labels: wontfix

#22 - Write/improve documentation

Issue - State: closed - Opened by reece over 5 years ago - 2 comments
Labels: wontfix

#21 - Expanded and reformatted for Sphinx the docstrings in normalize.py

Pull Request - State: closed - Opened by trentwatt over 5 years ago - 2 comments

#20 - Implement refget digest format

Issue - State: closed - Opened by reece over 5 years ago

#19 - Remove support for Python 2.7

Issue - State: closed - Opened by reece over 5 years ago

#18 - Implement flexible sequence normalization

Issue - State: closed - Opened by reece over 5 years ago - 5 comments
Labels: wontfix

#17 - Release last 2.7 version with pinned dependencies

Issue - State: closed - Opened by reece over 5 years ago - 1 comment

#16 - seqfetcher: Retry after rate limit error

Issue - State: closed - Opened by reece over 5 years ago

#15 - logging http error if detected

Pull Request - State: closed - Opened by bmrobin almost 6 years ago

#14 - Removing Biopython dependency

Pull Request - State: closed - Opened by afrubin about 6 years ago - 1 comment

#13 - Implement origin inference using identifiers.org information

Issue - State: closed - Opened by reece about 6 years ago - 2 comments
Labels: wontfix

#12 - Add function to infer origin from accession

Issue - State: closed - Opened by reece about 6 years ago

#11 - Fixes #10 add support for the 'ncbi_api_key' environment variable.

Pull Request - State: closed - Opened by timothyjlaurent over 6 years ago - 1 comment

#10 - Add support for eutils' api_key parameter

Issue - State: closed - Opened by timothyjlaurent over 6 years ago

#9 - Make seqfetcher use an appropriate tool and email, and register them

Issue - State: closed - Opened by reece about 7 years ago - 4 comments
Labels: wontfix

#8 - Email address and tool name missing from seqfetcher eutils call

Issue - State: closed - Opened by reece about 7 years ago

#6 - seqrepo tests fail due to removal of unicode coercion

Issue - State: closed - Opened by reece over 7 years ago

#5 - seqhash disappeared from bioutils.digests

Issue - State: closed - Opened by reece over 7 years ago

#4 - Update REAMDE links to point to github.com

Pull Request - State: closed - Opened by lucaswiman over 7 years ago

#3 - seqfetcher fails with protein accessions

Issue - State: closed - Opened by reece almost 8 years ago

#2 - migrate from recordtype to attrs

Issue - State: closed - Opened by reece almost 8 years ago - 1 comment

#1 - test issue

Issue - State: closed - Opened by reece over 8 years ago