Ecosyste.ms: Issues

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

GitHub / dib-lab/screed issues and pull requests

#110 - Bump codecov/codecov-action from 3 to 4

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

#109 - Bump actions/cache from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies, github_actions

#108 - Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: dependencies, github_actions

#107 - Docs: system_packages is deprecated in RTD

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

#106 - Close sequencefile if an error happens in open_reader

Pull Request - State: closed - Opened by luizirber about 1 year ago - 2 comments

#105 - MRG: switch screed tests to run monthly

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

#104 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies, github_actions

#103 - MRG: rename test methods -> pytest; remove issue template

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

#102 - MRG: fix codecov upload

Pull Request - State: closed - Opened by ctb over 1 year ago - 3 comments

#101 - WIP: switch to ubuntu latest for CI

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

#100 - Remove pkg_resources usage

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

#99 - [MRG] remove `bz2file` in favor of `bz2`

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

#98 - remove bz2file dependency!

Issue - State: closed - Opened by ctb almost 2 years ago

#97 - [MRG] bump pip/tox cache version numbers

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

#96 - [MRG] add patch to semver versioning in release notes

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

#95 - [MRG] update release checklist after v1.1

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

#94 - Bump actions/cache from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, github_actions

#93 - Bump actions/setup-python from 2 to 4

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, github_actions

#92 - Bump actions/checkout from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies, github_actions

#91 - [MRG] add dependabot

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

#90 - [MRG] fix ResourceWarning from unclosed file

Pull Request - State: closed - Opened by ctb almost 3 years ago - 1 comment

#89 - Add badges for Debian packages

Pull Request - State: closed - Opened by mr-c almost 4 years ago - 1 comment

#88 - Update the release process & checklist.

Pull Request - State: closed - Opened by ctb almost 4 years ago - 2 comments

#87 - [MRG] make CI actually run, by configuring tox correctly

Pull Request - State: closed - Opened by ctb almost 4 years ago - 2 comments

#86 - [MRG] switch to using GitHub actions

Pull Request - State: closed - Opened by ctb almost 4 years ago - 1 comment

#85 - [MRG] Switch version config from versioneer to setuptools_scm

Pull Request - State: closed - Opened by ctb almost 4 years ago - 1 comment

#84 - [MRG] Update Python code in a few simple ways.

Pull Request - State: closed - Opened by ctb almost 4 years ago - 1 comment

#83 - [MRG] use pyproject.toml and setup.cfg instead of setup.py

Pull Request - State: closed - Opened by ctb almost 4 years ago - 12 comments

#82 - Fix deprecation warning in screedRecord

Pull Request - State: closed - Opened by luizirber almost 5 years ago - 1 comment

#81 - Fix travis

Pull Request - State: closed - Opened by luizirber almost 6 years ago - 1 comment

#80 - Use collections.abc for MutableMapping

Pull Request - State: closed - Opened by mandel01 almost 6 years ago - 1 comment

#79 - Remove deprecation warning (will stop working in Python 3.8)

Issue - State: closed - Opened by luizirber about 6 years ago - 2 comments

#78 - Screed version?

Issue - State: open - Opened by johnsolk over 6 years ago

#76 - screed docs e-mail address is [email protected]

Issue - State: open - Opened by ctb over 6 years ago

#75 - add bgzf/random access code from biopython to screed

Issue - State: open - Opened by ctb about 7 years ago

#74 - make write_fastx a method on Record, or import at top of screed

Issue - State: open - Opened by ctb about 7 years ago

#73 - Problems with deepcopy

Issue - State: open - Opened by luizirber over 7 years ago

#72 - post demultiplexing script as example

Issue - State: open - Opened by ctb over 7 years ago

#70 - author list in screed docs is wrong.

Issue - State: open - Opened by ctb over 7 years ago - 2 comments

#69 - Fix release notes generation; add recommonmark dependency

Pull Request - State: closed - Opened by luizirber over 7 years ago - 2 comments

#68 - Passing dict for Record should work

Pull Request - State: closed - Opened by luizirber over 7 years ago - 4 comments
Labels: wontfix

#67 - [MRG] Release 1.0 updates

Pull Request - State: closed - Opened by luizirber over 7 years ago - 2 comments

#66 - Add cleaned_seq attribute to Record

Pull Request - State: closed - Opened by betatim almost 8 years ago - 5 comments
Labels: wontfix

#65 - simplify use of 'open' internally

Pull Request - State: closed - Opened by ctb almost 8 years ago - 3 comments

#64 - Revert Record changes that break with khmer 2.0

Pull Request - State: closed - Opened by ctb almost 8 years ago - 2 comments

#63 - Add missing import for make_db

Pull Request - State: closed - Opened by luizirber almost 8 years ago - 2 comments

#62 - Cleanup user docs

Pull Request - State: closed - Opened by standage almost 8 years ago - 3 comments

#61 - Fix test execution when calling as a module

Pull Request - State: closed - Opened by luizirber almost 8 years ago - 6 comments

#60 - Release notes for 1.0

Pull Request - State: closed - Opened by ctb almost 8 years ago - 5 comments

#59 - Simpler changelog format

Pull Request - State: closed - Opened by standage almost 8 years ago - 2 comments

#58 - Make sure docs are tested in CI build

Pull Request - State: closed - Opened by standage almost 8 years ago - 3 comments

#57 - Code cleanup

Pull Request - State: closed - Opened by standage almost 8 years ago - 8 comments

#56 - allow sqlite3 import to fail

Pull Request - State: closed - Opened by ctb almost 8 years ago - 3 comments

#55 - Shell command for screed functions and simplified API for DB creation

Pull Request - State: closed - Opened by luizirber almost 8 years ago - 16 comments

#54 - Update tests & constrain behavior in various ways.

Pull Request - State: closed - Opened by ctb almost 8 years ago - 3 comments

#53 - Replace *_Writer with write_fastx

Pull Request - State: closed - Opened by standage about 8 years ago - 11 comments

#52 - Reduce build matrix

Pull Request - State: closed - Opened by standage about 8 years ago - 3 comments

#51 - Fix imports on screed.fadbm

Pull Request - State: closed - Opened by luizirber about 8 years ago

#50 - Use pytest as test runner

Pull Request - State: closed - Opened by luizirber about 8 years ago - 4 comments

#49 - Build improvements

Pull Request - State: closed - Opened by luizirber about 8 years ago - 3 comments

#48 - Fix operator comparison

Pull Request - State: closed - Opened by luizirber about 8 years ago - 4 comments

#47 - add fix for RC problems in Python 2.7

Pull Request - State: closed - Opened by ctb over 8 years ago - 2 comments

#46 - v0.9 release notes

Pull Request - State: closed - Opened by mr-c over 9 years ago - 2 comments

#45 - update known-issues

Pull Request - State: closed - Opened by mr-c over 9 years ago - 2 comments

#44 - Update versioneer & known-issues

Pull Request - State: closed - Opened by mr-c over 9 years ago - 2 comments

#43 - changed default behavior of screed.open to parse_description=False

Pull Request - State: closed - Opened by ctb over 9 years ago - 5 comments

#42 - Record slicing, take 2

Pull Request - State: closed - Opened by luizirber over 9 years ago - 6 comments

#41 - Add missing close method to screed.open

Pull Request - State: closed - Opened by luizirber over 9 years ago - 5 comments

#40 - ship relocated test data & unbreak Record rename

Pull Request - State: closed - Opened by mr-c over 9 years ago - 5 comments

#39 - screed.open as a context manager

Pull Request - State: closed - Opened by luizirber over 9 years ago - 8 comments

#38 - Fix/760 endless screed

Pull Request - State: closed - Opened by proteasome over 9 years ago - 6 comments

#37 - changed streaming test to fail for missing imports before starting threads

Pull Request - State: closed - Opened by anotherthomas over 9 years ago - 5 comments

#36 - added handling of '-' as shortcut for stdin to screed.open

Pull Request - State: closed - Opened by anotherthomas over 9 years ago - 4 comments

#35 - renamed _screed_record_dict()

Pull Request - State: closed - Opened by sguermond over 9 years ago - 5 comments

#34 - Python 3/2 compatibility

Pull Request - State: closed - Opened by luizirber over 9 years ago - 12 comments

#33 - Updated release docs to include instructions on making a final release

Pull Request - State: closed - Opened by bocajnotnef over 9 years ago - 12 comments

#32 - Restore release checklist

Pull Request - State: closed - Opened by bocajnotnef over 9 years ago

#31 - Tests for attribute equality/non-equality errors

Pull Request - State: closed - Opened by bocajnotnef over 9 years ago - 12 comments

#30 - Make screed tests use tmpdirs where applicable, addresses khmer/748

Pull Request - State: closed - Opened by bocajnotnef over 9 years ago - 17 comments

#29 - Screed Record Slicing

Pull Request - State: closed - Opened by themangoemoji over 9 years ago - 22 comments

#28 - Added release notes for v0.8

Pull Request - State: closed - Opened by bocajnotnef over 9 years ago - 14 comments

#27 - Fix a typo in screedRecord

Pull Request - State: closed - Opened by kdm9 over 9 years ago - 9 comments

#26 - make doc gen repro

Pull Request - State: closed - Opened by mr-c almost 10 years ago - 3 comments

#25 - correct typos

Pull Request - State: closed - Opened by mr-c almost 10 years ago - 1 comment

#24 - Fix release docs formatting & expand MANIFEST.in

Pull Request - State: closed - Opened by mr-c almost 10 years ago - 4 comments

#23 - work around versioneer bug

Pull Request - State: closed - Opened by mr-c almost 10 years ago - 3 comments

#22 - Docs cleanup

Pull Request - State: closed - Opened by bocajnotnef almost 10 years ago - 10 comments

#21 - Add a Gitter chat badge to README.md

Pull Request - State: closed - Opened by gitter-badger almost 10 years ago - 1 comment

#20 - fix build status badge

Pull Request - State: closed - Opened by mr-c almost 10 years ago

#19 - Cleanup for v0.8rc2

Pull Request - State: closed - Opened by bocajnotnef almost 10 years ago - 1 comment

#18 - Fix/705

Pull Request - State: closed - Opened by gpratt almost 10 years ago - 9 comments

#17 - screed release prep work

Pull Request - State: closed - Opened by bocajnotnef almost 10 years ago - 16 comments

#16 - Revert "Screed 1.0 Release Candidate Prep work"

Pull Request - State: closed - Opened by bocajnotnef almost 10 years ago

#15 - initial jenkins-build.sh

Pull Request - State: closed - Opened by mr-c almost 10 years ago - 1 comment

#14 - Screed 1.0 Release Candidate Prep work

Pull Request - State: closed - Opened by bocajnotnef almost 10 years ago - 5 comments

#13 - add Doxygen support

Pull Request - State: closed - Opened by mr-c about 10 years ago - 1 comment

#12 - Changed all instances of accuracy to quality. Nosetests still pass.

Pull Request - State: closed - Opened by brtaylor92 about 10 years ago - 2 comments

#11 - eliminate seek()s

Pull Request - State: closed - Opened by mr-c about 10 years ago - 23 comments