Ecosyste.ms: Issues

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

GitHub / rki-mf1/covsonar issues and pull requests

#129 - Bump conda-incubator/setup-miniconda from 3.0.4 to 3.1.0

Pull Request - State: open - Opened by dependabot[bot] 3 months ago
Labels: dependencies

#128 - Bump psf/black from 24.8.0 to 24.10.0

Pull Request - State: open - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#127 - Bump psf/black from 24.4.2 to 24.8.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#126 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#125 - Bump psf/black from 23.10.1 to 24.4.2

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#124 - Bump conda-incubator/setup-miniconda from 2.1.1 to 3.0.4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#123 - Allow match query parameters to be read from a file

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

#122 - If match returns no rows, still output column names

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

#121 - Automatically update parent-child lineage info

Pull Request - State: closed - Opened by matthuska over 1 year ago
Labels: covsonar1

#120 - Switch to nextstrain SARS-CoV-2 gene annotation as default

Issue - State: open - Opened by matthuska over 1 year ago
Labels: covsonar1

#119 - Update lineage information whenever a user does a match query with sublineages

Issue - State: closed - Opened by matthuska over 1 year ago
Labels: covsonar1

#118 - Check formatting with black on push or pull requests

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

#116 - Add covsonar 1 precommit hook to run black and zimports, etc.

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

#115 - Allow matching by seqhash (including negation with '^')

Pull Request - State: closed - Opened by matthuska over 1 year ago
Labels: covsonar1

#114 - Fix match command

Pull Request - State: closed - Opened by silenus092 over 1 year ago - 6 comments
Labels: bug, covsonar2

#113 - Don't crash when filtering empty profile. Closes #112

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

#112 - Match query fails with AttributeError: 'NoneType' object has no attribute 'split'

Issue - State: closed - Opened by matthuska over 1 year ago
Labels: covsonar1

#111 - Import cache takes up a lot of disk space

Issue - State: closed - Opened by matthuska over 1 year ago - 2 comments
Labels: covsonar2

#110 - Rewrite property handling to use a simple table rather than an entity-attribute-value table

Pull Request - State: closed - Opened by matthuska over 1 year ago - 4 comments
Labels: covsonar2

#108 - GISAID sequences cause errors when importing into a database

Issue - State: closed - Opened by matthuska over 1 year ago - 2 comments
Labels: covsonar1

#107 - refix: avoid deletion of identical sequences

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

#106 - Sublineage queries silently fail when `update-lineages` has never been run for a database

Issue - State: closed - Opened by matthuska over 1 year ago - 1 comment
Labels: covsonar2

#105 - "pango" property type not document in README.md

Issue - State: closed - Opened by matthuska over 1 year ago - 2 comments
Labels: documentation, covsonar2

#104 - Allow lineages to also be updated from local files

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

#103 - Avoid bug when deleting sequences which are identical to others

Pull Request - State: closed - Opened by matthuska over 1 year ago
Labels: covsonar1

#102 - Match by `seqhash`

Issue - State: closed - Opened by MarieLataretu over 1 year ago
Labels: feature request, covsonar1, covsonar2

#101 - Fix matching on multiple properties and profiles

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

#100 - Broken pipe error on using `head` on output of `match` command

Issue - State: open - Opened by matthuska over 1 year ago
Labels: covsonar1

#99 - Initial table with all commands we are using regularly from covsonar 1

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

#98 - covsonar 2 runtime (and memory usage?)

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

#95 - Add --only-frameshifts and --no-frameshifts arguments

Issue - State: closed - Opened by matthuska over 1 year ago - 1 comment
Labels: covsonar2

#94 - Option to output all unique elements of a given metadata field

Issue - State: open - Opened by matthuska over 1 year ago
Labels: feature request

#93 - Add workflow diagram to README

Issue - State: open - Opened by matthuska over 1 year ago
Labels: documentation

#92 - Optionally mask the start/end of sequences

Issue - State: open - Opened by matthuska over 1 year ago
Labels: feature request

#91 - Stats about blind spots (N) when matching genomic profiles

Issue - State: open - Opened by matthuska over 1 year ago
Labels: feature request

#90 - Match accessions by list of accessions in a file

Issue - State: closed - Opened by MarieLataretu over 1 year ago - 2 comments
Labels: feature request, covsonar2

#89 - Special case for properties starting in '.', lstrip() them.

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

#88 - Bump package and tooling dependencies

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

#87 - zimports: split imports over multiple lines

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

#86 - --only_frameshifts reports empty files, if none found

Issue - State: closed - Opened by oliverdrechsel over 1 year ago
Labels: covsonar1

#84 - VCF file restored from covsonar and Usher pre-processing

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

#83 - covsonar2.alpha-3 for testing

Pull Request - State: closed - Opened by silenus092 almost 2 years ago

#82 - Error when extracting TSV from rki.db 2021-12-07

Issue - State: closed - Opened by hoelzer almost 2 years ago - 7 comments
Labels: covsonar1

#81 - Error when extracting a certain lineage

Issue - State: closed - Opened by hoelzer almost 2 years ago - 6 comments

#79 - Fix delete samples

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#78 - querying for a specific mutation returns also genomes that do not contain this mutation

Issue - State: closed - Opened by akifoss over 2 years ago - 6 comments
Labels: covsonar1

#77 - Test/note/testing script

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#76 - Test/note/testing script

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#75 - covSonar1: Branch "Fix/v.1"- Update Sept. V.1.1.7

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#74 - --platform not working

Issue - State: closed - Opened by AliceWi over 2 years ago - 1 comment
Labels: bug

#73 - Fix Readme and Add feature

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#72 - Allow to select output columns

Issue - State: closed - Opened by silenus092 over 2 years ago - 2 comments
Labels: feature request

#71 - Update master to 1.16 from Fix/v.1 branch

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#70 - Test/note/testing script

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#69 - Test/note/testing script: Update to 92% overall test coverage.

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#68 - Update Feature/note/cov2_mpire

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#67 - Update Test Script

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#66 - Revert "Dev/cov2 mpire sf"

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#65 - Feature/k2/readme

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#64 - Dev/cov2 mpire sf

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

#63 - Add mamba to GitHub actions environments, so testing works

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

#62 - Fix crasher when importing sequences inside pytest --cov

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

#61 - Add missing newline to end of paranoid alignment output

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

#60 - Add pre-commit hooks to update formatting and run linter

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

#59 - Releases to PyPI

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

#58 - Enable test.pypi.org upload action for dev/cov2_mpire branch

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

#57 - Prepare packing and automated testing

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

#56 - July Patch - Bug Fix

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#55 - Fix parent-child construction script

Issue - State: closed - Opened by silenus092 over 2 years ago
Labels: bug

#54 - Decrease memory usage when outputting mutation profiles from large databases

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

#53 - Information on NNNNN stretches

Issue - State: closed - Opened by hoelzer over 2 years ago - 1 comment
Labels: enhancement

#52 - Create ci-v1.yml

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#51 - Create ci-v1x.yml

Pull Request - State: closed - Opened by silenus092 over 2 years ago

#50 - --no_frameshifts does not work with --tsv

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

#49 - Dev/cov2 mpire - [merged]

Issue - State: closed - Opened by silenus092 almost 3 years ago - 1 comment
Labels: gitlab merge request

#48 - First > dev/cov2_mpire to covsonar2_mpire

Pull Request - State: closed - Opened by silenus092 almost 3 years ago

#47 - Update to [covSonar 1.1.4] - [merged]

Issue - State: closed - Opened by silenus092 almost 3 years ago - 3 comments
Labels: gitlab merge request

#46 - HotFix - [merged]

Issue - State: closed - Opened by silenus092 almost 3 years ago - 1 comment
Labels: gitlab merge request

#45 - Update to [covSonar 1.1.3] - [merged]

Issue - State: closed - Opened by silenus092 about 3 years ago - 10 comments
Labels: gitlab merge request

#44 - Update to [covSonar V.1.1.2] - [merged]

Issue - State: closed - Opened by silenus092 about 3 years ago - 10 comments
Labels: gitlab merge request

#43 - Dev delete function - [merged]

Issue - State: closed - Opened by silenus092 about 3 years ago - 6 comments
Labels: gitlab merge request

#42 - Dev/v.1 - [merged]

Issue - State: closed - Opened by silenus092 about 3 years ago - 1 comment
Labels: gitlab merge request

#41 - Fix and Add features - [merged]

Issue - State: closed - Opened by silenus092 about 3 years ago - 4 comments
Labels: gitlab merge request

#40 - Zero length Hot Fix - [merged]

Issue - State: closed - Opened by silenus092 over 3 years ago - 1 comment
Labels: gitlab merge request

#39 - fix #14 (conda env working on mac) - [merged]

Issue - State: closed - Opened by silenus092 over 3 years ago - 1 comment
Labels: gitlab merge request

#38 - TSV Export - [closed]

Issue - State: closed - Opened by silenus092 over 3 years ago
Labels: gitlab merge request

#37 - Draft: Matts wishlist - [closed]

Issue - State: closed - Opened by silenus092 over 3 years ago
Labels: gitlab merge request

#36 - Matts wishlist - [merged]

Issue - State: closed - Opened by silenus092 over 3 years ago - 1 comment
Labels: gitlab merge request

#35 - v1.0.0 - [merged]

Issue - State: closed - Opened by silenus092 over 3 years ago - 1 comment
Labels: gitlab merge request

#34 - Improvements - [merged]

Issue - State: closed - Opened by silenus092 over 3 years ago - 1 comment
Labels: gitlab merge request

#33 - WIP class overhaul - [merged]

Issue - State: closed - Opened by silenus092 almost 4 years ago - 1 comment
Labels: gitlab merge request

#32 - ORF1ab fix to support non-linear CDS - [merged]

Issue - State: closed - Opened by silenus092 almost 4 years ago - 3 comments
Labels: gitlab merge request

#31 - improvements - [merged]

Issue - State: closed - Opened by silenus092 almost 4 years ago - 4 comments
Labels: gitlab merge request

#30 - Issues - [merged]

Issue - State: closed - Opened by silenus092 almost 4 years ago - 3 comments
Labels: gitlab merge request