Ecosyste.ms: Issues

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

GitHub / griffithlab/civicpy issues and pull requests

#155 - Add --version support

Pull Request - State: open - Opened by acoffman 2 months ago

#154 - GKS support

Issue - State: open - Opened by ahwagner 2 months ago

#151 - Update civicpy to support all types of Features

Pull Request - State: closed - Opened by susannasiebert 4 months ago

#148 - civicpy cache truncated?

Issue - State: closed - Opened by zhanyinx 5 months ago - 9 comments

#100 - Fix import statement

Pull Request - State: closed - Opened by susannasiebert over 4 years ago

#99 - update requirements files

Pull Request - State: closed - Opened by ahwagner over 4 years ago

#99 - update requirements files

Pull Request - State: closed - Opened by ahwagner over 4 years ago

#98 - Support reference build NCBI36/hg18

Pull Request - State: closed - Opened by susannasiebert over 4 years ago

#98 - Support reference build NCBI36/hg18

Pull Request - State: closed - Opened by susannasiebert over 4 years ago

#97 - A few variant coordinate search improvements

Pull Request - State: closed - Opened by susannasiebert over 4 years ago

#96 - Implement variant search by HGVS expression

Pull Request - State: closed - Opened by susannasiebert over 4 years ago

#95 - Throw fatal error when using `-` as the alt or ref in a coordinate query

Pull Request - State: closed - Opened by susannasiebert over 4 years ago - 1 comment

#94 - Add deprecation warnings to civic.get_all_x_ids methods

Pull Request - State: closed - Opened by susannasiebert over 4 years ago - 1 comment

#93 - speed up tests

Issue - State: open - Opened by ahwagner over 4 years ago - 1 comment
Labels: enhancement

#93 - speed up tests

Issue - State: open - Opened by ahwagner over 4 years ago - 1 comment
Labels: enhancement

#91 - Make CIViCpy Python >=3.5 compatible

Pull Request - State: closed - Opened by susannasiebert over 4 years ago - 2 comments

#90 - Deprecate the `get_all_x_ids` methods

Issue - State: closed - Opened by susannasiebert almost 5 years ago

#90 - Deprecate the `get_all_x_ids` methods

Issue - State: closed - Opened by susannasiebert almost 5 years ago

#89 - Improve tests coverage

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

#89 - Improve tests coverage

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

#88 - Add more fields to the VCF annotation output

Issue - State: closed - Opened by susannasiebert almost 5 years ago

#88 - Add more fields to the VCF annotation output

Issue - State: closed - Opened by susannasiebert almost 5 years ago

#87 - Add command to annotate an existing VCF with CIViC variants

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago

#86 - Patch for vcf_annotator2 to sanitize coordinate inputs

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

#86 - Patch for vcf_annotator2 to sanitize coordinate inputs

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

#85 - merge master to 1.0 ahead of 1.0.1 release

Pull Request - State: closed - Opened by ahwagner almost 5 years ago

#85 - merge master to 1.0 ahead of 1.0.1 release

Pull Request - State: closed - Opened by ahwagner almost 5 years ago

#84 - Use '*' as a wildcard for coordinate exact searches

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago

#84 - Use '*' as a wildcard for coordinate exact searches

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago

#83 - Download test pkl file from symlink

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago

#83 - Download test pkl file from symlink

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago

#82 - Documentation patch

Pull Request - State: closed - Opened by ahwagner almost 5 years ago

#82 - Documentation patch

Pull Request - State: closed - Opened by ahwagner almost 5 years ago

#81 - Fix bug in VCF coordinate retrieval for complex indels

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago - 3 comments

#81 - Fix bug in VCF coordinate retrieval for complex indels

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago - 3 comments

#80 - bump version to 1.0.0

Pull Request - State: closed - Opened by ahwagner almost 5 years ago

#79 - Fix bugs that prevent generation of valid VCF

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago

#79 - Fix bugs that prevent generation of valid VCF

Pull Request - State: closed - Opened by susannasiebert almost 5 years ago

#78 - Allow users to mistakenly use '-' for empty ref/alt

Issue - State: closed - Opened by ahwagner almost 5 years ago
Labels: enhancement

#78 - Allow users to mistakenly use '-' for empty ref/alt

Issue - State: closed - Opened by ahwagner almost 5 years ago
Labels: enhancement

#77 - Add ref and build as optional parameters to CoordinateQuery

Pull Request - State: closed - Opened by susannasiebert about 5 years ago

#77 - Add ref and build as optional parameters to CoordinateQuery

Pull Request - State: closed - Opened by susannasiebert about 5 years ago

#76 - Various bugfixes to coordinate search

Pull Request - State: closed - Opened by susannasiebert about 5 years ago

#75 - Remove pubchem_id field on Drug and replace with ncit_id

Pull Request - State: closed - Opened by susannasiebert about 5 years ago

#75 - Remove pubchem_id field on Drug and replace with ncit_id

Pull Request - State: closed - Opened by susannasiebert about 5 years ago

#74 - No remote queries option

Issue - State: open - Opened by ahwagner about 5 years ago - 1 comment
Labels: enhancement

#74 - No remote queries option

Issue - State: open - Opened by ahwagner about 5 years ago - 1 comment
Labels: enhancement

#73 - Add new variant search capabilities

Pull Request - State: closed - Opened by susannasiebert about 5 years ago - 1 comment

#73 - Add new variant search capabilities

Pull Request - State: closed - Opened by susannasiebert about 5 years ago - 1 comment

#72 - Gene provenance

Pull Request - State: closed - Opened by ahwagner about 5 years ago

#72 - Gene provenance

Pull Request - State: closed - Opened by ahwagner about 5 years ago

#71 - add prov / lifecycle documentation

Pull Request - State: closed - Opened by ahwagner about 5 years ago - 1 comment

#71 - add prov / lifecycle documentation

Pull Request - State: closed - Opened by ahwagner about 5 years ago - 1 comment

#70 - Partial support for issue 65

Pull Request - State: closed - Opened by ahwagner about 5 years ago - 4 comments

#70 - Partial support for issue 65

Pull Request - State: closed - Opened by ahwagner about 5 years ago - 4 comments

#69 - civicpy-specific endpoints on CIViC production

Issue - State: closed - Opened by ahwagner about 5 years ago - 2 comments

#69 - civicpy-specific endpoints on CIViC production

Issue - State: closed - Opened by ahwagner about 5 years ago - 2 comments

#68 - Documentation of coordinate search

Pull Request - State: closed - Opened by ahwagner about 5 years ago

#68 - Documentation of coordinate search

Pull Request - State: closed - Opened by ahwagner about 5 years ago

#67 - Mock tests for update behavior

Issue - State: closed - Opened by ahwagner about 5 years ago
Labels: high priority

#66 - closes #59

Pull Request - State: closed - Opened by ahwagner about 5 years ago - 1 comment

#66 - closes #59

Pull Request - State: closed - Opened by ahwagner about 5 years ago - 1 comment

#65 - add provenance information

Issue - State: closed - Opened by ahwagner about 5 years ago - 2 comments

#65 - add provenance information

Issue - State: closed - Opened by ahwagner about 5 years ago - 2 comments

#64 - run erro

Issue - State: closed - Opened by fanyucai1 about 5 years ago - 8 comments

#64 - run erro

Issue - State: closed - Opened by fanyucai1 about 5 years ago - 8 comments

#62 - Add testing for example Jupyter notebooks

Issue - State: closed - Opened by susannasiebert about 5 years ago - 1 comment
Labels: question

#62 - Add testing for example Jupyter notebooks

Issue - State: closed - Opened by susannasiebert about 5 years ago - 1 comment
Labels: question

#61 - Add a basic example Jupyter notenbook

Pull Request - State: closed - Opened by susannasiebert about 5 years ago - 1 comment

#61 - Add a basic example Jupyter notenbook

Pull Request - State: closed - Opened by susannasiebert about 5 years ago - 1 comment

#60 - Update documentation

Issue - State: closed - Opened by ahwagner about 5 years ago - 2 comments

#60 - Update documentation

Issue - State: closed - Opened by ahwagner about 5 years ago - 2 comments

#59 - update_cache and load_cache behavior

Issue - State: closed - Opened by ahwagner about 5 years ago

#58 - Separate out requirements in setup.py

Issue - State: closed - Opened by ahwagner about 5 years ago

#58 - Separate out requirements in setup.py

Issue - State: closed - Opened by ahwagner about 5 years ago

#57 - Create figure of code example

Issue - State: closed - Opened by ahwagner about 5 years ago

#57 - Create figure of code example

Issue - State: closed - Opened by ahwagner about 5 years ago

#56 - Consider support for all active versions of Python 3

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

#55 - Add reference build check to the VCFWriter

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

#55 - Add reference build check to the VCFWriter

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

#54 - Update master remote cache pkl file path

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

#54 - Update master remote cache pkl file path

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

#53 - VCFWriter improvements

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

#53 - VCFWriter improvements

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

#52 - closes #45

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

#51 - Cleanup

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

#51 - Cleanup

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

#50 - add support for revisions and projections

Issue - State: open - Opened by ahwagner over 5 years ago - 1 comment
Labels: enhancement

#49 - closes #38

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

#48 - refactor object retrieval from cache

Issue - State: open - Opened by ahwagner over 5 years ago
Labels: bug

#47 - evidence and variants filter out assertions based on include_filter

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

#46 - add revision retrieval method to CivicRecord

Issue - State: closed - Opened by ahwagner over 5 years ago - 1 comment
Labels: duplicate

#46 - add revision retrieval method to CivicRecord

Issue - State: closed - Opened by ahwagner over 5 years ago - 1 comment
Labels: duplicate

#45 - add variant_group support

Issue - State: closed - Opened by ahwagner over 5 years ago
Labels: high priority

#45 - add variant_group support

Issue - State: closed - Opened by ahwagner over 5 years ago
Labels: high priority

#44 - Update the VCFWriter to handle indels

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