biocommons/eutils issues and pull requests

#182 - docs: fix examples

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

#181 - chore: add ignore revs file

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

#180 - style: format with Ruff

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

#179 - chore: fix license classifier

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

#178 - Add Biocommons CICD actions

Issue - State: open - Opened by jsstevenson 6 months ago - 1 comment
Labels: enhancement

#177 - Fix failing tests

Issue - State: open - Opened by jsstevenson 6 months ago
Labels: bug

#176 - build!: configure with pyproject.toml using biocommons.example parameters

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

#175 - "Examples" in docs are broken

Issue - State: closed - Opened by jsstevenson 6 months ago
Labels: bug

#174 - Implement client interface for `elink`

Issue - State: open - Opened by jsstevenson 6 months ago - 1 comment
Labels: enhancement, keep alive

#173 - ModuleNotFoundError (pkg_resources) on import in fresh 3.12 environment

Issue - State: closed - Opened by jsstevenson 6 months ago - 1 comment
Labels: bug

#172 - Expose SQLiteCache

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

#171 - .efetch() fails silently when batch query exceeds 250 IDs

Issue - State: closed - Opened by safay over 3 years ago - 2 comments
Labels: stale, closed-by-stale

#170 - installing from tarball failed

Issue - State: closed - Opened by shouldsee over 4 years ago - 1 comment
Labels: not-a-bug

#169 - Update queryservice.py docstrings

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

#168 - Update README.rst

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

#167 - Address issues found by Deepsource

Issue - State: closed - Opened by reece almost 5 years ago - 5 comments
Labels: stale, closed-by-stale

#166 - Remove python 2.7 support code

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

#165 - Replace deprecated time.clock function

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

#164 - EutilsRequestError handling raises AttributeError:

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

#163 - Add .deepsource.toml, Fix issues raised by DeepSource

Pull Request - State: closed - Opened by mohi7solanki over 5 years ago

#162 - Release last 2.7 version with pinned dependencies

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

#161 - modernize eutils development practice

Issue - State: closed - Opened by reece almost 6 years ago - 3 comments

#160 - hide internal submodules

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

#159 - Medcitations qualifiers types

Pull Request - State: closed - Opened by VincentMatthys almost 6 years ago - 2 comments

#158 - closes #157: edge case results in error being thrown when extracting abstract text

Pull Request - State: closed - Opened by pmartin23 almost 6 years ago - 4 comments

#157 - Edge case results in error being thrown when extracting abstract text in medlinecitation.py

Issue - State: closed - Opened by pmartin23 over 6 years ago - 1 comment

#156 - closes #132: Fix functions default argument

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

#155 - Call name typo

Pull Request - State: closed - Opened by ShriramK over 6 years ago

#154 - Fixes #152 - add support for ncbi_api_key

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

#153 - efetch for protein db

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

#152 - option to specify API key for QueryService instances

Issue - State: closed - Opened by pmartin23 over 6 years ago - 3 comments

#151 - Fix for #150

Pull Request - State: closed - Opened by andreasprlic almost 7 years ago - 1 comment

#150 - Can't efetch gi

Issue - State: closed - Opened by andreasprlic almost 7 years ago - 1 comment

#149 - A bug in the abstract property in medlinecitation.py

Issue - State: closed - Opened by jinseonyou about 7 years ago - 1 comment

#148 - A bug in abstract property in Medlinecitation.py

Pull Request - State: closed - Opened by jinseonyou about 7 years ago

#147 - Client: Don't use cache by default

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

#146 - use vcrpy to eliminate/reduce remote calls during testing

Issue - State: closed - Opened by reece over 7 years ago - 1 comment

#145 - update dbSNP for the change to https

Pull Request - State: closed - Opened by cariaso over 7 years ago - 1 comment

#144 - Nucest support

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

#143 - include error message from XML parser when can't parse NCBI response

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

#142 - QueryService treats all error responses from NCBI as being encoded as XML

Issue - State: closed - Opened by diekhans over 7 years ago - 1 comment

#141 - Wrong URL in Warning

Issue - State: closed - Opened by LLCampos almost 8 years ago - 2 comments

#140 - Fails to install with pip on Windows

Issue - State: closed - Opened by baoilleach almost 8 years ago - 6 comments

#139 - Wrap error handling and parsing with try catch - added test

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

#138 - Key Error with today's NCBI 'testing'

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

#137 - NCBI switching exclusively to https as of 9/26/2016

Issue - State: closed - Opened by nthmost about 8 years ago - 2 comments

#136 - Use https for NCBI E-utilities

Issue - State: closed - Opened by reece about 8 years ago - 1 comment
Labels: critical

#135 - basic support for pubmedcentral

Pull Request - State: closed - Opened by cariaso about 8 years ago - 2 comments

#134 - Eutils sqlite cache can store NCBI error page

Issue - State: closed - Opened by naomifox about 8 years ago
Labels: bug

#133 - extract authors information

Issue - State: closed - Opened by reece almost 9 years ago - 3 comments
Labels: enhancement, xmlfacades, trivial, stale, closed-by-stale

#132 - Functions have a dict as a default argument

Issue - State: closed - Opened by reece almost 9 years ago
Labels: bug, minor

#131 - add support for fetching sequence slices

Issue - State: closed - Opened by reece about 9 years ago - 2 comments
Labels: enhancement, minor, stale, closed-by-stale

#130 - move clientx to submodule

Issue - State: closed - Opened by reece about 9 years ago - 1 comment
Labels: enhancement, major, querying

#129 - create sphinx project documentation

Issue - State: closed - Opened by reece about 9 years ago - 2 comments
Labels: enhancement, minor, docs

#128 - implement GBFeature

Issue - State: closed - Opened by reece about 9 years ago - 1 comment
Labels: enhancement, major, xmlfacades

#127 - sqlite3 fails if directory ~/.cache is not previously created

Issue - State: closed - Opened by reece about 9 years ago - 2 comments
Labels: bug, minor

#126 - IndexError retrieving "comment" field from GBSeq object

Issue - State: closed - Opened by reece about 9 years ago - 3 comments
Labels: bug, minor

#125 - PubMedArticle parsing fails in case of CollectiveName authors

Issue - State: closed - Opened by reece over 9 years ago - 1 comment
Labels: bug, major

#124 - Support large search result sets

Issue - State: open - Opened by reece over 9 years ago - 11 comments
Labels: enhancement, keep alive

#123 - refactor queryservice to separate querying, throttling, and caching

Issue - State: closed - Opened by reece over 9 years ago - 2 comments
Labels: enhancement, minor, querying, stale, closed-by-stale

#122 - implement TTL support in cache

Issue - State: closed - Opened by reece over 9 years ago - 2 comments
Labels: enhancement, minor, querying, stale, closed-by-stale

#121 - update xmlfacades to better match xml tags and cardinality

Issue - State: closed - Opened by reece over 9 years ago - 1 comment
Labels: enhancement, major

#120 - "Documentation" is unclear

Issue - State: closed - Opened by reece over 9 years ago - 4 comments
Labels: critical, proposal