Ecosyste.ms: Issues

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

GitHub / harmslab/topiary issues and pull requests

#49 - AttributeError with toytree

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

#48 - Recurring TypeError with PrettyTree

Issue - State: open - Opened by auroraab 3 months ago - 2 comments

#47 - Update python-app.yml

Pull Request - State: closed - Opened by harmsm 7 months ago

#46 - bug fixing

Pull Request - State: open - Opened by harmsm 7 months ago

#45 - Cleanup

Pull Request - State: closed - Opened by harmsm 8 months ago

#44 - Problem with pulling proteome from NCBI--solution found!

Issue - State: open - Opened by ani-sch 9 months ago - 3 comments

#43 - No bootstrap MSA files written in "Alignment to Ancestors" step

Issue - State: closed - Opened by jmayoral1 about 1 year ago - 2 comments

#41 - Running topiary for species that are not on NCBI

Issue - State: open - Opened by cyhkim almost 2 years ago

#40 - Notebook fails to build on pycairo

Issue - State: open - Opened by HWaymentSteele almost 2 years ago

#39 - seed-to-alignment unable to retrieve proteome for key species

Issue - State: open - Opened by benclifton almost 2 years ago - 1 comment

#38 - updated for pandas 2

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

#37 - bugfix: right response to seed species not found on ott

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

#36 - All aditional sequences removed in seed-to-alignment step

Issue - State: open - Opened by lbleicher almost 2 years ago - 8 comments

#35 - minor bug fixes

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

#34 - bugfix for partial md5 ncbi downloads

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

#33 - Error in topiary-seed-to-alignment

Issue - State: open - Opened by lbleicher almost 2 years ago - 25 comments

#32 - Ncbi api key

Pull Request - State: closed - Opened by harmsm about 2 years ago

#31 - Sets entrez API key from environment

Pull Request - State: closed - Opened by odcambc about 2 years ago - 1 comment

#30 - Add support for Entrez.api_key

Issue - State: closed - Opened by odcambc about 2 years ago - 4 comments

#29 - fixed np.float and nfs bugs

Pull Request - State: closed - Opened by harmsm about 2 years ago

#28 - numpy 1.24 doesn't like np.float()

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

#27 - OSError: [Errno 39] Directory not empty

Issue - State: closed - Opened by jkaczmarski about 2 years ago - 7 comments

#26 - clean up to docs

Pull Request - State: closed - Opened by harmsm about 2 years ago

#25 - ready for pre-release

Pull Request - State: closed - Opened by harmsm about 2 years ago

#24 - major updates to docs

Pull Request - State: closed - Opened by harmsm about 2 years ago

#23 - Minor edits to protocol.rst

Pull Request - State: closed - Opened by Kona-O about 2 years ago

#22 - wrap chdir functions, bug fixes

Pull Request - State: closed - Opened by harmsm about 2 years ago

#21 - much improved final report code

Pull Request - State: closed - Opened by harmsm about 2 years ago

#20 - discard_key definition updated

Pull Request - State: closed - Opened by Kona-O about 2 years ago

#19 - ready for beta release

Pull Request - State: closed - Opened by harmsm about 2 years ago

#18 - Updated example seed dataset in this repo

Pull Request - State: closed - Opened by Kona-O about 2 years ago - 1 comment

#17 - new features

Pull Request - State: closed - Opened by harmsm about 2 years ago

#16 - intermediate commit; blocked in reports and updated mpi for cola

Pull Request - State: closed - Opened by harmsm about 2 years ago

#14 - Updated documentation

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

#13 - Filled in docs

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

#12 - functional reconciliation bootstrapping

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

#11 - clean up and refactor

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

#10 - docs updates, fixing apidoc for readthedocs

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

#9 - Pre-release commits

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

#8 - pre-release draft

Pull Request - State: closed - Opened by harmsm over 2 years ago - 1 comment

#7 - final draft of release API

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

#6 - updated reverse blasting

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

#5 - fixed reverse blast

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

#4 - stitched together final pipeline architecture before submission

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

#3 - now checks all models

Pull Request - State: closed - Opened by harmsm over 3 years ago

#2 - update test yaml

Pull Request - State: closed - Opened by harmsm over 3 years ago

#1 - now passing flake and pytest

Pull Request - State: closed - Opened by harmsm over 3 years ago