Ecosyste.ms: Issues

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

GitHub / volkamerlab/kissim issues and pull requests

#118 - Bump up env/CI to Python >=3.8

Issue - State: open - Opened by dominiquesydow over 1 year ago

#117 - Update black formatting

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

#116 - Update GHA CI configs

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

#115 - Citation

Pull Request - State: closed - Opened by t-kimber almost 2 years ago
Labels: documentation

#114 - Check if ipywidgets pin is working

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

#113 - Pin `ipywidgets` to <8

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

#112 - Reminder: Remove pin for `ipywidgets<8`

Issue - State: open - Opened by dominiquesydow about 2 years ago

#111 - Update CI schedule to Mondays 3 am (UTC)

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

#110 - Add CITATION.cff

Issue - State: open - Opened by dominiquesydow over 2 years ago

#109 - Fix docs CI

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

#108 - Add residue subset by Martin et al.

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

#107 - Update CI (OS and Python versions)

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

#106 - Add test file!

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

#105 - Fix failing CI

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

#104 - Update test_env.yaml

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

#103 - Add conda-forge channel to installation docs

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

#101 - Pin matplotlib to <3.5

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

#100 - Fix `kissim.viewer` discrete colorbar

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

#99 - `kissim.viewer`: With `matplotlib` 3.5 categorial cbar colorbar incorrect

Issue - State: closed - Opened by dominiquesydow almost 3 years ago
Labels: bug

#98 - Update `kissim.viewer` (NGL GUI optional + absolute FP diff)

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

#97 - Add Phylo tree to docs

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

#96 - Fix bug in `viewer` module

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

#95 - Compress fingerprint/feature distances output files (`csv.bz2`)

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago - 1 comment

#93 - Minor repo improvements (env, README, docs)

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago - 1 comment

#92 - Update README + docs

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago

#91 - Install opencadd from conda!

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago - 1 comment

#90 - Set logger level + clean up unit tests output

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago - 1 comment

#89 - Implement min-max normalization (coarse/fine)

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago - 1 comment

#88 - Add docs badges

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago

#87 - Update subpocket colors in kissim TOC

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

#86 - Mini-PR: Remove print statement

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

#85 - Fix bugs (FingerprintNormalized.kinase_name empty)

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

#83 - KiSSim variation: Comparison: Use L2 norm only

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#82 - KiSSim variation: Comparison: Use L1 norm only

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#81 - KiSSim variation: Use continuous values for SCO/EXP

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

#80 - Subset fingerprints based on selected pocket residues

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment
Labels: enhancement

#79 - FIX: Sort kinase pairs alphabetically before groupby

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment
Labels: bug

#78 - Add workarounds for problematic structures in 2021-06-30 KLIFS dataset

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment
Labels: bug

#77 - Subset fingerprint by ligand-interacting residues

Issue - State: closed - Opened by dominiquesydow over 3 years ago - 2 comments
Labels: enhancement

#76 - Move FingerprintDistanceGenerator.*_matrix methods to matrix module

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#75 - Extend 3D viewer: Add all ligand(s) and structure(s)

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#74 - Fix SiteAlign definitions for THR (set charge 1 to 0)

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#73 - Check docstrings coverage with interrogate

Issue - State: open - Opened by dominiquesydow over 3 years ago

#72 - Change default branch from master to main

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

#71 - Optional coverage minimum in FingerprintDistanceGenerator

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment
Labels: enhancement

#70 - Add 3D fingerprint view

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 6 comments

#69 - Add SCO cutoffs to definitions

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

#68 - Remove dataset.filters/explorer

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#67 - Add SCO cutoffs to definitions

Issue - State: closed - Opened by dominiquesydow over 3 years ago

#66 - Rename `master` to `main`

Issue - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#65 - Generate fingerprint from PDB file + pocket indices

Issue - State: open - Opened by dominiquesydow over 3 years ago - 1 comment
Labels: enhancement

#64 - Add more default output files to compare API/CLI

Issue - State: closed - Opened by dominiquesydow over 3 years ago
Labels: enhancement

#63 - Solve minor issues (enhancements + updates)

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#62 - Fix failing CI

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#61 - Schedule CI once a week (not daily)

Issue - State: closed - Opened by dominiquesydow over 3 years ago

#60 - CLI extension

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#59 - Fix MemoryError in `comparison` module

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#58 - Refine kinase matrix generation

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#57 - Integrate `kissim_to_newick` tool into `kissim` code base

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 4 comments

#56 - Correct typos in document example code

Issue - State: closed - Opened by Gumgo91 over 3 years ago - 2 comments
Labels: enhancement

#55 - TOOL: kissim_to_newick for processing KISSIM matrix into clustered tree

Pull Request - State: closed - Opened by AJK-dev over 3 years ago - 6 comments
Labels: enhancement

#54 - Exposure feature cutoff

Issue - State: closed - Opened by dominiquesydow over 3 years ago

#53 - All one-against-all comparisons

Issue - State: open - Opened by dominiquesydow over 3 years ago
Labels: enhancement

#52 - Change default for feature weights

Issue - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#51 - Change default for Fingerprint.values_array()

Issue - State: closed - Opened by dominiquesydow over 3 years ago

#50 - Add FingerprintDistanceGenerator.from_fingerprint_generator()

Issue - State: closed - Opened by dominiquesydow over 3 years ago
Labels: enhancement

#49 - Add windows to CI

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 7 comments

#48 - Fix kinase distance matrix diagonal

Issue - State: closed - Opened by dominiquesydow over 3 years ago - 2 comments

#47 - Reduce memory load

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

#46 - Exploratory notebook: NoSQL > MongoDB > mongoengine

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#45 - Fix typo + rewording in README/docs index

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

#44 - Fill kissim docs

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#43 - Fix: CodeCov's omitted files show up in report

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 14 comments

#42 - Add tests for CLI

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 2 comments

#41 - CodeCov: Ignore unit tests

Issue - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#40 - Fix bugs

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 2 comments

#39 - Refactor comparison part 2

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

#38 - Refactor comparison

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 1 comment

#37 - Clean up encoding module

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

#36 - Remove windows from CI

Pull Request - State: closed - Opened by dominiquesydow almost 4 years ago

#35 - Add back windows to CI

Issue - State: closed - Opened by dominiquesydow almost 4 years ago

#34 - Why are CLI unit tests not run on GHA?

Issue - State: open - Opened by dominiquesydow almost 4 years ago - 2 comments
Labels: question

#33 - Fix wrongly included files in codecov report

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

#32 - More testing

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

#31 - Reduce testing from KLIFS remote

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

#30 - Refactor comparison module (round 1)

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

#29 - Trigger codecov

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

#28 - Trigger codecov (attempt 1)

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

#27 - Some fingerprints fail due to Bio.PDB.HSExposure error

Issue - State: closed - Opened by dominiquesydow almost 4 years ago - 1 comment

#26 - Refactor encoding

Pull Request - State: closed - Opened by dominiquesydow about 4 years ago - 1 comment

#25 - Update sco

Pull Request - State: closed - Opened by dominiquesydow about 4 years ago - 1 comment

#23 - Setup CI / docs

Pull Request - State: closed - Opened by dominiquesydow about 4 years ago

#19 - Finish #18 (merged before pushing local changes)

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

#17 - Create pythonapp.yml (to run GitHub Actions)

Pull Request - State: closed - Opened by dominiquesydow almost 5 years ago - 2 comments

#8 - Exclude distance extrema from analysis

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

#7 - Add log info to empty bits

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

#4 - Visualize features in NGLview

Issue - State: closed - Opened by dominiquesydow about 5 years ago - 1 comment
Labels: enhancement