Ecosyste.ms: Issues

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GitHub / dwhswenson/contact_map issues and pull requests

#135 - Update Python versions in CI

Pull Request - State: closed - Opened by dwhswenson 7 months ago - 2 comments
Labels: misc PR, ci

#133 - tests: `setup`,`teardown` -> `setup_method`, etc

Pull Request - State: closed - Opened by dwhswenson about 1 year ago - 3 comments

#132 - Regenerate webhook for read the docs

Issue - State: open - Opened by sroet about 1 year ago - 2 comments

#129 - How to display contacts of atoms within the same residue?

Issue - State: closed - Opened by sam-mahdi over 1 year ago - 7 comments

#128 - Update RTD config

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 5 comments
Labels: misc PR, docs

#127 - how to extract some special contacts

Issue - State: closed - Opened by wayuer19 over 1 year ago - 3 comments

#126 - fix matplotlib 3.6 'Unable to determine Axes to steal space for Colorbar

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

#125 - How to calculate the CA distance between two residues？

Issue - State: closed - Opened by FYY99117 almost 3 years ago - 2 comments

#124 - use new way of checking for no warnings

Pull Request - State: closed - Opened by sroet almost 3 years ago - 2 comments
Labels: misc PR, upstream_changed

#123 - update copyright to 2022

Pull Request - State: closed - Opened by sroet about 3 years ago - 1 comment
Labels: misc PR

#122 - swap from codecov bash uploader to their github action

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

#121 - also drop appveyor badge

Pull Request - State: closed - Opened by sroet over 3 years ago - 1 comment
Labels: misc PR

#120 - CI Cleanup: Windows builds on GitHub Actions; drop Python 3.6; better requirements handling

Pull Request - State: closed - Opened by dwhswenson over 3 years ago - 4 comments
Labels: misc PR, ci

#119 - Discussion: Moving off of AppVeyor

Issue - State: closed - Opened by dwhswenson over 3 years ago - 5 comments

#118 - Actually test for the Userwarning on custom cmaps

Pull Request - State: closed - Opened by sroet over 3 years ago - 1 comment
Labels: misc PR

#117 - Remove genindex from docs

Pull Request - State: closed - Opened by dwhswenson over 3 years ago - 2 comments
Labels: misc PR, docs

#116 - define forgotten ne

Pull Request - State: closed - Opened by sroet over 3 years ago - 2 comments
Labels: bugfix

#115 - [WIP]: cythonisation

Pull Request - State: open - Opened by sroet over 3 years ago - 1 comment

#114 - Update GA badge

Pull Request - State: closed - Opened by sroet over 3 years ago - 1 comment
Labels: misc PR

#113 - Renaming `master` branch to `main`

Issue - State: open - Opened by dwhswenson almost 4 years ago - 2 comments

#112 - [Security] invalidate all CI secrets

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

#111 - Fix lines missing from test coverage

Pull Request - State: closed - Opened by dwhswenson almost 4 years ago - 2 comments
Labels: misc PR

#110 - Automatically detect diverging color maps

Pull Request - State: closed - Opened by dwhswenson almost 4 years ago - 5 comments
Labels: enhancement, api break

#109 - DOCS: Add matplotlib tips to custom_plotting

Pull Request - State: closed - Opened by dwhswenson almost 4 years ago - 1 comment
Labels: misc PR, docs

#108 - Changing colorbar font size

Issue - State: closed - Opened by retlaw-1 almost 4 years ago - 2 comments

#107 - update GA

Pull Request - State: closed - Opened by sroet almost 4 years ago - 2 comments
Labels: misc PR, ci

#106 - New example notebooks

Pull Request - State: closed - Opened by dwhswenson almost 4 years ago - 5 comments
Labels: misc PR, docs

#105 - How are "contacts" defined?

Issue - State: closed - Opened by victorprincipe almost 4 years ago - 4 comments

#104 - Switch to GitHub Actions and CodeCov

Pull Request - State: closed - Opened by dwhswenson about 4 years ago - 9 comments
Labels: misc PR, ci

#103 - What to do with the new travis.com plan?

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

#102 - Smarter loading for Dask based implementations

Issue - State: open - Opened by sroet about 4 years ago

#101 - DaskContactTrajectory

Pull Request - State: closed - Opened by sroet about 4 years ago - 20 comments
Labels: enhancement

#100 - Update Travis badge to .com instead of .org

Pull Request - State: closed - Opened by sroet over 4 years ago
Labels: misc PR

#99 - Move from travis.org -> travis.com/github actions

Issue - State: closed - Opened by sroet over 4 years ago - 4 comments

#98 - Bump 0.7.1.dev0

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

#97 - Fix spaces in links

Pull Request - State: closed - Opened by sroet over 4 years ago - 1 comment
Labels: misc PR, docs

#96 - Release 0.7

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

#95 - Future proof ParameterFixer

Pull Request - State: closed - Opened by sroet over 4 years ago - 2 comments
Labels: misc PR

#94 - [non-public API-break] Autozoom plots

Pull Request - State: closed - Opened by sroet over 4 years ago - 14 comments
Labels: enhancement

#93 - Add binder links

Pull Request - State: closed - Opened by sroet over 4 years ago - 7 comments
Labels: misc PR, docs

#92 - Enable binder

Pull Request - State: closed - Opened by sroet over 4 years ago - 12 comments
Labels: misc PR

#91 - API cleanup: private `ContactObject._contact_map`; remove `frames` from `ContactFrequency`

Pull Request - State: closed - Opened by dwhswenson over 4 years ago
Labels: misc PR, api break

#90 - ContactCount.to_networkx

Pull Request - State: closed - Opened by dwhswenson over 4 years ago - 2 comments
Labels: enhancement

#89 - "Autozoom" plotting

Issue - State: closed - Opened by dwhswenson over 4 years ago - 8 comments

#88 - Remove `ContactMap` (allowing rename `ContactFrequency` => `ContactMap`)

Pull Request - State: closed - Opened by dwhswenson over 4 years ago - 2 comments
Labels: misc PR, api break, deprecation

#87 - IndexManagers for atom slicing

Pull Request - State: closed - Opened by dwhswenson over 4 years ago - 2 comments
Labels: misc PR, api break

#86 - Bump version to 0.6.1.dev0

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

#85 - Release 0.6.0

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

#84 - Deprecate `ContactMap` (allowing rename `ContactFrequency` => `ContactMap`)

Pull Request - State: closed - Opened by dwhswenson over 4 years ago - 2 comments
Labels: misc PR, deprecation

#83 - Coveralls cleanup

Pull Request - State: closed - Opened by dwhswenson over 4 years ago - 1 comment
Labels: misc PR, ci

#82 - Renaming `ContactFrequency` to `ContactMap`; removing old `ContactMap`

Issue - State: open - Opened by dwhswenson over 4 years ago - 2 comments

#81 - Contact trajectories

Pull Request - State: closed - Opened by dwhswenson over 4 years ago - 3 comments
Labels: enhancement

#80 - Bump 0.6.0.dev0

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

#79 - rework plotting to allow for plot_axes

Pull Request - State: closed - Opened by sroet over 4 years ago - 16 comments
Labels: enhancement

#78 - Subplots for ContactFrequency

Issue - State: closed - Opened by nffaruk over 4 years ago - 3 comments

#77 - Allow mismatched ContactDifference

Pull Request - State: closed - Opened by sroet over 4 years ago - 18 comments
Labels: enhancement

#76 - Release 0.5.1

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

#75 - Drop Py27 and Win32; add Py38

Pull Request - State: closed - Opened by dwhswenson over 4 years ago - 2 comments
Labels: misc PR, upstream_changed

#74 - ContactFrequency to pandas dataframe

Issue - State: open - Opened by PeptideSimulator01 over 4 years ago - 7 comments

#73 - Contact Difference of two trajectories

Issue - State: closed - Opened by PeptideSimulator01 over 4 years ago - 6 comments

#72 - Fix RTD docs build

Pull Request - State: closed - Opened by dwhswenson almost 5 years ago - 1 comment
Labels: misc PR, docs

#71 - Bump 0.5.1.dev0

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

#70 - pin pandas<1.0

Pull Request - State: closed - Opened by dwhswenson almost 5 years ago
Labels: misc PR, upstream_changed

#69 - Fixes for sparse matrix in Pandas 1.0

Pull Request - State: closed - Opened by dwhswenson almost 5 years ago - 6 comments
Labels: misc PR, upstream_changed

#68 - Release 0.5.0

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

#66 - Move to Autorelease 0.1.0

Pull Request - State: closed - Opened by dwhswenson about 5 years ago - 2 comments
Labels: misc PR

#65 - Added test for non_periodic systems

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

#64 - Fix for lack of unitcell; better colorbar scaling

Pull Request - State: closed - Opened by nffaruk about 5 years ago - 3 comments
Labels: misc PR

#63 - Fix coveralls reporting

Pull Request - State: closed - Opened by dwhswenson over 5 years ago - 1 comment
Labels: misc PR

#62 - Example: Plot drug binding hotspots w/ NGLView

Pull Request - State: open - Opened by dwhswenson over 5 years ago - 9 comments

#61 - Rename to Contact Map Explorer

Pull Request - State: closed - Opened by dwhswenson over 5 years ago - 6 comments
Labels: misc PR

#60 - Option to turn off topology compatibility check in `ContactDifference`

Issue - State: closed - Opened by dwhswenson over 5 years ago - 5 comments

#59 - ContactMap/ContactFrequency on a set of individual pdb (not trajectory)

Issue - State: closed - Opened by aparente-nurix over 5 years ago - 6 comments

#58 - [WIP] make google colab versions of the notebooks

Pull Request - State: closed - Opened by sroet over 5 years ago - 1 comment

#57 - Use Google Colab to load ipynb examples directly from documentation?

Issue - State: closed - Opened by sroet over 5 years ago - 11 comments

#56 - Bump to 0.5.0.dev0

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

#55 - Release 0.4.0

Pull Request - State: closed - Opened by dwhswenson over 5 years ago - 2 comments

#54 - Fix dask+atom_slice

Pull Request - State: closed - Opened by sroet over 5 years ago - 1 comment
Labels: bug

#53 - Enhancement: ContactTrajectory class (with movies!)

Issue - State: open - Opened by dwhswenson almost 6 years ago - 6 comments

#52 - Fix docs

Pull Request - State: closed - Opened by dwhswenson almost 6 years ago
Labels: misc PR

#51 - dask example not working

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

#50 - Warn when there is less than 1 pixel per contact

Pull Request - State: closed - Opened by sroet almost 6 years ago - 8 comments
Labels: misc PR, api break

#49 - Fix docs build problems

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

#48 - Always show at least one pixel for plotting

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

#47 - Add example for concurrences

Pull Request - State: closed - Opened by dwhswenson about 6 years ago - 2 comments
Labels: enhancement, misc PR, docs

#46 - Release 0.3.3

Pull Request - State: closed - Opened by dwhswenson about 6 years ago - 2 comments

#45 - Fix problems with pytest

Pull Request - State: closed - Opened by dwhswenson about 6 years ago - 1 comment
Labels: misc PR, upstream_changed

#44 - Handle dask TimeoutError exception in tests

Pull Request - State: closed - Opened by dwhswenson about 6 years ago - 1 comment
Labels: misc PR

#43 - Easy access to haystack/query residue indices and range

Pull Request - State: closed - Opened by dwhswenson about 6 years ago - 2 comments
Labels: enhancement

#42 - [WIP] FrozenSetDict; FrozenSetCounter

Pull Request - State: open - Opened by dwhswenson over 6 years ago
Labels: misc PR

#41 - Add Python 3.7 support

Pull Request - State: closed - Opened by dwhswenson over 6 years ago - 4 comments
Labels: misc PR

#40 - fix dask travis error

Pull Request - State: closed - Opened by sroet over 6 years ago - 2 comments
Labels: misc PR

#39 - Bump to 0.4.0.dev0

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

#38 - Release 0.3.1

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

#37 - fixed pandas future warn about as_matrix

Pull Request - State: closed - Opened by sroet over 6 years ago
Labels: misc PR, upstream_changed

#36 - Drop Python 3.4 support [travis]

Pull Request - State: closed - Opened by dwhswenson almost 7 years ago - 1 comment
Labels: misc PR