pierrepo/PBxplore issues and pull requests

#181 - Add Zenodo and SH badge for code archives

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

#180 - Update CI badges

Pull Request - State: closed - Opened by HubLot almost 4 years ago - 10 comments

#179 - Update citation with code archives

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

#178 - Update badge for CI

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

#177 - Add Zenodo badge

Pull Request - State: closed - Opened by pierrepo almost 4 years ago - 3 comments

#176 - Update CI to GitHub Actions

Pull Request - State: closed - Opened by HubLot almost 4 years ago - 7 comments

#175 - Fix few bugs and bump to v1.4.0

Pull Request - State: closed - Opened by gabrielctn almost 4 years ago - 12 comments

#174 - Fix pytest

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

#173 - new Weblogo library issue

Issue - State: closed - Opened by alexdb27 over 5 years ago - 1 comment

#172 - Bumb the minimal MDAnalysis version required

Pull Request - State: open - Opened by jbarnoud almost 7 years ago - 7 comments
Labels: install

#171 - Add citation info

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

#170 - Link the paper and explain how to cite

Issue - State: closed - Opened by jbarnoud about 7 years ago - 3 comments

#169 - Add an example plot with RMSF and Neq superposed

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

#168 - Pierre's and Hubert's affiliations are outdated on the README

Issue - State: closed - Opened by jbarnoud about 7 years ago
Labels: documentation

#167 - Two tests 'xfailed'

Issue - State: closed - Opened by pierrepo over 7 years ago - 2 comments
Labels: bug

#166 - Mordernize the tests

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

#165 - Conda update

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

#164 - Fix the usage string of PBassign

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

#163 - Remove gromacs word for trajectory and use more generic ones.

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

#162 - Update installation doc

Pull Request - State: closed - Opened by pierrepo over 7 years ago - 5 comments

#161 - Update PBassign version

Pull Request - State: closed - Opened by pierrepo over 7 years ago - 6 comments

#160 - Fix display image notebook

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

#159 - Yet another update on the documentation

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

#158 - Travis python 3.6

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

#157 - Update license to BSD?

Issue - State: closed - Opened by pierrepo over 7 years ago - 2 comments

#156 - Update travis to build doc also for Python 3.x (up to 3.6)

Issue - State: closed - Opened by pierrepo over 7 years ago - 7 comments
Labels: documentation

#155 - Add example files for documentation

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

#154 - Remove remaining PBdata stuff

Pull Request - State: closed - Opened by HubLot almost 8 years ago - 2 comments

#153 - Fix encoding issue with weblogo file (#152)

Pull Request - State: closed - Opened by HubLot almost 8 years ago - 1 comment

#152 - PBstat does not generate weblogo anymore

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

#151 - Add a progress bar during PB assignment of a trajectory (#150)

Pull Request - State: closed - Opened by HubLot almost 8 years ago - 6 comments

#150 - Missing progress in MD trajectory PBs assignment

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

#149 - Fix #148

Pull Request - State: closed - Opened by HubLot almost 8 years ago - 5 comments

#148 - visualization functions fail when the first residue of the count matrix is not equal to 1

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

#147 - Improve drawing of PBs map

Pull Request - State: closed - Opened by pierrepo almost 8 years ago - 4 comments

#146 - PBstat with `--map` option crash when the number of residus is < 20

Issue - State: closed - Opened by HubLot almost 8 years ago - 3 comments

#145 - Check PEP8 compliance

Issue - State: closed - Opened by pierrepo almost 8 years ago - 9 comments

#144 - Handle production of NaN during angle calculations.

Pull Request - State: closed - Opened by HubLot almost 8 years ago - 5 comments

#143 - Remove R clustering in main code, tests and doc

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

#142 - Fix weblogo weblogolib.SymbolColor/ColorGroup import

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

#141 - Matplotlib is a mandatory requirement

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

#140 - MDAnalysis as a mandatory requirement

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

#139 - Support of file extension .pdb.gz

Pull Request - State: closed - Opened by HubLot about 8 years ago

#138 - PBxplore from PyPI (v1.0) does not seem to read *.pdb.gz anymore

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

#137 - Add doc for PyPI release

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

#136 - Remove Clustering

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

#135 - [WIP] Release Procedure

Pull Request - State: closed - Opened by HubLot about 8 years ago - 1 comment

#134 - compatibility check for weblogo versions

Pull Request - State: closed - Opened by HubLot about 8 years ago - 4 comments

#133 - Tests fail with he latest version of weblogo

Issue - State: closed - Opened by jbarnoud about 8 years ago - 4 comments

#132 - installation difficulties and PBxplore philosphy

Issue - State: closed - Opened by alexdb27 over 8 years ago - 2 comments

#131 - conda package

Pull Request - State: closed - Opened by HubLot over 8 years ago - 4 comments

#130 - `pbxplore.test()` doesn't work outside PBxplore folder

Pull Request - State: closed - Opened by HubLot over 8 years ago

#129 - test function is not working outside PBxplore folder

Issue - State: closed - Opened by HubLot over 8 years ago - 1 comment

#128 - Install pandoc through deb package

Pull Request - State: closed - Opened by HubLot over 8 years ago - 1 comment

#127 - Travis failed while building docs

Issue - State: closed - Opened by pierrepo over 8 years ago - 5 comments

#126 - Add version number

Pull Request - State: closed - Opened by pierrepo over 8 years ago - 1 comment

#125 - pip installation failed on a Python setup without numpy

Issue - State: closed - Opened by pierrepo over 8 years ago

#124 - Fix build doc

Pull Request - State: closed - Opened by pierrepo over 8 years ago

#123 - Crash while building doc with Jupyter-nbconvert 4.2.0

Issue - State: closed - Opened by pierrepo over 8 years ago

#122 - [WIP] Add unit tests

Pull Request - State: closed - Opened by HubLot over 8 years ago - 7 comments

#121 - Remove test dir from PyPi package?

Issue - State: closed - Opened by pierrepo over 8 years ago - 14 comments

#120 - Remove --phipsi option

Pull Request - State: closed - Opened by HubLot over 8 years ago - 8 comments

#119 - Remove --flat option

Pull Request - State: closed - Opened by pierrepo over 8 years ago - 4 comments

#118 - Remove --phipsi option

Issue - State: closed - Opened by pierrepo over 8 years ago

#117 - Remove --flat option

Issue - State: closed - Opened by pierrepo over 8 years ago

#116 - Improve the calculation of angle RMSD for assignation.

Pull Request - State: closed - Opened by HubLot over 8 years ago - 3 comments

#115 - [Proposal] Optimize PBassign when reading xtc trajectory

Pull Request - State: closed - Opened by HubLot over 8 years ago - 4 comments

#114 - Fix performance issues when dealing with large xtc trajectories

Pull Request - State: closed - Opened by HubLot over 8 years ago - 1 comment

#113 - Update README and MANIFEST

Pull Request - State: closed - Opened by HubLot over 8 years ago - 1 comment

#112 - Fix the doc in Travis

Pull Request - State: closed - Opened by jbarnoud almost 9 years ago

#111 - Travis failed when building the doc

Issue - State: closed - Opened by HubLot almost 9 years ago - 6 comments

#110 - [WIP] Rewrite of old documentation

Pull Request - State: closed - Opened by HubLot almost 9 years ago - 16 comments
Labels: documentation

#109 - Specify the version number of pandoc for Travis build

Pull Request - State: closed - Opened by HubLot almost 9 years ago - 1 comment

#108 - Travis build for doc fails

Issue - State: closed - Opened by HubLot almost 9 years ago - 1 comment

#107 - Check if matplotlib is present in PBstat.py

Pull Request - State: closed - Opened by HubLot almost 9 years ago

#106 - [WIP] K-means

Pull Request - State: open - Opened by jbarnoud almost 9 years ago - 22 comments
Labels: enhancement, clustering

#105 - Doc is broken on Read the docs

Issue - State: closed - Opened by jbarnoud about 9 years ago - 1 comment
Labels: documentation

#104 - Document the limitation of the PDB and PDBx parsers

Issue - State: open - Opened by jbarnoud about 9 years ago
Labels: documentation

#103 - Get a doi

Issue - State: closed - Opened by jbarnoud about 9 years ago - 1 comment

#102 - Create package for Anaconda

Issue - State: closed - Opened by jbarnoud about 9 years ago - 1 comment
Labels: install

#101 - Update the install documentation

Issue - State: closed - Opened by jbarnoud about 9 years ago - 1 comment
Labels: documentation, install

#100 - Cannot_Generate_Plots_Using_PBstat.py

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

#99 - [WIP] Group demo files

Pull Request - State: closed - Opened by jbarnoud about 9 years ago - 2 comments

#98 - Have Travis build the doc

Pull Request - State: closed - Opened by jbarnoud about 9 years ago - 1 comment

#97 - Regroup demo files ?

Issue - State: closed - Opened by HubLot about 9 years ago - 4 comments

#96 - [WIP] Packaging Pbxplore

Pull Request - State: closed - Opened by HubLot about 9 years ago - 10 comments

#95 - folder demo_paper

Issue - State: closed - Opened by HubLot about 9 years ago - 4 comments

#94 - Add a link to the API doc to the README

Pull Request - State: closed - Opened by jbarnoud about 9 years ago

#93 - Fix few issues with Sphinx

Pull Request - State: closed - Opened by jbarnoud about 9 years ago

#90 - Set Readthedocs

Issue - State: closed - Opened by jbarnoud about 9 years ago - 7 comments
Labels: documentation

#89 - Ignore the content of lines which starts by a comment when comparing files

Pull Request - State: closed - Opened by HubLot about 9 years ago

#87 - Document the dependancies for the concerned functions

Issue - State: closed - Opened by jbarnoud about 9 years ago - 1 comment
Labels: documentation

#67 - Consider using docker to ease installation, distribution and OS compatibility

Issue - State: open - Opened by jmaupetit over 9 years ago - 6 comments
Labels: install

#66 - PBclust is not compatible with most recent versions of R

Issue - State: closed - Opened by jbarnoud over 9 years ago - 12 comments
Labels: wontfix, clustering

#64 - PB-k means something / hc issue

Issue - State: open - Opened by alexdb27 over 9 years ago - 25 comments
Labels: clustering

#31 - clusters

Issue - State: closed - Opened by alexdb27 over 9 years ago - 10 comments
Labels: wontfix, documentation, clustering

#30 - Mac

Issue - State: closed - Opened by alexdb27 over 9 years ago - 6 comments
Labels: documentation

#22 - PBxplore should be available on Pypi

Issue - State: closed - Opened by jbarnoud almost 10 years ago - 3 comments
Labels: enhancement, install

#21 - Make PBxplore installable

Issue - State: closed - Opened by jbarnoud almost 10 years ago - 1 comment
Labels: enhancement, install

#13 - Get rid of R

Issue - State: closed - Opened by jbarnoud about 10 years ago - 11 comments
Labels: duplicate, enhancement

GitHub / pierrepo/PBxplore issues and pull requests