patrickfuchs/buildH issues and pull requests

#167 - Fix pdb writer

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

#166 - add the correct myst extension for math expressions

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

#165 - Latex formulas are not rendered correctly on readthedoc

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

#164 - Missing carbon atoms

Issue - State: closed - Opened by larabort over 2 years ago - 5 comments

#163 - Update Read the Docs configuration (automatic)

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

#162 - Fix beta H reconstruction in PS lipids

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

#161 - Add an example of ignore_CH3s to Notebook04

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

#160 - Add doc for -igch3 option

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

#159 - Beta hydrogens in PS

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

#158 - Add feature to ignore CH3 groups

Pull Request - State: closed - Opened by HubLot almost 3 years ago - 9 comments

#157 - CH3 groups

Issue - State: closed - Opened by ohsOllila almost 3 years ago - 8 comments
Labels: enhancement

#156 - Update Software Heritage link

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

#155 - Update swh link to the new version 1.6.0

Issue - State: closed - Opened by patrickfuchs about 3 years ago

#154 - Improve docstrings in buildh files

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

#153 - Simplify workflow file and add support of Python 3.9

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

#152 - Test and update to MDAnalysis 2.0.0

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

#151 - Python versions and dependencies.

Issue - State: closed - Opened by ojeda-e about 3 years ago - 3 comments

#150 - Improvements on API documentation

Issue - State: closed - Opened by ojeda-e about 3 years ago - 2 comments

#149 - Minor wording or grammar nitpicks with paper

Issue - State: closed - Opened by lilyminium about 3 years ago - 2 comments

#148 - Which OSs are supported?

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

#147 - Contributing credit?

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

#146 - Which three things? (docs)

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

#145 - Fixing box dimensions and trajectory output with Hs

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

#144 - [Request] Add documentation for building from source with minimal dependencies

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

#143 - Update release and archive IDs

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

#142 - Fix xtc writer

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

#141 - Fix python version for readthedocs

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

#140 - Doc no longer compiles

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

#139 - Add support for DPPC CHARMM36UA

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

#138 - Limit python version

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

#137 - Restrict BuildH for Python >= 3.6 and <= 3.8

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

#136 - add dt information on the output trajectory

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

#135 - add support for different lipids

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

#134 - Update MDAnalysis to 1.1.1

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 10 comments

#133 - Add references to archives

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

#132 - Add CLI prompt

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

#131 - add pandoc installation

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

#130 - Update doc and notebooks with -v option

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

#129 - Archive repository to Software Heritage

Pull Request - State: closed - Opened by pierrepo over 3 years ago - 9 comments

#128 - Automate archiving in Software Heritage upon release

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

#127 - Update documentation regarding -v option

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

#126 - Test: new release and automatic package deployment

Issue - State: closed - Opened by pierrepo over 3 years ago - 11 comments

#125 - Add link to doc in the upper right corner of the GitHub page

Issue - State: closed - Opened by pierrepo over 3 years ago - 8 comments

#124 - Add community guidelines

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

#123 - Edit paper text / fix some typos

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

#122 - Create GitHub action to build and publish package on PyPI

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

#121 - Handle warnings

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

#120 - Add version option in command line

Pull Request - State: closed - Opened by pierrepo over 3 years ago - 5 comments

#119 - Add `-v` and `--version` options

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

#118 - Update authors order

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

#117 - Update authors order

Issue - State: closed - Opened by pierrepo over 3 years ago
Labels: packaging, paper

#116 - Add community guidelines

Issue - State: closed - Opened by pierrepo over 3 years ago - 1 comment
Labels: documentation, paper

#115 - Update zenodo swh badges

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

#114 - Paper Modifications

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

#113 - Clean subtitles hierarchy

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

#112 - Bug in hierarchical organization of items in doc

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

#111 - Add logo in left menu header

Pull Request - State: closed - Opened by pierrepo over 3 years ago - 9 comments

#110 - Reorder C-H in Berger cholesterol def file

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

#109 - JOSS paper

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 10 comments
Labels: paper

#108 - buildH logo

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 9 comments
Labels: documentation

#107 - Proposal of doc's modifications

Pull Request - State: closed - Opened by HubLot over 3 years ago - 13 comments

#106 - Update H naming convention

Issue - State: closed - Opened by patrickfuchs over 3 years ago
Labels: documentation

#105 - Update doc and procedure for Bioconda package

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

#104 - Fix setup.cfg to include json files

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

#103 - Folder "buildh/lipids/" is missing when building buildh archive

Issue - State: closed - Opened by HubLot over 3 years ago
Labels: bug, packaging

#102 - Fix readthedocs sphinx book theme

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

#101 - Compilation of documentation with MyST on readthedocs

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 5 comments
Labels: bug, documentation

#100 - More expicit message when def and json file don't match.

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

#99 - Fix residue number exceeding 9999

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

#98 - Residue number in PDB > 9999

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 1 comment
Labels: bug

#97 - Register buildH to bio.tools

Issue - State: closed - Opened by pierrepo over 3 years ago - 3 comments
Labels: Registry & archive

#96 - Be more explicit on error message

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

#95 - Fix typo in env name

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

#94 - Add an example on a mixture of lipids

Issue - State: closed - Opened by patrickfuchs over 3 years ago
Labels: documentation

#93 - Use MyST parser to handle LaTeX equation in Sphinx

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

#92 - Automate PyPI package deployment upon release

Issue - State: closed - Opened by pierrepo over 3 years ago - 1 comment
Labels: packaging

#91 - Update license text

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

#90 - Output test files to temp directory

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

#89 - Simplify CH reconstruction

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

#88 - Simplify CH calculation in hydrogens.py

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

#87 - add tests for UI module

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

#86 - Getting rid of MDAnalysis warnings

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 20 comments

#85 - Order parameter formula

Issue - State: closed - Opened by patrickfuchs over 3 years ago
Labels: documentation

#84 - Equations in the doc

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 6 comments
Labels: documentation

#83 - Write doc about command line options

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 1 comment
Labels: documentation

#82 - Update doc about Numba

Issue - State: closed - Opened by patrickfuchs over 3 years ago - 1 comment
Labels: documentation

#81 - Implement feature to use buildh as a module

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

#79 - Numba Optimization

Pull Request - State: closed - Opened by HubLot over 3 years ago - 9 comments

#77 - Implement a way to use buildH as a simple module

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

#74 - Implement cholesterol

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

#73 - Advertise buildH

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

#67 - Document the use of the json files

Issue - State: closed - Opened by HubLot almost 4 years ago - 1 comment
Labels: documentation

#50 - Specify the type of trajectory supported

Issue - State: closed - Opened by HubLot almost 4 years ago - 1 comment
Labels: documentation

#44 - Add json files for other UA force fields and lipids

Issue - State: open - Opened by patrickfuchs almost 4 years ago - 8 comments
Labels: enhancement

#38 - Update licence text

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

#34 - Register buildH to Software Heritage

Issue - State: closed - Opened by pierrepo almost 4 years ago
Labels: Registry & archive

#21 - Update doc (Calculate OP on a subpart)

Issue - State: closed - Opened by patrickfuchs almost 5 years ago
Labels: documentation

#18 - Create Bioconda package and update procedure

Issue - State: closed - Opened by pierrepo almost 5 years ago - 3 comments
Labels: packaging

#15 - Add a message that PBC are not taken (yet) into account

Issue - State: closed - Opened by patrickfuchs about 5 years ago - 2 comments
Labels: documentation

#10 - Update vectors.png

Issue - State: closed - Opened by patrickfuchs over 5 years ago
Labels: documentation

GitHub / patrickfuchs/buildH issues and pull requests