Ecosyste.ms: Issues

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GitHub / Becksteinlab/GromacsWrapper issues and pull requests

#287 - codecov coverage dropped to 0%

Issue - State: open - Opened by orbeckst 14 days ago
Labels: CI

#286 - fix "DeprecationWarning: invalid escape sequence '\s'"

Pull Request - State: closed - Opened by orbeckst 14 days ago - 1 comment

#285 - DeprecationWarning: invalid escape sequence '\s'

Issue - State: closed - Opened by orbeckst 14 days ago - 1 comment

#284 - use importlib.resources instead of pkg_resources

Pull Request - State: closed - Opened by orbeckst 15 days ago - 3 comments

#282 - replace pkg_resources everywhere

Issue - State: closed - Opened by orbeckst 15 days ago - 2 comments
Labels: tests, configuration, refactor

#281 - release 0.9.0

Issue - State: closed - Opened by orbeckst 15 days ago - 3 comments
Labels: release

#280 - full pyproject.toml support

Pull Request - State: closed - Opened by orbeckst 16 days ago - 1 comment

#279 - no console scripts installed in 0.9.0

Issue - State: open - Opened by orbeckst 16 days ago - 2 comments
Labels: wontfix

#278 - update to using pyproject.toml only

Issue - State: closed - Opened by orbeckst 16 days ago

#277 - remove support for old and ancient python versions

Issue - State: closed - Opened by orbeckst 16 days ago - 2 comments

#276 - "Unknown command-line option -include" with cbook.add_mdp_includes()

Issue - State: open - Opened by a-ws-m 19 days ago - 1 comment

#275 - fix TestAttributeDict

Pull Request - State: closed - Opened by njzjz about 2 months ago - 1 comment

#274 - fix `SyntaxWarning: invalid escape sequence`

Pull Request - State: closed - Opened by njzjz about 2 months ago - 1 comment

#273 - refactor: use importlib instead of pkg_resources

Pull Request - State: closed - Opened by jandom 8 months ago - 5 comments

#272 - ci: try a simple ci.yaml (experiment)

Pull Request - State: closed - Opened by jandom 8 months ago - 4 comments

#271 - fix #263: No module named 'pkg_resources'

Pull Request - State: closed - Opened by jandom 8 months ago - 1 comment

#270 - fix #252: handle keyboard interrupts

Pull Request - State: closed - Opened by jandom 8 months ago - 2 comments

#269 - fix #214: AttributeDict does not support hasattr

Pull Request - State: closed - Opened by jandom 8 months ago - 3 comments

#268 - updated CI environments

Pull Request - State: closed - Opened by orbeckst 8 months ago - 1 comment

#267 - RTD failing

Issue - State: closed - Opened by orbeckst 8 months ago - 1 comment
Labels: documentation, bug, CI

#266 - updated to versioneer 0.29

Pull Request - State: closed - Opened by orbeckst 8 months ago - 1 comment

#265 - removed support for Python <= 3.7

Pull Request - State: closed - Opened by orbeckst 8 months ago - 10 comments

#264 - fix #216: angle parameters are not being read from topology file

Pull Request - State: closed - Opened by jandom 8 months ago - 12 comments

#263 - Python 3.12: No module named 'pkg_resources'

Issue - State: closed - Opened by njzjz 8 months ago - 5 comments
Labels: installation, bug, Python3

#262 - AttributeError: module 'gromacs.tools' has no attribute 'Grompp' when using `gmx_mpi` only

Issue - State: open - Opened by oliviertrottier 8 months ago - 6 comments
Labels: documentation, configuration

#261 - angle parameters are not being read from topology file

Issue - State: closed - Opened by brgstfzj 9 months ago - 9 comments
Labels: fileformats, bug

#259 - drop support for very old Python versions

Issue - State: closed - Opened by orbeckst 10 months ago
Labels: Python3

#258 - updated RTD config

Pull Request - State: closed - Opened by orbeckst 10 months ago - 1 comment

#257 - RTD docs build failed

Issue - State: closed - Opened by orbeckst 10 months ago
Labels: documentation

#256 - make final 0.8.x release

Issue - State: closed - Opened by orbeckst 10 months ago

#255 - test GROMACS 2023.1 (and use Py 3.11 for the all version test)

Pull Request - State: closed - Opened by orbeckst 10 months ago - 1 comment

#254 - modernized CI workflow

Pull Request - State: closed - Opened by orbeckst 10 months ago - 2 comments

#253 - mamba installation fails on macOS GH runner

Issue - State: closed - Opened by orbeckst 10 months ago - 1 comment

#252 - Handle KeyboardInterrupts when using `MDRunner.run()`

Issue - State: closed - Opened by a-ws-m 10 months ago - 1 comment

#251 - add GROMACS 2023 to test matrix

Issue - State: closed - Opened by orbeckst 10 months ago - 1 comment
Labels: tests

#250 - use pandas.testing.assert_frame_equal

Pull Request - State: closed - Opened by orbeckst 10 months ago - 4 comments

#249 - do_dssp was replaced by gmx dssp

Issue - State: closed - Opened by orbeckst 10 months ago - 1 comment
Labels: bug

#248 - `pandas.util.testing import assert_frame_equal` not found

Issue - State: closed - Opened by orbeckst 10 months ago - 1 comment
Labels: tests, bug

#247 - Blacken

Pull Request - State: closed - Opened by orbeckst 10 months ago - 5 comments

#246 - use black for formatting

Issue - State: closed - Opened by orbeckst 10 months ago
Labels: refactor

#244 - unclosed file in `config.py`

Issue - State: closed - Opened by njzjz 11 months ago - 1 comment

#243 - genion option

Issue - State: closed - Opened by yychuang about 1 year ago - 1 comment

#242 - Legend and title are not shown

Issue - State: closed - Opened by pacho2 about 1 year ago - 4 comments

#241 - "neutral" option in gromacs.genion

Issue - State: closed - Opened by marcodigennaro about 1 year ago - 3 comments

#239 - release 0.8.4

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

#236 - missing Improp. Dihedrals section in AMBER FF topology tests

Issue - State: closed - Opened by orbeckst over 1 year ago - 1 comment
Labels: bug

#235 - update for Python >= 3.10

Issue - State: closed - Opened by orbeckst over 1 year ago - 1 comment

#234 - fix removal of deprecated np.bool

Issue - State: closed - Opened by orbeckst over 1 year ago

#233 - release 0.8.3

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

#232 - rename master branch to main

Issue - State: closed - Opened by orbeckst over 1 year ago - 2 comments

#231 - xpm read not properly

Issue - State: closed - Opened by aspitaleri over 1 year ago - 1 comment

#229 - replace deprecated logger.warn() with logger.warning()

Issue - State: closed - Opened by orbeckst almost 2 years ago - 1 comment

#227 - Hi there. error for gmx.pdb2gmx()

Issue - State: closed - Opened by lichman0405 almost 2 years ago - 1 comment
Labels: question

#219 - Use of try option with gmx insert-molecules?

Issue - State: closed - Opened by dpadula85 about 2 years ago - 3 comments
Labels: question

#218 - use gromologist?

Issue - State: open - Opened by orbeckst about 2 years ago - 6 comments
Labels: enhancement

#217 - release 0.8.2

Issue - State: closed - Opened by orbeckst almost 3 years ago - 3 comments
Labels: release

#216 - use and document conda packages

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

#215 - update installation instructions for conda

Issue - State: closed - Opened by orbeckst almost 3 years ago
Labels: installation, documentation

#214 - Can we redirect the output of terminal to .log or .txt file?

Issue - State: closed - Opened by MeetXinZhang almost 3 years ago - 1 comment

#213 - replaced logger.warn() (DEPRECATED) with logger.warning()

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

#212 - fixed stop_logging() NameError

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

#211 - stop_logging() fails with NameError

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

#210 - AttributeDict does not support hasattr()

Issue - State: closed - Opened by orbeckst almost 3 years ago - 1 comment
Labels: bug

#209 - codecov failure "'Too many uploads to this commit.'"

Issue - State: closed - Opened by orbeckst almost 3 years ago - 2 comments
Labels: tests

#208 - Solvate function doesn't support nn and np input

Issue - State: open - Opened by VOD555 almost 3 years ago - 4 comments
Labels: enhancement

#207 - Finalize for 0.8.1 release

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

#206 - doc updates

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

#205 - extend testing

Pull Request - State: closed - Opened by orbeckst almost 3 years ago - 2 comments

#204 - cut release 0.8.1

Issue - State: closed - Opened by orbeckst almost 3 years ago
Labels: release

#203 - test on MacOS

Issue - State: closed - Opened by orbeckst almost 3 years ago
Labels: tests

#202 - test multiple GROMACS versions

Issue - State: closed - Opened by orbeckst almost 3 years ago
Labels: tests

#201 - switch CI from Travis to GitHub actions

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

#200 - transition from Travis CI to GitHub actions

Issue - State: closed - Opened by orbeckst almost 3 years ago
Labels: tests

#199 - fix cbook.portable_topology() for Python 2/3

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

#198 - Python 3 failure on tempfile: TypeError

Issue - State: closed - Opened by orbeckst almost 3 years ago - 1 comment
Labels: bug, Python3

#197 - How to use GROMACS wrapper with `mpirun`?

Issue - State: closed - Opened by wehs7661 almost 3 years ago - 5 comments
Labels: question

#195 - fix xvg plotting with matplotlib colors/cmaps

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

#194 - xvg.plot_coarsened fails with incompatible matplotlib colors

Issue - State: closed - Opened by orbeckst about 3 years ago - 1 comment
Labels: fileformats, tests, bug, Python3

#193 - problem with pickle

Issue - State: open - Opened by PolyachenkoYA over 3 years ago - 4 comments
Labels: fileformats, bug

#192 - Fix Readme, to have the same PDB ID

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

#191 - How to run mdrun with mpiexec?

Issue - State: closed - Opened by dpadula85 over 3 years ago - 3 comments
Labels: documentation, question

#190 - update CHANGES

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

#189 - Made tests uninstallable

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

#188 - Fix file open

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

#187 - xvg.plot fix

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

#186 - additional checks for gmx output when importing

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

#185 - CI is broken aka "need to update so that gw works with new packages"

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

#184 - func_name support for python 3.0 added in xvg.py

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

#183 - func.func_name is not used in Python 3

Issue - State: closed - Opened by PolyachenkoYA almost 4 years ago - 4 comments
Labels: bug, Python3

#182 - Package installs 'tests' package which is likely a bug in the build system

Issue - State: closed - Opened by pacho2 about 4 years ago - 4 comments
Labels: installation, bug

#181 - Bug in Python3 - Capture Output File

Issue - State: closed - Opened by rochoa85 over 4 years ago - 2 comments
Labels: bug, Python3

#180 - MDP files should not be written as binary

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

#179 - various fixes due to upstream updates

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

#178 - how to handle interactive data analysis?

Issue - State: closed - Opened by Wade2016 over 4 years ago - 2 comments

#177 - MissingSectionHeaderError:

Issue - State: closed - Opened by poojitharamachandra about 5 years ago - 3 comments

#176 - expand test matrix

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

#175 - new virtual tool gromacs.tools.Release

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

#174 - don't call `logger` directly, fix #173

Pull Request - State: closed - Opened by theavey about 5 years ago - 2 comments