Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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
#238 - setup.py metadata does not include all supported Python versions
Issue -
State: closed - Opened by orbeckst over 1 year ago
#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
#196 - some tests fail with "FileNotFoundError: [Errno 2] No such file or directory: '/home/travis/miniconda/envs/test/bin.AVX2_256'"
Issue -
State: closed - Opened by orbeckst about 3 years ago
- 1 comment
Labels: tests
#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