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wehs7661 / ensemble_md

A python package for performing GROMACS simulation ensembles
MIT License
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Fixed the bugs relevant to coordinate modification #21

Closed wehs7661 closed 1 year ago

wehs7661 commented 1 year ago

This PR aims to resolve issue #15 and is a part of the work in the project EEXE for serial mutations.

wehs7661 commented 1 year ago

Note that the recent builds of CI and documentation have been failing because a recent update in mdtraj broke the installation process. (See the issue https://github.com/mdtraj/mdtraj/issues/1800.) Using mdtraj==1.9.7 did not work and we'll probably just wait for the fix of the issue on the side of mdtraj. If the issue persists longer, we might want to consider temporarily adjusting the dependencies of the package to pass the builds, as the minimal case of data analysis might not need mdtraj and pyemma (which requires installing mdtraj.)

mattwthompson commented 1 year ago

An MDTraj release probably won't happen until the weekend, you might want to add something like Cython==0.29.36 into your build system 😅

wehs7661 commented 1 year ago

Thanks for the suggestion @mattwthompson! I wrote the comment above just to provide some context, and there is no rush. I'll use Cython==0.29.36 in the next commit. Looking forward to the new MDTraj release!

mattwthompson commented 1 year ago

No harm done, just want to make sure upstream issues aren't holding you back!

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 31.46% and project coverage change: -1.06 :warning:

Comparison is base (164bb98) 60.56% compared to head (3d2a63d) 59.50%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #21 +/- ## ========================================== - Coverage 60.56% 59.50% -1.06% ========================================== Files 7 7 Lines 1321 1363 +42 ========================================== + Hits 800 811 +11 - Misses 521 552 +31 ``` | [Impacted Files](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/21?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Wei-Tse+Hsu) | Coverage Δ | | |---|---|---| | [ensemble\_md/utils/utils.py](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/21?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Wei-Tse+Hsu#diff-ZW5zZW1ibGVfbWQvdXRpbHMvdXRpbHMucHk=) | `59.00% <16.66%> (-9.30%)` | :arrow_down: | | [ensemble\_md/ensemble\_EXE.py](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/21?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Wei-Tse+Hsu#diff-ZW5zZW1ibGVfbWQvZW5zZW1ibGVfRVhFLnB5) | `77.77% <35.21%> (-1.91%)` | :arrow_down: |

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