wehs7661 / ensemble_md

A python package for performing GROMACS simulation ensembles
MIT License
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Rename the EEXE method as REXEE method #27

Closed wehs7661 closed 1 year ago

wehs7661 commented 1 year ago

We decided to rename the EEXE method as REXEE, which stands for replica exchange (REX) of expanded ensembles (EE). This requires updating the names of some modules and classes, as well as the docstrings and the documentation.

codecov[bot] commented 1 year ago

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (9cb910f) 55.09% compared to head (a95ea2d) 55.09%. Report is 5 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #27 +/- ## ======================================= Coverage 55.09% 55.09% ======================================= Files 7 7 Lines 1552 1552 ======================================= Hits 855 855 Misses 697 697 ``` | [Files](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/27?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/analysis/analyze\_matrix.py](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Wei-Tse+Hsu#diff-ZW5zZW1ibGVfbWQvYW5hbHlzaXMvYW5hbHl6ZV9tYXRyaXgucHk=) | `99.08% <ø> (ø)` | | | [ensemble\_md/replica\_exchange\_EE.py](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Wei-Tse+Hsu#diff-ZW5zZW1ibGVfbWQvcmVwbGljYV9leGNoYW5nZV9FRS5weQ==) | `74.13% <100.00%> (ø)` | | | [ensemble\_md/utils/gmx\_parser.py](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Wei-Tse+Hsu#diff-ZW5zZW1ibGVfbWQvdXRpbHMvZ214X3BhcnNlci5weQ==) | `85.86% <ø> (ø)` | | | [ensemble\_md/utils/utils.py](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Wei-Tse+Hsu#diff-ZW5zZW1ibGVfbWQvdXRpbHMvdXRpbHMucHk=) | `63.44% <100.00%> (ø)` | | | [ensemble\_md/analysis/analyze\_traj.py](https://app.codecov.io/gh/wehs7661/ensemble_md/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Wei-Tse+Hsu#diff-ZW5zZW1ibGVfbWQvYW5hbHlzaXMvYW5hbHl6ZV90cmFqLnB5) | `5.49% <50.00%> (ø)` | |

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