NAMD parser for FEP files #72
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For issue #7 |
Codecov Report
@@ Coverage Diff @@
## master #72 +/- ##
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+ Coverage 98.33% 98.42% +0.09%
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Files 10 11 +1
Lines 539 572 +33
Branches 105 109 +4
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+ Hits 530 563 +33
Misses 4 4
Partials 5 5
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This looks very nice already. Apart from the one comment that I found on a quick parse, please also integrate your code into the docs:
- add a file to docs/parsing/ (follow the examples), name it
alchemlyb.parsing.namd.rst - add "namd" to the bottom of docs/parsing.rst
- Try building the docs with
python setup.py build_sphinxand look at the locally generated HTML files (see output to find path to the top levelindex.html)
src/alchemlyb/parsing/namd.py
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| def extract_dHdl(fepout): |
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If it's not implemented then leave it out, better than a pass and weird failures down the line.
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Also, removing it will improve your coverage ;-)
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Got it, I'll take out this placeholder function.
This pull request parses NAMD .fepout files to extract the work values (
dEcolumn) into a pandas dataframe in line with the overall API proposal. I also added a few tests to check the dimensions of the imported data and verify the results of BAR analysis on the data inalchemtest.