Use bar_intervall instead of ntpr for parsing AMBER MBAR timestamps #429
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #429 +/- ##
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Coverage 98.80% 98.80%
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Files 28 28
Lines 2008 2010 +2
Branches 356 356
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+ Hits 1984 1986 +2
Misses 2 2
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Thanks for the PR, do you mind
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I assume the test file needs to be put in https://github.com/alchemistry/alchemtest. Could you help me with it? see the output attached! |
| @@ -282,3 +282,13 @@ def test_concatenated_amber_dhdl(tmp_path): | |||
| match="TI Energy detected after the TIMINGS section.", | |||
| ): | |||
| extract(tmp_path / "amber.out", 298) | |||
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| def test_correct_timestamp_u_nk(testfiles): | |||
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@yuxuanzhuang Thanks for adding the test. I think it is fine to just adapt this test to use an existing file and check if the timestep is correct would be enough. No need to add a new file.
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thanks. then I think test_u_nk_time_reading(single_u_nk) is already checking it.
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Ok, so it was already checked, I was thinking something along the line of
def test_u_nk_time_reading_bar_intervall(single_u_nk, tmp_path):
"""Test if time information is read correctly when extracting u_nk"""
with bz2.open(single_u_nk, 'rt') as bz2_file:
content = bz2_file.read()
with open(tmp_path / 'amber.log', 'w') as text_file:
text_file.write(content.replace("bar_intervall = 1000", "bar_intervall = 100"))
u_nk = extract_u_nk(tmp_path / 'amber.log', T=298.0)
assert_allclose(u_nk.index.values[0][0], ??)
Then you show that changing the bar_intervall in the log file will change the time stamp in the generated dataframe.
AUTHORS
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| @@ -59,3 +59,6 @@ Chronological list of authors | |||
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| 2024 | |||
| - Jennifer A. Clark (@jaclark5) | |||
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| 2025 | |||
| - Yuxuan Zhuang (@yuxuanzhuang) | |||
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blank line after this
Fix #428