Linting iii #235
Linting iii #235
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This reverts commit 35dec99.
| @@ -1,4 +1,4 @@ | |||
| import os | |||
| from pathlib import Path | |||
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Is this a thing? that Path is prefered over os?
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yes.. imho it makes path operations much more readable,
I especially like the overloading of the / operator when it comes to using it (e.g. Path("/home/") / "user").
I especially dislike the overloading of the / operator when it comes to mocking it :-)
| @@ -18,8 +18,8 @@ | |||
| warnings.filterwarnings("always") | |||
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| mod_to_unimod_dict = {} | |||
| for mod_name, unimod_id in MOD_DF[["mod_name", "unimod_id"]].values: | |||
| unimod_id = int(unimod_id) | |||
| for mod_name, unimod_id_ in MOD_DF[["mod_name", "unimod_id"]].to_numpy(): | |||
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is this suffix thing a known pattern? I only now it as private prefix
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I use it to avoid name clashes, e.g. with built-ins or other variables
| @@ -292,7 +292,7 @@ def _lookup_modification( | |||
| The name of the matched modification in alphabase format. | |||
| """ | |||
| mass_distance = mod_annotated_df["mass"].values - mass_observed | |||
| mass_distance = mod_annotated_df["mass"].to_numpy() - mass_observed | |||
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This is a bit of a tricky change. It might have some performance implications as it performas a copy.
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If you wish, we can disable the rule and revert? however, pandas docs recommend using to_numpy()
https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.values.html
| frag_num -= 1 | ||
| elif frag_type in "xyz": | ||
| frag_num = nAA - frag_num - 1 | ||
| ].to_numpy(): |
manual fixes for a first bunch of linting rules ..
see individual commits
edit: made all start imports in notebooks explicit as tests started to fail due to removal of
osfrom some readers