Delete unused variables

dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.

MIT License

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Delete unused variables #124

Closed piterand closed 1 year ago

piterand commented 1 year ago

I have deleted all unused variables. Please, review these changes, and decide what to do with these lines.

piterand commented 1 year ago

Also in src/rpbp/analysis/profile_construction/create_read_length_orf_profiles.py: in line 142 format(...) has unused arguments at position(s): 8 and in line 162 format(...) has unused arguments at position(s): 5. Can you check these lines, please?

eboileau commented 1 year ago

Regarding https://github.com/dieterich-lab/rp-bp/pull/124/commits/076f3e4763e016185d77937186b09b93f79d76cd, I think most of them are fine, except:

src/rpbp/analysis/profile_construction/create_read_length_metagene_profile_plot.py, where removed lines modify axes created at fig, axes = plt.subplots(ncols=2, figsize=(10, 5), sharey=True) line 158, so no changes should be made.
src/rpbp/analysis/profile_construction/visualize_read_filtering_counts.py, where mpl_utils.create_stacked_bar_graph modify ax, so no changes should be made.
src/rpbp/analysis/rpbp_predictions/visualize_orf_type_metagene_profiles.py, where removed lines modify axes created at fig, axes = plt.subplots(ncols=3, sharey=True, sharex=True, figsize=(10, 5)) line 92, so no changes should be made.

eboileau commented 1 year ago

Regarding unused arguments, indeed the last one is missing, I can correct that.

eboileau commented 1 year ago

Can you commit back the unmodified files, or is there a way for me to cherry pick only parts of your commit? Would I need to split your commit? Never done that before...

piterand commented 1 year ago

Can you commit back the unmodified files, or is there a way for me to cherry pick only parts of your commit? Would I need to split your commit? Never done that before...

Here you can accept or decline all changes at once. I will submit a new commit with the changes that you mention above here.

piterand commented 1 year ago

Can you commit back the unmodified files, or is there a way for me to cherry pick only parts of your commit? Would I need to split your commit? Never done that before...

I back all changes in these 3 files: src/rpbp/analysis/profile_construction/create_read_length_metagene_profile_plot.py src/rpbp/analysis/profile_construction/visualize_read_filtering_counts.py, src/rpbp/analysis/rpbp_predictions/visualize_orf_type_metagene_profiles.py

eboileau commented 1 year ago

Great, thanks. I will merge this PR, fix the unused arguments, and push.

piterand commented 1 year ago

Great, thanks. I will merge this PR, fix the unused arguments, and push.

Should I preserve logging_str arguments or delete them from cmd?

eboileau commented 1 year ago

I just merged this PR, and manually added your last commit hide F841 and F523 errors. The unused arguments has been fixed.