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Document code structure in dev guide #832

Merged
merged 5 commits into from Jan 11, 2020
Merged

Document code structure in dev guide #832

merged 5 commits into from Jan 11, 2020

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@luizirber
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luizirber commented Jan 7, 2020

First draft of documenting code structure, wondering how much detail to add (describing all files seems a bit excessive and easy to get outdated).

Fixes #831

Checklist

  • Is it mergeable?
  • make test Did it pass the tests?
  • make coverage Is the new code covered?
  • Did it change the command-line interface? Only additions are allowed
    without a major version increment. Changing file formats also requires a
    major version number increment.
  • Was a spellchecker run on the source code and documentation after
    changes were made?
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codecov bot commented Jan 7, 2020

Codecov Report

Merging #832 into master will increase coverage by 0.23%.
The diff coverage is 97.46%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #832      +/-   ##
==========================================
+ Coverage   79.13%   79.36%   +0.23%     
==========================================
  Files          83       83              
  Lines        7016     7017       +1     
  Branches      469      469              
==========================================
+ Hits         5552     5569      +17     
+ Misses       1164     1148      -16     
  Partials      300      300
Flag Coverage Δ
#pytests 89.95% <97.46%> (ø) ⬆️
#rusttests 48.71% <ø> (ø) ⬆️
Impacted Files Coverage Δ
sourmash/lca/command_summarize.py 80.24% <ø> (ø) ⬆️
sourmash/commands.py 83.69% <ø> (ø) ⬆️
sourmash/lca/command_rankinfo.py 89.13% <ø> (ø) ⬆️
sourmash/lca/command_compare_csv.py 92.3% <ø> (ø) ⬆️
sourmash/sourmash_args.py 96.03% <ø> (ø) ⬆️
sourmash/sbt.py 86.61% <ø> (+0.29%) ⬆️
sourmash/lca/command_classify.py 84.21% <ø> (ø) ⬆️
sourmash/lca/command_gather.py 83.76% <ø> (ø) ⬆️
sourmash/__main__.py 92.3% <100%> (ø) ⬆️
sourmash/cli/lca/classify.py 100% <100%> (ø) ⬆️
... and 58 more

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luizirber commented Jan 7, 2020

I also plan to write about py-spy and heaptrack for CPU and memory profiling, but probably as blog posts and link to doc/developer.md. Both have been hugely important leading to 3.0 and for changes that have been landing in master for 3.1.

@ctb
ctb approved these changes Jan 8, 2020
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ctb left a comment

This looks great! I agree with you that describing all files is excessive and will get out of date, tho, unless we somehow automatically flag file name/directory changes (which also seems excessive).

luizirber added 3 commits Jan 10, 2020
@luizirber luizirber changed the title [WIP] Document code structure in dev guide Document code structure in dev guide Jan 11, 2020
@luizirber luizirber merged commit 86e1105 into master Jan 11, 2020
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@luizirber luizirber deleted the doc_code_structure branch Jan 11, 2020
@luizirber luizirber added this to the 3.1 milestone Jan 14, 2020
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