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[REF,ENH] Adds new abagen.probes module #67

Merged
merged 6 commits into from
Aug 16, 2019
Merged

[REF,ENH] Adds new abagen.probes module #67

merged 6 commits into from
Aug 16, 2019

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rmarkello
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@rmarkello rmarkello commented Aug 6, 2019

Closes #51.

Moves all functions operating on probes to abagen.probes module (i.e., reannotate_probes() and filter_probes(), previously in abagen.process) and adds new probe selection methods (previously limited to differential stability).

New selection methods have been integrated into primary workflow (i.e., abagen.get_expression()) via the optional probe_selection keyword argument. Relevant references and description of the different methods have been added to the Notes of the doc-strings.

To do:

  • Add tests for all new probe selection methods
  • Update docs to reflect new options

Moves all functions operating on probes to `abagen.probes` module (i.e.,
reannotate_probes() and filter_probes(), previously in `abagen.process`)
and adds new probe selection methods (previously limited to differential
stability).

New selection methods have been integrated into primary workflow (i.e.,
abagen.get_expression()) via the optional `probe_selection` keyword
argument. Relevant references and description of the different methods
have been added to the Notes of the doc-strings.
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coveralls commented Aug 6, 2019

Pull Request Test Coverage Report for Build 257

  • 204 of 209 (97.61%) changed or added relevant lines in 4 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage increased (+0.3%) to 95.315%

Changes Missing Coverage Covered Lines Changed/Added Lines %
abagen/allen.py 12 14 85.71%
abagen/probes.py 102 105 97.14%
Totals Coverage Status
Change from base Build 247: 0.3%
Covered Lines: 1119
Relevant Lines: 1174

💛 - Coveralls

@rmarkello
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rmarkello commented Aug 7, 2019

Despite having no new tests, the builds are failing due to timeout errors trying to connect to the Allen Insitute API... Seems a bit strange, but hopefully it was an isolated event 🤞

Perhaps it would be worthwhile investigating how to run the test suite on simulated / test data so we don't have to pull everything from the Allen Institute every time? Will open an issue...

Edit: issue #68 created to address this.

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codecov bot commented Aug 14, 2019

Codecov Report

Merging #67 into master will decrease coverage by 3.29%.
The diff coverage is 67.47%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master      #67     +/-   ##
=========================================
- Coverage   95.01%   91.72%   -3.3%     
=========================================
  Files          24       25      +1     
  Lines        1024     1088     +64     
=========================================
+ Hits          973      998     +25     
- Misses         51       90     +39
Impacted Files Coverage Δ
abagen/process.py 100% <100%> (ø) ⬆️
abagen/probes.py 62.74% <62.74%> (ø)
abagen/allen.py 98.34% <85.71%> (-0.83%) ⬇️

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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codecov bot commented Aug 14, 2019

Codecov Report

Merging #67 into master will increase coverage by 0.29%.
The diff coverage is 97.6%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #67      +/-   ##
==========================================
+ Coverage   95.01%   95.31%   +0.29%     
==========================================
  Files          24       26       +2     
  Lines        1024     1174     +150     
==========================================
+ Hits          973     1119     +146     
- Misses         51       55       +4
Impacted Files Coverage Δ
abagen/process.py 100% <100%> (ø) ⬆️
abagen/tests/test_probes.py 100% <100%> (ø)
abagen/allen.py 98.34% <85.71%> (-0.83%) ⬇️
abagen/probes.py 97.14% <97.14%> (ø)

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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Including at least basic testing of most functionality. Limited edge
cases included as of yet, but I think those can come later since these
mostly aren't "public" functions... /shrug
One of the tests in abagen.probes was using dicts to instantiate a
dataframe and I _think_ that's what caused the issue
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Include other metrics for probe selection
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