[REF,ENH] Adds new abagen.probes module #67
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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.
Pull Request Test Coverage Report for Build 257
💛 - Coveralls |
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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. |
Codecov Report
@@ Coverage Diff @@
## master #67 +/- ##
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- Coverage 95.01% 91.72% -3.3%
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Files 24 25 +1
Lines 1024 1088 +64
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+ Hits 973 998 +25
- Misses 51 90 +39
Continue to review full report at Codecov.
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Codecov Report
@@ 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
Continue to review full report at Codecov.
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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
Closes #51.
Moves all functions operating on probes to
abagen.probesmodule (i.e.,reannotate_probes()andfilter_probes(), previously inabagen.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 optionalprobe_selectionkeyword argument. Relevant references and description of the different methods have been added to the Notes of the doc-strings.To do: