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NEW: Adds core beta diversity measures #6

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merged 48 commits into from
Jun 11, 2020
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06d4d61
adds @_safely_count_cpus, tests
ChrisKeefe Oct 12, 2019
ef17a8b
MAINT: tidies var names of expected results in test_alpha
ChrisKeefe Oct 17, 2019
4da3de4
adds vscode workspace files to gitignore
ChrisKeefe Oct 17, 2019
b294120
guards against empty table passed as fp, fixes CPU count decorator
ChrisKeefe Feb 5, 2020
5ac73ad
MAINT: replaces copy.deepcopy() with biom 'inplace=False'
ChrisKeefe Feb 7, 2020
7205ed2
adds registrations, citations, init for core beta diversity
ChrisKeefe Feb 7, 2020
fb4e59a
NEW: adds core beta diversity measures, basic tests
ChrisKeefe Feb 8, 2020
9d04464
adds test data for faith_pd refactor, fixes broken rel. freq table
ChrisKeefe Feb 10, 2020
d9b9b91
refactors faith_pd to use biocore's Unifrac
ChrisKeefe Feb 10, 2020
a390a5f
BUG: corrects filename mismatch
ChrisKeefe Feb 10, 2020
7db2de7
BUG: corrects non-firing test cases
ChrisKeefe Feb 10, 2020
1b75089
Adds n_jobs edge case handling, temp test for running methods through…
ChrisKeefe May 9, 2020
aef7749
HACK: patches inconsistent error messages from Unifrac
ChrisKeefe May 13, 2020
4e81604
properly adds method and test data for weighted unifrac
ChrisKeefe May 13, 2020
cdcda1c
minor comment cleanup
ChrisKeefe May 13, 2020
ee5eaf2
removes fancy unifracs. see draft_fancy_unifracs branch if needed
ChrisKeefe May 13, 2020
bec18de
hides variance_adjusted parameter in unifrac to prevent adjusting wit…
ChrisKeefe May 14, 2020
2b1ad18
LINT: reorganize imports to PEP8
ChrisKeefe May 14, 2020
1ebe57b
combines empty_tables decorators, moves it to decorator.docorator, vi…
ChrisKeefe May 15, 2020
96e4388
switches n_jobs decorator over to decorator.decorator, first through-…
ChrisKeefe May 15, 2020
e244509
adds decorator to ci meta.yaml, missing-lines report to make test-cov…
ChrisKeefe May 18, 2020
27df8f0
fixes _disallow_empty_tables bad view_type error message
ChrisKeefe May 18, 2020
fd7c695
BUG: test_alpha and test_util now pass proper view types
ChrisKeefe May 19, 2020
2bd531a
MAINT: organizes table/tree data consistently
ChrisKeefe May 19, 2020
9744ccd
simplifies type handling, removes invalid filepath testing
ChrisKeefe May 20, 2020
e8c74f2
adds dependencies to recipe
ChrisKeefe May 21, 2020
d59aab3
LINT: updates copyright headers
ChrisKeefe May 20, 2020
e06eb57
adds test data assets to setup.py
ChrisKeefe May 21, 2020
e85651e
removes travis.yml, removes travis build badge from README
ChrisKeefe May 22, 2020
c4c91e5
REVERT ME: testing a theory
thermokarst May 22, 2020
acc4daa
Revert "REVERT ME: testing a theory"
thermokarst May 22, 2020
c33b977
adds github actions workflow
ChrisKeefe May 20, 2020
0e3ec5e
ENH: Adds lint-build-test badge to readme (#4)
ChrisKeefe May 22, 2020
ab22b7f
SQUASH: naming, comment placement
ChrisKeefe May 27, 2020
a96c04d
BUG: fixes patch-related test issue visible on Darwin (#5)
ChrisKeefe May 27, 2020
229e79f
BUG: actually fixes patch-related test (#6)
ChrisKeefe May 28, 2020
ad5967b
SQUASH: fixes poorly-named variable mock_cpu_affinity
ChrisKeefe May 28, 2020
ae674f3
MAINT: gitignore notes directory and contents
ChrisKeefe May 29, 2020
fd0e24e
Makes quoting consistent: user-facing strings double, keys etc single
ChrisKeefe May 27, 2020
47daa08
SQUASH: minor comment cleanup
ChrisKeefe Jun 5, 2020
750836d
preliminary review changes, not incl n_jobs
ChrisKeefe Jun 8, 2020
6fcd5b7
renames 'n_jobs' to 'threads' as needed, improves semantic type
ChrisKeefe Jun 8, 2020
f3e9056
Handles 'auto' passed to cpu-request params, renames tests from 'n_jobs'
ChrisKeefe Jun 9, 2020
687401d
Wordsmiths cpu-request parameter descriptions
ChrisKeefe Jun 9, 2020
d5fdd8e
MAINT: Test-data file lint, removes two_feature_table.tsv
ChrisKeefe Jun 9, 2020
b9f5168
test data file paths not instance vars, fixes tree view type
ChrisKeefe Jun 10, 2020
b662efd
LINT: removes unused io import
ChrisKeefe Jun 10, 2020
226be5b
Updates requested_cpuss test class name
ChrisKeefe Jun 10, 2020
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adds decorator to ci meta.yaml, missing-lines report to make test-cov…
… target
ChrisKeefe committed Jun 1, 2020

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commit e244509ecd1f97402afcbb01b98073c90a666b79
2 changes: 1 addition & 1 deletion Makefile
Original file line number Diff line number Diff line change
@@ -11,7 +11,7 @@ test: all
py.test

test-cov: all
py.test --cov=q2_diversity_lib
py.test --cov-report=term-missing --cov=q2_diversity_lib

install:
$(PYTHON) setup.py install
1 change: 1 addition & 0 deletions ci/recipe/meta.yaml
Original file line number Diff line number Diff line change
@@ -23,6 +23,7 @@ requirements:
- biom-format >=2.1.5,<2.2.0
- qiime2 {{ release }}.*
- q2-types {{ release }}.*
- decorator

test:
imports: