Merge pf7 package updates to master - #2

Merged

kathrynmurie merged 70 commits into

kathrynmurie:masterfrom

malariagen:master

Feb 21, 2022

Commits on Oct 8, 2021

Commits on Nov 26, 2021

Add integration tests to test data in staging bucket
kathrynmurie
committed
5bc9538

Commits on Dec 7, 2021

Change path to util module in pf7 module
kathrynmurie
committed
857d647

Commits on Jan 11, 2022

Update changes to util module
kathrynmurie
committed
398039c
Merge remote-tracking branch 'origin/master' into add_pf_module
kathrynmurie
committed
9b5f6d3
Update pf7 module to be in line with ag3 and amin1 changes
kathrynmurie
committed
b994b6e
remove empty columns
cclarkson
committed
8a52097
Add extra entries to default xarray returned and add option to extend
kathrynmurie
committed
e5f95e8
add option to extend dataset returned by variant_calls
kathrynmurie
committed
6fafbec
Extend fields in xarray with extended flag
kathrynmurie
committed
ac48af3
Merge pull request #120 from malariagen/118-drop
cclarkson
authored
2a2e399
fix compress bug (#121)
alimanfoo
authored
681399b

Commits on Jan 13, 2022

Add variables to extended version of xarray from zarr
kathrynmurie
committed
2bdc4e2

Commits on Jan 14, 2022

aa freq method plus test
cclarkson
committed
ccfa903

Commits on Jan 21, 2022

Commits on Jan 24, 2022

Commits on Jan 25, 2022

updated aa freqs method, plus basic test
cclarkson
committed
2619dc8

Commits on Jan 26, 2022

improves test
cclarkson
committed
493f1ec

Commits on Jan 27, 2022

doc string corrections
cclarkson
committed
a825e41

Commits on Jan 28, 2022

Slimline unit tests for pf7
kathrynmurie
committed
f48a8e9
Remove objects not used from pf7 test setup
kathrynmurie
committed
94e04b8
added other aa altering effects
cclarkson
committed
7bd1f69
reduce repeated code in variant calls
kathrynmurie
committed
69dff96
Merge pull request #124 from malariagen/101-aafrq
cclarkson
authored
ce4c7a8
Change extension option to default to an empty list with the option of setting it to '*' or a list of variables to add to the default set
kathrynmurie
committed
a0bf876
Add tests for new functions for adding data
kathrynmurie
committed
177d028

Commits on Feb 7, 2022

Commits on Feb 8, 2022

Remove subset extended function as it isn't used anymore
kathrynmurie
committed
7ba504d
Change zarr to variant_calls_zarr in function, cache, and config to provide more clarity
kathrynmurie
committed
f88b5db
Make add_data_vars a private function
kathrynmurie
committed
92be104
Add sample_query parameter to allele frequencies (#126)

alimanfoo
and
cclarkson
authored
1ec701e
Extend documentation
kathrynmurie
committed
02ea8f6
ag3.plot_frequencies_heatmap() (#125)

cclarkson
and
alimanfoo
authored
ca44c97
Zarr 2.11.0 compatibility (#130)
alimanfoo
authored
01229cd
v1.0.0 release notes (#131)
alimanfoo
authored
37a3ce0
Refactor region support and add region support to Amin1 (#132)
alimanfoo
authored
9de39a2
add missing release notes
alimanfoo
committed
8aebfc1
bump version to 1.0.0
alimanfoo
committed
a293215

Commits on Feb 9, 2022

expose more imshow parameters in plot_frequencies_heatmap (#134)
alimanfoo
authored
38db46f
release notes
alimanfoo
committed
46fc934
bump version
alimanfoo
committed
7afc494

Commits on Feb 10, 2022

Remove unnecessary test for init and check tests for load config test specifically that the path can be overridden
kathrynmurie
committed
2910e0e
Remove excess test for testing open zarr as same is tested when using cache
kathrynmurie
committed
06ef68d
Improve doc strings by adding examples of using functions
kathrynmurie
committed
a1f83a1
Set default url in config so user doesn't have to specify every time
kathrynmurie
committed
8500442
Update malariagen_data/pf7.py

kathrynmurie
and
alimanfoo
authored
ddfe6ca
Update malariagen_data/pf7.py

kathrynmurie
and
alimanfoo
authored
324f981
Change documentation to be in line with numpydoc style as in ag3
kathrynmurie
committed
ebf7736
Change documentation to be in line with numpydoc style as in ag3
kathrynmurie
committed
1ff4a30
Put text on same indent level sample_metadata docstring
kathrynmurie
committed
a37684e
Update malariagen_data/pf7.py

kathrynmurie
and
alimanfoo
authored
049af11
Update malariagen_data/pf7.py

kathrynmurie
and
alimanfoo
authored
f055578
Remove trailing white space causing linting to fail
kathrynmurie
committed
3b052f8
Merge pull request #69 from kathryn1995/add_pf_module
kathrynmurie
authored
4c65f37

Commits on Feb 15, 2022

Update version for pf7 pre-release
kathrynmurie
committed
16a53ae

Commits on Feb 21, 2022

Merge pull request #137 from malariagen/update_version_for_pf7_prerelease
kathrynmurie
authored
9ba91f5