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2021-05-06Used a list comprehension for perm_vals as mentioned in Bonface's commentzsloan
2021-05-06Merge branch 'testing' into bug/fix_rqtl_covariateszsloan
2021-05-06Because each permutations value is returned as an array, need to just take ↵zsloan
the first item to convert to numbers
2021-05-06Fixed vertical position of loading text so that it should be positioned in ↵zsloan
the center vertically
2021-05-06Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2021-05-06Include group and species in form parameters for mapping results page, so ↵zsloan
they can be included in the loading page if the map is reloaded
2021-05-06Include group/species in form parameters on trait page so they can be ↵zsloan
displayed on mapping loading page
2021-05-06Changed the way metadata is displayed on the mapping loading pagezsloan
2021-05-06Delete model.py and it's referencesBonfaceKilz
* wqflask/wqflask/database.py (init_db): Remove references to "wqflask.model" * wqflask/wqflask/model.py: Delete it.
2021-05-06wqflask: user_manager: Delete usermanager.py and it's referencesBonfaceKilz
This module is not used anywhere.
2021-05-06wqflask: database: Remove loggingBonfaceKilz
2021-05-05Added whether GEMMA is using LOCO to mapping loading pagezsloan
2021-05-05Added genotype file to mapping loading pagezsloan
2021-05-05Removed an unused item from mapping_input_listzsloan
2021-05-05Added a number of new metadata items to the mapping loading page, such as ↵zsloan
covariates and permutation/bootstrap numbers
2021-05-05Added mapping download button above the results tablezsloan
2021-05-05Made change that should cause clicking the R/qtl tab to make it compute; ↵zsloan
also removed a console.log
2021-05-05Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2021-05-05Removed broken Genome Browser link from index pagezsloan
2021-05-05base: species: Remove redundant assignmentBonfaceKilz
2021-05-05api: gen_menu: Remove "+" when concatenating strings inside bracketsBonfaceKilz
2021-05-05tests: test_species: Update failing testsBonfaceKilz
2021-05-05base: chromosomes: Fetch the chromosomes lazilyBonfaceKilz
2021-05-05base: species: Rewrite Chromosomes using a dataclassBonfaceKilz
2021-05-05base: species: Rewrite IndChromosome using a dataclassBonfaceKilz
2021-05-05base: trait: Remove logging informationBonfaceKilz
The log adds unnecessary noise in addition to creating unwanted side-effects.
2021-05-05base: species: Rewrite TheSpecies class using a dataclassBonfaceKilz
2021-05-05base: species: Remove unused importBonfaceKilz
2021-05-05base: species: Format SQL queriesBonfaceKilz
2021-05-05templates: test_species: Add tests for instantiating ChromosomesBonfaceKilz
2021-05-05tests: test_species: Test that IndChromosome instantiates correctlyBonfaceKilz
2021-05-05tests: test_species: Add test cases for TestTheSpecies classBonfaceKilz
2021-05-04Removed unused rpy import in run_mapping.pyzsloan
2021-05-03Account for the possibility of the R being returned as 0.999... by scipy ↵zsloan
when a trait is correlated against itself - before the 0.999... was preventing it from switching to calculating Spearman for the values above the diagonal in the correlation matrix
2021-04-30Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2021-04-30Fixed issue where Network Graph wouldn't show edges if multiple nodes had ↵zsloan
the same trait name; instead use combo of trait name and dataset name as the edge IDs
2021-04-30webtests: Delete itBonfaceKilz
These are no longer used
2021-04-30autopep8: Run autopep8 100 times with target rulesBonfaceKilz
Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix E101, E11BonfaceKilz
2021-04-30autopep8: Fix W504BonfaceKilz
2021-04-30autopep8: Fix W291, W292, W293, W391BonfaceKilz
2021-04-30autopep8: Fix E70 and E701BonfaceKilz
2021-04-30autopep8: Fix E501BonfaceKilz
2021-04-30autopep8: Fix E401BonfaceKilz
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2021-04-30autopep8: Fix E20-E27BonfaceKilz
Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
2021-04-29I think the import of collect.py got removed with recent changes, so I'm ↵zsloan
adding it back
2021-04-29Merge pull request #569 from zsloan/bug/network_graph_fixeszsloan
Bug/network graph fixes
2021-04-29Merge branch 'testing' into bug/network_graph_fixeszsloan
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