Improve GWAS documentation#217
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karenfeng merged 19 commits intoprojectglow:masterfrom Jun 8, 2020
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@@ Coverage Diff @@
## master #217 +/- ##
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Coverage 93.63% 93.63%
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Files 88 88
Lines 4258 4258
Branches 397 397
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Hits 3987 3987
Misses 271 271 Continue to review full report at Codecov.
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…ument-multiple-phenos Signed-off-by: Karen Feng <karen.feng@databricks.com>
…ument-multiple-phenos Signed-off-by: Karen Feng <karen.feng@databricks.com>
…ument-multiple-phenos Signed-off-by: Karen Feng <karen.feng@databricks.com>
Signed-off-by: Karen Feng <karen.feng@databricks.com>
Signed-off-by: Karen Feng <karen.feng@databricks.com>
Signed-off-by: Karen Feng <karen.feng@databricks.com>
Signed-off-by: Karen Feng <karen.feng@databricks.com>
Signed-off-by: Karen Feng <karen.feng@databricks.com>
Signed-off-by: Karen Feng <karen.feng@databricks.com>
Signed-off-by: Karen Feng <karen.feng@databricks.com>
henrydavidge
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Jun 22, 2020
* Improve GWAS docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Compress Signed-off-by: Karen Feng <karen.feng@databricks.com> * Gzip Signed-off-by: Karen Feng <karen.feng@databricks.com> * Intercept Signed-off-by: Karen Feng <karen.feng@databricks.com> * lit Signed-off-by: Karen Feng <karen.feng@databricks.com> * fixup binary phenos Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add tip Signed-off-by: Karen Feng <karen.feng@databricks.com> * lit Signed-off-by: Karen Feng <karen.feng@databricks.com> * comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Set up PySpark from github Signed-off-by: Karen Feng <karen.feng@databricks.com> * clone Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't specify rev Signed-off-by: Karen Feng <karen.feng@databricks.com> * Docs fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Move setup Signed-off-by: Karen Feng <karen.feng@databricks.com> * ordering of struct Signed-off-by: Karen Feng <karen.feng@databricks.com> * enable legacy conf PYSPARK_ROW_FIELD_SORTING_ENABLED Signed-off-by: Karen Feng <karen.feng@databricks.com> Signed-off-by: Henry Davidge <hhd@databricks.com>
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What changes are proposed in this pull request?
Changes the GWAS documentation to read covariates and phenotypes from CSVs in order to better match a realistic workflow and document that the user can pass literal numpy arrays as a result of #213.
Due to incompatibility between the most recent release of PySpark 3.0 and the current Spark 3.0.1 snapshot that broke Pandas functionality, I also modified the build to create our own pip-installable
.tar.gzoff the latest Sparkbranch-3.0. This required us to create our ownsetup.pyfile, as the existing one in Spark requires jarsThis change necessitated enabling the env var
PYSPARK_ROW_FIELD_SORTING_ENABLEDdue to the changes in apache/spark#26496, which modified the row ordering and broke the Python tests when the row elements were unsorted.How is this patch tested?