[HLS-351] Release prep #1

karenfeng · 2019-10-07T15:25:10Z

What changes are proposed in this pull request?

Make sure tests pass with Java (not Kryo) serialization
Move README from md to rst to play nice with pip descriptions
Prune (mostly GATK) dependencies to reduce package resolution time
Set up pipeline to release maven artifacts to Bintray
Set up Python wheel creation (temporarily disabled install_requires as Databricks does not resolve from different repos, and typeguard exists in PyPi but not TestPyPi)

Instructions

To create a maven artifact and publish to Bintray
- Prereq: get Bintray creds (via Lastpass)
- Run sbt release from glow
To create a wheel and publish to TestPyPi
- Prereq: update your conda environment so that you can use setuptools and twine
- Run python setup.py bdist_wheel from glow/python
- Run twine upload --repository-url https://test.pypi.org/legacy/ dist/*

How is this patch tested?

Unit tests
Integration tests
Manual tests

A DBR cluster was set up with the maven artifacts and wheel, and basic functionality was tested.

Don't use Kryo serializer Don't parallelize un-serializable Hadoop FileStatus Change descrip WIP Whoops bintray Not local Quiet logs Remove tmp file Actually rename bintray Setting version to 0.1.0 WIP WIP License fixup Resolver WIP Change version Setting version to 0.1.1 WIP Setting version to 0.1.2 Setting version to 0.1.3-SNAPSHOT WIP Setting version to 0.1.2 Setting version to 0.1.3-SNAPSHOT Exclude many GATK deps Setting version to 0.1.3 Setting version to 0.1.4-SNAPSHOT Setting version to 0.1.4 Setting version to 0.1.5-SNAPSHOT Whoops Setting version to 0.1.3 Setting version to 0.1.4-SNAPSHOT Setting version to 0.1.4 Setting version to 0.1.5-SNAPSHOT Setting version to 0.1.6 Setting version to 0.1.7-SNAPSHOT Yay deps Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.1 Setting version to 0.1.2-SNAPSHOT Setting version to 0.1.10 Setting version to 0.1.11-SNAPSHOT Setting version to 0.1.15 Setting version to 0.1.16-SNAPSHOT Setting version to 0.1.9 Setting version to 0.1.10-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Add tests back Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Setting version to 0.1.13 Setting version to 0.1.14-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT WIP Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT WIP Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT Setting version to 0.1.11 Setting version to 0.1.12-SNAPSHOT Setting version to 0.1.7 Setting version to 0.1.8-SNAPSHOT Exclude findbugs Setting version to 0.1.8 Setting version to 0.1.9-SNAPSHOT WIP Cleanup

henrydavidge

Nice work! I had a bunch of questions.

henrydavidge · 2019-10-08T16:17:40Z

README.rst

@@ -0,0 +1,10 @@
+==================================


Can you migrate over the rest of the readme contents?

And delete the old one?

To clean everything up for publishing (PyPi uses readme.rst), I put everything in Building and Testing in the wiki.

henrydavidge · 2019-10-08T16:18:55Z

build.sbt

+    .exclude("biz.k11i", "xgboost-predictor")
+    .exclude("com.esotericsoftware", "kryo")
+    .exclude("com.esotericsoftware", "reflectasm")
+    .exclude("com.github.fommil.netlib", "netlib-native_ref-osx-x86_64")


Are you sure we should exclude these? These are the blas bindings I believe. cc @fnothaft

henrydavidge · 2019-10-08T16:21:06Z

build.sbt


-// Uncomment the following for publishing to Sonatype.
-// See https://www.scala-sbt.org/1.x/docs/Using-Sonatype.html for more detail.
+// Publish to Bintray


I get that bintray is helpful for testing, but why would we publish to bintray vs maven central? I think it's easier for users to download from maven central because they don't need to add a repo to their pom (please correct me if that's wrong).

As discussed offline, this is what Delta does with their OSS release - stage in bintray before pushing to Maven Central.

core/src/test/resources/log4j.properties

core/src/test/scala/com/databricks/hls/sql/HLSBaseTest.scala

python/environment.yml

henrydavidge · 2019-10-08T16:22:22Z

python/setup.py

+from setuptools import setup
+
+setup(
+    name='glowpy',


can we just call it glow?

As discussed offline, both glow and pyglow have been taken on PyPi.

python/setup.py

* feat: ridge models for wgr added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Changes made to accessing the sample ID map and more docstrings The map_normal_eqn and score_models functions previously expected the sample IDs for a given sample block to be found in the Pandas DataFrame, which mean we had to join them on before the .groupBy().apply(). These functions now expect the sample block to sample IDs mapping to be provided separately as a dict, so that the join is no longer required. RidgeReducer and RidgeRegression APIs remain unchanged. docstrings have been added for RidgeReducer and RidgeRegression classes. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Refactored object names and comments to reflect new terminology Where 'block' was previously used to refer to the set of columns in a block, we now use 'header_block' Where 'group' was previously used to refer to the set of samples in a block, we now use 'sample_block' Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com>

* feat: ridge models for wgr added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Changes made to accessing the sample ID map and more docstrings The map_normal_eqn and score_models functions previously expected the sample IDs for a given sample block to be found in the Pandas DataFrame, which mean we had to join them on before the .groupBy().apply(). These functions now expect the sample block to sample IDs mapping to be provided separately as a dict, so that the join is no longer required. RidgeReducer and RidgeRegression APIs remain unchanged. docstrings have been added for RidgeReducer and RidgeRegression classes. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Refactored object names and comments to reflect new terminology Where 'block' was previously used to refer to the set of columns in a block, we now use 'header_block' Where 'group' was previously used to refer to the set of samples in a block, we now use 'sample_block' Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> Signed-off-by: Henry Davidge <hhd@databricks.com>

* Add Leland's demo notebook * block_variants_and_samples Transformer to create genotype DataFrame for WGR (#2) * blocks Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test vcf Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * transformer Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * refactor and conform with ridge namings Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test files Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra file Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * sort_key Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * feat: ridge models for wgr added (#1) * feat: ridge models for wgr added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Changes made to accessing the sample ID map and more docstrings The map_normal_eqn and score_models functions previously expected the sample IDs for a given sample block to be found in the Pandas DataFrame, which mean we had to join them on before the .groupBy().apply(). These functions now expect the sample block to sample IDs mapping to be provided separately as a dict, so that the join is no longer required. RidgeReducer and RidgeRegression APIs remain unchanged. docstrings have been added for RidgeReducer and RidgeRegression classes. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Refactored object names and comments to reflect new terminology Where 'block' was previously used to refer to the set of columns in a block, we now use 'header_block' Where 'group' was previously used to refer to the set of samples in a block, we now use 'sample_block' Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * [HLS-539] Fix compatibility between blocked GT transformer and WGR (#6) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Spark 3 needs more recent PyArrow, reduce mem consumption by removing unnecessary caching Signed-off-by: Karen Feng <karen.feng@databricks.com> * PyArrow 0.15.1 only with PySpark 3 Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't use toPandas() Signed-off-by: Karen Feng <karen.feng@databricks.com> * Upgrade pyarrow Signed-off-by: Karen Feng <karen.feng@databricks.com> * Only register once Signed-off-by: Karen Feng <karen.feng@databricks.com> * Minimize memory usage Signed-off-by: Karen Feng <karen.feng@databricks.com> * Select before head Signed-off-by: Karen Feng <karen.feng@databricks.com> * set up/tear down Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try limiting pyspark memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * No teardown Signed-off-by: Karen Feng <karen.feng@databricks.com> * Extend timeout Signed-off-by: Karen Feng <karen.feng@databricks.com> * Simplify ordering logic in levels code (#7) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * start changing for readability * use input label ordering * rename create_row_indexer * undo column sort * change reduce Signed-off-by: Henry D <henrydavidge@gmail.com> * further simplify reduce * sorted alpha names * remove ordering * comments Signed-off-by: Henry D <henrydavidge@gmail.com> * Set arrow env var in build Signed-off-by: Henry D <henrydavidge@gmail.com> * faster sort * add test file * undo test data change * >= * formatting * empty Co-authored-by: Karen Feng <karen.feng@databricks.com> * Limit Spark memory conf in tests (#9) * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf transform Signed-off-by: Karen Feng <karen.feng@databricks.com> * Set driver memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try changing spark mem Signed-off-by: Karen Feng <karen.feng@databricks.com> * match java tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * remove driver memory flag Signed-off-by: Karen Feng <karen.feng@databricks.com> * Improve partitioning in block_variants_and_samples transformer (#11) Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * Remove unnecessary header_block grouping (#10) * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Create sample ID blocking helper functions (#12) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * simplify tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * index map compat Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add more tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * pass args as ints Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't roll our own splitter Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename sample_index to sample_blocks Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add type-checking to WGR APIs (#14) * Add type-checking to APIs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check valid alphas Signed-off-by: Karen Feng <karen.feng@databricks.com> * check 0 sig Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add to install_requires list Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add covariate support (#13) * Added necessary modifications to accomodate covariates in model fitting. The initial formulation of the WGR model assumed a form y ~ Xb, however in general we would like to use a model of the form y ~ Ca + Xb, where C is some matrix of covariates that are separate from the genomic features X. This PR makes numerous changes to accomodate covariate matrix C. Adding covariates required the following breaking changes to the APIs: * indexdf is now a required argument for RidgeReducer.transform() and RidgeRegression.transform(): * RidgeReducer.transform(blockdf, labeldf, modeldf) -> RidgeReducer.transform(blockdf, labeldf, indexdf, modeldf) * RidgeRegression.transform(blockdf, labeldf, model, cvdf) -> RidgeRegression.transform(blockdf, labeldf, indexdf, model, cvdf) Additionally, the function signatures for the fit and transform methods of RidgeReducer and RidgeRegression have all been updated to accomodate an optional covariate DataFrame as the final argument. Two new tests have been added to test_ridge_regression.py to test run modes with covariates: * test_ridge_reducer_transform_with_cov * test_two_level_regression_with_cov Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Cleaned up one unnecessary Pandas import Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Small changes for clarity and consistence with the rest of the code. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Forgot one usage of coalesce Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Added a couple of comments to explain logic and replaced usages of .values with .array Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Fixed one instance of the change .values -> .array where it was made in error. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Typo in test_ridge_regression.py. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Style auto-updates with yapfAll Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> * Flatten estimated phenotypes (#15) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Order to match labeldf Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check we tie-break Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * test var name Signed-off-by: Karen Feng <karen.feng@databricks.com> * clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add fit_transform function to models (#17) Signed-off-by: Karen Feng <karen.feng@databricks.com> * Rename levels (#20) * Rename levels to wgr Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename test files Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add license headers (#21) * headers * executable * fix template rendering * yapf * add header to template * add header to template Signed-off-by: Henry D <henrydavidge@gmail.com> Co-authored-by: Kiavash Kianfar <kiavash.kianfar@databricks.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> Co-authored-by: Leland <leland.barnard@gmail.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com>

* Add Leland's demo notebook * block_variants_and_samples Transformer to create genotype DataFrame for WGR (#2) * blocks Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test vcf Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * transformer Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * refactor and conform with ridge namings Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test files Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra file Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * sort_key Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * feat: ridge models for wgr added (#1) * feat: ridge models for wgr added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Changes made to accessing the sample ID map and more docstrings The map_normal_eqn and score_models functions previously expected the sample IDs for a given sample block to be found in the Pandas DataFrame, which mean we had to join them on before the .groupBy().apply(). These functions now expect the sample block to sample IDs mapping to be provided separately as a dict, so that the join is no longer required. RidgeReducer and RidgeRegression APIs remain unchanged. docstrings have been added for RidgeReducer and RidgeRegression classes. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Refactored object names and comments to reflect new terminology Where 'block' was previously used to refer to the set of columns in a block, we now use 'header_block' Where 'group' was previously used to refer to the set of samples in a block, we now use 'sample_block' Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * [HLS-539] Fix compatibility between blocked GT transformer and WGR (#6) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Spark 3 needs more recent PyArrow, reduce mem consumption by removing unnecessary caching Signed-off-by: Karen Feng <karen.feng@databricks.com> * PyArrow 0.15.1 only with PySpark 3 Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't use toPandas() Signed-off-by: Karen Feng <karen.feng@databricks.com> * Upgrade pyarrow Signed-off-by: Karen Feng <karen.feng@databricks.com> * Only register once Signed-off-by: Karen Feng <karen.feng@databricks.com> * Minimize memory usage Signed-off-by: Karen Feng <karen.feng@databricks.com> * Select before head Signed-off-by: Karen Feng <karen.feng@databricks.com> * set up/tear down Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try limiting pyspark memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * No teardown Signed-off-by: Karen Feng <karen.feng@databricks.com> * Extend timeout Signed-off-by: Karen Feng <karen.feng@databricks.com> * Simplify ordering logic in levels code (#7) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * start changing for readability * use input label ordering * rename create_row_indexer * undo column sort * change reduce Signed-off-by: Henry D <henrydavidge@gmail.com> * further simplify reduce * sorted alpha names * remove ordering * comments Signed-off-by: Henry D <henrydavidge@gmail.com> * Set arrow env var in build Signed-off-by: Henry D <henrydavidge@gmail.com> * faster sort * add test file * undo test data change * >= * formatting * empty Co-authored-by: Karen Feng <karen.feng@databricks.com> * Limit Spark memory conf in tests (#9) * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf transform Signed-off-by: Karen Feng <karen.feng@databricks.com> * Set driver memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try changing spark mem Signed-off-by: Karen Feng <karen.feng@databricks.com> * match java tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * remove driver memory flag Signed-off-by: Karen Feng <karen.feng@databricks.com> * Improve partitioning in block_variants_and_samples transformer (#11) Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * Remove unnecessary header_block grouping (#10) * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Create sample ID blocking helper functions (#12) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * simplify tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * index map compat Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add more tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * pass args as ints Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't roll our own splitter Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename sample_index to sample_blocks Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add type-checking to WGR APIs (#14) * Add type-checking to APIs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check valid alphas Signed-off-by: Karen Feng <karen.feng@databricks.com> * check 0 sig Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add to install_requires list Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add covariate support (#13) * Added necessary modifications to accomodate covariates in model fitting. The initial formulation of the WGR model assumed a form y ~ Xb, however in general we would like to use a model of the form y ~ Ca + Xb, where C is some matrix of covariates that are separate from the genomic features X. This PR makes numerous changes to accomodate covariate matrix C. Adding covariates required the following breaking changes to the APIs: * indexdf is now a required argument for RidgeReducer.transform() and RidgeRegression.transform(): * RidgeReducer.transform(blockdf, labeldf, modeldf) -> RidgeReducer.transform(blockdf, labeldf, indexdf, modeldf) * RidgeRegression.transform(blockdf, labeldf, model, cvdf) -> RidgeRegression.transform(blockdf, labeldf, indexdf, model, cvdf) Additionally, the function signatures for the fit and transform methods of RidgeReducer and RidgeRegression have all been updated to accomodate an optional covariate DataFrame as the final argument. Two new tests have been added to test_ridge_regression.py to test run modes with covariates: * test_ridge_reducer_transform_with_cov * test_two_level_regression_with_cov Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Cleaned up one unnecessary Pandas import Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Small changes for clarity and consistence with the rest of the code. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Forgot one usage of coalesce Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Added a couple of comments to explain logic and replaced usages of .values with .array Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Fixed one instance of the change .values -> .array where it was made in error. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Typo in test_ridge_regression.py. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Style auto-updates with yapfAll Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> * Flatten estimated phenotypes (#15) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Order to match labeldf Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check we tie-break Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * test var name Signed-off-by: Karen Feng <karen.feng@databricks.com> * clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add fit_transform function to models (#17) Signed-off-by: Karen Feng <karen.feng@databricks.com> * support alpha inference Signed-off-by: Karen Feng <karen.feng@databricks.com> * test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * more test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * test fixups Signed-off-by: Karen Feng <karen.feng@databricks.com> * sub-sample Signed-off-by: Karen Feng <karen.feng@databricks.com> * test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments - only infer alphas during fit Signed-off-by: Karen Feng <karen.feng@databricks.com> * exception varies Signed-off-by: Karen Feng <karen.feng@databricks.com> * Rename levels (#20) * Rename levels to wgr Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename test files Signed-off-by: Karen Feng <karen.feng@databricks.com> * Errors vary by Spark version Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add license headers (#21) * headers * executable * fix template rendering * yapf Co-authored-by: Kiavash Kianfar <kiavash.kianfar@databricks.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> Co-authored-by: Leland <leland.barnard@gmail.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com>

* Add Leland's demo notebook * block_variants_and_samples Transformer to create genotype DataFrame for WGR (#2) * blocks Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test vcf Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * transformer Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * refactor and conform with ridge namings Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test files Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra file Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * sort_key Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * feat: ridge models for wgr added (#1) * feat: ridge models for wgr added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Changes made to accessing the sample ID map and more docstrings The map_normal_eqn and score_models functions previously expected the sample IDs for a given sample block to be found in the Pandas DataFrame, which mean we had to join them on before the .groupBy().apply(). These functions now expect the sample block to sample IDs mapping to be provided separately as a dict, so that the join is no longer required. RidgeReducer and RidgeRegression APIs remain unchanged. docstrings have been added for RidgeReducer and RidgeRegression classes. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Refactored object names and comments to reflect new terminology Where 'block' was previously used to refer to the set of columns in a block, we now use 'header_block' Where 'group' was previously used to refer to the set of samples in a block, we now use 'sample_block' Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * [HLS-539] Fix compatibility between blocked GT transformer and WGR (#6) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Spark 3 needs more recent PyArrow, reduce mem consumption by removing unnecessary caching Signed-off-by: Karen Feng <karen.feng@databricks.com> * PyArrow 0.15.1 only with PySpark 3 Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't use toPandas() Signed-off-by: Karen Feng <karen.feng@databricks.com> * Upgrade pyarrow Signed-off-by: Karen Feng <karen.feng@databricks.com> * Only register once Signed-off-by: Karen Feng <karen.feng@databricks.com> * Minimize memory usage Signed-off-by: Karen Feng <karen.feng@databricks.com> * Select before head Signed-off-by: Karen Feng <karen.feng@databricks.com> * set up/tear down Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try limiting pyspark memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * No teardown Signed-off-by: Karen Feng <karen.feng@databricks.com> * Extend timeout Signed-off-by: Karen Feng <karen.feng@databricks.com> * Simplify ordering logic in levels code (#7) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * start changing for readability * use input label ordering * rename create_row_indexer * undo column sort * change reduce Signed-off-by: Henry D <henrydavidge@gmail.com> * further simplify reduce * sorted alpha names * remove ordering * comments Signed-off-by: Henry D <henrydavidge@gmail.com> * Set arrow env var in build Signed-off-by: Henry D <henrydavidge@gmail.com> * faster sort * add test file * undo test data change * >= * formatting * empty Co-authored-by: Karen Feng <karen.feng@databricks.com> * Limit Spark memory conf in tests (#9) * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf transform Signed-off-by: Karen Feng <karen.feng@databricks.com> * Set driver memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try changing spark mem Signed-off-by: Karen Feng <karen.feng@databricks.com> * match java tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * remove driver memory flag Signed-off-by: Karen Feng <karen.feng@databricks.com> * Improve partitioning in block_variants_and_samples transformer (#11) Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * Remove unnecessary header_block grouping (#10) * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Create sample ID blocking helper functions (#12) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * simplify tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * index map compat Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add more tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * pass args as ints Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't roll our own splitter Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename sample_index to sample_blocks Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add type-checking to WGR APIs (#14) * Add type-checking to APIs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check valid alphas Signed-off-by: Karen Feng <karen.feng@databricks.com> * check 0 sig Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add to install_requires list Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add covariate support (#13) * Added necessary modifications to accomodate covariates in model fitting. The initial formulation of the WGR model assumed a form y ~ Xb, however in general we would like to use a model of the form y ~ Ca + Xb, where C is some matrix of covariates that are separate from the genomic features X. This PR makes numerous changes to accomodate covariate matrix C. Adding covariates required the following breaking changes to the APIs: * indexdf is now a required argument for RidgeReducer.transform() and RidgeRegression.transform(): * RidgeReducer.transform(blockdf, labeldf, modeldf) -> RidgeReducer.transform(blockdf, labeldf, indexdf, modeldf) * RidgeRegression.transform(blockdf, labeldf, model, cvdf) -> RidgeRegression.transform(blockdf, labeldf, indexdf, model, cvdf) Additionally, the function signatures for the fit and transform methods of RidgeReducer and RidgeRegression have all been updated to accomodate an optional covariate DataFrame as the final argument. Two new tests have been added to test_ridge_regression.py to test run modes with covariates: * test_ridge_reducer_transform_with_cov * test_two_level_regression_with_cov Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Cleaned up one unnecessary Pandas import Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Small changes for clarity and consistence with the rest of the code. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Forgot one usage of coalesce Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Added a couple of comments to explain logic and replaced usages of .values with .array Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Fixed one instance of the change .values -> .array where it was made in error. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Typo in test_ridge_regression.py. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Style auto-updates with yapfAll Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> * Flatten estimated phenotypes (#15) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Order to match labeldf Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check we tie-break Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * test var name Signed-off-by: Karen Feng <karen.feng@databricks.com> * clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * remove accidental files Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add fit_transform function to models (#17) Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Rename levels (#20) * Rename levels to wgr Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename test files Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add license headers (#21) * headers * executable * fix template rendering * yapf * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * More work Signed-off-by: Karen Feng <karen.feng@databricks.com> * More cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Fix docs tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * fix regression fit description Signed-off-by: Karen Feng <karen.feng@databricks.com> * fix capitalization Signed-off-by: Karen Feng <karen.feng@databricks.com> * address some comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * more cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * More cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * add notebook Signed-off-by: Karen Feng <karen.feng@databricks.com> * update notebook Signed-off-by: Karen Feng <karen.feng@databricks.com> Co-authored-by: Henry D <henrydavidge@gmail.com> Co-authored-by: Kiavash Kianfar <kiavash.kianfar@databricks.com> Co-authored-by: Leland <leland.barnard@gmail.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com>

karenfeng added 12 commits September 27, 2019 13:35

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karenfeng requested a review from henrydavidge October 8, 2019 09:15

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karenfeng changed the title ~~Release prep~~ [HLS-351] Release prep Oct 10, 2019

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karenfeng commented Oct 7, 2019 •

edited

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