From 677241a66a5539653752b95642e71d7e57035e02 Mon Sep 17 00:00:00 2001 From: Alyssa Morrow Date: Wed, 30 Aug 2017 14:15:39 -0700 Subject: [PATCH] moved bdgenomics.adam package to bdgenomics-adam --- adam-python/Makefile | 2 +- adam-python/setup.py | 2 +- adam-python/src/{bdgenomics => }/__init__.py | 0 .../src/{bdgenomics/adam => bdgenomics_adam}/.gitignore | 0 .../src/{bdgenomics/adam => bdgenomics_adam}/__init__.py | 0 .../src/{bdgenomics/adam => bdgenomics_adam}/adamContext.py | 2 +- adam-python/src/{bdgenomics/adam => bdgenomics_adam}/rdd.py | 2 +- .../src/{bdgenomics/adam => bdgenomics_adam}/stringency.py | 0 .../{bdgenomics/adam => bdgenomics_adam}/test/__init__.py | 0 .../adam => bdgenomics_adam}/test/adamContext_test.py | 4 ++-- .../test/alignmentRecordRdd_test.py | 6 +++--- .../adam => bdgenomics_adam}/test/featureRdd_test.py | 4 ++-- .../adam => bdgenomics_adam}/test/genotypeRdd_test.py | 4 ++-- .../adam => bdgenomics_adam}/test/variantRdd_test.py | 4 ++-- 14 files changed, 15 insertions(+), 15 deletions(-) rename adam-python/src/{bdgenomics => }/__init__.py (100%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/.gitignore (100%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/__init__.py (100%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/adamContext.py (99%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/rdd.py (99%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/stringency.py (100%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/test/__init__.py (100%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/test/adamContext_test.py (97%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/test/alignmentRecordRdd_test.py (96%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/test/featureRdd_test.py (96%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/test/genotypeRdd_test.py (95%) rename adam-python/src/{bdgenomics/adam => bdgenomics_adam}/test/variantRdd_test.py (92%) diff --git a/adam-python/Makefile b/adam-python/Makefile index e8284bd386..fd2bd47298 100644 --- a/adam-python/Makefile +++ b/adam-python/Makefile @@ -32,7 +32,7 @@ The 'clean' target undoes the effect of 'develop'. The 'test' target runs ADAM's unit tests. Set the 'tests' variable to run a particular test, e.g. - make test tests=src/adam/test/sort/sortTest.py::SortTest::testSort + make test tests=src/bdgenomics_adam/test/sort/sortTest.py::SortTest::testSort The 'pypi' target publishes the current commit of ADAM to PyPI after enforcing that the working copy and the index are clean, and tagging it as an unstable .dev build. diff --git a/adam-python/setup.py b/adam-python/setup.py index fa6b161f4e..77b9ad98cc 100644 --- a/adam-python/setup.py +++ b/adam-python/setup.py @@ -20,7 +20,7 @@ from version import version as adam_version setup( - name='bdgenomics.adam', + name='bdgenomics_adam', version=adam_version, description='A fast, scalable genome analysis system', author='Frank Austin Nothaft', diff --git a/adam-python/src/bdgenomics/__init__.py b/adam-python/src/__init__.py similarity index 100% rename from adam-python/src/bdgenomics/__init__.py rename to adam-python/src/__init__.py diff --git a/adam-python/src/bdgenomics/adam/.gitignore b/adam-python/src/bdgenomics_adam/.gitignore similarity index 100% rename from adam-python/src/bdgenomics/adam/.gitignore rename to adam-python/src/bdgenomics_adam/.gitignore diff --git a/adam-python/src/bdgenomics/adam/__init__.py b/adam-python/src/bdgenomics_adam/__init__.py similarity index 100% rename from adam-python/src/bdgenomics/adam/__init__.py rename to adam-python/src/bdgenomics_adam/__init__.py diff --git a/adam-python/src/bdgenomics/adam/adamContext.py b/adam-python/src/bdgenomics_adam/adamContext.py similarity index 99% rename from adam-python/src/bdgenomics/adam/adamContext.py rename to adam-python/src/bdgenomics_adam/adamContext.py index f818f66dbb..6536151572 100644 --- a/adam-python/src/bdgenomics/adam/adamContext.py +++ b/adam-python/src/bdgenomics_adam/adamContext.py @@ -16,7 +16,7 @@ # limitations under the License. # -from bdgenomics.adam.rdd import AlignmentRecordRDD, \ +from bdgenomics_adam.rdd import AlignmentRecordRDD, \ CoverageRDD, \ FeatureRDD, \ FragmentRDD, \ diff --git a/adam-python/src/bdgenomics/adam/rdd.py b/adam-python/src/bdgenomics_adam/rdd.py similarity index 99% rename from adam-python/src/bdgenomics/adam/rdd.py rename to adam-python/src/bdgenomics_adam/rdd.py index c800d11206..3dda101438 100644 --- a/adam-python/src/bdgenomics/adam/rdd.py +++ b/adam-python/src/bdgenomics_adam/rdd.py @@ -21,7 +21,7 @@ from pyspark.rdd import RDD from pyspark.sql import DataFrame, SQLContext -from bdgenomics.adam.stringency import LENIENT, _toJava +from bdgenomics_adam.stringency import LENIENT, _toJava _log = logging.getLogger(__name__) diff --git a/adam-python/src/bdgenomics/adam/stringency.py b/adam-python/src/bdgenomics_adam/stringency.py similarity index 100% rename from adam-python/src/bdgenomics/adam/stringency.py rename to adam-python/src/bdgenomics_adam/stringency.py diff --git a/adam-python/src/bdgenomics/adam/test/__init__.py b/adam-python/src/bdgenomics_adam/test/__init__.py similarity index 100% rename from adam-python/src/bdgenomics/adam/test/__init__.py rename to adam-python/src/bdgenomics_adam/test/__init__.py diff --git a/adam-python/src/bdgenomics/adam/test/adamContext_test.py b/adam-python/src/bdgenomics_adam/test/adamContext_test.py similarity index 97% rename from adam-python/src/bdgenomics/adam/test/adamContext_test.py rename to adam-python/src/bdgenomics_adam/test/adamContext_test.py index 8208b7448e..b97d0ad09f 100644 --- a/adam-python/src/bdgenomics/adam/test/adamContext_test.py +++ b/adam-python/src/bdgenomics_adam/test/adamContext_test.py @@ -17,8 +17,8 @@ # -from bdgenomics.adam.adamContext import ADAMContext -from bdgenomics.adam.test import SparkTestCase +from bdgenomics_adam.adamContext import ADAMContext +from bdgenomics_adam.test import SparkTestCase class ADAMContextTest(SparkTestCase): diff --git a/adam-python/src/bdgenomics/adam/test/alignmentRecordRdd_test.py b/adam-python/src/bdgenomics_adam/test/alignmentRecordRdd_test.py similarity index 96% rename from adam-python/src/bdgenomics/adam/test/alignmentRecordRdd_test.py rename to adam-python/src/bdgenomics_adam/test/alignmentRecordRdd_test.py index 64a38fafd3..6540d1969f 100644 --- a/adam-python/src/bdgenomics/adam/test/alignmentRecordRdd_test.py +++ b/adam-python/src/bdgenomics_adam/test/alignmentRecordRdd_test.py @@ -17,9 +17,9 @@ # -from bdgenomics.adam.adamContext import ADAMContext -from bdgenomics.adam.rdd import AlignmentRecordRDD, CoverageRDD -from bdgenomics.adam.test import SparkTestCase +from bdgenomics_adam.adamContext import ADAMContext +from bdgenomics_adam.rdd import AlignmentRecordRDD, CoverageRDD +from bdgenomics_adam.test import SparkTestCase from pyspark.sql.types import DoubleType diff --git a/adam-python/src/bdgenomics/adam/test/featureRdd_test.py b/adam-python/src/bdgenomics_adam/test/featureRdd_test.py similarity index 96% rename from adam-python/src/bdgenomics/adam/test/featureRdd_test.py rename to adam-python/src/bdgenomics_adam/test/featureRdd_test.py index 2f1d040109..d78234fefd 100644 --- a/adam-python/src/bdgenomics/adam/test/featureRdd_test.py +++ b/adam-python/src/bdgenomics_adam/test/featureRdd_test.py @@ -17,8 +17,8 @@ # -from bdgenomics.adam.adamContext import ADAMContext -from bdgenomics.adam.test import SparkTestCase +from bdgenomics_adam.adamContext import ADAMContext +from bdgenomics_adam.test import SparkTestCase class FeatureRDDTest(SparkTestCase): diff --git a/adam-python/src/bdgenomics/adam/test/genotypeRdd_test.py b/adam-python/src/bdgenomics_adam/test/genotypeRdd_test.py similarity index 95% rename from adam-python/src/bdgenomics/adam/test/genotypeRdd_test.py rename to adam-python/src/bdgenomics_adam/test/genotypeRdd_test.py index 2b58c6bdb2..f983c16551 100644 --- a/adam-python/src/bdgenomics/adam/test/genotypeRdd_test.py +++ b/adam-python/src/bdgenomics_adam/test/genotypeRdd_test.py @@ -17,8 +17,8 @@ # -from bdgenomics.adam.adamContext import ADAMContext -from bdgenomics.adam.test import SparkTestCase +from bdgenomics_adam.adamContext import ADAMContext +from bdgenomics_adam.test import SparkTestCase class GenotypeRDDTest(SparkTestCase): diff --git a/adam-python/src/bdgenomics/adam/test/variantRdd_test.py b/adam-python/src/bdgenomics_adam/test/variantRdd_test.py similarity index 92% rename from adam-python/src/bdgenomics/adam/test/variantRdd_test.py rename to adam-python/src/bdgenomics_adam/test/variantRdd_test.py index f89ccd2767..71aec9d89b 100644 --- a/adam-python/src/bdgenomics/adam/test/variantRdd_test.py +++ b/adam-python/src/bdgenomics_adam/test/variantRdd_test.py @@ -17,8 +17,8 @@ # -from bdgenomics.adam.adamContext import ADAMContext -from bdgenomics.adam.test import SparkTestCase +from bdgenomics_adam.adamContext import ADAMContext +from bdgenomics_adam.test import SparkTestCase class VariantRDDTest(SparkTestCase):