moved bdgenomics.adam package to bdgenomics-adam

bigdatagenomics · Aug 30, 2017 · 677241a · 677241a
1 parent 511f925
commit 677241a
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Showing 14 changed files with 15 additions and 15 deletions.
diff --git 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
@@ -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 → adam-python/src/__init__.py b/adam-python/src/bdgenomics/__init__.py → adam-python/src/__init__.py
diff --git a/adam-python/src/bdgenomics/adam/.gitignore → adam-python/src/bdgenomics_adam/.gitignore b/adam-python/src/bdgenomics/adam/.gitignore → adam-python/src/bdgenomics_adam/.gitignore
diff --git a/adam-python/src/bdgenomics/adam/__init__.py → adam-python/src/bdgenomics_adam/__init__.py b/adam-python/src/bdgenomics/adam/__init__.py → adam-python/src/bdgenomics_adam/__init__.py
diff --git a/...python/src/bdgenomics/adam/adamContext.py → ...python/src/bdgenomics_adam/adamContext.py b/...python/src/bdgenomics/adam/adamContext.py → ...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 → adam-python/src/bdgenomics_adam/rdd.py b/adam-python/src/bdgenomics/adam/rdd.py → 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/...-python/src/bdgenomics/adam/stringency.py → ...-python/src/bdgenomics_adam/stringency.py b/...-python/src/bdgenomics/adam/stringency.py → ...-python/src/bdgenomics_adam/stringency.py
diff --git a/...thon/src/bdgenomics/adam/test/__init__.py → ...thon/src/bdgenomics_adam/test/__init__.py b/...thon/src/bdgenomics/adam/test/__init__.py → ...thon/src/bdgenomics_adam/test/__init__.py
diff --git a/.../bdgenomics/adam/test/adamContext_test.py → .../bdgenomics_adam/test/adamContext_test.py b/.../bdgenomics/adam/test/adamContext_test.py → .../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/...mics/adam/test/alignmentRecordRdd_test.py → ...mics_adam/test/alignmentRecordRdd_test.py b/...mics/adam/test/alignmentRecordRdd_test.py → ...mics_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/...c/bdgenomics/adam/test/featureRdd_test.py → ...c/bdgenomics_adam/test/featureRdd_test.py b/...c/bdgenomics/adam/test/featureRdd_test.py → ...c/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/.../bdgenomics/adam/test/genotypeRdd_test.py → .../bdgenomics_adam/test/genotypeRdd_test.py b/.../bdgenomics/adam/test/genotypeRdd_test.py → .../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/...c/bdgenomics/adam/test/variantRdd_test.py → ...c/bdgenomics_adam/test/variantRdd_test.py b/...c/bdgenomics/adam/test/variantRdd_test.py → ...c/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):