Merge pull request #22 from dcolligan/namespace

Hierarchical namespace

.gitignore

@@ -12,7 +12,7 @@ scripts/auth.yml
 *.bak
 *.db-shm
 *.db-wal
-ga4gh_client/_version.py
+_version.py
 tests/data/registry.db
 
 # Below based off of https://gist.github.com/octocat/9257657

.travis.yml

@@ -21,9 +21,9 @@ before_script:
 # run_tests.py runs everything under the script: tag so only put commands
 # under it that we want to run (and want to be able to run) as local tests
 script: 
-  - flake8 client_dev.py setup.py tests ga4gh_client scripts
+  - flake8 client_dev.py setup.py tests ga4gh scripts
   - nosetests tests
-              --with-coverage --cover-package ga4gh_client
+              --with-coverage --cover-package ga4gh.client
               --cover-inclusive --cover-min-percentage=50
               --cover-branches --cover-erase
   - make clean -C docs

client_dev.py

@@ -1,7 +1,7 @@
 """
 Simple shim for running the client program during development.
 """
-import ga4gh_client.cli as cli
+import ga4gh.client.cli as cli
 
 if __name__ == "__main__":
     cli.client_main()

docs/api.rst

@@ -29,7 +29,7 @@ Client API
 
 .. todo:: Add overview documentation for the client API.
 
-.. autoclass:: ga4gh_client.client.HttpClient
+.. autoclass:: ga4gh.client.client.HttpClient
     :members: get_reference_set, get_reference,
         get_dataset, get_variant_set, get_variant,
         get_read_group_set, get_read_group,

docs/conf.py

@@ -19,7 +19,7 @@
 import os
 import sys
 sys.path.insert(0, os.path.abspath('..'))
-import ga4gh_client
+import ga4gh.client
 
 # -- General configuration ------------------------------------------------
 

ga4gh/__init__.py

@@ -0,0 +1,8 @@
+"""
+Client for servers implementing the GA4GH api
+"""
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+__import__('pkg_resources').declare_namespace(__name__)

ga4gh_client/__init__.py → ga4gh/client/__init__.py

@@ -1,6 +1,9 @@
 """
 Reference implementation of the GA4GH client
 """
+# Don't include future imports here; we don't want to export them as
+# part of the package
+
 __version__ = "undefined"
 try:
     from . import _version

ga4gh_client/cli.py → ga4gh/client/cli.py

@@ -9,12 +9,12 @@
 import logging
 import requests
 
-import ga4gh_client
-import ga4gh_client.client as client
-import ga4gh_client.exceptions as exceptions
-import ga4gh_client.protocol as protocol
+import ga4gh.client
+import ga4gh.client.client as client
+import ga4gh.client.exceptions as exceptions
+import ga4gh.client.protocol as protocol
 
-import ga4gh_common.cli as cli
+import ga4gh.common.cli as cli
 
 
 ###############
@@ -36,7 +36,7 @@ def addVersionArgument(parser):
     versionString = (
         "GA4GH Client Version {}\n"
         "(Protocol Version {})".format(
-            ga4gh_client.__version__, protocol.version))
+            ga4gh.client.__version__, protocol.version))
     parser.add_argument(
         "--version", version=versionString, action="version")
 

ga4gh_client/client.py → ga4gh/client/client.py

@@ -9,10 +9,10 @@
 import posixpath
 import logging
 
-import ga4gh_client.protocol as protocol
-import ga4gh_client.exceptions as exceptions
+import ga4gh.client.protocol as protocol
+import ga4gh.client.exceptions as exceptions
 
-import ga4gh_schemas.pb as pb
+import ga4gh.schemas.pb as pb
 
 
 class AbstractClient(object):

ga4gh_client/protocol.py → ga4gh/client/protocol.py

@@ -14,29 +14,29 @@
 import google.protobuf.message as message
 import google.protobuf.struct_pb2 as struct_pb2
 
-import ga4gh_schemas.pb as pb
-
-from ga4gh_schemas._protocol_version import version  # noqa
-from ga4gh_schemas.ga4gh.common_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.assay_metadata_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.metadata_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.metadata_service_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.read_service_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.reads_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.reference_service_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.references_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.variant_service_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.variants_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.allele_annotations_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.allele_annotation_service_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.sequence_annotations_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.sequence_annotation_service_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.bio_metadata_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.bio_metadata_service_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.genotype_phenotype_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.genotype_phenotype_service_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.rna_quantification_pb2 import *  # noqa
-from ga4gh_schemas.ga4gh.rna_quantification_service_pb2 import *  # noqa
+import ga4gh.schemas.pb as pb
+
+from ga4gh.schemas._protocol_version import version  # noqa
+from ga4gh.schemas.ga4gh.common_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.assay_metadata_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.metadata_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.metadata_service_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.read_service_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.reads_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.reference_service_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.references_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.variant_service_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.variants_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.allele_annotations_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.allele_annotation_service_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.sequence_annotations_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.sequence_annotation_service_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.bio_metadata_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.bio_metadata_service_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.genotype_phenotype_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.genotype_phenotype_service_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.rna_quantification_pb2 import *  # noqa
+from ga4gh.schemas.ga4gh.rna_quantification_service_pb2 import *  # noqa
 
 
 # A map of response objects to the name of the attribute used to

requirements.txt

@@ -3,7 +3,7 @@
 #
 # These requirements are read directly into setup.py, so specify them
 # in the order that they should be in in setup.py
-ga4gh_common==0.0.4
-ga4gh_schemas==0.0.7
+ga4gh_common==0.0.5
+ga4gh_schemas==0.0.8
 requests
 protobuf==3.0.0b3

setup.py

@@ -27,12 +27,13 @@
     # END BOILERPLATE
     name="ga4gh_client",
     description="A client for the GA4GH reference server",
-    packages=["ga4gh_client"],
+    packages=["ga4gh", "ga4gh.client"],
+    namespace_packages=["ga4gh"],
     url="https://github.com/ga4gh/ga4gh-client",
-    use_scm_version={"write_to": "ga4gh_client/_version.py"},
+    use_scm_version={"write_to": "ga4gh/client/_version.py"},
     entry_points={
         'console_scripts': [
-            'ga4gh_client=ga4gh_client.cli:client_main',
+            'ga4gh_client=ga4gh.client.cli:client_main',
         ]
     },
     # BEGIN BOILERPLATE

tests/unit/test_cli.py

@@ -9,11 +9,12 @@
 import mock
 import unittest
 
-import ga4gh_client.cli as cli_client
-import ga4gh_client.protocol as protocol
 import google.protobuf.descriptor as descriptor
 import google.protobuf.internal.python_message as python_message
-import ga4gh_common.utils as utils
+
+import ga4gh.client.cli as cli_client
+import ga4gh.client.protocol as protocol
+import ga4gh.common.utils as utils
 
 
 class TestClientArguments(unittest.TestCase):

tests/unit/test_client.py

@@ -9,9 +9,9 @@
 
 import mock
 
-import ga4gh_client.protocol as protocol
-import ga4gh_client.client as client
-import ga4gh_client.exceptions as exceptions
+import ga4gh.client.protocol as protocol
+import ga4gh.client.client as client
+import ga4gh.client.exceptions as exceptions
 
 
 class TestSearchMethodsCallRunRequest(unittest.TestCase):