Doc changes for github URL rename (#853)

schemas -> ga4gh-schemas

Author: dcolligan

CONTRIBUTING.rst

@@ -23,7 +23,7 @@ Issues
 @@@@@@
 
 The project's `Issues Page
-<https://github.com/ga4gh/schemas/issues>`__ is a forum to discuss
+<https://github.com/ga4gh/ga4gh-schemas/issues>`__ is a forum to discuss
 both major and minor issues related to developing the standards,
 formats, and APIs. It also serves as the means for collaborating with
 the group and discussing contributions that will ultimately lead to

doc/source/api/genotypephenotype.rst

@@ -57,12 +57,12 @@ G2P servers are planned to be implemented in three different contexts:
 Approach
 --------
 
-We based our original work on the model captured in `ga4gh/schemas
+We based our original work on the model captured in `ga4gh/ga4gh-schemas
 commit of Jul 30,
-2015 <https://github.com/ga4gh/schemas/tree/be171b00a5f164836dfd40ea5ae75ea56924d316>`__.
+2015 <https://github.com/ga4gh/ga4gh-schemas/tree/be171b00a5f164836dfd40ea5ae75ea56924d316>`__.
 This version of the schema predates the `separated genotype to phenotype
 files from
-baseline <https://github.com/ga4gh/schemas/commit/846b711fdcf544bf889cc7dbab19c6c48e9a9428>`__.
+baseline <https://github.com/ga4gh/ga4gh-schemas/commit/846b711fdcf544bf889cc7dbab19c6c48e9a9428>`__.
 After on review of the schemas and code, the team had feedback about
 separation of responsibility in the original API. The API was refactored
 to separate the searches for genotype, phenotype, feature and
@@ -89,10 +89,10 @@ their original context i.e. the source ontology.
 
 Due to the flexibility of the data model, users have a number of options
 for specifying each query term
-`feature <https://github.com/ga4gh/schemas/blob/be171b00a5f164836dfd40ea5ae75ea56924d316/src/main/resources/avro/genotypephenotypemethods.avdl#L105>`__,
-`phenotype <https://github.com/ga4gh/schemas/blob/be171b00a5f164836dfd40ea5ae75ea56924d316/src/main/resources/avro/genotypephenotypemethods.avdl#L108>`__,
+`feature <https://github.com/ga4gh/ga4gh-schemas/blob/be171b00a5f164836dfd40ea5ae75ea56924d316/src/main/resources/avro/genotypephenotypemethods.avdl#L105>`__,
+`phenotype <https://github.com/ga4gh/ga4gh-schemas/blob/be171b00a5f164836dfd40ea5ae75ea56924d316/src/main/resources/avro/genotypephenotypemethods.avdl#L108>`__,
 and
-`evidence <https://github.com/ga4gh/schemas/blob/be171b00a5f164836dfd40ea5ae75ea56924d316/src/main/resources/avro/genotypephenotypemethods.avdl#L111>`__.
+`evidence <https://github.com/ga4gh/ga4gh-schemas/blob/be171b00a5f164836dfd40ea5ae75ea56924d316/src/main/resources/avro/genotypephenotypemethods.avdl#L111>`__.
 
 API
 ---
@@ -152,7 +152,7 @@ Usage
 3. Repeat 1-2 as necessary, collating responses on the client.
 
 Many types rely heavily on the concept of an
-`OntologyTerm <https://github.com/ga4gh/schemas/blob/be171b00a5f164836dfd40ea5ae75ea56924d316/src/main/resources/avro/ontologies.avdl#L10>`__
+`OntologyTerm <https://github.com/ga4gh/ga4gh-schemas/blob/be171b00a5f164836dfd40ea5ae75ea56924d316/src/main/resources/avro/ontologies.avdl#L10>`__
 (see end of document for discussion on usage of OntologyTerms).
 
 Implementation

pom.xml

@@ -8,7 +8,7 @@
 
   <name>GA4GH: Schemas</name>
   <description>Data models and APIs for Genomic data.</description>
-  <url>https://github.com/ga4gh/schemas</url>
+  <url>https://github.com/ga4gh/ga4gh-schemas</url>
   <inceptionYear>2014</inceptionYear>
   <organization>
     <name>Global Alliance for Genomics and Health</name>
@@ -21,9 +21,9 @@
     </license>
   </licenses>
   <scm>
-    <connection>scm:git:https://github.com/ga4gh/schemas</connection>
-    <developerConnection>scm:git:https://github.com/ga4gh/schemas</developerConnection>
-    <url>https://github.com/ga4gh/schemas</url>
+    <connection>scm:git:https://github.com/ga4gh/ga4gh-schemas</connection>
+    <developerConnection>scm:git:https://github.com/ga4gh/ga4gh-schemas</developerConnection>
+    <url>https://github.com/ga4gh/ga4gh-schemas</url>
   </scm>
   <developers>
     <developer>

python/README.rst

@@ -38,7 +38,7 @@ releases `here <https://github.com/google/protobuf>`_.
 
 .. code-block:: bash
 
-    git clone [email protected]:ga4gh/schemas.git
+    git clone [email protected]:ga4gh/ga4gh-schemas.git
     cd schemas
     virtualenv env
     source env/bin/activate
@@ -75,18 +75,18 @@ Release Notes
 
 `0.6.0a9.post2 <https://pypi.python.org/pypi/ga4gh-schemas/0.6.0a9.post2>`_ 2016-1-20 
 
-* Set the release version (`#790 <https://github.com/ga4gh/schemas/pull/790>`_).
+* Set the release version (`#790 <https://github.com/ga4gh/ga4gh-schemas/pull/790>`_).
 
 `0.6.0a9.post1 <https://pypi.python.org/pypi/ga4gh-schemas/0.6.0a9.post1>`_ 2016-1
 
-* Remove protoc from install path (`#781 <https://github.com/ga4gh/schemas/pull/751>`_).
+* Remove protoc from install path (`#781 <https://github.com/ga4gh/ga4gh-schemas/pull/751>`_).
 
 0.6.0a9 2016-1
 
-* "BioSample" refactored to "Biosample" (`#697 <https://github.com/ga4gh/schemas/pull/697>`_).
-* Calls list supports if no genotype is reported (`#735 <https://github.com/ga4gh/schemas/pull/697>`_).
-* Introduces a new versioning scheme to match `ga4gh/schemas <https://github.com/ga4gh/schemas>`_ protocol version.
-* Improve setup process (`#751 <https://github.com/ga4gh/schemas/pull/751>`_, `#746 <https://github.com/ga4gh/schemas/pull/746>`_).
+* "BioSample" refactored to "Biosample" (`#697 <https://github.com/ga4gh/ga4gh-schemas/pull/697>`_).
+* Calls list supports if no genotype is reported (`#735 <https://github.com/ga4gh/ga4gh-schemas/pull/697>`_).
+* Introduces a new versioning scheme to match `ga4gh/schemas <https://github.com/ga4gh/ga4gh-schemas>`_ protocol version.
+* Improve setup process (`#751 <https://github.com/ga4gh/ga4gh-schemas/pull/751>`_, `#746 <https://github.com/ga4gh/ga4gh-schemas/pull/746>`_).
 
 0.0.8 2016-11-02
 

setup.py

@@ -57,7 +57,7 @@
         "ga4gh.schemas.google.api"
     ],
     namespace_packages=["ga4gh"],
-    url="https://github.com/ga4gh/schemas",
+    url="https://github.com/ga4gh/ga4gh-schemas",
     use_scm_version={"write_to": "python/ga4gh/schemas/_version.py"},
     entry_points={},
     package_dir={'': 'python'},