Add constraints for private repos

Add dependency links to setup py
Remove version pin from schemas and client requirements
Add protoc to travis for building schemas
Add guard if no constraints are found

.travis.yml

@@ -6,13 +6,14 @@ sudo: false
 cache:
   directories:
     - $HOME/.cache/pip
+    - /tmp/proto3.1.0
 
 install:
   - pip install pip --upgrade
 # RDFLib requres html5lib;  html5lib requires setuptools version 18.5 or above;
   - pip install setuptools==25.1.0
   - python setup.py sdist
-  - pip install dist/ga4gh*.tar.gz
+  - pip install dist/ga4gh*.tar.gz  -c constraints.txt
 # every installable in setup.py's entry_points should be tested here
   - ga4gh_configtest --version
   - ga4gh_server --version
@@ -21,9 +22,12 @@ install:
   - ga4gh_repo --version
 
 before_script:
-  - pip install -r dev-requirements.txt
+  - pip install -r dev-requirements.txt -c constraints.txt
   - python scripts/build_test_data.py 
-
+
+before_install:
+    - bash tools/travis-install-protoc.sh 3.1.0
+    - export PATH=/tmp/proto3.1.0/bin:$PATH
 
 # 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

constraints.txt

@@ -0,0 +1,2 @@
+git+git://github.com/david4096/ga4gh-client.git@protobuf31#egg=ga4gh_client
+git+git://github.com/david4096/schemas.git@protobuf31#egg=ga4gh_schemas

dev-requirements.txt

@@ -26,7 +26,7 @@ PyVCF==0.6.7
 freezegun==0.3.6
 guppy==0.1.10
 snakefood==1.4
-Sphinx==1.3.1
+Sphinx==1.4.6
 
 # Requirements for OIDC provider
 pyaml==15.03.1

requirements.txt

@@ -9,9 +9,8 @@
 # that are dependencies of libraries listed in the next section
 
 ga4gh-common==0.0.5
-ga4gh-schemas==0.0.8
-#ga4gh-client==0.0.3
-git+git://github.com/david4096/ga4gh-client.git@protobuf31#egg=ga4gh-client
+ga4gh-schemas
+ga4gh-client
 
 Werkzeug==0.11.5
 MarkupSafe==0.23
@@ -41,7 +40,7 @@ pyjwkest==1.0.1
 # prefix due to a setuptools bug.
 Flask-Cors==2.0.1
 Flask==0.10.1
-protobuf==3.1
+protobuf==3.1.0.post1
 humanize==0.5.1
 pysam==0.9.0
 requests==2.7.0

setup.py

@@ -23,10 +23,24 @@
         pinnedVersion = line.split()[0]
         install_requires.append(pinnedVersion)
 
+dependency_links = []
+try:
+    with open("constraints.txt") as constraintsFile:
+        for line in constraintsFile:
+            line = line.strip()
+            if len(line) == 0:
+                continue
+            if line[0] == '#':
+                continue
+            if line.find('git') != -1:
+                dependency_links.append(line)
+except EnvironmentError:
+    print('No constraints file found, proceeding without '
+          'creating dependency links.')
+
 setup(
-    # END BOILERPLATE
     name="ga4gh",
-    description="A reference implementation of the ga4gh API",
+    description="A reference implementation of the GA4GH API",
     packages=["ga4gh", "ga4gh.server", "ga4gh.server.datamodel",
               "ga4gh.server.templates"],
     namespace_packages=["ga4gh"],
@@ -42,9 +56,9 @@
             'ga4gh_repo=ga4gh.server.cli.repomanager:repo_main',
         ]
     },
-    # BEGIN BOILERPLATE
     long_description=long_description,
     install_requires=install_requires,
+    dependency_links=dependency_links,
     license='Apache License 2.0',
     include_package_data=True,
     author="Global Alliance for Genomics and Health",

tools/travis-install-protoc.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+# ensure that the specified version of protoc is installed in
+# /tmp/proto$PROTO_VERSION/bin/protoc, which maybe cached
+
+# bash tools/travis-install-protoc.sh 3.0.0-beta-3.1
+#   
+
+
+# make bash more robust.
+set -beEux -o pipefail
+
+if [ $# != 1 ] ; then
+    echo "wrong # of args: $0 protoversion" >&2
+    exit 1
+fi
+
+PROTO_VERSION="$1"
+PROTO_DIR="/tmp/proto$PROTO_VERSION"
+
+# Can't check for presence of directory as cache auto-creates it.
+if [ ! -f "$PROTO_DIR/bin/protoc" ]; then
+  wget -O - "https://github.com/google/protobuf/archive/v${PROTO_VERSION}.tar.gz" | tar xz -C /tmp
+  cd "/tmp/protobuf-${PROTO_VERSION}"
+  ./autogen.sh
+  ./configure --prefix="$PROTO_DIR" --disable-shared
+  make -j 4
+  make install
+fi
+