Merge pull request #534 from Sage-Bionetworks/develop

release 1.8.0 to master

Author: zimingd

.travis.yml

@@ -1,12 +1,43 @@
-sudo: false
+sudo: required
 language: python
 
-script:
-- python setup.py install
-- nosetests -vs tests/unit
-- 'if [ "${TRAVIS_PULL_REQUEST}" = "false" ]; then nosetests -vs tests/integration; else echo "Skipping integration tests"; fi'
+matrix:
+  include:
+    - os: linux
+      python: 2.7.14
+      env:
+      # workaround for the dbus-python package installation not being able to find python shared object files for compilation when using virtualenv.
+      # source: https://github.com/willprice/python-omxplayer-wrapper/pull/101/files
+      - 'PYTHON_LIBS="-L$(python-config --prefix)/lib $(python-config --libs)"'
+      - PY_ENABLE_SHARD=0
+    - os: linux
+      python: 3.5.3
+      env:
+      - 'PYTHON_LIBS="-L$(python-config --prefix)/lib $(python-config --libs)"'
+      - PY_ENABLE_SHARD=0
+    - os: linux
+      python: 3.6.2
+      env:
+      - 'PYTHON_LIBS="-L$(python-config --prefix)/lib $(python-config --libs)"'
+      - PY_ENABLE_SHARD=0
+
+
+    - os: osx
+      language: generic
+      env: PY_VERSION=2.7.14
+    - os: osx
+      language: generic
+      env: PY_VERSION=3.5.3
+    - os: osx
+      language: generic
+      env: PY_VERSION=3.6.2
+
+addons:
+  #This is used for SFTP integration tests
+  ssh_known_hosts: ec2-54-212-85-156.us-west-2.compute.amazonaws.com
 
-before_install: |
+before_install:
+- |
   if [ "$TRAVIS_OS_NAME" == "osx" ]; then
     brew update
     brew outdated pyenv || brew upgrade pyenv
@@ -19,31 +50,44 @@ before_install: |
     pip install nose mock
   fi
 
+install:
+- |
+  if [ "$TRAVIS_OS_NAME" == "linux" ]; then
+    sudo apt-get update
+    sudo apt-get install gnome-keyring python-gnomekeyring libdbus-glib-1-dev
+    pip install --no-cache-dir --upgrade --force-reinstall dbus-python
+  fi
+- pip install -U setuptools
+- travis_wait pip install pysftp pandas boto3
+- python setup.py install
+
+before_script:
+- | # decrypt credentials used in tests
   if [[ "${TRAVIS_PULL_REQUEST}" = "false" ]]; then
     openssl aes-256-cbc -K $encrypted_d17283647768_key -iv $encrypted_d17283647768_iv -in test.synapseConfig.enc -out test.synapseConfig -d
     mv test.synapseConfig ~/.synapseConfig
     openssl aes-256-cbc -K $encrypted_d17283647768_key -iv $encrypted_d17283647768_iv -in test.awscredentials.enc -out test.awscredentials -d
     mkdir -p ~/.aws && mv test.awscredentials ~/.aws/credentials
   fi
-  travis_wait pip install pysftp cython pandas boto3
 
-addons:
-  ssh_known_hosts: ec2-54-212-85-156.us-west-2.compute.amazonaws.com
 
-matrix:
-  include:
-    - os: linux
-      python: 2.7.14
-    - os: linux
-      python: 3.5.3
-    - os: linux
-      python: 3.6.2
-    - os: osx
-      language: generic
-      env: PY_VERSION=2.7.14
-    - os: osx
-      language: generic
-      env: PY_VERSION=3.5.3
-    - os: osx
-      language: generic
-      env: PY_VERSION=3.6.2
+script:
+- nosetests -vs tests/unit
+- |
+  if [ "${TRAVIS_PULL_REQUEST}" = "false" ];then
+    if [ "$TRAVIS_OS_NAME" == "linux" ]; then
+      # set up the dbus daemon used to connect to the keyring. create default "login" keyring.
+      # TODO: once Travis uses Ubuntu Xenial instead of Trusty, remove python-gnomekeyring and just use 'gnome-keyring-daemon --unlock'
+      eval $(dbus-launch --sh-syntax)
+      echo -n "hunter2" | eval $(gnome-keyring-daemon --login)
+      eval $(gnome-keyring-daemon --components=secrets --start)
+      /usr/bin/python -c "import gnomekeyring;gnomekeyring.create_sync('login', '');";
+    fi
+
+    nosetests -vs tests/integration
+  else
+    echo "Skipping integration tests";
+  fi
+
+
+

appveyor.yml

@@ -18,7 +18,7 @@ test_script:
     - ps: |
         if ( -Not $env:APPVEYOR_PULL_REQUEST_NUMBER ){
           openssl aes-256-cbc -K $env:encrypted_d17283647768_key -iv $env:encrypted_d17283647768_iv -in test.synapseConfig.enc -out test.synapseConfig -d
-          move test.synapseConfig ${env:userprofile}\\.synapseConfig
+          move -force test.synapseConfig ${env:userprofile}\\.synapseConfig
           openssl aes-256-cbc -K $env:encrypted_d17283647768_key -iv $env:encrypted_d17283647768_iv -in test.awscredentials.enc -out test.awscredentials -d
           mkdir ${env:userprofile}\\.aws
           move test.awscredentials ${env:userprofile}\\.aws\\credentials

doc/conf.py

@@ -48,9 +48,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.7.5'
+version = '1.8.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.7.5'
+release = '1.8.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

release_notes/release-1.8.0.md

@@ -0,0 +1,40 @@
+# Release notes - Synapse Python Client - Version 1.8.0
+
+**Install Instructions:** `pip install --upgrade synapseclient` or see [http://docs.synapse.org/python/#installation](http://docs.synapse.org/python/#installation)  
+**Documentation:** [http://docs.synapse.org/python/](http://docs.synapse.org/python/)
+
+**Release Date:** 7-May-2018 
+
+--------------------------------------------------
+
+This release has 2 major changes:
+* The client will no longer store your saved credentials in your synapse cache (`~/synapseCache/.session`). The python client now relies on [keyring](https://pypi.org/project/keyring/) to handle credential storage of your Synapse credentials. 
+
+* The client also now uses connection pooling, which means that all method calls that connect to Synapse should now be faster.
+
+The remaining changes are bugfixes and cleanup of test code.
+
+
+Below are the full list of issues addressed by this release:
+
+Bug
+---
+
+*   \[[SYNPY-654](https://sagebionetworks.jira.com/browse/SYNPY-654)\] \- syn.getColumns does not terminate
+*   \[[SYNPY-658](https://sagebionetworks.jira.com/browse/SYNPY-658)\] \- Security vunerability on clusters
+*   \[[SYNPY-689](https://sagebionetworks.jira.com/browse/SYNPY-689)\] \- Wiki's attachments cannot be None
+*   \[[SYNPY-692](https://sagebionetworks.jira.com/browse/SYNPY-692)\] \- synapseutils.sync.generateManifest() sets contentType incorrectly
+*   \[[SYNPY-693](https://sagebionetworks.jira.com/browse/SYNPY-693)\] \- synapseutils.sync.generateManifest() UnicodeEncodingError in python 2
+
+Task
+----
+
+*   \[[SYNPY-617](https://sagebionetworks.jira.com/browse/SYNPY-617)\] \- Remove use of deprecated service to delete table rows
+*   \[[SYNPY-673](https://sagebionetworks.jira.com/browse/SYNPY-673)\] \- Fix Integration Tests being run on Appveyor
+*   \[[SYNPY-683](https://sagebionetworks.jira.com/browse/SYNPY-683)\] \- Clean up print()s used in unit/integration tests
+
+Improvement
+-----------
+
+*   \[[SYNPY-408](https://sagebionetworks.jira.com/browse/SYNPY-408)\] \- Add bettter error messages when /filehandle/batch fails.
+*   \[[SYNPY-647](https://sagebionetworks.jira.com/browse/SYNPY-647)\] \- Use connection pooling for Python client's requests

setup.py

@@ -41,12 +41,14 @@
         'requests>=1.2',
         'six',
         'future',
-        'backports.csv'
+        'backports.csv',
+        'keyring',
     ],
     extras_require = {
         'pandas':  ["pandas"],
         'pysftp': ["pysftp>=0.2.8"],
-        'boto3' : ["boto3"]
+        'boto3' : ["boto3"],
+        ':sys_platform=="linux2" or sys_platform=="linux"': ['keyrings.alt'],
     },
     test_suite='nose.collector',
     tests_require=['nose', 'mock'],