Python 3.7 Upgrade ( Issue #73 )

.gitignore

@@ -7,3 +7,4 @@ current-docs.zip
 intermine-docs-1.00.03.zip
 build
 MANIFEST
+.idea

.travis.yml

@@ -1,20 +1,22 @@
+---
+os: linux
 language: python
-sudo: false # use container based infrastructure
-jdk:
-- openjdk8
-dist: 
-- trusty
+jdk: openjdk11
+dist: bionic
+services: postgresql
+addons:
+  postgresql: 11
 env:
-    global:
-        - TESTMODEL_URL=http://localhost:8080/intermine-demo
-        - TESTMODEL_PATH=intermine-demo
+  global:
+    - TESTMODEL_URL=http://localhost:8080/intermine-demo
+    - TESTMODEL_PATH=intermine-demo
 before_script:
-- "./config/travis/init-solr.sh"
-- "./config/travis/init.sh"
-script: 
-    - python setup.py test
-    - python setup.py livetest
+  - "./config/travis/init-solr.sh"
+  - "./config/travis/init.sh"
+script:
+  - python setup.py test
+  - python setup.py livetest
 python:
-    - "2.7"
-    - "3.4"
-    - "3.5" 
+  - "3.6"
+  - "3.7"
+

README.md

@@ -25,7 +25,7 @@ to perform queries. Some examples of sites that
 are powered by InterMine software, and thus offer
 a compatible webservice API, are:
 
-  * [FlyMine](http://www.flymine.org)
+  * [FlyMine](https://www.flymine.org)
   * [MouseMine](http://www.mousemine.org)
   * [YeastMine](http://yeastmine.yeastgenome.org)
   * [ZebrafishMine](http://zebrafishmine.org)

config/travis/init-solr.sh

@@ -1,7 +1,7 @@
 # set up solr for testmine
 # testmine's setup script populates these empty indexes
 
-wget http://archive.apache.org/dist/lucene/solr/7.2.1/solr-7.2.1.tgz  
-tar xzf solr-7.2.1.tgz && ./solr-7.2.1/bin/solr start
-./solr-7.2.1/bin/solr create -c intermine-search
-./solr-7.2.1/bin/solr create -c intermine-autocomplete
+wget http://archive.apache.org/dist/lucene/solr/8.6.2/solr-8.6.2.tgz
+tar xzf solr-8.6.2.tgz && ./solr-8.6.2/bin/solr start
+./solr-8.6.2/bin/solr create -c intermine-search
+./solr-8.6.2/bin/solr create -c intermine-autocomplete

config/travis/init.sh

@@ -12,7 +12,6 @@ fi
 # Pull in the server code.
 git clone --single-branch --depth 1 https://github.com/intermine/intermine.git server
 
-
 export PSQL_USER=postgres
 
 # Set up properties
@@ -29,7 +28,8 @@ sed -i -e $SED_SCRIPT $TESTMODEL_PROPS
 # We will need a fully operational web-application
 echo '#---> Building and releasing web application to test against'
 (cd server/testmine && ./setup.sh)
-sleep 60 # let webapp startup
+# Travis is so slow
+sleep 90 # let webapp startup
 
 # Warm up the keyword search by requesting results, but ignoring the results
 $GET "$TESTMODEL_URL/service/search" > /dev/null

docs/make.bat

@@ -1,36 +1,36 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=Intermine
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=Intermine
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/conf.py

@@ -196,4 +196,3 @@
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
-\n

intermine.egg-info/PKG-INFO

@@ -0,0 +1,30 @@
+Metadata-Version: 1.1
+Name: intermine
+Version: 1.12.0
+Summary: InterMine WebService client
+Home-page: http://www.intermine.org
+Author: InterMine team
+Author-email: all@intermine.org
+License: LGPL, BSD
+Description: InterMine Webservice Client
+        ----------------------------
+
+        A Python API to access bioinformatics
+         data warehouses powered by the InterMine platform.
+
+
+Keywords: webservice,genomic,bioinformatics
+Platform: UNKNOWN
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Internet :: WWW/HTTP
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Operating System :: OS Independent
+Provides: intermine

intermine.egg-info/SOURCES.txt

@@ -0,0 +1,26 @@
+LICENSE-BSD
+LICENSE-LGPL
+MANIFEST.in
+README.md
+setup.py
+intermine/__init__.py
+intermine/bar_chart.py
+intermine/constraints.py
+intermine/decorators.py
+intermine/errors.py
+intermine/idresolution.py
+intermine/model.py
+intermine/pathfeatures.py
+intermine/query.py
+intermine/query_manager.py
+intermine/registry.py
+intermine/results.py
+intermine/util.py
+intermine/webservice.py
+intermine.egg-info/PKG-INFO
+intermine.egg-info/SOURCES.txt
+intermine.egg-info/dependency_links.txt
+intermine.egg-info/top_level.txt
+intermine/lists/__init__.py
+intermine/lists/list.py
+intermine/lists/listmanager.py

intermine.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

intermine.egg-info/top_level.txt

@@ -0,0 +1 @@
+intermine

intermine/__init__.py

@@ -1 +1 @@
-VERSION = "1.11.0"
+VERSION = "1.12.0"