Merge pull request #109 from intermine/1.14-update

Bump version to v1.14.0

Author: martinburchell

.github/workflows/im-build.yml

@@ -2,8 +2,9 @@ name: InterMine WS Python CI
 
 on:
   push:
-  pull_request:
 
+env:
+  SOLR_VERSION: 8.6.2
 jobs:
   build:
 
@@ -34,6 +35,11 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: '3.10'
+    - name: Setup Apache Solr
+      uses: DhavalGojiya/setup-solr-action@v1.2.0
+      with:
+        solr-version: ${{ env.SOLR_VERSION }}
+        solr-core-name: 'intermine-search'
     - name: Change apt mirror
       run: |
           set -euo pipefail
@@ -44,7 +50,7 @@ jobs:
     - name: Install dependencies
       run: |
         set -euo pipefail
-        sudo apt-get install libxml2-dev libxslt-dev python3-dev
+        sudo apt-get install -y libxml2-dev libxslt-dev python3-dev wait-for-it
         python -m pip install --upgrade pip
         pip install -U setuptools
         pip install -r requirements.txt
@@ -54,10 +60,16 @@ jobs:
         sudo apt-get update -y
         sudo apt-get install -y libpq-dev postgresql-client
         sudo service postgresql start
+    - name: Create additional Solr core
+      run: |
+        set -euo pipefail
+        wait-for-it localhost:8983
+        docker ps
+        SOLR_CONTAINER=$(docker ps -f ancestor=solr:"$SOLR_VERSION" --format '{{.ID}}' | head -n1)
+        docker exec "$SOLR_CONTAINER" /opt/solr/bin/solr create -c intermine-autocomplete
     - name: Run unit tests
       run: |
         set -euo pipefail
-        ./config/ci/init-solr.sh ${GITHUB_WORKSPACE}
-        ./config/ci/init.sh ${GITHUB_WORKSPACE} http://localhost:8080/intermine-demo
+        ./config/ci/init.sh ${GITHUB_WORKSPACE} $(which python3) http://localhost:8080/intermine-demo
         python setup.py test
         python setup.py livetest

README.md

@@ -2,25 +2,25 @@ The InterMine Python Webservice Client
 =====================================
 
 
-[![Build Status][badge]][ci] 
+[![Build Status][badge]][ci]
 ![Version](http://img.shields.io/badge/version-1.12.0-blue.svg?style=flat)
-[![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/intermine/intermine/blob/master/LICENSE) 
+[![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/intermine/intermine/blob/master/LICENSE)
 [![Research software impact](http://depsy.org/api/package/pypi/intermine/badge.svg)](http://depsy.org/package/python/intermine)
 
 [![Conda](https://anaconda.org/intermine/intermine/badges/installer/conda.svg)](https://anaconda.org/bioconda/intermine)
 [![Anaconda-Server Badge](https://anaconda.org/bioconda/intermine/badges/version.svg)](https://anaconda.org/bioconda/intermine)
 [![Downloads](https://anaconda.org/bioconda/intermine/badges/downloads.svg)](https://anaconda.org/bioconda/intermine)
 
 
-An implementation of a webservice client 
+An implementation of a webservice client
 for InterMine webservices, written in Python
 
 Who should use this software?
 -----------------------------
 
-This software is intended for people who make 
+This software is intended for people who make
 use of InterMine datawarehouses (ie. Biologists)
-and who want a quicker, more automated way 
+and who want a quicker, more automated way
 to perform queries. Some examples of sites that
 are powered by InterMine software, and thus offer
 a compatible webservice API, are:
@@ -36,9 +36,9 @@ a compatible webservice API, are:
 
 See the [InterMine registry](http://registry.intermine.org/) for the full list of available InterMines.
 
-Queries here refer to database queries over the 
-integrated datawarehouse. Instead of using 
-SQL, InterMine services use a flexible and 
+Queries here refer to database queries over the
+integrated datawarehouse. Instead of using
+SQL, InterMine services use a flexible and
 powerful sub-set of database query language
 to enable wide-ranging and arbitrary queries.
 
@@ -67,7 +67,7 @@ the following command: (from the source directory)
   python setup.py test
 ```
 
-If you want to run the suite against a live server (e.g. as deployed by the testmodel/setup.sh in 
+If you want to run the suite against a live server (e.g. as deployed by the testmodel/setup.sh in
 the InterMine distribution, then you can run:
 
 ```
@@ -122,6 +122,7 @@ For example:
 Changes:
 --------
 
+    1.14.00   Add Python 3.10 support
     1.13.00   Added get_template_by_user method
 			  Added property view_types to the template
     1.12.00   Added organism to list upload
@@ -152,7 +153,7 @@ Changes:
               Ensure lists and queries share the same overloading
     0.99.02   Allow sort-orders which are not in the view but are on selected classes
     0.99.01   Better representation of multiple sort-orders.
-    0.99.00   Fixed bug with subclasses not being included in clones 
+    0.99.00   Fixed bug with subclasses not being included in clones
               Added support for new json format for ws versions >= 8.
     0.98.16   Fixed bug with XML parsing and subclasses where the subclass is mentioned in the first view.
               better result format documentation and tests
@@ -184,7 +185,5 @@ Please cite
 
 [Nucleic Acids Res. 2014 Jul;42(Web Server issue):W468-72](https://academic.oup.com/nar/article/42/W1/W468/2435235)
 
-[![doi](http://img.shields.io/badge/doi-10.1093/nar/gku301-blue.svg?style=flat)](https://doi.org/10.1093/nar/gku301) 
+[![doi](http://img.shields.io/badge/doi-10.1093/nar/gku301-blue.svg?style=flat)](https://doi.org/10.1093/nar/gku301)
 [![pubmed](http://img.shields.io/badge/pubmed-24753429-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/24753429)
-
-

config/ci/init.sh

@@ -2,13 +2,14 @@
 
 set -euo pipefail
 
-if [ "$#" != "2" ]; then
-   echo "Usage: $0 <workspace_dir> <testmodel_url>"
+if [ "$#" != "3" ]; then
+   echo "Usage: $0 <workspace_dir> <python executable> <testmodel_url>"
    exit 2
 fi
 
 WORKSPACE_DIR=$1
-TESTMODEL_URL=$2
+PYTHON=$2
+TESTMODEL_URL=$3
 
 INTERMINE_DIR=${WORKSPACE_DIR}/server
 TESTMINE_DIR=${INTERMINE_DIR}/testmine
@@ -48,6 +49,7 @@ sed -i -e "s/PSQL_HOST/${PSQL_HOST}/" "$TESTMODEL_PROPS"
 sed -i -e "s/PSQL_USER/${PSQL_USER}/" "$TESTMODEL_PROPS"
 sed -i -e "s/PSQL_PWD/${PSQL_PWD}/" "$TESTMODEL_PROPS"
 
+${PYTHON} "${INTERMINE_DIR}"/config/lib/install_intermine.py
 
 # We will need a fully operational web-application
 echo '#---> Building and releasing web application to test against'

intermine/__init__.py

@@ -1 +1 @@
-VERSION = "1.13.0"
+VERSION = "1.14.0"