Merge pull request #5 from genouest/20.05

See if tests pass with 20.05

.github/workflows/lint_test.yml

@@ -27,13 +27,13 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Python install
       run: |
-        pip install -U pip setuptools nose
+        pip install -U pip setuptools nose ephemeris
         python setup.py install
     - name: Launch containers
       run: |
         export BM2G_GLOBAL_CONFIG_PATH=`pwd`/test-data/bm2g.yml
-        GAL_DOCKER=$(docker run -d -p 8080:80 -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True -v `pwd`/test-data/:/data/ quay.io/bgruening/galaxy:19.09)
-        sleep 180 # Wait for the container to be ready
+        GAL_DOCKER=$(docker run -d -p 8080:80 -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True -v `pwd`/test-data/:/data/ quay.io/bgruening/galaxy:20.05)
+        galaxy-wait -g http://localhost:8080 --timeout 300
         docker exec -i $GAL_DOCKER install-tools /data/tools.yml
         docker exec -i $GAL_DOCKER supervisorctl restart galaxy:
         echo "-------------"

README.md

@@ -95,6 +95,9 @@ By default, relative file paths will be interpreted as relative to `${data.dir}/
 
 ## Changes
 
+- 2.2.0
+    - Fixed errors with Galaxy 20.05
+
 - 2.1.0
     - Fixed errors with Galaxy >19.05 (also fixes in Galaxy: https://github.com/galaxyproject/galaxy/issues/8792 and in IUC: https://github.com/galaxyproject/tools-iuc/pull/2634)
 

biomaj2galaxy/__init__.py

@@ -13,7 +13,7 @@
 
 standard_library.install_aliases()
 
-__version__ = '2.1.0'
+__version__ = '2.2.0'
 
 
 CONTEXT_SETTINGS = dict(auto_envvar_prefix='BM2G', help_option_names=['-h', '--help'])

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name="biomaj2galaxy",
-    version='2.1.0',
+    version='2.2.0',
     description="Command-line utility to assist in interconnecting BioMAJ (https://biomaj.genouest.org/) with Galaxy (http://galaxyproject.org/).",
     author="Anthony Bretaudeau",
     author_email="[email protected]",
@@ -22,9 +22,6 @@
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
         "Topic :: Scientific/Engineering",
-        "Programming Language :: Python :: 2",
-        "Programming Language :: Python :: 2.7",
-        "Programming Language :: Python :: 3.4",
-        "Programming Language :: Python :: 3.5",
         "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
     ])

test-data/bm2g.yml

@@ -2,4 +2,4 @@ __default: local
 
 local:
     url: "http://localhost:8080/"
-    apikey: "admin"
+    apikey: "fakekey"