Pin moto to <5

.github/workflows/tests.yml

@@ -26,21 +26,19 @@ jobs:
         key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-    # Set up Python 3.7
-    - name: Set up Python 3.7
+    # Set up Python 3.8
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
     # Install EMMAA/test dependencies
     - name: Install dependencies
       run: |
         sudo apt-get install libpq-dev
         psql --no-password -h localhost -c 'create database emmaadb_test;' -U postgres
-        wget -nv https://files.pythonhosted.org/packages/91/a1/55b8224cbc9986bbad4b8f0f2dd11892845156b759b3495202d457ca0b73/kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.whl
-        mv kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.whl kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.zip
-        unzip kappy-4.0.94-cp37-cp37m-manylinux2010_x86_64.zip
         sudo apt-get install graphviz libgraphviz-dev pkg-config
         python -m pip install --upgrade pip
+        pip install kappy==4.1.2
         pip install nose coverage flask pyyaml boto3 openpyxl
         pip install git+https://github.com/sorgerlab/indra.git
         pip uninstall -y enum34
@@ -60,7 +58,7 @@ jobs:
         # cd automates
         # git checkout claytonm/gromet
         # cd ..
-        pip install boto3 jsonpickle pygraphviz fnvhash inflection pybel==0.15 flask_jwt_extended==3.25.0 gilda tweepy nose coverage moto[iam] sqlalchemy_utils termcolor flask-cors
+        pip install boto3 jsonpickle pygraphviz fnvhash inflection pybel==0.15 flask_jwt_extended==3.25.0 gilda tweepy nose coverage 'moto[iam]<5' sqlalchemy_utils termcolor flask-cors 'markupsafe<2.1.0'
         pip install --no-dependencies .
         pip install -U sqlalchemy==1.3.23
         wget "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.4.0/BioNetGen-2.4.0-Linux.tgz" -O bionetgen.tar.gz -nv

emmaa/tests/test_xdd.py

@@ -4,11 +4,11 @@
 
 @attr('nonpublic')
 def test_document_figures_doi():
-    doi = '10.1016/j.apsb.2020.09.003'
+    doi = '10.1136/bmj.n436'
     fig_list = get_document_figures(doi, 'DOI')
     assert fig_list
     # Should be a list of tuples with title and image bytes
-    assert len(fig_list[0]) == 2
+    assert len(fig_list[0]) == 8
 
 
 # This would call database

setup.py

@@ -30,14 +30,14 @@
       author_email='benjamin_gyori@hms.harvard.edu',
       classifiers=[
         'Development Status :: 4 - Beta',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7'
+        'Programming Language :: Python :: 3.8'
         ],
       packages=find_packages(),
       install_requires=['indra', 'boto3', 'jsonpickle', 'kappy==4.1.2',
                         'pygraphviz', 'fnvhash', 'sqlalchemy<1.4',
                         'inflection', 'pybel==0.15',
-                        'flask_jwt_extended==3.25.0', 'gilda', 'tweepy'],
-      extras_require={'test': ['nose', 'coverage', 'moto[iam]',
+                        'flask_jwt_extended==3.25.0', 'gilda', 'tweepy',
+                        'markupsafe<2.1.0'],
+      extras_require={'test': ['nose', 'coverage', 'moto[iam]<5',
                                'sqlalchemy_utils']}
       )