diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c76fb165..53b073f6 100644 --- a/.github/workflows/tests.yml +++ b/.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 diff --git a/emmaa/tests/test_xdd.py b/emmaa/tests/test_xdd.py index 7371e714..e642427f 100644 --- a/emmaa/tests/test_xdd.py +++ b/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 diff --git a/setup.py b/setup.py index 23cfc1af..4be494e2 100644 --- a/setup.py +++ b/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']} )