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Pin moto to <5 #279

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12 changes: 5 additions & 7 deletions .github/workflows/tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
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4 changes: 2 additions & 2 deletions emmaa/tests/test_xdd.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
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8 changes: 4 additions & 4 deletions setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -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']}
)
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