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Update dependencies #1417

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merged 4 commits into from
Aug 30, 2023
Merged

Update dependencies #1417

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0c11dbe
Use latest protmapper
bgyori Aug 29, 2023
5f1bb7e
Limit cython version
bgyori Aug 29, 2023
5bc5d89
Limit cython version on GHA
bgyori Aug 29, 2023
f4cd97f
Update test for new resources
bgyori Aug 30, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
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Expand Up @@ -39,7 +39,7 @@ jobs:
tar xzf bionetgen.tar.gz
pip install git+https://github.com/pysb/pysb.git
# Temporary fix. Ensure cython is installed before pyjnius
pip install cython
pip install "cython<3"
# Now install INDRA with all its extras
pip install .[all]
# Run slow tests only if we're in the cron setting
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2 changes: 1 addition & 1 deletion indra/tests/test_uniprot_client.py
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Expand Up @@ -92,7 +92,7 @@ def test_get_gene_name_no_gene_name():

def test_get_gene_name_multiple_gene_names():
gene_name = uniprot_client.get_gene_name('Q5VWM5')
assert gene_name == 'PRAMEF9'
assert gene_name == 'PRAMEF15'


def test_is_human():
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6 changes: 3 additions & 3 deletions setup.py
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Expand Up @@ -13,14 +13,14 @@ def main():
'requests>=2.11', 'lxml', 'ipython', 'future',
'networkx>=2,<3', 'pandas<2', 'ndex2==2.0.1', 'jinja2',
'markupsafe<2.1.0',
'protmapper>=0.0.27', 'obonet',
'protmapper>=0.0.28', 'obonet',
'tqdm', 'pybiopax>=0.0.5']

extras_require = {
# Inputs and outputs
'trips_offline': ['pykqml'],
'reach_offline': ['cython', 'pyjnius==1.1.4'],
'eidos_offline': ['cython', 'pyjnius==1.1.4'],
'reach_offline': ['cython<3', 'pyjnius==1.1.4'],
'eidos_offline': ['cython<3', 'pyjnius==1.1.4'],
'hypothesis': ['gilda>=0.10.2'],
'geneways': ['stemming', 'nltk<3.6'],
'bel': ['pybel>=0.15.0,<0.16.0'],
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