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fix simularium file generation #140

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fix simularium file generation #140

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00f75ab
fix: removed biosimulators simularium for native content
AlexPatrie Aug 22, 2024
fa78311
re-added biosimulators simularium for new version and updated exec
AlexPatrie Aug 22, 2024
dbd1b8f
updated setup to include latest simularium converter content
AlexPatrie Aug 23, 2024
c1743e8
chore: rm whitespace
AlexPatrie Aug 23, 2024
bcdb71e
updated linux build for exact python versions in gh cache
AlexPatrie Aug 26, 2024
f2b8091
updated linux build for spec python cache version
AlexPatrie Aug 26, 2024
04e4d8d
updated osx workflow to ensure cache versions
AlexPatrie Aug 26, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/linux.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11' ]
python-version: [ '3.7.15', '3.8.12', '3.9.7', '3.10.4', '3.11.0' ]
# python-version: [ '3.7', '3.8', '3.9', '3.10' ]

steps:
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2 changes: 1 addition & 1 deletion .github/workflows/osx.yml
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Expand Up @@ -15,7 +15,7 @@ jobs:
runs-on: macos-latest
strategy:
matrix:
python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11' ]
python-version: [ '3.7.15', '3.8.12', '3.9.7', '3.10.4', '3.11.0' ]
# python-version: [ '3.7', '3.8', '3.9', '3.10' ]

steps:
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2 changes: 1 addition & 1 deletion source/python/setup.py.in
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Expand Up @@ -63,7 +63,7 @@ setuptools.setup(
"biosimulators-utils[logging]>=0.1.124",
"numpy",
"pandas",
"biosimulators-simularium>=0.5.29"
"biosimulators-simularium>=0.6.3"
],
"biosimulators-dev": [
"flake8",
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37 changes: 21 additions & 16 deletions source/python/smoldyn/biosimulators/combine.py
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Expand Up @@ -59,27 +59,32 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None):
* :obj:`SedDocumentResults`: results
* :obj:`CombineArchiveLog`: log
'''

print('GENERATING A SIMULARIUM FILE ------------- ')
# extract contents from archive
temp_archive_root = tempfile.mkdtemp()
with zipfile.ZipFile(archive_filename, 'r') as ref:
ref.extractall(temp_archive_root)

# process simularium file generation
exec_biosimularium(
working_dir=temp_archive_root,
output_dir=out_dir,
use_json=True
)

print('RUNNING A SEDML SIMULATION ------------------ ')
# process sed result
print('RUNNING A SEDML SIMULATION ------------------ ')
results, log = exec_sedml_docs_in_archive(exec_sed_doc, archive_filename, out_dir,
apply_xml_model_changes=False,
config=config)

return results, log
# generate a simularium file
try:
print('GENERATING A SIMULARIUM FILE ------------- ')
# extract contents from archive
temp_archive_root = tempfile.mkdtemp()
with zipfile.ZipFile(archive_filename, 'r') as ref:
ref.extractall(temp_archive_root)

# process simularium file generation
exec_biosimularium(
working_dir=temp_archive_root,
output_dir=out_dir,
use_json=True
)
except Exception as e:
if config.LOG:
log.exception = e
else:
print(str(e))
return results, log


def exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None,
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