move biosimulations_pipeline and vcell_pipeline to python-utils

.gitignore

@@ -119,7 +119,7 @@ stdOut.txt
 *.rar
 
 # need this file for testing
-!vcell-cli-utils/tests/fixtures/modeldb-206365-outputs.zip
+!python-utils/tests/fixtures/modeldb-206365-outputs.zip
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*

vcell-cli-utils/biosimulations_pipeline/README.md → python-utils/README.md

@@ -13,7 +13,7 @@ OMEX_OUTPUT_DIR=<<path-to-output-artifacts>>
 ```
 
 ```bash
-poetry run python biosimulations_pipeline/cli.py --help
+poetry run python vcutils/biosimulations_pipeline/cli.py --help
 ```
 
 ```
@@ -39,7 +39,7 @@ poetry run python biosimulations_pipeline/cli.py --help
 ## upload OMEX files
 
 ```bash
-poetry run python biosimulations_pipeline/cli.py upload_omex --help
+poetry run python vcutils/biosimulations_pipeline/cli.py upload_omex --help
 ```
 
 ```
@@ -60,7 +60,7 @@ Options:
 ## download runs
 
 ```bash
-poetry run python biosimulations_pipeline/cli.py download_runs --help
+poetry run python vcutils/biosimulations_pipeline/cli.py download_runs --help
 ```
 
 ```
@@ -80,7 +80,7 @@ Options:
 ## refresh status
 
 ```bash
-poetry run python biosimulations_pipeline/cli.py refresh_status --help
+poetry run python vcutils/biosimulations_pipeline/cli.py refresh_status --help
 ```
 
 ```
@@ -96,7 +96,7 @@ Options:
 ## compare runs
 
 ```bash
-poetry run python biosimulations_pipeline/cli.py compare_runs --help
+poetry run python vcutils/biosimulations_pipeline/cli.py compare_runs --help
 ```
 
 ```
@@ -114,7 +114,7 @@ Options:
 ## publish
 
 ```bash
-poetry run python biosimulations_pipeline/cli.py publish --help
+poetry run python vcutils/biosimulations_pipeline/cli.py publish --help
 ```
 
 ```

python-utils/mypy.ini

@@ -0,0 +1,11 @@
+[mypy]
+ignore_missing_imports = True
+ignore_errors = False
+
+[vcell_opt]
+ingore_errors = False
+disallow_untyped_defs = True
+disallow_untyped_calls = True
+
+;[copasi-basico]
+;ignore_errors = False

python-utils/pyproject.toml

@@ -0,0 +1,39 @@
+[tool.poetry]
+name = "vcutils"
+version = "0.7.2"
+description = "Python general utility package for VCell"
+authors = ["Virtual Cell"]
+license = "MIT"
+repository = "https://github.com/virtualcell/vcell"
+keywords = ["HDF5", "SBML", "VCell"]
+classifiers = [
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT License',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3 :: Only",
+]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+requests = "^2.31.0"
+pydantic = "^2.5.2"
+python-dotenv = "^1.0.0"
+typer = "^0.9.0"
+h5py = "^3.10.0"
+
+
+[tool.poetry.dev-dependencies]
+pytest = "^7.4.0"
+mypy = "^1.4.1"
+
+[tool.poetry.group.dev.dependencies]
+types-requests = "^2.31.0.10"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

vcell-cli-utils/tests/citation_test.py → python-utils/tests/citation_test.py

@@ -1,5 +1,5 @@
 from typing import Optional
-from vcell_pipeline.citation import getCitation, CitationInfo, getSuggestedProjectName
+from vcutils.vcell_pipeline.citation import getCitation, CitationInfo, getSuggestedProjectName
 
 
 def test_citation() -> None:

vcell-cli-utils/tests/hdf5_test.py → python-utils/tests/hdf5_test.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from biosimulations_pipeline.hdf5_compare import get_results, compare_arrays, compare_datasets
+from vcutils.biosimulations_pipeline.hdf5_compare import get_results, compare_arrays, compare_datasets
 
 
 def test_compare_arrays() -> None:

vcell-cli-utils/tests/vcell_datamodels_test.py → python-utils/tests/vcell_datamodels_test.py

@@ -1,6 +1,6 @@
 import json
 
-from vcell_pipeline.vcell_datamodels import Publication
+from vcutils.vcell_pipeline.vcell_datamodels import Publication
 
 testdata = '''
 [ 

vcell-cli-utils/biosimulations_pipeline/biosim_api.py → python-utils/vcutils/biosimulations_pipeline/biosim_api.py

@@ -46,7 +46,7 @@ def run_project(
 
     print(source_omex.omex_file)
     with open(source_omex.omex_file, 'rb') as omex_file_handle:
-        multipart_form_data: dict[str, Union[tuple[str, BinaryIO],  tuple[None, str]] = {
+        multipart_form_data: dict[str, Union[tuple[str, BinaryIO],  tuple[None, str]]] = {
             'file': (source_omex.project_id + '.omex', omex_file_handle),
             'simulationRun': (None, simulation_run_request.json()),
         }

vcell-cli-utils/biosimulations_pipeline/cli.py → python-utils/vcutils/biosimulations_pipeline/cli.py

@@ -10,7 +10,7 @@
 from biosim_api import run_project, check_run_status, publish_project
 from data_manager import DataManager
 from datamodels import Simulator, SimulationRun, SimulatorComparison
-from vcell_common.api_utils import download_file
+from vcutils.vcell_common.api_utils import download_file
 from hdf5_compare import compare_datasets, get_results
 
 

vcell-cli-utils/biosimulations_pipeline/data_manager.py → python-utils/vcutils/biosimulations_pipeline/data_manager.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Optional
 
-from biosimulations_pipeline.datamodels import (
+from vcutils.biosimulations_pipeline.datamodels import (
     BiosimulationsProject,
     SourceOmex,
     SimulationRun,

vcell-cli-utils/vcell_pipeline/citation.py → python-utils/vcutils/vcell_pipeline/citation.py

@@ -1,7 +1,7 @@
 from typing import Optional
 import requests
 import time
-from vcell_pipeline.vcell_datamodels import Publication
+from vcutils.vcell_pipeline.vcell_datamodels import Publication
 
 
 class CitationInfo:

vcell-cli-utils/vcell_pipeline/download_vcell_omex.py → python-utils/vcutils/vcell_pipeline/download_vcell_omex.py

@@ -5,8 +5,8 @@
 from typing import Optional
 
 from citation import getCitation, CitationInfo, getSuggestedProjectName
-from vcell_common.api_utils import download_file
-from vcell_pipeline.vcell_datamodels import Publication
+from vcutils.vcell_common.api_utils import download_file
+from vcutils.vcell_pipeline.vcell_datamodels import Publication
 
 
 class ExportStatus(BaseModel):
@@ -63,8 +63,8 @@ def download_published_omex(api_base_url: str, out_dir: Path) -> None:
 
         except requests.exceptions.HTTPError as e:
             error_msg = str(e)
-            error_response: requests.Response = e.response
-            if error_response.status_code == 500:
+            error_response: requests.Response | None = e.response
+            if error_response is not None and error_response.status_code >= 400:
                 error_msg += " "+error_response.text
             print(error_msg)
             exportStatus.exception = error_msg