Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

reorganize pyvcell packages #11

Merged
merged 21 commits into from
Mar 3, 2025
Merged

reorganize pyvcell packages #11

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
21 commits
Select commit Hold shift + click to select a range
ba0cf10
move pyvcell.api to pyvcell.core.api
jcschaff Feb 28, 2025
7d054bc
move pyvcell.simdata to pyvcell.core.simdata
jcschaff Feb 28, 2025
a758a4b
move pyvcell.solvers to pyvcell.core.solvers
jcschaff Feb 28, 2025
17eea47
remove foo.py
jcschaff Feb 28, 2025
655fb1c
move utils.py to data_model/zarr_utils.py
jcschaff Feb 28, 2025
77428e3
move all sbml code to pyvcell/sbml and all vcml code to pyvcell/vcml
jcschaff Feb 28, 2025
656fe41
rename pyvcell/data_model to pyvcell/sim_results
jcschaff Feb 28, 2025
3915a40
remove VcmlSpatialModel, use Biomodel instead
jcschaff Feb 28, 2025
faec8d0
remove unused method
jcschaff Feb 28, 2025
8f9e53c
fixed plot labels in Plotter.plot_conentrations()
jcschaff Feb 28, 2025
0d06f35
move notebooks and scripts to sep folders, fix some api calls
jcschaff Feb 28, 2025
5959cda
remove notebook output files from repo
jcschaff Feb 28, 2025
f15dc8a
gitignore for all test_output files
jcschaff Feb 28, 2025
c0d56bb
move solver_input files to tests/fixtures/data
jcschaff Feb 28, 2025
d5cc9f6
fix formatting in test data - should really be excluded
jcschaff Mar 3, 2025
cdc1df2
rename pyvcell.core.* to pyvcell._internal.* to guide end users and devs
jcschaff Mar 3, 2025
c7c3143
rename notebooks and example scripts to _internal if use _internal api
jcschaff Mar 3, 2025
0f6b84a
rename Spacial to Spatial - hurts my eyes
jcschaff Mar 3, 2025
0a89203
better error message if create SbmlSpatialModel with non-existent file
jcschaff Mar 3, 2025
d0a7bfb
moved example models to examples/models, renamed sbml notebook
jcschaff Mar 3, 2025
dc5ff0c
add simple vcml_workflow example script
jcschaff Mar 3, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
2 changes: 2 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -176,3 +176,5 @@ test_output_1/
/.venv_jupyter/

examples/test_output/SimID_*
/examples/notebooks/*.py
/examples/solver_output/zarr/
203 changes: 102 additions & 101 deletions .openapi-generator/FILES
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,102 +1,103 @@
pyvcell/__init__.py
pyvcell/api/__init__.py
pyvcell/api/vcell_client/__init__.py
pyvcell/api/vcell_client/api/__init__.py
pyvcell/api/vcell_client/api/admin_resource_api.py
pyvcell/api/vcell_client/api/bio_model_resource_api.py
pyvcell/api/vcell_client/api/field_data_resource_api.py
pyvcell/api/vcell_client/api/hello_world_api.py
pyvcell/api/vcell_client/api/publication_resource_api.py
pyvcell/api/vcell_client/api/simulation_resource_api.py
pyvcell/api/vcell_client/api/solver_resource_api.py
pyvcell/api/vcell_client/api/users_resource_api.py
pyvcell/api/vcell_client/api_client.py
pyvcell/api/vcell_client/api_response.py
pyvcell/api/vcell_client/configuration.py
pyvcell/api/vcell_client/docs/AccesTokenRepresentationRecord.md
pyvcell/api/vcell_client/docs/AdminResourceApi.md
pyvcell/api/vcell_client/docs/AnalyzedResultsFromFieldData.md
pyvcell/api/vcell_client/docs/BatchSystemType.md
pyvcell/api/vcell_client/docs/BioModel.md
pyvcell/api/vcell_client/docs/BioModelResourceApi.md
pyvcell/api/vcell_client/docs/BiomodelRef.md
pyvcell/api/vcell_client/docs/DataIdentifier.md
pyvcell/api/vcell_client/docs/DetailedState.md
pyvcell/api/vcell_client/docs/Domain.md
pyvcell/api/vcell_client/docs/Extent.md
pyvcell/api/vcell_client/docs/ExternalDataIdentifier.md
pyvcell/api/vcell_client/docs/FieldDataReference.md
pyvcell/api/vcell_client/docs/FieldDataResourceApi.md
pyvcell/api/vcell_client/docs/FieldDataSaveResults.md
pyvcell/api/vcell_client/docs/FieldDataShape.md
pyvcell/api/vcell_client/docs/HelloWorldApi.md
pyvcell/api/vcell_client/docs/HelloWorldMessage.md
pyvcell/api/vcell_client/docs/HtcJobID.md
pyvcell/api/vcell_client/docs/ISize.md
pyvcell/api/vcell_client/docs/Identity.md
pyvcell/api/vcell_client/docs/KeyValue.md
pyvcell/api/vcell_client/docs/MathmodelRef.md
pyvcell/api/vcell_client/docs/Origin.md
pyvcell/api/vcell_client/docs/Publication.md
pyvcell/api/vcell_client/docs/PublicationResourceApi.md
pyvcell/api/vcell_client/docs/SchedulerStatus.md
pyvcell/api/vcell_client/docs/SimulationExecutionStatusRecord.md
pyvcell/api/vcell_client/docs/SimulationJobStatusRecord.md
pyvcell/api/vcell_client/docs/SimulationMessage.md
pyvcell/api/vcell_client/docs/SimulationQueueEntryStatusRecord.md
pyvcell/api/vcell_client/docs/SimulationQueueID.md
pyvcell/api/vcell_client/docs/SimulationResourceApi.md
pyvcell/api/vcell_client/docs/SimulationStatusPersistentRecord.md
pyvcell/api/vcell_client/docs/SolverResourceApi.md
pyvcell/api/vcell_client/docs/Status.md
pyvcell/api/vcell_client/docs/StatusMessage.md
pyvcell/api/vcell_client/docs/User.md
pyvcell/api/vcell_client/docs/UserIdentityJSONSafe.md
pyvcell/api/vcell_client/docs/UserLoginInfoForMapping.md
pyvcell/api/vcell_client/docs/UserRegistrationInfo.md
pyvcell/api/vcell_client/docs/UsersResourceApi.md
pyvcell/api/vcell_client/docs/VCSimulationIdentifier.md
pyvcell/api/vcell_client/docs/VariableDomain.md
pyvcell/api/vcell_client/docs/VariableType.md
pyvcell/api/vcell_client/exceptions.py
pyvcell/api/vcell_client/models/__init__.py
pyvcell/api/vcell_client/models/acces_token_representation_record.py
pyvcell/api/vcell_client/models/analyzed_results_from_field_data.py
pyvcell/api/vcell_client/models/batch_system_type.py
pyvcell/api/vcell_client/models/bio_model.py
pyvcell/api/vcell_client/models/biomodel_ref.py
pyvcell/api/vcell_client/models/data_identifier.py
pyvcell/api/vcell_client/models/detailed_state.py
pyvcell/api/vcell_client/models/domain.py
pyvcell/api/vcell_client/models/extent.py
pyvcell/api/vcell_client/models/external_data_identifier.py
pyvcell/api/vcell_client/models/field_data_reference.py
pyvcell/api/vcell_client/models/field_data_save_results.py
pyvcell/api/vcell_client/models/field_data_shape.py
pyvcell/api/vcell_client/models/hello_world_message.py
pyvcell/api/vcell_client/models/htc_job_id.py
pyvcell/api/vcell_client/models/i_size.py
pyvcell/api/vcell_client/models/identity.py
pyvcell/api/vcell_client/models/key_value.py
pyvcell/api/vcell_client/models/mathmodel_ref.py
pyvcell/api/vcell_client/models/origin.py
pyvcell/api/vcell_client/models/publication.py
pyvcell/api/vcell_client/models/scheduler_status.py
pyvcell/api/vcell_client/models/simulation_execution_status_record.py
pyvcell/api/vcell_client/models/simulation_job_status_record.py
pyvcell/api/vcell_client/models/simulation_message.py
pyvcell/api/vcell_client/models/simulation_queue_entry_status_record.py
pyvcell/api/vcell_client/models/simulation_queue_id.py
pyvcell/api/vcell_client/models/simulation_status_persistent_record.py
pyvcell/api/vcell_client/models/status.py
pyvcell/api/vcell_client/models/status_message.py
pyvcell/api/vcell_client/models/user.py
pyvcell/api/vcell_client/models/user_identity_json_safe.py
pyvcell/api/vcell_client/models/user_login_info_for_mapping.py
pyvcell/api/vcell_client/models/user_registration_info.py
pyvcell/api/vcell_client/models/variable_domain.py
pyvcell/api/vcell_client/models/variable_type.py
pyvcell/api/vcell_client/models/vc_simulation_identifier.py
pyvcell/api/vcell_client/rest.py
pyvcell/api/vcell_client/test/__init__.py
pyvcell/api/vcell_client_README.md
pyvcell/_internal/__init__.py
pyvcell/_internal/api/__init__.py
pyvcell/_internal/api/vcell_client/__init__.py
pyvcell/_internal/api/vcell_client/api/__init__.py
pyvcell/_internal/api/vcell_client/api/admin_resource_api.py
pyvcell/_internal/api/vcell_client/api/bio_model_resource_api.py
pyvcell/_internal/api/vcell_client/api/field_data_resource_api.py
pyvcell/_internal/api/vcell_client/api/hello_world_api.py
pyvcell/_internal/api/vcell_client/api/publication_resource_api.py
pyvcell/_internal/api/vcell_client/api/simulation_resource_api.py
pyvcell/_internal/api/vcell_client/api/solver_resource_api.py
pyvcell/_internal/api/vcell_client/api/users_resource_api.py
pyvcell/_internal/api/vcell_client/api_client.py
pyvcell/_internal/api/vcell_client/api_response.py
pyvcell/_internal/api/vcell_client/configuration.py
pyvcell/_internal/api/vcell_client/docs/AccesTokenRepresentationRecord.md
pyvcell/_internal/api/vcell_client/docs/AdminResourceApi.md
pyvcell/_internal/api/vcell_client/docs/AnalyzedResultsFromFieldData.md
pyvcell/_internal/api/vcell_client/docs/BatchSystemType.md
pyvcell/_internal/api/vcell_client/docs/BioModel.md
pyvcell/_internal/api/vcell_client/docs/BioModelResourceApi.md
pyvcell/_internal/api/vcell_client/docs/BiomodelRef.md
pyvcell/_internal/api/vcell_client/docs/DataIdentifier.md
pyvcell/_internal/api/vcell_client/docs/DetailedState.md
pyvcell/_internal/api/vcell_client/docs/Domain.md
pyvcell/_internal/api/vcell_client/docs/Extent.md
pyvcell/_internal/api/vcell_client/docs/ExternalDataIdentifier.md
pyvcell/_internal/api/vcell_client/docs/FieldDataReference.md
pyvcell/_internal/api/vcell_client/docs/FieldDataResourceApi.md
pyvcell/_internal/api/vcell_client/docs/FieldDataSaveResults.md
pyvcell/_internal/api/vcell_client/docs/FieldDataShape.md
pyvcell/_internal/api/vcell_client/docs/HelloWorldApi.md
pyvcell/_internal/api/vcell_client/docs/HelloWorldMessage.md
pyvcell/_internal/api/vcell_client/docs/HtcJobID.md
pyvcell/_internal/api/vcell_client/docs/ISize.md
pyvcell/_internal/api/vcell_client/docs/Identity.md
pyvcell/_internal/api/vcell_client/docs/KeyValue.md
pyvcell/_internal/api/vcell_client/docs/MathmodelRef.md
pyvcell/_internal/api/vcell_client/docs/Origin.md
pyvcell/_internal/api/vcell_client/docs/Publication.md
pyvcell/_internal/api/vcell_client/docs/PublicationResourceApi.md
pyvcell/_internal/api/vcell_client/docs/SchedulerStatus.md
pyvcell/_internal/api/vcell_client/docs/SimulationExecutionStatusRecord.md
pyvcell/_internal/api/vcell_client/docs/SimulationJobStatusRecord.md
pyvcell/_internal/api/vcell_client/docs/SimulationMessage.md
pyvcell/_internal/api/vcell_client/docs/SimulationQueueEntryStatusRecord.md
pyvcell/_internal/api/vcell_client/docs/SimulationQueueID.md
pyvcell/_internal/api/vcell_client/docs/SimulationResourceApi.md
pyvcell/_internal/api/vcell_client/docs/SimulationStatusPersistentRecord.md
pyvcell/_internal/api/vcell_client/docs/SolverResourceApi.md
pyvcell/_internal/api/vcell_client/docs/Status.md
pyvcell/_internal/api/vcell_client/docs/StatusMessage.md
pyvcell/_internal/api/vcell_client/docs/User.md
pyvcell/_internal/api/vcell_client/docs/UserIdentityJSONSafe.md
pyvcell/_internal/api/vcell_client/docs/UserLoginInfoForMapping.md
pyvcell/_internal/api/vcell_client/docs/UserRegistrationInfo.md
pyvcell/_internal/api/vcell_client/docs/UsersResourceApi.md
pyvcell/_internal/api/vcell_client/docs/VCSimulationIdentifier.md
pyvcell/_internal/api/vcell_client/docs/VariableDomain.md
pyvcell/_internal/api/vcell_client/docs/VariableType.md
pyvcell/_internal/api/vcell_client/exceptions.py
pyvcell/_internal/api/vcell_client/models/__init__.py
pyvcell/_internal/api/vcell_client/models/acces_token_representation_record.py
pyvcell/_internal/api/vcell_client/models/analyzed_results_from_field_data.py
pyvcell/_internal/api/vcell_client/models/batch_system_type.py
pyvcell/_internal/api/vcell_client/models/bio_model.py
pyvcell/_internal/api/vcell_client/models/biomodel_ref.py
pyvcell/_internal/api/vcell_client/models/data_identifier.py
pyvcell/_internal/api/vcell_client/models/detailed_state.py
pyvcell/_internal/api/vcell_client/models/domain.py
pyvcell/_internal/api/vcell_client/models/extent.py
pyvcell/_internal/api/vcell_client/models/external_data_identifier.py
pyvcell/_internal/api/vcell_client/models/field_data_reference.py
pyvcell/_internal/api/vcell_client/models/field_data_save_results.py
pyvcell/_internal/api/vcell_client/models/field_data_shape.py
pyvcell/_internal/api/vcell_client/models/hello_world_message.py
pyvcell/_internal/api/vcell_client/models/htc_job_id.py
pyvcell/_internal/api/vcell_client/models/i_size.py
pyvcell/_internal/api/vcell_client/models/identity.py
pyvcell/_internal/api/vcell_client/models/key_value.py
pyvcell/_internal/api/vcell_client/models/mathmodel_ref.py
pyvcell/_internal/api/vcell_client/models/origin.py
pyvcell/_internal/api/vcell_client/models/publication.py
pyvcell/_internal/api/vcell_client/models/scheduler_status.py
pyvcell/_internal/api/vcell_client/models/simulation_execution_status_record.py
pyvcell/_internal/api/vcell_client/models/simulation_job_status_record.py
pyvcell/_internal/api/vcell_client/models/simulation_message.py
pyvcell/_internal/api/vcell_client/models/simulation_queue_entry_status_record.py
pyvcell/_internal/api/vcell_client/models/simulation_queue_id.py
pyvcell/_internal/api/vcell_client/models/simulation_status_persistent_record.py
pyvcell/_internal/api/vcell_client/models/status.py
pyvcell/_internal/api/vcell_client/models/status_message.py
pyvcell/_internal/api/vcell_client/models/user.py
pyvcell/_internal/api/vcell_client/models/user_identity_json_safe.py
pyvcell/_internal/api/vcell_client/models/user_login_info_for_mapping.py
pyvcell/_internal/api/vcell_client/models/user_registration_info.py
pyvcell/_internal/api/vcell_client/models/variable_domain.py
pyvcell/_internal/api/vcell_client/models/variable_type.py
pyvcell/_internal/api/vcell_client/models/vc_simulation_identifier.py
pyvcell/_internal/api/vcell_client/rest.py
pyvcell/_internal/api/vcell_client/test/__init__.py
pyvcell/_internal/api/vcell_client_README.md
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ repos:
hooks:
- id: ruff
args: [--exit-non-zero-on-fix]
exclude: 'pyvcell/api/.*\.py'
exclude: 'pyvcell/_internal/api/.*\.py'
- id: ruff-format

- repo: https://github.com/pre-commit/mirrors-prettier
Expand Down
Loading