Merge pull request #11 from virtualcell/reorganize-repo

tests still need updating, good place to stop for now.

Author: jcschaff

.gitignore

@@ -176,3 +176,5 @@ test_output_1/
 /.venv_jupyter/
 
 examples/test_output/SimID_*
+/examples/notebooks/*.py
+/examples/solver_output/zarr/

.openapi-generator/FILES

@@ -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

.pre-commit-config.yaml

@@ -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