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.

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

experimenting with high level wrappers #3

Merged
merged 27 commits into from
Feb 18, 2025
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
27 commits
Select commit Hold shift + click to select a range
53e3ec6
experimented with high level wrappers
AlexPatrie Jan 28, 2025
7538eeb
fetched latest api changes
AlexPatrie Jan 30, 2025
61a6b13
update to workflow
AlexPatrie Jan 31, 2025
6f4ee74
updated run in workflow
AlexPatrie Jan 31, 2025
ad57dfb
added plot slice 3d
AlexPatrie Jan 31, 2025
6a526f6
added post processing parameters as generalizable attributes of Result
AlexPatrie Jan 31, 2025
0af9a98
fix: times data for x axis in plot concentrations
AlexPatrie Jan 31, 2025
52bf155
added 3d animator
AlexPatrie Jan 31, 2025
e3e34ce
fixed image animator
AlexPatrie Jan 31, 2025
6acbdb7
updated fv solver notebook
AlexPatrie Jan 31, 2025
ecde1ff
updates to fv solver ntbk
AlexPatrie Feb 3, 2025
70e4e2a
fixed to add zarr dataset to generalized get dataset method
AlexPatrie Feb 14, 2025
9420f82
fixed typing in spatial model
AlexPatrie Feb 14, 2025
8d9c662
chore: added ignores where needed and types for returns
AlexPatrie Feb 14, 2025
ca94a12
fix: added client fv input file getter to simulation and adjusted typing
AlexPatrie Feb 16, 2025
55c04a9
added pyvista unstructured grid constructor
AlexPatrie Feb 16, 2025
52bb0ee
update to POST verb for getFVSolverInput endpoint
jcschaff Feb 17, 2025
3c2eeb6
WIP - functional, but rough
jcschaff Feb 18, 2025
bfc9cc1
added z coordinate to plot rather than slice number
jcschaff Feb 18, 2025
7eca7d7
add missing .log file previously ignored
jcschaff Feb 18, 2025
13f6ee4
clean up imports
jcschaff Feb 18, 2025
660c495
add another missing log file
jcschaff Feb 18, 2025
7ae4727
fixed some numpy typing
jcschaff Feb 18, 2025
36cf50d
moved NDArray types to remove import cycle
jcschaff Feb 18, 2025
ad91fed
fix prettier, ruff, mypy
jcschaff Feb 18, 2025
56c2056
fix implicit dependencies
jcschaff Feb 18, 2025
eb27caf
no deptry in test directory, complained about pytest import in fixture
jcschaff Feb 18, 2025
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 23 additions & 0 deletions .openapi-generator-ignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
# OpenAPI Generator Ignore
# Generated by openapi-generator https://github.com/openapitools/openapi-generator

# Use this file to prevent files from being overwritten by the generator.
# The patterns follow closely to .gitignore or .dockerignore.

# As an example, the C# client generator defines ApiClient.cs.
# You can make changes and tell OpenAPI Generator to ignore just this file by uncommenting the following line:
#ApiClient.cs

# You can match any string of characters against a directory, file or extension with a single asterisk (*):
#foo/*/qux
# The above matches foo/bar/qux and foo/baz/qux, but not foo/bar/baz/qux

# You can recursively match patterns against a directory, file or extension with a double asterisk (**):
#foo/**/qux
# This matches foo/bar/qux, foo/baz/qux, and foo/bar/baz/qux

# You can also negate patterns with an exclamation (!).
# For example, you can ignore all files in a docs folder with the file extension .md:
#docs/*.md
# Then explicitly reverse the ignore rule for a single file:
#!docs/README.md
104 changes: 104 additions & 0 deletions .openapi-generator/FILES
Original file line number Diff line number Diff line change
@@ -0,0 +1,104 @@
.openapi-generator-ignore
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/test/test_solver_resource_api.py
pyvcell/api/vcell_client_README.md
1 change: 1 addition & 0 deletions .openapi-generator/VERSION
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
7.10.0
2 changes: 1 addition & 1 deletion Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ check: ## Run code quality tools.
@echo "🚀 Static type checking: Running mypy"
@poetry run mypy
@echo "🚀 Checking for obsolete dependencies: Running deptry"
@poetry run deptry --exclude=.venv --exclude=.venv_jupyter --exclude=examples .
@poetry run deptry --exclude=.venv --exclude=.venv_jupyter --exclude=examples --exclude=tests .

.PHONY: test
test: ## Test the code with pytest
Expand Down
Loading
Loading