Skip to content

Release v1.0.3 #279

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

Merged
briandrawert merged 62 commits into from
Jun 10, 2022
Merged

Release v1.0.3 #279

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
62 commits
Select commit Hold shift + click to select a range
17e8118
Added quotes around invalid characters in type_id check.
BryanRumsey May 2, 2022
18528c1
Updated version to v1.0.3
BryanRumsey May 3, 2022
0ca2433
Added a run coverage script.
BryanRumsey May 20, 2022
13530f1
Added a module to contain the unittest files.
BryanRumsey May 20, 2022
d2f9a6a
Moved the unittest files into the unittests module.
BryanRumsey May 20, 2022
976725a
Added source args to coverage calls in testing github actions.
BryanRumsey May 20, 2022
5f9a469
Added unittests for the new timespan module.
BryanRumsey May 20, 2022
5492923
Added the error class for the timespan module.
BryanRumsey May 20, 2022
02c39ca
Added the timespan module to the core directory.
BryanRumsey May 20, 2022
c736547
Fixed import error with timespan error class.
BryanRumsey May 20, 2022
7fb2abc
Added the timespan to the core init.
BryanRumsey May 20, 2022
2a76aa0
Added a timespan module.
BryanRumsey May 22, 2022
54f376b
Added unittest for the new timespan module.
BryanRumsey May 22, 2022
cb3a4d5
Integrated the new timespan module into the package.
BryanRumsey May 22, 2022
4a447ba
Updated the unittests for the species module and added a validate fun…
BryanRumsey May 22, 2022
599665a
Added a validate function to the parameter class to handle all parame…
BryanRumsey May 23, 2022
ea5ebd5
Updated the unittests for the parameter module to test the updates.
BryanRumsey May 23, 2022
9a14edb
Re-organized the model class functions.
BryanRumsey May 25, 2022
9afb31c
Moved imports to the top of the model module.
BryanRumsey May 25, 2022
efc1e21
Updated Model.update_namespace().
BryanRumsey May 25, 2022
56fa78d
Refactored and re-organized the component functions. Added missing co…
BryanRumsey Jun 1, 2022
b47ee66
Fixed issue in solver caused by the change in the data functions data…
BryanRumsey Jun 1, 2022
5c51d77
Refactored the reaction class to be more consistent with GillesPy2.Re…
BryanRumsey Jun 2, 2022
bcb8c18
Refactored the unit test to cover the changes in reaction.py.
BryanRumsey Jun 2, 2022
69622c8
Converted all model subclasses with create functions.
BryanRumsey Jun 3, 2022
37338bb
Example updates part one.
BryanRumsey Jun 6, 2022
853b12b
Added the __str__ and _ipython_display_ function to the TimeSapn Module.
BryanRumsey Jun 6, 2022
4f95fd0
Fixed issue in compile prep function.
BryanRumsey Jun 6, 2022
f6e1888
Merge branch 'timespan-module' of https://github.com/StochSS/SpatialP…
BryanRumsey Jun 6, 2022
a90611d
Merge branch 'update-species-module' of https://github.com/StochSS/Sp…
BryanRumsey Jun 6, 2022
27e6a4f
Resolved merge conflicts.
BryanRumsey Jun 6, 2022
d4982ff
Merge branch 'update-model-reaction' of https://github.com/StochSS/Sp…
BryanRumsey Jun 6, 2022
8d592de
Merge branch 'update-model-reaction' of https://github.com/StochSS/Sp…
BryanRumsey Jun 6, 2022
e4b9fed
Merge branch 'update-model-reaction' of https://github.com/StochSS/Sp…
BryanRumsey Jun 6, 2022
2568e8f
Silenced isuniform check for coverage=="all"
BryanRumsey Jun 6, 2022
a80dbd2
Merge pull request #266 from StochSS/timespan-module
briandrawert Jun 6, 2022
1e03087
Merge branch 'develop' of https://github.com/StochSS/SpatialPy into u…
BryanRumsey Jun 6, 2022
65ed293
Merge branch 'develop' of https://github.com/StochSS/SpatialPy into u…
BryanRumsey Jun 6, 2022
6d59d77
Merge pull request #267 from StochSS/update-species-module
briandrawert Jun 6, 2022
277b34f
Merge branch 'develop' of https://github.com/StochSS/SpatialPy into u…
BryanRumsey Jun 6, 2022
a1c9c94
Merge pull request #268 from StochSS/update-parameter-modeule
briandrawert Jun 6, 2022
3ade2f7
Merge branch 'develop' of https://github.com/StochSS/SpatialPy into u…
BryanRumsey Jun 6, 2022
e032174
Merge pull request #272 from StochSS/update-model-module
briandrawert Jun 6, 2022
b9121f2
Merge pull request #273 from StochSS/update-reaction-module
briandrawert Jun 6, 2022
8425322
Added missing functions to reaction bug and fixed issue with resolvin…
BryanRumsey Jun 6, 2022
756c225
Merge branch 'update-model-reaction' of https://github.com/StochSS/Sp…
BryanRumsey Jun 6, 2022
c3942d5
Added check to ensure that the marate is a str before checking if its…
BryanRumsey Jun 6, 2022
171747f
Merge branch 'update-model-reaction' of https://github.com/StochSS/Sp…
BryanRumsey Jun 6, 2022
f55e8dd
Resticted the isuniform check to build and replaced StochKit with Spa…
BryanRumsey Jun 6, 2022
e0b2910
Fixed divide by zero error when particle vols are equal.
BryanRumsey Jun 6, 2022
131bbbf
Fixed the tspan validation in compile prep.
BryanRumsey Jun 6, 2022
6b911ef
Added missing ptp calculation.
BryanRumsey Jun 6, 2022
246661f
Merge pull request #271 from StochSS/update-model-reaction
seanebum Jun 7, 2022
82eb3f2
Example updates part two.
BryanRumsey Jun 7, 2022
98dde9e
Merge branch 'develop' of https://github.com/StochSS/SpatialPy into b…
BryanRumsey Jun 7, 2022
efd5021
Final examples update for working models.
BryanRumsey Jun 7, 2022
670741b
Fixed type issue for default timestep size.
BryanRumsey Jun 8, 2022
47dbbc5
Final updates to test examples.
BryanRumsey Jun 8, 2022
858992d
Fixed my dummy mistake of casting the timestep_size to the wrong type.
BryanRumsey Jun 8, 2022
ce01890
Removed duplicate examples
BryanRumsey Jun 9, 2022
00968de
Merge pull request #274 from StochSS/build-model
seanebum Jun 10, 2022
c3511aa
Merge pull request #255 from StochSS/develop
BryanRumsey Jun 10, 2022
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
2 changes: 1 addition & 1 deletion .github/workflows/run-integration-tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,4 +27,4 @@ jobs:
python3 -m pip install coverage

- name: Run tests
run: coverage run test/run_integration_tests.py
run: coverage run --source=spatialpy test/run_integration_tests.py
2 changes: 1 addition & 1 deletion .github/workflows/run-unit-tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,4 +25,4 @@ jobs:
python3 -m pip install coverage

- name: Run tests
run: coverage run test/run_unit_tests.py
run: coverage run --source=spatialpy test/run_unit_tests.py
254 changes: 124 additions & 130 deletions examples/3D_Cylinder_Demo.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

Loading