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Stage Release v1.0.3 - #255

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BryanRumsey merged 61 commits into
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Jun 10, 2022
Merged

Stage Release v1.0.3#255
BryanRumsey merged 61 commits into
stagingfrom
develop

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@BryanRumsey

@BryanRumseyBryanRumsey commented May 3, 2022•
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closes#251
closes#254
closes#256
closes#257
closes#258
closes#259
closes#260
closes#261
closes#262
closes#263
closes#264
closes#269
closes#270

@BryanRumseyBryanRumsey added this to the 1.0.3 Release milestone May 3, 2022
@BryanRumsey
BryanRumsey changed the base branch from main to stagingMay 3, 2022 13:36
@BryanRumseyBryanRumsey changed the title Release v1.0.3Stage Release v1.0.3May 3, 2022
@BryanRumsey
Added a run coverage script.
0ca2433
@BryanRumsey
Added a module to contain the unittest files.
13530f1
@BryanRumsey
Moved the unittest files into the unittests module.
d2f9a6a
@BryanRumsey
Added source args to coverage calls in testing github actions.
976725a
@BryanRumsey
Added unittests for the new timespan module.
5f9a469
@BryanRumsey
Added the error class for the timespan module.
5492923
@BryanRumsey
Added the timespan module to the core directory.
02c39ca
@BryanRumsey
Fixed import error with timespan error class.
c736547
@BryanRumsey
Added the timespan to the core init.
7fb2abc
@BryanRumsey
Added a timespan module.
2a76aa0
@BryanRumsey
Added unittest for the new timespan module.
54f376b
@BryanRumsey
Integrated the new timespan module into the package.
cb3a4d5
@BryanRumsey
Updated the unittests for the species module and added a validate fun…
4a447ba
…ction.
@BryanRumsey
Added a validate function to the parameter class to handle all parame…
599665a
…ter validation.
@BryanRumsey
Updated the unittests for the parameter module to test the updates.
ea5ebd5
@BryanRumsey
Re-organized the model class functions.
9a14edb
@BryanRumsey
Moved imports to the top of the model module.
9afb31c
@BryanRumsey
Updated Model.update_namespace().
efc1e21
@BryanRumsey
Refactored and re-organized the component functions. Added missing co…
56fa78d
…mponent functions. Added a __getitem__ function. Added resolve functions for parameters and reactions.
@BryanRumsey
Fixed issue in solver caused by the change in the data functions data…
b47ee66
… structure.
@BryanRumsey
Refactored the reaction class to be more consistent with GillesPy2.Re…
5c51d77
…action.
@BryanRumsey
Refactored the unit test to cover the changes in reaction.py.
bcb8c18
@BryanRumsey
Converted all model subclasses with create functions.
69622c8
@BryanRumsey
Example updates part one.
37338bb
@BryanRumsey
Added the __str__ and _ipython_display_ function to the TimeSapn Module.
853b12b
BryanRumseyand others added 29 commits June 6, 2022 11:04
@BryanRumsey
Merge branch 'update-model-reaction' ofhttps://github.com/StochSS/Sp…
8d592de
…atialPy into update-reaction-module
@BryanRumsey
Merge branch 'update-model-reaction' ofhttps://github.com/StochSS/Sp…
e4b9fed
…atialPy into build-model
@BryanRumsey
Silenced isuniform check for coverage=="all"
2568e8f
@briandrawert
Merge pull request#266from StochSS/timespan-module
a80dbd2
Timespan module
@BryanRumsey
Merge branch 'develop' ofhttps://github.com/StochSS/SpatialPyinto u…
1e03087
…pdate-species-module
@BryanRumsey
Merge branch 'develop' ofhttps://github.com/StochSS/SpatialPyinto u…
65ed293
…pdate-parameter-modeule
@briandrawert
Merge pull request#267from StochSS/update-species-module
6d59d77
Updates to the species module
@BryanRumsey
Merge branch 'develop' ofhttps://github.com/StochSS/SpatialPyinto u…
277b34f
…pdate-parameter-modeule
@briandrawert
Merge pull request#268from StochSS/update-parameter-modeule
a1c9c94
Update parameter modeule
@BryanRumsey
Merge branch 'develop' ofhttps://github.com/StochSS/SpatialPyinto u…
3ade2f7
…pdate-model-reaction
@briandrawert
Merge pull request#272from StochSS/update-model-module
e032174
Update model module
@briandrawert
Merge pull request#273from StochSS/update-reaction-module
b9121f2
Update reaction module
@BryanRumsey
Added missing functions to reaction bug and fixed issue with resolvin…
8425322
…g reactions.
@BryanRumsey
Merge branch 'update-model-reaction' ofhttps://github.com/StochSS/Sp…
756c225
…atialPy into build-model
@BryanRumsey
Added check to ensure that the marate is a str before checking if its…
c3942d5
… a digit.
@BryanRumsey
Merge branch 'update-model-reaction' ofhttps://github.com/StochSS/Sp…
171747f
…atialPy into build-model
@BryanRumsey
Resticted the isuniform check to build and replaced StochKit with Spa…
f55e8dd
…tialPy.
@BryanRumsey
Fixed divide by zero error when particle vols are equal.
e0b2910
@BryanRumsey
Fixed the tspan validation in compile prep.
131bbbf
@BryanRumsey
Added missing ptp calculation.
6b911ef
@seanebum
Merge pull request#271from StochSS/update-model-reaction
246661f
Updates to the Model and Reaction modules
@BryanRumsey
Example updates part two.
82eb3f2
@BryanRumsey
Merge branch 'develop' ofhttps://github.com/StochSS/SpatialPyinto b…
98dde9e
…uild-model
@BryanRumsey
Final examples update for working models.
efd5021
@BryanRumsey
Fixed type issue for default timestep size.
670741b
@BryanRumsey
Final updates to test examples.
47dbbc5
@BryanRumsey
Fixed my dummy mistake of casting the timestep_size to the wrong type.
858992d
@BryanRumsey
Removed duplicate examples
ce01890
@seanebum
Merge pull request#274from StochSS/build-model
00968de
Conversion of model subclasses to create functions
@BryanRumsey
BryanRumsey merged commit c3511aa into stagingJun 10, 2022
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Need clearer error message when a type_id contains a space

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@BryanRumsey@briandrawert@seanebum