1.0 Release - #124

Merged

BryanRumsey merged 629 commits into

Mar 1, 2022

This pull request is big! We're only showing the most recent 250 commits

Commits on Oct 18, 2021

Refactored and cleaned up Parameter.__init__.
BryanRumsey
committed
0e9c7d1
Refactored Parameter._evaluate to raise an exception if Parameter.expression could not be evaluated.
BryanRumsey
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7bc4cb6
Removed set_expression from Parameter.
BryanRumsey
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91d2bc0
Refactored Model._resolve_parameters to no longer raise a ParameterError.
BryanRumsey
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013604f
Reactored Model.add_parameter to update the models namespace and evauate a new param before adding it to the model.
BryanRumsey
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34d8439
Removed set_paramter function from Model.
BryanRumsey
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a82f335
Removed expressions from Model.
BryanRumsey
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1845dad
Merge pull request #178 from StochSS/tspan-fix
briandrawert
authored
96004a0
Merge pull request #179 from StochSS/ipython-display
briandrawert
authored
8adad3c
Merge branch 'develop' into per-particle-rho0
BryanRumsey
authored
d09921a
Merge pull request #187 from StochSS/per-particle-rho0
seanebum
authored
1d570a3
Merge branch 'develop' into per-particle-c
BryanRumsey
authored
dc18a89
Merge pull request #188 from StochSS/per-particle-c
seanebum
authored
3f26af1
Merge branch 'develop' into vol-in-set-type
BryanRumsey
authored
ed7d78d
Merge pull request #189 from StochSS/plot-type-list
briandrawert
authored
1fc2eeb
Resolved review comments
BryanRumsey
authored
9b22872
Merge pull request #192 from StochSS/vol-in-set-type
seanebum
authored
53d0def
Added status print statements.
BryanRumsey
committed
2ca235c
Resolved review comments
BryanRumsey
authored
8387f98
Resolved 'Sean's' review comment
BryanRumsey
authored
b0c2ca4
resolved review comments.
BryanRumsey
committed
66e908d
Merge pull request #193 from StochSS/cleanup_functions
briandrawert
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19f713f
Added resolve parameters call to Model.__str__.
BryanRumsey
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0426b57
Added expression back to error message
BryanRumsey
authored
e928ad5
Added ':' to error
BryanRumsey
authored
9a96bb3
Merge pull request #194 from StochSS/params-in-param-expr
briandrawert
authored
fe8d9f9
Merge branch 'develop' of github.com:stochss/SpatialPy into natural-convection-example
briandrawert
committed
2ecdc2c

Commits on Oct 19, 2021

Fixing the [-Wreorder] warnings
briandrawert
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057be80

Commits on Oct 20, 2021

Commits on Oct 21, 2021

Full run of notebook
briandrawert
committed
f411d7b

Commits on Oct 26, 2021

sim_steps errors if dt is too small
briandrawert
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11d518e
removed debugging
briandrawert
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e35142f
adding Sploosh model
briandrawert
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e091e76

Commits on Oct 27, 2021

progress
briandrawert
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15b15c2

Commits on Nov 9, 2021

Commits on Nov 10, 2021

Commits on Nov 11, 2021

Fixed the core import.
BryanRumsey
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9464777
Added spatialpy errors file to fix model error circular import.
BryanRumsey
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17bfc4d
Fixed import issues.
BryanRumsey
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2c6a4bf
Pulled the Species, Parameter, and Reaction classes out of the model file and into their own files.
BryanRumsey
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f664881
Restructured the solver files.
BryanRumsey
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9cb1625
Added setter function for diffusion_coefficient.
BryanRumsey
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3326565
Added unit tests for species class.
BryanRumsey
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769dae9
Fixed Species unit tests. Added Parameter unit tests.
BryanRumsey
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884eb25

Commits on Nov 12, 2021

Commits on Nov 29, 2021

Commits on Nov 30, 2021

Commits on Dec 1, 2021

Move the name block to the Reaction class. Removed duplicate code from Model.add_reaction.
BryanRumsey
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04545d6
Added tests for Reaction.name. Added test for as string.
BryanRumsey
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79a34b1
Added test for marate as parameter.
BryanRumsey
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2257a66
Added missing import for reaction tests.
BryanRumsey
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3830177
Fixed the Reaction._create_mass_action function.
BryanRumsey
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75727a8
Fixed name references in error messages. Fixed marate tests.
BryanRumsey
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9f9632c
Fixed name type check.
BryanRumsey
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bde9296
Added missing re import.
BryanRumsey
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0daf7a5
Restuctured the Model.py file.
BryanRumsey
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99cb4ae
Added tests for Reaction._create_mass_action with marate as int and float.
BryanRumsey
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5f676d4
Fixed indentation issue.
BryanRumsey
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bf4d817
Added tests for propensity functions built using Reaction._create_mass_action.
BryanRumsey
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6545629
Restuctured the Reaction.py file. Fixed tests for propensity function built using Reaction._create_mass_action.
BryanRumsey
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174f4d5
Added additional type checking for Reaction.add_product and Reaction.add_reactant. Added support for string Species for Reaction.add_product and Reaction.add_reactant. Added tests for Reaction.ad…
BryanRumsey
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650f4ba
Added Species import.
BryanRumsey
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6f314e1
Added type check for the annotation arg of Reaction.annotation.
BryanRumsey
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c053db3
Added tests for Reaction.annotation. Fixed issue with species constructor. Updated docs.
BryanRumsey
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0d2e82f
Fixed incorrect tests.
BryanRumsey
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bd523f2
Fixed incorrect tests take two.
BryanRumsey
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8dcfc64
Fixed incorrect tests take three.
BryanRumsey
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a81e9ef
Fixed incorrect tests take four.
BryanRumsey
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7905267
Fixed incorrect tests take five.
BryanRumsey
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792d5ed

Commits on Dec 2, 2021

Commits on Dec 7, 2021

Commits on Dec 8, 2021

Updated examples to work with changes made for unit tests.
BryanRumsey
committed
b6fe71e

Commits on Dec 13, 2021

status commit
briandrawert
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16be907
Merge pull request #205 from StochSS/unit-test
briandrawert
authored
8e8384f
conflict resolution
briandrawert
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9bd56fd
undo debugging
briandrawert
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86c7cce

Commits on Jan 6, 2022

added equation for setting P0 from c0
seanebum
committed
17c72a8

Commits on Jan 12, 2022

Fixing the Shepard filter
briandrawert
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ae1ddb1
remove done TODOs
briandrawert
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8bac7a6

Commits on Feb 2, 2022

cleanup
briandrawert
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430c5b3
Updated copyright to 'Copyright (C) 2019 - 2022'.
BryanRumsey
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f5b6281
Added pylintrc file.
BryanRumsey
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5ce5f29
pylint updates to __init__.
BryanRumsey
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b85cb65
pylint changes to boundary conditions.
BryanRumsey
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31cc838

Commits on Feb 3, 2022

Renamed file to match module naming convention.
BryanRumsey
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a9d5910
Pylint changes to the cleanup script.
BryanRumsey
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7746112
Updated docs for boundarycounditions and datafunctions. Pylint changes to datafunction.
BryanRumsey
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984ec9d
Updated docs. Pylint changes.
BryanRumsey
committed
39d4ea0
Fixed import of non-dependant packages.
BryanRumsey
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735734f
Fixed imports in model file.
BryanRumsey
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a4766c4
Updated pylint rc file.
BryanRumsey
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ec8b1d0
updated docs, mostly putting in returns
seanebum
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982e76b
resolved merge conflicts
seanebum
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760a089
Merge pull request #210 from StochSS/copyright-update
seanebum
authored
76cb1a5
Pulled in changes from develop. Updated pylintrc file.
BryanRumsey
committed
6d1838f
Merge branch 'develop' of github.com:stochss/SpatialPy into fix/pressure
briandrawert
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3e3fe2c
Comnined property and species arguments.
BryanRumsey
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911667f
Merge pull request #206 from StochSS/fix/pressure
BryanRumsey
authored
71fe6a6
Pulled in changes from develop
BryanRumsey
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bfcb503
Fixed issue with boundaryconition value type check.
BryanRumsey
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84f0ab5
Added action items to domain.
BryanRumsey
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a0b7599
Fixed compatibility issues with action items.
BryanRumsey
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f294fc6
fixed import error
BryanRumsey
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7f6827a
fixed import error take 2.
BryanRumsey
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8573fb9

Commits on Feb 4, 2022

Pylint changes and updates to docs.
BryanRumsey
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d4614e2
Update docs and pylint changes for initialconditions.
BryanRumsey
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1322643
Fixed imports in __init__.
BryanRumsey
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c93acf1
Pylint changes to species.py.
BryanRumsey
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cfc39ed
Pylint changes and doc updates.
BryanRumsey
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f0563c7
Fixed imports.
BryanRumsey
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2363b64
pylint changes to reaction.py.
BryanRumsey
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75ff213

Commits on Feb 7, 2022

Pylint changes and docs update.
BryanRumsey
committed
f92e8f3
Fixed import issues.
BryanRumsey
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51d8cee
Renamed results.py. Refactored and based on review comments.
BryanRumsey
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d62ce2f
Renamed results.py. Refactored and based on review comments.
BryanRumsey
committed
23d89bb
Fixed import issues.
BryanRumsey
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7592653
Docs update and pylint changes.
BryanRumsey
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4b98f5a
Fixed matplotlib import error.
BryanRumsey
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97dc76c

Commits on Feb 8, 2022

Commits on Feb 9, 2022

Commits on Feb 10, 2022

Pylint changes and docs update for solver.py.
BryanRumsey
committed
b9c467c
Fixed import issues.
BryanRumsey
committed
2bf1f20
Pylint changes.
BryanRumsey
committed
4c6c1ec
Fixed inits for core and solver.
BryanRumsey
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1dbceea
Fixed circular import.
BryanRumsey
committed
6ce3acb
Fixed circular import in model.py.
BryanRumsey
committed
9b9f816
Fixed circular import in solver.py.
BryanRumsey
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2a2ba25
Fixed issue with build_dir is None in solver.py.
BryanRumsey
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f100721

Commits on Feb 11, 2022

Commits on Feb 14, 2022

Updated the weir example.
BryanRumsey
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464848a
Updated the Polarisome_1D example.
BryanRumsey
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acfb544
Updated the G-Protein_1D example.
BryanRumsey
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97559fa
Merge branch 'code-cleanup' of https://github.com/StochSS/SpatialPy into update-docs
seanebum
committed
d9d2ffb
Updated the cdc42 example.
BryanRumsey
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187d696
Restructured the Under Construction folder in examples.
BryanRumsey
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9846e09
Updates to paths in Under Construction examples.
BryanRumsey
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002988f

Commits on Feb 15, 2022

Fixed coords in Domain.fill_with_particles.
BryanRumsey
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3365445
Merge branch 'code-cleanup' of https://github.com/StochSS/SpatialPy into example-cleanup
BryanRumsey
committed
6fec66e
Restructured the 3d cylinder demo files.
BryanRumsey
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7e5c6da
Restructures the coral reef example.
BryanRumsey
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188e1c0
updating docstrings
seanebum
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59d675a
Restructured the hes1 example.
BryanRumsey
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3fdc3ee
Restructured the weir example.
BryanRumsey
committed
e9ec6fb
Merge pull request #217 from StochSS/update-docs
BryanRumsey
authored
ba098c0
Merge branch 'code-cleanup' of https://github.com/StochSS/SpatialPy into example-cleanup
BryanRumsey
committed
e13dff1
Updated the boundary conditions examples.
BryanRumsey
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16b1963
Updated the spatialpy gravity example.
BryanRumsey
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1ba83a8
initial build of docs 1.0
seanebum
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ed8e689

Commits on Feb 17, 2022

Switched Domain.type to Domain.type_id.
BryanRumsey
committed
6ff83c1

Commits on Feb 18, 2022

Commits on Feb 22, 2022

Updated examples.
BryanRumsey
committed
e7b0e4a
Updates to the type_id name scheme
BryanRumsey
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03e8a26
Fixed broken tests.
BryanRumsey
committed
be7f9fd
Added missing tests for restric_to.
BryanRumsey
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4e5043c
Fixed broken species tests.
BryanRumsey
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07fe9bd
Fixed broken species tests take 2.
BryanRumsey
committed
5e8909f
Fixed broken test models.
BryanRumsey
committed
9352991
Merge branch 'code-cleanup' of https://github.com/StochSS/SpatialPy into build-docs
seanebum
committed
773d3db
rebuilding docs
seanebum
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ee3c2bd
Merge branch 'code-cleanup' of https://github.com/StochSS/SpatialPy into example-cleanup
BryanRumsey
committed
df8f282
Final updates to the examples model.
BryanRumsey
committed
e6891c8
Moved start here model to its correct location.
BryanRumsey
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30b424f
Merge pull request #222 from StochSS/build-docs
briandrawert
authored
ba292bb
Fixed bug with get_property when property name is 'v'.
BryanRumsey
committed
f22494d
Updates to start here example.
BryanRumsey
committed
4e42cf9
Merge pull request #219 from StochSS/example-cleanup
seanebum
authored
6cbfa98
Merge pull request #211 from StochSS/code-cleanup
briandrawert
authored
56a6892
Merge branch 'main' into develop
briandrawert
authored
13b336a
Bumping version to 1.0
briandrawert
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81cdf10

Commits on Feb 23, 2022

Rebuilt docs for 1.0, added front page material
briandrawert
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2804389
cleanup, and add top level index.html for docs
briandrawert
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ceaece4
Created .nojekyll file
BryanRumsey
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8dccf29
Start here update.
BryanRumsey
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0a37ca9
update to conf.py for img
seanebum
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ab3aabb
rebuilt docs
seanebum
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b9a06d9
Added fonts and css directories for docs.
BryanRumsey
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65ef760
Merge branch 'docs_updates' of https://github.com/StochSS/SpatialPy into docs_updates
BryanRumsey
committed
0d90273
rebuild agian for css updates
seanebum
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611a316

Commits on Feb 24, 2022

Final updates to the StartHere, Gravity, and Weir examples.
BryanRumsey
committed
f801a46

Commits on Feb 25, 2022

Commits on Feb 28, 2022