1.0 Full Release - #231

Merged

briandrawert merged 664 commits into

mainfrom

Mar 7, 2022

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

Commits on Oct 26, 2021

adding Sploosh model
briandrawert
committed
e091e76

Commits on Oct 27, 2021

progress
briandrawert
committed
15b15c2

Commits on Nov 9, 2021

Commits on Nov 10, 2021

Consolidated duplicate code in plotting functions.
BryanRumsey
committed
aea0371
Moved all core files into a core directory. Setup module init files to maintain previous import syntax.
BryanRumsey
committed
83abc32

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
committed
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
committed
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
committed
75727a8
Fixed name references in error messages. Fixed marate tests.
BryanRumsey
committed
9f9632c
Fixed name type check.
BryanRumsey
committed
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
committed
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
committed
735734f
Fixed imports in model file.
BryanRumsey
committed
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
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76cb1a5
Pulled in changes from develop. Updated pylintrc file.
BryanRumsey
committed
6d1838f
Merge branch 'develop' of github.com:stochss/SpatialPy into fix/pressure
briandrawert
committed
3e3fe2c
Comnined property and species arguments.
BryanRumsey
committed
911667f
Merge pull request #206 from StochSS/fix/pressure
BryanRumsey
authored
71fe6a6
Pulled in changes from develop
BryanRumsey
committed
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
committed
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
committed
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
committed
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
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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
committed
acfb544
Updated the G-Protein_1D example.
BryanRumsey
committed
97559fa
Merge branch 'code-cleanup' of https://github.com/StochSS/SpatialPy into update-docs
seanebum
committed
d9d2ffb
Updated the cdc42 example.
BryanRumsey
committed
187d696
Restructured the Under Construction folder in examples.
BryanRumsey
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9846e09
Updates to paths in Under Construction examples.
BryanRumsey
committed
002988f

Commits on Feb 15, 2022

Fixed coords in Domain.fill_with_particles.
BryanRumsey
committed
3365445
Merge branch 'code-cleanup' of https://github.com/StochSS/SpatialPy into example-cleanup
BryanRumsey
committed
6fec66e
Restructured the 3d cylinder demo files.
BryanRumsey
committed
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
committed
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
committed
03e8a26
Fixed broken tests.
BryanRumsey
committed
be7f9fd
Added missing tests for restric_to.
BryanRumsey
committed
4e5043c
Fixed broken species tests.
BryanRumsey
committed
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
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e6891c8
Moved start here model to its correct location.
BryanRumsey
committed
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
authored
8dccf29
Start here update.
BryanRumsey
committed
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
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f801a46

Commits on Feb 25, 2022

Commits on Feb 28, 2022

Commits on Mar 1, 2022

Merge pull request #124 from StochSS/develop
BryanRumsey
authored
34e781c
Fixed start here notebook name.
BryanRumsey
committed
3372f96
Fixed doc strings for boundary conditions.
BryanRumsey
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a2585ed
Fixed doc strings for boundary conditions.
BryanRumsey
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05ad212
Added a missing raises doc tag for data functions.
BryanRumsey
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86c3647
Updated docs in domain. updated docs.
BryanRumsey
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4ca44ad
Updated docs in domain. updated docs.
BryanRumsey
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d5d489f
Updated docs in domain. updated docs.
BryanRumsey
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dffadb7
Updates to Geometry and Initial Condition docs.
BryanRumsey
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a9df60e
closes #225
briandrawert
committed
3fd6aa7

Commits on Mar 2, 2022

Updated docs.
BryanRumsey
committed
08b5a36
Updated docs html files.
BryanRumsey
committed
ac1c46b
Updated docs for initial conditions and model.
BryanRumsey
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a09f2e0
Updated docs html files.
BryanRumsey
committed
6e7d788
Updated docs for reactions.
BryanRumsey
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c142a95
Updated docs html files.
BryanRumsey
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b3639dd
Updated docs for results.
BryanRumsey
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0186da3
Updated docs html files.
BryanRumsey
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aaa1606
Updated docs for species.
BryanRumsey
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4a0d3d3
Updated docs html files.
BryanRumsey
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93511d4
Updated docs for stochss export.
BryanRumsey
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5f41717
Updated docs html files.
BryanRumsey
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dd077f1
Updated docs for solver.
BryanRumsey
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e9edd02
Updated docs html files.
BryanRumsey
committed
7d7f806

Commits on Mar 4, 2022

Split tests into unit tests and integration tests. Added new test script and yml file for integration tests.
BryanRumsey
committed
7b3f35d

Commits on Mar 7, 2022

updates to test 3d cylinder demo nb.
BryanRumsey
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e71ba96
update to domain docs
seanebum
committed
a60534d
added develop branch to integration test cation target.
BryanRumsey
committed
553652e
Merge pull request #233 from StochSS/split-tests
seanebum
authored
5d522c2
update link to example StartHere notebook
seanebum
committed
637527e
added explination of the validation plots
briandrawert
committed
a345465
Merge branch 'develop' of github.com:stochss/SpatialPy into develop
briandrawert
committed
774335d
Merge pull request #229 from StochSS/doc-edits
briandrawert
authored
02913a1
Merge pull request #232 from StochSS/develop
briandrawert
authored
c5f0509