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Refactor/mechanism/preprocess variable #530

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merged 185 commits into from
Nov 14, 2017
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Refactor/mechanism/preprocess variable #530

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250201b
Org/library/models (#483)
jdcpni Sep 28, 2017
ada0f63
Docs/mechanism/updated states fig (#484)
jdcpni Sep 29, 2017
bce23b4
adding all params of FHNIntegrator Function to the LCControlMechanism…
KristenManning Sep 29, 2017
1ea5333
passed in all arguments to the FHNIntegrator where the LCControlMecha…
KristenManning Sep 29, 2017
044293a
Merge pull request #485 from PrincetonUniversity/fix/FHN-integrator/f…
KristenManning Sep 29, 2017
628adb0
move tutorial notebook to its own dedicated folder
kmantel Sep 29, 2017
409b708
change test_notebooks to only test the notebooks in the tutorial fold…
kmantel Sep 29, 2017
b74eece
replace Adpative with Adaptive
kmantel Sep 29, 2017
a89f759
import ShellClass Mechanism directly instead of implicitly importing …
kmantel Oct 2, 2017
d184198
import ShellClass Projection directly instead of implicitly importing…
kmantel Oct 2, 2017
8d752cc
import ShellClass State directly instead of implicitly importing it t…
kmantel Oct 2, 2017
18660ab
import ShellClass Process directly instead of implicitly importing it…
kmantel Oct 2, 2017
7504cee
import ShellClass System directly instead of implicitly importing it …
kmantel Oct 2, 2017
31ea0fb
replace nonexistence ControlMechanism_Base uses with the real Control…
kmantel Oct 3, 2017
de9c124
optimize imports via pycharm
kmantel Oct 3, 2017
8ddd5d0
make IntegratorMechanism get its paramClassDefaults from its parent P…
kmantel Oct 3, 2017
7b98bbc
refactoring rk helper method to compute the two variables (v and w) c…
KristenManning Oct 3, 2017
ef95566
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
KristenManning Oct 3, 2017
634a7a2
adding pytest to verify FHNIntegrator function against Gilzenrat pape…
KristenManning Oct 4, 2017
841c73b
adding ipykernel>=4.6.1 to dev_requirements.txt
allieluu Oct 4, 2017
2d55c56
fixing Project Defaults
allieluu Oct 4, 2017
ecfdaca
removing toposort from ignoredPackages
allieluu Oct 4, 2017
9147ab5
adding Project_Default.xml to gitignore
allieluu Oct 4, 2017
42e1b93
revising FHN integrator docs comparisons to other models (Gilzenrat, …
KristenManning Oct 4, 2017
e68b4f9
Update Project_Default.xml
allieluu Oct 4, 2017
b2df5ad
Merge pull request #487 from PrincetonUniversity/fix/FHN-integrator/o…
KristenManning Oct 4, 2017
f9a6dde
Merge branch 'devel' into fix-deprecation-warning-test
allieluu Oct 4, 2017
9fde49e
Merge pull request #486 from PrincetonUniversity/fix-deprecation-warn…
allieluu Oct 4, 2017
5ab54e9
ensure that MechanismPreferenceSet imports its parent class
kmantel Oct 5, 2017
83f0e18
define undefined default values in MechanismPreferenceSet
kmantel Oct 5, 2017
53bb926
temporary fix: changing LCControlMechanism output to (gain(w_t), gain…
KristenManning Oct 9, 2017
705d2e6
Merge pull request #488 from PrincetonUniversity/fix/output-states/in…
KristenManning Oct 9, 2017
a486e94
replace calls to numpy typechecking from 64 bit to 64 or 32bit versions
kmantel Aug 11, 2017
10daff1
make TransferMechanism.paramClassDefaults copy its parent instead of …
kmantel Oct 9, 2017
87af69c
cleanup test_recurrent_mechanism.py imports
kmantel Oct 10, 2017
cb91cf4
replace crude assertions with numpy assert_allclose in test_recurrent…
kmantel Oct 10, 2017
f80cda3
test_recurrent_transfer_mechanism.py PEP8 format
kmantel Oct 10, 2017
48dd3e2
adding a new function called 'LCAIntegrator' which computes rate*prev…
KristenManning Oct 11, 2017
d9bd518
updating execute method of LCA to call LCAIntegrator and renaming tim…
KristenManning Oct 11, 2017
cb9fad3
Merge pull request #489 from PrincetonUniversity/fix/LCA/new-integrat…
KristenManning Oct 11, 2017
cdb0ddf
relaxing validation on LCAIntegrator rate param in order to create an…
KristenManning Oct 11, 2017
c782f0f
remove mechanismGenerator
kmantel Oct 3, 2017
13f1092
rename packages and modules to lowercase, and handle relevant import …
kmantel Oct 3, 2017
db4da11
remove old pyargs argument for pytest
kmantel Oct 5, 2017
ef5fbac
move typecheck for _get_modulated_param inside to avoid circular import
kmantel Oct 4, 2017
6b9e9a4
switch name of System and System_Base
kmantel Oct 6, 2017
abf3e7e
switch name of Process and Process_Base
kmantel Oct 6, 2017
559c86b
remove process factory in favor of just instantiating Process class
kmantel Oct 6, 2017
18249f6
remove system factory in favor of just instantiating System class
kmantel Oct 7, 2017
4bd5746
remove mechanism factory method
kmantel Oct 9, 2017
5251467
make LearningMechanism get its paramClassDefaults from its parent and…
kmantel Oct 5, 2017
19e4df5
rework imports to avoid circularities due to packaging
kmantel Oct 5, 2017
78cff05
replace paramClassDefaults PROJECTION_SENDER with OutputState class i…
kmantel Oct 6, 2017
73ffffc
clean up main package __init__.py
kmantel Sep 29, 2017
b9a28d2
rename globals/run.py to globals/environment.py to avoid namespace co…
kmantel Oct 9, 2017
4661a3c
add __all__ lists to modules
kmantel Oct 3, 2017
b13b6c3
update package __init__.py files for simple importing
kmantel Oct 4, 2017
dee7f13
update docs to handle new module/package format
kmantel Oct 6, 2017
ba47f38
update tutorial to new easier import style
kmantel Oct 6, 2017
cb73dfa
add docstrings to __init__.py files (for help command)
kmantel Oct 11, 2017
80759a2
remove extraneous files
kmantel Sep 21, 2017
d3ed7d0
remove SOFTWARE ARCHITECTURE and TODO List
kmantel Sep 27, 2017
fcc8e95
add MANIFEST.in
kmantel Aug 18, 2017
924d761
update setup.py packages
kmantel Aug 18, 2017
2c143bd
add requirements.txt mirroring setup.py requirements
kmantel Aug 18, 2017
6a6dfe4
add tutorial_requirements.txt mirroring setup.py requirements
kmantel Sep 21, 2017
19c24b0
update setup.py classifier for Apache license
kmantel Aug 18, 2017
240d8e3
update setup.py supported Python versions to include only 3.5 and 3.6…
kmantel Sep 21, 2017
9654b18
update setup.cfg for wheel creation and to include license file
kmantel Sep 21, 2017
8249299
update short description to match the title line in the long description
kmantel Sep 21, 2017
deb7d18
reformat README into .rst format so pypi can format it nicely
kmantel Sep 21, 2017
308e45a
update README and docs index.rst to new PyPI installation instruction…
kmantel Sep 21, 2017
6068a15
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
KristenManning Oct 11, 2017
55c9b9e
adding a new Integrator function that matches the decision and respon…
KristenManning Oct 12, 2017
bde2c10
adding gilzenrat changes onto new devel; fixing gilzenrat noise to be…
KristenManning Oct 12, 2017
3e591a1
updating value of LC control mechanism output before it runs to match…
KristenManning Oct 13, 2017
5f9991e
removing and re-adding gilzenrat transfer mechanism because name chan…
KristenManning Oct 13, 2017
9b34b65
remove DefaultProcessingMechanism from component/__init__.py because …
kmantel Oct 13, 2017
e7cc6ce
make Function_Base inherit its paramClassDefaults from its parent cla…
kmantel Oct 13, 2017
763a906
improving initial conditions by making first recurrent projections to…
KristenManning Oct 13, 2017
83dd2ff
Devel (#490)
jdcpni Oct 13, 2017
8fc887e
correcting LCAIntegrator function to match the papers (since it repre…
KristenManning Oct 16, 2017
2b9438d
Merge pull request #491 from PrincetonUniversity/fix/LCA-mechanism/co…
KristenManning Oct 16, 2017
c9179c6
fix link to the tutorial in docs that didn't get changed when tutoria…
kmantel Oct 16, 2017
4c47d9d
pulling changes from devel into gilzenrat branch
KristenManning Oct 16, 2017
7d698ee
fixing bug in NormalDist() function which was shifting the mean of th…
KristenManning Oct 16, 2017
b58c370
Merge branch 'devel' into temp/merge-gilzenrat-devel
KristenManning Oct 16, 2017
568f02d
Merge pull request #492 from PrincetonUniversity/temp/merge-gilzenrat…
KristenManning Oct 16, 2017
bc0d391
stop package-level __all__ assignments from accidentally overwriting …
kmantel Oct 17, 2017
a25a65b
skip notebook checkpoints in running notebook tests
kmantel Oct 17, 2017
dc1da78
fold keywords into first level hierarchy, because some keywords aren'…
kmantel Oct 17, 2017
f0142b8
add component module to main psyneulink package
kmantel Oct 20, 2017
a29ff25
indexing into the first element of the transfer mechanism's integrato…
KristenManning Oct 23, 2017
811dba5
updating mechanism pytests to reflect integrator_function shape chang…
KristenManning Oct 23, 2017
78383fa
Refactored instantiation of States and Projections (#494)
jdcpni Oct 25, 2017
8cd5f9d
Refactor/state and projection/specification bug fix 2 (#495)
jdcpni Oct 26, 2017
e37ce77
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
KristenManning Oct 27, 2017
1bd8107
Merge pull request #496 from PrincetonUniversity/fix/integrator-mode/…
KristenManning Oct 27, 2017
c17d464
replacing GilzenratIntegrator with LCAIntegrator (with rate=-1) in Gi…
KristenManning Oct 27, 2017
aa75df0
implementing noise on LCAIntegrator and cleaning up unnecessary integ…
KristenManning Oct 27, 2017
87fc0a2
adding progress statement ('% complete') to gilzenrat script
KristenManning Oct 27, 2017
4a6394c
Optimize registry duplicate naming
kmantel Oct 26, 2017
5cdb94c
fixing up a few model values in the gilzenrat model -- behavior is no…
KristenManning Oct 27, 2017
f713bbc
adding pytests that isolate the GilzenratTransferMechanism and moving…
KristenManning Oct 27, 2017
a0179a7
adding full gilzenrat model to pytests -- no comparison data to asser…
KristenManning Oct 27, 2017
e660260
moving imports to top of gilzenrat pytests file
KristenManning Oct 27, 2017
4b738c2
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
KristenManning Oct 27, 2017
48e93fe
requiring version 1.4 of toposort
KristenManning Oct 27, 2017
bf5a6b5
Merge pull request #499 from PrincetonUniversity/fix/gilzenrat-mechan…
KristenManning Oct 27, 2017
b152401
Refactor/state and projection/names and docs (#500)
jdcpni Oct 30, 2017
414cb26
Refactor/state and projections/unit tests (#501)
jdcpni Oct 30, 2017
0e9b84c
Refactor/state and projection/unit tests bug fixes (#502)
jdcpni Oct 30, 2017
bb02214
avoid using module-level Mechanisms in unit tests to avoid possible c…
kmantel Oct 30, 2017
e27a626
fix typo in ObjectiveMechanism docstring causing weird documentation …
kmantel Oct 31, 2017
1c0880f
Refactor/state and projection/clean up (#503)
jdcpni Nov 1, 2017
0079c1f
Refactor/projection/ instantiate sender (#504)
jdcpni Nov 1, 2017
af0e741
• Projection (#505)
jdcpni Nov 1, 2017
9237616
Refactor/gating mechanism/ instantiate gating signal (#506)
jdcpni Nov 2, 2017
069e8a7
Refactor/projection/connection specs (#507)
jdcpni Nov 2, 2017
c7f048c
Clean up/registry/ register category (#508)
jdcpni Nov 2, 2017
067318a
rename System and Process to add _Base suffix in shellclasses.__all__…
kmantel Nov 2, 2017
944af9d
Fix/utilities/iscompatible (#511)
jdcpni Nov 3, 2017
6711c2e
Fix/utilities/iscompatible final rev (#512)
jdcpni Nov 3, 2017
b748ca5
Leabra wrapper prototype (#513)
dcw3 Nov 3, 2017
a99ecda
Import leabra and run leabra tests only if leabra module is available.
kmantel Nov 4, 2017
e725a33
-
jdcpni Nov 4, 2017
3584eb5
Refactor/control and gating signals (#514)
jdcpni Nov 5, 2017
cb04745
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
jdcpni Nov 5, 2017
2063541
rename duplicate transfer mech test to avoid overwrite
kmantel Nov 7, 2017
0ed0c26
remove uses of self.variable. (it is vestigial and maintained only fo…
kmantel Nov 7, 2017
d0b94bb
Docs/state and projection (#515)
jdcpni Nov 7, 2017
c859a73
make test_transfer_mechanism tests use instance_defaults.variable ins…
kmantel Oct 31, 2017
0e905fd
update current input_state spec tests
kmantel Nov 6, 2017
a09240c
move input_states spec tests in test_transfer_mechanism to new file
kmantel Nov 6, 2017
2f668b1
hack mechanism to be able to accept instance_defaults.variable setup …
kmantel Oct 31, 2017
49146b3
Merge branch 'feat/default-variable/assign-with-input-states' into devel
kmantel Nov 7, 2017
0bfbd34
Naming/registry/default name 0 (#516)
jdcpni Nov 8, 2017
e29b026
scaling entire noise term by sqrt(dt) rather than scaling the standar…
KristenManning Nov 8, 2017
960b26e
switching FHNIntegrator to use euler integration
KristenManning Nov 8, 2017
caab90e
fixing some params to match matlab model; made it easier to swtich be…
KristenManning Nov 8, 2017
280fd33
adding 'integration_method' to LCControlMechanism so that user can sw…
KristenManning Nov 8, 2017
d9b610b
adding validation requiring integration_method to either be RK4 or EULER
KristenManning Nov 8, 2017
2211ad7
using new EULER option on the LCControlMechanism in GilzenratModel in…
KristenManning Nov 8, 2017
22ecfbc
Merge pull request #517 from PrincetonUniversity/fix/gilzenrat/match-…
KristenManning Nov 8, 2017
ea3b359
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
jdcpni Nov 9, 2017
0c24e98
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
jdcpni Nov 9, 2017
7b545b4
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
jdcpni Nov 9, 2017
84ce4fc
Fix/input state specs (#518)
jdcpni Nov 9, 2017
49bd299
Fix/input state specs (#519)
jdcpni Nov 9, 2017
913f0be
Fix/input state specs (#520)
jdcpni Nov 9, 2017
59c418e
Fix/input state specs (#521)
jdcpni Nov 10, 2017
0ef7b40
Docs/input state specs (#522)
jdcpni Nov 10, 2017
084c3e1
make self.name return unnamed .__class__ in case no name was set
kmantel Sep 1, 2017
2195293
Logo (#523)
jdcpni Nov 10, 2017
e6302b4
Docs/intro materials (#524)
jdcpni Nov 12, 2017
441b5b3
Docs/latex math (#525)
jdcpni Nov 12, 2017
6559fae
Refactor/distance metrics (#526)
jdcpni Nov 12, 2017
d5d6d6d
• State
jdcpni Nov 12, 2017
6f095fb
• State
jdcpni Nov 12, 2017
f4dd3d1
• State
jdcpni Nov 12, 2017
4a2cf96
Fixed/state/ parse state spec/projection spec (#528)
jdcpni Nov 12, 2017
d3df60b
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
jdcpni Nov 12, 2017
d96b946
• State
jdcpni Nov 13, 2017
04cdd30
• State
jdcpni Nov 13, 2017
a8b0f91
• State, Projection
jdcpni Nov 13, 2017
af796d2
-
jdcpni Nov 13, 2017
9186346
-
jdcpni Nov 13, 2017
78181d4
-
jdcpni Nov 13, 2017
f3f713c
• Utilities
jdcpni Nov 13, 2017
dd342e2
• Utilities
jdcpni Nov 13, 2017
ddbe7d3
• Utilities
jdcpni Nov 13, 2017
bbbe722
-
jdcpni Nov 13, 2017
9fa9ee6
-
jdcpni Nov 13, 2017
576800b
-
jdcpni Nov 13, 2017
95eea9a
change behavior of _parse_state_spec to not populate the state dict w…
kmantel Nov 13, 2017
c04a218
correct bug in _parse_arg_input_states where a non-list argument woul…
kmantel Nov 13, 2017
7ca2984
-
jdcpni Nov 14, 2017
fe18840
-
jdcpni Nov 14, 2017
fcebf28
Merge branches 'devel' and 'docs/State_and_Projections/docstring_revs…
jdcpni Nov 14, 2017
185dd85
-
jdcpni Nov 14, 2017
2d85143
-
jdcpni Nov 14, 2017
7475d25
-
jdcpni Nov 14, 2017
43adc5d
Docs/state and projections/docstring revs (#529)
jdcpni Nov 14, 2017
d428b97
-
jdcpni Nov 14, 2017
11ad8c4
• Mechanism, Component
jdcpni Nov 14, 2017
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4 changes: 0 additions & 4 deletions .buildinfo
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5 changes: 4 additions & 1 deletion .gitignore
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# Icon must end with two \r
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# Thumbnails
._*
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.idea/**/misc.xml
.idea/**/PsyNeuLink.iml
.idea/dictionaries
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.idea/inspectionProfiles/Project_Default.xml

# Sensitive or high-churn files:
.idea/**/dataSources/
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2 changes: 1 addition & 1 deletion .idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml
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20 changes: 20 additions & 0 deletions .idea/runConfigurations/Gating_Mechanism_Test_Script.xml
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2 changes: 1 addition & 1 deletion .idea/runConfigurations/_Integrator_scheduled_timescales.xml
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2 changes: 1 addition & 1 deletion .idea/runConfigurations/_Stroop_Demo_Script.xml
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