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Feature/oogpfa #287

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merged 38 commits into from
Feb 5, 2020
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2dd6d73
Refactor GPFA codes in an object oriented manner
Junji110 Jan 13, 2020
6a48cc1
Delete unnecessary lines which were left undeleted by mistake
Junji110 Jan 13, 2020
b782c25
Add fit_transform() method to the GPFA class
Junji110 Jan 13, 2020
761fc8d
Simplify the input structure
Junji110 Jan 14, 2020
0ec178a
Simplify the output structure
Junji110 Jan 14, 2020
8ccac93
Add a test for transforming testing data
Junji110 Jan 14, 2020
7d42cd6
Add score() method to the GPFA class
Junji110 Jan 14, 2020
5775cf7
Add a test for cross-validation
Junji110 Jan 14, 2020
bee9905
Remove 'trialId' in seqs object and adapt tests accordingly
essink Jan 15, 2020
6b71a95
Remove trialId from documentation
essink Jan 15, 2020
332d6c9
Move import to beginning of file
essink Jan 15, 2020
1c69ea9
Rename seqs_train to seqs where it could belong to either train or test
essink Jan 15, 2020
af53ed9
Restructure gpfa file locations
essink Jan 15, 2020
710fc33
Add explicit test for returned_data option of transform()
essink Jan 15, 2020
ef77516
Add a first draft of a tutorial notebook
essink Jan 16, 2020
8ae763c
Minor change in documentation
essink Jan 16, 2020
041893b
Revise documentation and refactor variable names
Junji110 Jan 17, 2020
45c236c
Revise documentation further
Junji110 Jan 17, 2020
a48aac4
PEP8ify the codes
Junji110 Jan 17, 2020
3346e99
import GPFA only if requirements-extras are installed; added __future…
dizcza Jan 17, 2020
20db3e4
added GPFA reference to doc/modules
dizcza Jan 17, 2020
c1cb242
import gpfa safely
dizcza Jan 17, 2020
02530f1
fixed codefactor
dizcza Jan 17, 2020
2ff7c31
fixed conda numpy 1.18.1 breaking change
dizcza Jan 17, 2020
46fe61d
Relax the condition for log-likelihood in test_data1() to pass the test
Junji110 Jan 20, 2020
f8abcc2
Merge branch 'feature/oogpfa' of github.com:INM-6/elephant into featu…
Junji110 Jan 20, 2020
040f49f
pep8
dizcza Jan 22, 2020
925ad24
first refactor of GPFA.gpfa to follow doc guidelines
dizcza Jan 22, 2020
3491c87
Reorganize how parameters are stored in the GPFA() class
Junji110 Jan 28, 2020
866ab19
pep8
dizcza Jan 28, 2020
fa74aef
Disable the tqdm output if verbose=False
essink Jan 29, 2020
b9db3df
Improve tutorial
essink Jan 29, 2020
4e79b44
added explanations to tutorial sections
dizcza Jan 29, 2020
3daf030
Revise module documentation
Junji110 Feb 5, 2020
c8acf82
Revise tutorial
Junji110 Feb 5, 2020
540f890
Revise tutorial again
Junji110 Feb 5, 2020
59fcbc2
Merge branch 'master' into feature/oogpfa
dizcza Feb 5, 2020
8a26d44
fixed manual github conflict resolving dummy issue
dizcza Feb 5, 2020
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1 change: 1 addition & 0 deletions doc/modules.rst
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ Function Reference by Module
reference/conversion
reference/cubic
reference/current_source_density
reference/gpfa
reference/kernels
reference/neo_tools
reference/pandas_bridge
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2 changes: 1 addition & 1 deletion doc/reference/gpfa.rst
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@
`GPFA` - Gaussian-process factor analysis
=========================================

.. automodule:: elephant.gpfa
.. automodule:: elephant.gpfa.gpfa
:members:
964 changes: 964 additions & 0 deletions doc/tutorials/gpfa.ipynb

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5 changes: 4 additions & 1 deletion elephant/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -23,14 +23,17 @@
conversion,
neo_tools,
cell_assembly_detection,
waveform_features)
spade,
waveform_features,
gpfa)

try:
from . import pandas_bridge
from . import asset
from . import spade
except ImportError:
# requirements-extras are missing
# please run command `pip install -r requirements-extras.txt`
pass


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