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Refactoring and documentation of SympNets #88

Merged
merged 81 commits into from
Dec 4, 2023
Merged

Refactoring and documentation of SympNets #88

merged 81 commits into from
Dec 4, 2023

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benedict-96
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Updated the SympNet documentation: split the file into theoty and a tutorial. Also updated the Documenter, added a logo and got rid of all tikz images.

@benedict-96
Copied Makefile from GI.
efad4e6
@benedict-96
Started adding bibliography.
c95c6d1
@benedict-96
Copied Makefile from GI.
7f80823
@benedict-96
Added more references (on symplectic integrators).
355ba99
@benedict-96
Started to rework this section. Fixed typos.
dca1b52
@benedict-96
Continued changing relevant bits and corrected typos. The file still …
bbe8c30 
…uses old syntax.
@benedict-96
Updated Hairer reference.
5823466
@benedict-96
Started adding descriptions to the various layers.
2776bc6
@benedict-96
Started refactoring this file. It still uses the old syntax.
daa8765
@benedict-96
Added routines such that the SympNet layers can now deal with NamedTu…
7866c07 
…ples.
@benedict-96
File containing SympNet architecture.
bbddca5
@benedict-96
Added necessary tikz files.
0c86757
@benedict-96
Fixed typo.
1cf6ff7
@benedict-96
images -> tikz.
504e841
@benedict-96
Added (empty file) references.
fd4a232
@benedict-96
Added tikz picture that visualizes dependencies of various structs an…
411c20a 
…d types that are relevant for SympNets.
@benedict-96
Updated file path.
a8e92fb
@benedict-96
Added the bibliography with DocumenterCitations.
7eed150
@benedict-96
Fixed some typos.
c3d365e
@benedict-96
Updated file path.
48ea7d3
@benedict-96
Added new files.
37b0444
@benedict-96
Updated pendulum script to reflect new data types.
9c840bc
@benedict-96
Updated SympNet architectures.:
2e82681
@benedict-96
Started adding the option of symplectic data to the DataLoader.
950565d
@benedict-96
Made layers work with symplectic data.
f543742
@benedict-96
Added more description and a routine that can be initialized with a N…
704b39f 
…euralNetwork.
@benedict-96
Added some comments.
d3aa016
@benedict-96
Reorganized the DataLoader and Batch for NamedTuples.
4376166
@benedict-96
Fixed some typos in the code section.
998a1a9
@benedict-96
Extened routines to NamedTuples and fixed some typos.
772bd3a
@benedict-96
Added ENV line for correct plotting.
ebd35ac
@benedict-96
Updated according to new data structures in sympnets.jl
5af1ab9
@benedict-96
Updated file path to png.
1953f39
@benedict-96
Added comment.
e0fe713
@benedict-96
Split the theory and the tutorial sections up into two parts.
1008491
@benedict-96
Played around with the parameters a bit to make the LASympnet work (h…
c45adf5 
…opefully).
@benedict-96
Added the sympnet tutorial.
60673e7
@benedict-96
Added various cross-references and updated the tikz picture to use th…
acdb284 
…e same notation what is used in the text.
@benedict-96
Changed the default values of the LA SympNet parameters.
87cfccc
@benedict-96
Updated the makefile to include the new logos.
acdaf0b
@benedict-96
Replaced the name with our logo (also dark mode).
c669e8f
@benedict-96
Added an optional argument (sidebar_sitename=false) to better display…
350205b 
… the logo.
@benedict-96
Added generation of tikz images.
c8f869e
@benedict-96
Added .yaml file to generate logos.
f52d258
@benedict-96
Got rid of extra clean command (should already be included in make all).
1e1d4db
@benedict-96
Added logos (you shouldn't include bitstype).
1455922
@benedict-96
Added logo.
a514b2a
@benedict-96
Added logo for darkmode.
ee17db8
@benedict-96
Deleted Readme workflow again.
fed1520
@benedict-96
type -> GeometricMachineLearning.type
9fce2b7
@benedict-96
Fixed a problem with tests that appeared because of the new syntax.
dd0596c
@benedict-96
Added an extra option just to generate logos.
6c42e9c
@benedict-96
Updated names of exported structs.
d707115
@benedict-96
Deleted test that appeared double for some reason.
b15bc2f
@codecov Codecov
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codecov bot commented Nov 23, 2023 •
edited
Loading

Codecov Report

Attention: 150 lines in your changes are missing coverage. Please review.

Comparison is base (9445c71) 69.35% compared to head (56b08c5) 66.23%.

Files Patch % Lines
src/architectures/sympnet.jl 9.63% 75 Missing ⚠️
src/data_loader/batch.jl 3.03% 32 Missing ⚠️
src/arrays/symmetric.jl 72.60% 20 Missing ⚠️
src/data_loader/data_loader.jl 0.00% 15 Missing ⚠️
src/layers/sympnets.jl 88.88% 5 Missing ⚠️
src/optimizers/optimizer.jl 0.00% 2 Missing ⚠️
src/arrays/skew_symmetric.jl 0.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #88      +/-   ##
==========================================
- Coverage   69.35%   66.23%   -3.13%     
==========================================
  Files          96       96              
  Lines        2382     2535     +153     
==========================================
+ Hits         1652     1679      +27     
- Misses        730      856     +126

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@michakraus michakraus merged commit cdfd554 into main Dec 4, 2023
9 of 14 checks passed
@michakraus michakraus deleted the refactoring_and_documentation branch December 4, 2023 14:38
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@michakraus michakraus Awaiting requested review from michakraus

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@benedict-96 @michakraus