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Issue 56: Add pathfinder init #117

Merged
merged 46 commits into from
Mar 8, 2024
Merged

Issue 56: Add pathfinder init #117

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0b7c8e1
update
SamuelBrand1 Mar 1, 2024
d86b12d
added doc deps
SamuelBrand1 Mar 4, 2024
dfeaf54
started `getting started` notebook
SamuelBrand1 Mar 4, 2024
2ce57b4
Update getting_started.jl
SamuelBrand1 Mar 4, 2024
9089270
Getting started example
SamuelBrand1 Mar 5, 2024
e163b15
Add generated Pluto notebooks to gitignore
SamuelBrand1 Mar 5, 2024
5774a21
remove old version of example
SamuelBrand1 Mar 5, 2024
e7c60ce
add Pluto and PlutoStaticHTML as deps
SamuelBrand1 Mar 5, 2024
ee9e1ca
Adapt make and build files to generate Pluto notebooks statically and…
SamuelBrand1 Mar 5, 2024
fd5d554
Merge branch 'main' into add-doc-examples
SamuelBrand1 Mar 5, 2024
359a3c2
include build step for rendering Pluto notebooks
SamuelBrand1 Mar 5, 2024
ca2707e
remove old version of the getting started example
SamuelBrand1 Mar 5, 2024
f7816de
update
SamuelBrand1 Mar 1, 2024
0b4bfe2
added doc deps
SamuelBrand1 Mar 4, 2024
36fd0ea
started `getting started` notebook
SamuelBrand1 Mar 4, 2024
58e9744
Update getting_started.jl
SamuelBrand1 Mar 4, 2024
6513caf
Getting started example
SamuelBrand1 Mar 5, 2024
1c740db
Add generated Pluto notebooks to gitignore
SamuelBrand1 Mar 5, 2024
a37c77a
remove old version of example
SamuelBrand1 Mar 5, 2024
66782b8
add Pluto and PlutoStaticHTML as deps
SamuelBrand1 Mar 5, 2024
6853614
Adapt make and build files to generate Pluto notebooks statically and…
SamuelBrand1 Mar 5, 2024
2fbe618
include build step for rendering Pluto notebooks
SamuelBrand1 Mar 5, 2024
d97c92a
remove old version of the getting started example
SamuelBrand1 Mar 5, 2024
6019674
Merge branch 'main' into add-doc-examples
SamuelBrand1 Mar 6, 2024
e805792
Update EpiAware/docs/src/examples/getting_started.jl
seabbs Mar 6, 2024
0189ac1
Merge branch 'add-doc-examples' of https://github.com/CDCgov/Rt-witho…
SamuelBrand1 Mar 6, 2024
14b5d30
Remove unnecessary `CSV` dep in test
SamuelBrand1 Mar 6, 2024
f825d38
fix getting started
SamuelBrand1 Mar 6, 2024
0853042
Merge branch 'main' into add-pathfinder-init
SamuelBrand1 Mar 6, 2024
ac788d0
pathfinder first pass
SamuelBrand1 Mar 6, 2024
f6b8926
add deps which are required for `_epi_aware`
SamuelBrand1 Mar 6, 2024
2586edc
add `_epi_aware` function
SamuelBrand1 Mar 6, 2024
c21df4c
Add _epi_aware unit test
SamuelBrand1 Mar 6, 2024
30173c6
add project dep compat
SamuelBrand1 Mar 6, 2024
dbb655f
remove old notebooks so doesn't waste time trying to render
SamuelBrand1 Mar 6, 2024
5611ebc
Update getting started to include inference loop function
SamuelBrand1 Mar 6, 2024
4af04ac
manypathfinder approach with new getting started and tests
SamuelBrand1 Mar 7, 2024
93e3673
Merge branch 'main' into add-pathfinder-init
SamuelBrand1 Mar 7, 2024
40f3a5b
change to generated_y_t approach
SamuelBrand1 Mar 7, 2024
9b2b509
Update EpiAware/docs/src/examples/getting_started.jl
SamuelBrand1 Mar 7, 2024
a8ca3e8
fix rw_init
SamuelBrand1 Mar 7, 2024
957944a
Merge branch 'add-pathfinder-init' of https://github.com/CDCgov/Rt-wi…
SamuelBrand1 Mar 7, 2024
42b0b1b
Add warning about fail of all initial pathfinder runs
SamuelBrand1 Mar 7, 2024
902d206
Increased testing cases for manypathfinder
SamuelBrand1 Mar 7, 2024
67427fb
Make total fail a verbose exception error
SamuelBrand1 Mar 7, 2024
6deb30a
Change `manypathfinder` to have some API as `multipathfinder`
SamuelBrand1 Mar 8, 2024
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6 changes: 6 additions & 0 deletions EpiAware/Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,27 +7,33 @@ version = "0.1.0-DEV"
DataFramesMeta = "1313f7d8-7da2-5740-9ea0-a2ca25f37964"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
Optim = "429524aa-4258-5aef-a3af-852621145aeb"
Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
Pathfinder = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454"
QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Transducers = "28d57a85-8fef-5791-bfe6-a80928e7c999"
Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"

[compat]
DataFramesMeta = "0.14"
Distributions = "0.25"
DocStringExtensions = "0.9"
DynamicPPL = "0.24"
LinearAlgebra = "1.9"
LogExpFunctions = "0.3"
Optim = "1.9"
Parameters = "0.12"
Pathfinder = "0.8"
QuadGK = "2.9"
Random = "1.9"
ReverseDiff = "1.15"
SparseArrays = "1.10"
Transducers = "0.4"
Turing = "0.30"
julia = "1.10"
2 changes: 2 additions & 0 deletions EpiAware/docs/Project.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,10 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Pathfinder = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454"
Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
PlutoStaticHTML = "359b1769-a58e-495b-9770-312e911026ad"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
Transducers = "28d57a85-8fef-5791-bfe6-a80928e7c999"
Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
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