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Feat cookbook recipe articles #99

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merged 105 commits into from
Feb 9, 2024
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782d0ca
adding retro recipe
MOshima-PIFSC Jul 22, 2023
1d16a45
add get SS to pkgdown.yaml
MOshima-PIFSC Jul 25, 2023
362c5c7
remove ss executable for clean up
MOshima-PIFSC Jul 25, 2023
ce1c2f2
add retrospective article
MOshima-PIFSC Jul 26, 2023
dc04397
add FEAT branch to workflow to trigger pkgdown update
MOshima-PIFSC Jul 26, 2023
df3d0f8
update retro article
MOshima-PIFSC Jul 26, 2023
f590741
removing clean up ss exe bc seems like not necessary
MOshima-PIFSC Jul 26, 2023
1f98d4b
update retro article
MOshima-PIFSC Jul 27, 2023
5cd30c2
remove retro stuff from readme
MOshima-PIFSC Jul 27, 2023
26f16b8
minor fix
MOshima-PIFSC Jul 27, 2023
2c84f43
debug
MOshima-PIFSC Jul 27, 2023
f2dca88
turn off r -cmd-checks on this branch
MOshima-PIFSC Jul 27, 2023
3948341
change years for xlim
MOshima-PIFSC Jul 27, 2023
f21c04e
adding render rmd and commit to repo to workflow
MOshima-PIFSC Jul 27, 2023
02b66de
change file name in workflow
MOshima-PIFSC Jul 27, 2023
3304e6d
update gh action
MOshima-PIFSC Jul 27, 2023
70184b5
small fix
MOshima-PIFSC Jul 28, 2023
a8c38d0
update workflow
MOshima-PIFSC Jul 28, 2023
9d20fca
fix render command
MOshima-PIFSC Jul 28, 2023
59f0b48
installing depends
MOshima-PIFSC Jul 28, 2023
e5d7264
update article
MOshima-PIFSC Jul 28, 2023
1979c8d
update workflow
MOshima-PIFSC Jul 28, 2023
b6edd5e
ignore ss.exe
MOshima-PIFSC Jul 28, 2023
e2b690b
debugging
MOshima-PIFSC Jul 28, 2023
6918d1e
debug
MOshima-PIFSC Jul 28, 2023
9afb90c
debug
MOshima-PIFSC Jul 28, 2023
e15e114
debug
MOshima-PIFSC Jul 28, 2023
f969224
debug
MOshima-PIFSC Jul 28, 2023
631aca2
debug
MOshima-PIFSC Jul 28, 2023
63ebaff
update readme.md
MOshima-PIFSC Jul 28, 2023
e784350
check ss
MOshima-PIFSC Jul 29, 2023
0eafe25
copy ss over to dir_retro
MOshima-PIFSC Jul 29, 2023
c966ee3
run retro in rmd
MOshima-PIFSC Jul 29, 2023
9e88e5e
add residual analysis and some readme changes
MOshima-PIFSC Aug 9, 2023
0253b8f
likelihood profile article
MOshima-PIFSC Aug 9, 2023
d0b4c47
update likelihood
MOshima-PIFSC Aug 9, 2023
0563e6d
updating readme
MOshima-PIFSC Aug 10, 2023
f054745
finish likelihood
MOshima-PIFSC Aug 10, 2023
33a3e76
add hcxval
MOshima-PIFSC Aug 10, 2023
af6380f
add SSmase to hcxval
MOshima-PIFSC Aug 10, 2023
e306144
running retro in hcxval
MOshima-PIFSC Aug 10, 2023
377fad8
clean up readme
MOshima-PIFSC Aug 10, 2023
9ca9397
add SSrmse function to resids article
MOshima-PIFSC Aug 10, 2023
ff0ffff
remove duplicate check badge and add bootstrap theme
MOshima-PIFSC Aug 11, 2023
95e1654
add jitter article
MOshima-PIFSC Aug 11, 2023
73c7c53
add tidyverse dependency in ghaction
MOshima-PIFSC Aug 11, 2023
85a4a84
add more depends
MOshima-PIFSC Aug 11, 2023
3f1436d
minor fix
MOshima-PIFSC Aug 11, 2023
b40f40f
add aspm vignette
MOshima-PIFSC Jan 4, 2024
64a3e10
fix ss name
MOshima-PIFSC Jan 4, 2024
58b77de
removing incorrect r4ss version
MOshima-PIFSC Jan 4, 2024
7e67c18
update r4ss version
MOshima-PIFSC Jan 4, 2024
811af67
update ss3 url
MOshima-PIFSC Jan 4, 2024
0941d10
minor fix
MOshima-PIFSC Jan 4, 2024
fc85ac9
file path
MOshima-PIFSC Jan 4, 2024
94642ec
use get_ss3_exe function
MOshima-PIFSC Jan 5, 2024
e9b0e36
remove r4ss from Imports
MOshima-PIFSC Jan 5, 2024
a1694cf
r4ss version
MOshima-PIFSC Jan 5, 2024
499d67a
r4ss version
MOshima-PIFSC Jan 5, 2024
f9796c7
r4ss version
MOshima-PIFSC Jan 5, 2024
095bfdd
add get_ss3_exe fun to vingettes
MOshima-PIFSC Jan 5, 2024
d3f87c8
r4ss@main in description
MOshima-PIFSC Jan 5, 2024
e049f4a
change exe name
MOshima-PIFSC Jan 5, 2024
fa7d4b4
change ss3 version
MOshima-PIFSC Jan 5, 2024
3df3f30
fix file paths
MOshima-PIFSC Jan 5, 2024
15e78c6
debug jitter
MOshima-PIFSC Jan 5, 2024
9e2779e
aspm file path
MOshima-PIFSC Jan 5, 2024
cf3be86
aspm file path
MOshima-PIFSC Jan 10, 2024
1058060
update paths
MOshima-PIFSC Jan 10, 2024
27265d7
jitter debug
MOshima-PIFSC Jan 10, 2024
c348eea
jitter debug
MOshima-PIFSC Jan 10, 2024
04738ba
eval jitter
MOshima-PIFSC Jan 11, 2024
aeb5995
minor fixes to aspm
MOshima-PIFSC Jan 11, 2024
5ce861d
add future pkg to setup
MOshima-PIFSC Jan 16, 2024
2dd0f16
don't install future in rmarkdown
MOshima-PIFSC Jan 16, 2024
6eebe1b
install future in rmd
MOshima-PIFSC Jan 16, 2024
494f029
add updates to pkgdown yml
MOshima-PIFSC Jan 17, 2024
f8b30b8
add purrr and furrr
MOshima-PIFSC Jan 17, 2024
91d5e24
change pak to install_github
MOshima-PIFSC Jan 17, 2024
e05adae
add codespace
MOshima-PIFSC Jan 17, 2024
d1322f0
remove r4ss from devcontainer setup
MOshima-PIFSC Jan 17, 2024
bcb330d
remove extra package installs
MOshima-PIFSC Jan 17, 2024
f88e755
switch to windows machine
MOshima-PIFSC Jan 18, 2024
6c1d37b
Update devcontainer.json
MOshima-PIFSC Jan 30, 2024
683680f
use jitter-fix r4ss branch
MOshima-PIFSC Jan 31, 2024
60027fa
Merge branch 'FEAT-cookbook-recipe-articles' of https://github.com/PI…
MOshima-PIFSC Jan 31, 2024
bf48907
use fork of r4ss
MOshima-PIFSC Jan 31, 2024
29fe8a4
use ubuntu-latest
MOshima-PIFSC Jan 31, 2024
fb53bc3
use try-fix-jitter branch
MOshima-PIFSC Feb 2, 2024
e6aaee2
fix SSgetoutput index
MOshima-PIFSC Feb 2, 2024
d46ae17
small changes in vignettes
MOshima-PIFSC Feb 2, 2024
fcd5afe
clean up vignettes
MOshima-PIFSC Feb 2, 2024
993f1a1
fix in jitter file names
MOshima-PIFSC Feb 6, 2024
0b6d369
increase Njitter
MOshima-PIFSC Feb 6, 2024
41f586c
text fixes
MOshima-PIFSC Feb 6, 2024
4796cce
remove example data, deprecated Vignette, and cookbook recipe code
MOshima-PIFSC Feb 8, 2024
d483d8d
Merge branch 'main' into FEAT-cookbook-recipe-articles
efletcherPIFSC Feb 8, 2024
a1dce53
removed branches from workflows
MOshima-PIFSC Feb 8, 2024
21fe902
test-HCxval
MOshima-PIFSC Feb 9, 2024
6785f5e
style and docs: run devtools::document() and styler::style_pkg()
MOshima-PIFSC Feb 9, 2024
ebc8fb1
change retroSimple to retrosum.simple
MOshima-PIFSC Feb 9, 2024
986ae3f
Merge branch 'FEAT-cookbook-recipe-articles' of https://github.com/PI…
MOshima-PIFSC Feb 9, 2024
b2ab645
use retroModels object
MOshima-PIFSC Feb 9, 2024
84b8d26
adjust test values to match new model
MOshima-PIFSC Feb 9, 2024
a04721f
style and docs: run devtools::document() and styler::style_pkg()
MOshima-PIFSC Feb 9, 2024
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3 changes: 2 additions & 1 deletion .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -13,4 +13,5 @@ CONTRIBUTING.md
^docs$
^pkgdown$
^README\.Rmd$
^model_recipes$
^model_recipes$
^vignettes/articles$
59 changes: 59 additions & 0 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,59 @@
// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
// https://github.com/microsoft/vscode-dev-containers/tree/v0.234.0/containers/r
{
"name": "R (rocker/r-ver base)",
// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
"image": "ghcr.io/rocker-org/devcontainer/r-ver:4.3", //commma needed if other sections are used.

// hostRequirements to set a minimum for machine type
//"hostRequirements": {
// "cpus": 8,
// "memory": "8gb",
// "storage": "32gb"
// },

// Features to add to the dev container. More info: https://containers.dev/features.
"features": {

// to install r packages using pak
// more info: https://github.com/rocker-org/devcontainer-features/blob/main/src/r-packages/README.md
"ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
"packages": "tidyverse,future,purrr,rmarkdown",
"installSystemRequirements": true
},
//to install ss3 via wget
"ghcr.io/devcontainers-contrib/features/wget-apt-get:1.0.15":{
"-O ss3 https://github.com/nmfs-ost/ss3-source-code/releases/latest/download/ss_linux"
}
// // for quarto cli
// more info: https://github.com/rocker-org/devcontainer-features/blob/main/src/quarto-cli/README.md
// "ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {}

//to use Rstudio as IDE instead of VS code
//"ghcr.io/rocker-org/devcontainer-features/rstudio-server:0": {}
},

// Use 'forwardPorts' to make a list of ports inside the container available locally.
// "forwardPorts": [],

//"postAttachCommand": {
// "rstudio-start": "rserver"
//},
// Use 'postCreateCommand' to run commands after the container is created.
//"postCreateCommand": "echo 'options(repos = c(CRAN = \"https://cloud.r-project.org\"))' | sudo sh -c 'cat - >>\"${R_HOME}/etc/Rprofile.site\"'",

// Configure tool-specific properties.
"customizations": {
"vscode": {
// Set *default* container specific settings.json values on container create.
// Add the IDs of extensions you want installed when the container is created.
"extensions": [
"GitHub.codespaces"
]
}


// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
// "remoteUser": "root"
}
}
2 changes: 1 addition & 1 deletion .github/workflows/R-CMD-check.yaml
efletcherPIFSC marked this conversation as resolved.
Show resolved Hide resolved
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ on:
- 'README.md'
pull_request:

name: build-ss-R-CMD-check
name: R-CMD-check

jobs:
R-CMD-check:
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/pkgdown.yaml
MOshima-PIFSC marked this conversation as resolved.
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ jobs:

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::pkgdown, local::.
extra-packages: any::pkgdown, local::., any::tidyverse, any::future, any::rmarkdown, any::purrr, any::furrr
needs: website

- name: Deploy package
Expand Down
196 changes: 0 additions & 196 deletions Cookbook/Jitter_test_example.R

This file was deleted.

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