boettiger-lab · cboettig · Jun 26, 2020 · Jun 26, 2020 · Jul 7, 2020 · Jul 7, 2020
diff --git a/.github/workflows/rocker.yml b/.github/workflows/rocker.yml
@@ -0,0 +1,19 @@
+name: Docker Actions
+on: [push]
+jobs:
+  render: 
+    runs-on: ubuntu-latest
+    container: rocker/verse:4.0.0
+    steps:
+      - uses: actions/checkout@v1
+      - name: Install dependencies
+        run: |-
+          Rscript -e "remotes::install_deps(dependencies = TRUE)"
+          install2.r -r https://packagemanager.rstudio.com/all/291 igraph
+      - name: Render mansucript
+        run: |-
+          Rscript -e "lapply(fs::dir_ls('.', glob='*.Rmd', recurse=TRUE), rmarkdown::render, envir = globalenv())"
+
+## remarkably(?), we can use the standard checkout action, actions/checkout@v1
+## even inside this Docker container.
+
diff --git a/.travis.yml b/.travis.yml
@@ -1,11 +1,11 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
-#language: R
-#cache: packages
-#script: 
+language: R
+cache: packages
+script: 
 #  - travis_wait 120 R -e 'rmarkdown::render("appendix/appendixA.Rmd")'
 #  - travis_wait 60 R -e 'rmarkdown::render("appendix/appendixB.Rmd")'
-#  - R -e 'rmarkdown::render("manuscripts/manuscript.Rmd")'
+  - R -e 'rmarkdown::render("manuscripts/manuscript.Rmd")'
 
 ## Travis lacks enough memory to handle appendices
 ## test that all .Rmd files can render 
@@ -15,14 +15,14 @@
 
 
 ## Alternate recipe: use Docker instead of R travis
-sudo: required
-services:
-  - docker
-script:
+# sudo: required
+# services:
+#  - docker
+#script:
 # Test on locked version
-  - docker run -ti -v $(pwd):/home/rstudio/repo -w /home/rstudio/repo \
-    rocker/verse:3.4.3 \
-    R -e 'lapply(list.files(pattern=".*.Rmd", recursive=TRUE), rmarkdown::render)'
+#  - docker run -ti -v $(pwd):/home/rstudio/repo -w /home/rstudio/repo \
+#    rocker/verse:3.4.3 \
+#    R -e 'lapply(list.files(pattern=".*.Rmd", recursive=TRUE), rmarkdown::render)'
 
 
 
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Compendium
 Package: pomdpintro
-Version: 0.1.0
+Version: 0.2.0
 Depends: nimble, tidyverse, sarsop, MDPtoolbox, rmarkdown, printr, parallel, gridExtra, rticles, furrr, ramlegacy
-Suggests: extrafont, hrbrthemes, Cairo, ggthemes, tictoc, devtools
+Suggests: extrafont, hrbrthemes, Cairo, ggthemes, tictoc, devtools, igraph
 Remotes: boettiger-lab/sarsop
 
diff --git a/appendix/appendixA.pdf b/appendix/appendixA.pdf
diff --git a/appendix/appendixA_files/figure-latex/S1-1.pdf b/appendix/appendixA_files/figure-latex/S1-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/S2-1.pdf b/appendix/appendixA_files/figure-latex/S2-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/S3-1.pdf b/appendix/appendixA_files/figure-latex/S3-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/S4-1.pdf b/appendix/appendixA_files/figure-latex/S4-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/S5-1.pdf b/appendix/appendixA_files/figure-latex/S5-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/S6-1.pdf b/appendix/appendixA_files/figure-latex/S6-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/S7-1.pdf b/appendix/appendixA_files/figure-latex/S7-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/S8-1.pdf b/appendix/appendixA_files/figure-latex/S8-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/S9-1.pdf b/appendix/appendixA_files/figure-latex/S9-1.pdf
diff --git a/appendix/appendixA_files/figure-latex/unnamed-chunk-25-1.pdf b/appendix/appendixA_files/figure-latex/unnamed-chunk-25-1.pdf
diff --git a/data/appendixA/17e46780a9255acd02d317e1e9d42787.policyx b/data/appendixA/17e46780a9255acd02d317e1e9d42787.policyx
diff --git a/data/appendixA/187f76eda89296ae43caf96c8aa5e51a.policyx b/data/appendixA/187f76eda89296ae43caf96c8aa5e51a.policyx
diff --git a/data/appendixA/2e4b2e31f0a4c26b415d67fbd00bc400.policyx b/data/appendixA/2e4b2e31f0a4c26b415d67fbd00bc400.policyx
diff --git a/data/appendixA/34f4dc82d07faa9cf1ff8d7bb660ad3c.policyx b/data/appendixA/34f4dc82d07faa9cf1ff8d7bb660ad3c.policyx
diff --git a/data/appendixA/3725732eaf3d7c36d380c15ba9f63f6a.policyx b/data/appendixA/3725732eaf3d7c36d380c15ba9f63f6a.policyx
diff --git a/data/appendixA/4d369d534dbdcd6cde642aecb4bbc47d.policyx b/data/appendixA/4d369d534dbdcd6cde642aecb4bbc47d.policyx
diff --git a/data/appendixA/80482da84e3a2850840e525b98f0a516.policyx b/data/appendixA/80482da84e3a2850840e525b98f0a516.policyx
diff --git a/data/appendixA/ae21d46583b6e8713485d4f3967d4f75.policyx b/data/appendixA/ae21d46583b6e8713485d4f3967d4f75.policyx
diff --git a/data/appendixA/all_policies.csv b/data/appendixA/all_policies.csv
diff --git a/data/appendixA/e295b4a5f659ee1856b1198217689114.policyx b/data/appendixA/e295b4a5f659ee1856b1198217689114.policyx
diff --git a/data/appendixA/meta.csv b/data/appendixA/meta.csv
@@ -9,3 +9,12 @@ ff4e0d39dd2ae26eae45c1b03a9b061e,4.03,1.38,15000,2.79364e-05,  Preset timeout re
 0b5c68b7134afe0ae438824ad37d0292,5.39,410.68,15406.2,0.052506,  Preset timeout reached,100,100,100,0.95,2019-06-10 09:00:08,gs,0.75,1,0.02,0.15,normal,7
 cfa85b3302e4726205b6cc1bc695ee10,5.7,1238.57,15400.5,0.0195831,  Preset timeout reached,100,100,100,0.95,2019-06-10 09:01:45,gs,0.75,1,0.1,0.1,normal,5
 3db3ecc8830d87e0f4469a67e47a4a37,5.36,367.65,15227.1,0.0261569,  Preset timeout reached,100,100,100,0.95,2019-06-11 07:49:07,gs,0.75,1,0.02,0.1,normal,4
+e295b4a5f659ee1856b1198217689114,2.15,1.6,15000,2.79364e-05,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:44:17,gs,0.75,1,0.02,0,normal,1
+17e46780a9255acd02d317e1e9d42787,2.34,5.32,15000.1,7.48622e-05,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:44:44,gs,0.75,1,0.1,0,normal,2
+4d369d534dbdcd6cde642aecb4bbc47d,2.42,7.34,15000.1,4.59653e-05,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:44:46,gs,0.75,1,0.15,0,normal,3
+3725732eaf3d7c36d380c15ba9f63f6a,2.79,455.68,15168.8,0.0258481,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:52:21,gs,0.75,1,0.02,0.1,normal,4
+34f4dc82d07faa9cf1ff8d7bb660ad3c,3.03,2491.21,15165.7,0.0595409,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:52:52,gs,0.75,1,0.15,0.15,normal,9
+80482da84e3a2850840e525b98f0a516,2.95,1741.93,15174.8,0.0178336,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:53:04,gs,0.75,1,0.1,0.1,normal,5
+ae21d46583b6e8713485d4f3967d4f75,2.91,2431.3,15234.2,0.0138554,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:54:01,gs,0.75,1,0.15,0.1,normal,6
+187f76eda89296ae43caf96c8aa5e51a,2.82,466.9,15306,0.050797,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:54:35,gs,0.75,1,0.02,0.15,normal,7
+2e4b2e31f0a4c26b415d67fbd00bc400,2.9,1783.88,15392.2,0.0662396,  Preset timeout reached,100,100,100,0.95,2020-06-26 09:56:44,gs,0.75,1,0.1,0.15,normal,8