Merge pull request #1 from jjc2718/add_optimizers

[ci skip] This build is based on 3c54414. This commit was created by the following CI build and job: https://github.com/greenelab/jake_dissertation/commit/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/checks https://github.com/greenelab/jake_dissertation/actions/runs/6001912086
greenelab · Aug 28, 2023 · 7d8585a · 7d8585a
1 parent 854f647
commit 7d8585a
Show file tree

Hide file tree

Showing 60 changed files with 39,804 additions and 847 deletions.
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/greenelab/jake_dissertation/tree/gh-pages) branch hosts the contents of this directory at <https://greenelab.github.io/jake_dissertation/>.
-The permalink for this webpage version is <https://greenelab.github.io/jake_dissertation/v/8c1a803748961dcf6b7e8ed4d5ec8f8ce6d5a2a9/>.
+The permalink for this webpage version is <https://greenelab.github.io/jake_dissertation/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://greenelab.github.io/jake_dissertation/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`8c1a803748961dcf6b7e8ed4d5ec8f8ce6d5a2a9`](https://github.com/greenelab/jake_dissertation/commit/8c1a803748961dcf6b7e8ed4d5ec8f8ce6d5a2a9).
+[`3c54414f867d8b2fbddc5390e79b2142dfb8fe29`](https://github.com/greenelab/jake_dissertation/commit/3c54414f867d8b2fbddc5390e79b2142dfb8fe29).
diff --git a/images/optimizers/figure_1.png b/images/optimizers/figure_1.png
diff --git a/images/optimizers/figure_1.svg b/images/optimizers/figure_1.svg
diff --git a/images/optimizers/figure_2.png b/images/optimizers/figure_2.png
diff --git a/images/optimizers/figure_2.svg b/images/optimizers/figure_2.svg
diff --git a/images/optimizers/figure_3.png b/images/optimizers/figure_3.png
diff --git a/images/optimizers/figure_3.svg b/images/optimizers/figure_3.svg
diff --git a/images/optimizers/supp_figure_1.png b/images/optimizers/supp_figure_1.png
diff --git a/images/optimizers/supp_figure_1.svg b/images/optimizers/supp_figure_1.svg
diff --git a/images/optimizers/supp_figure_2.png b/images/optimizers/supp_figure_2.png
diff --git a/images/optimizers/supp_figure_2.svg b/images/optimizers/supp_figure_2.svg
diff --git a/images/optimizers/supp_figure_3.png b/images/optimizers/supp_figure_3.png
diff --git a/images/optimizers/supp_figure_3.svg b/images/optimizers/supp_figure_3.svg
diff --git a/images/optimizers/supp_figure_4.png b/images/optimizers/supp_figure_4.png
diff --git a/images/optimizers/supp_figure_4.svg b/images/optimizers/supp_figure_4.svg
diff --git a/index.html b/index.html
diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/github.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/github.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/mastodon.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/mastodon.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_1.png b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_1.png
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_1.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_1.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_2.png b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_2.png
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_2.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_2.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_3.png b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_3.png
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_3.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/figure_3.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_1.png b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_1.png
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_1.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_1.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_2.png b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_2.png
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_2.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_2.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_3.png b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_3.png
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_3.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_3.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_4.png b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_4.png
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_4.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/optimizers/supp_figure_4.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/orcid.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/orcid.svg
diff --git a/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/twitter.svg b/v/3c54414f867d8b2fbddc5390e79b2142dfb8fe29/images/twitter.svg