differences for PR #18

Author: actions-user

basic-targets.md

@@ -278,12 +278,12 @@ tar_make()
 
 ```{.output}
 ▶ start target penguins_csv_file
-● built target penguins_csv_file [0.002 seconds]
+● built target penguins_csv_file [0.001 seconds]
 ▶ start target penguins_data_raw
-● built target penguins_data_raw [0.148 seconds]
+● built target penguins_data_raw [0.161 seconds]
 ▶ start target penguins_data
-● built target penguins_data [0.011 seconds]
-▶ end pipeline [0.244 seconds]
+● built target penguins_data [0.012 seconds]
+▶ end pipeline [0.269 seconds]
 ```
 
 Congratulations, you've run your first workflow with `targets`!

branch.md

@@ -79,8 +79,8 @@ tar_plan(
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
 ▶ start target combined_model
-● built target combined_model [0.033 seconds]
-▶ end pipeline [0.115 seconds]
+● built target combined_model [0.056 seconds]
+▶ end pipeline [0.153 seconds]
 ```
 
 Let's have a look at the model. We will use the `glance()` function from the `broom` package. Unlike base R `summary()`, this function returns output as a tibble (the tidyverse equivalent of a dataframe), which as we will see later is quite useful for downstream analyses.
@@ -151,12 +151,12 @@ tar_plan(
 ▶ start target species_model
 ● built target species_model [0.002 seconds]
 ▶ start target combined_summary
-● built target combined_summary [0.008 seconds]
+● built target combined_summary [0.009 seconds]
 ▶ start target interaction_summary
-● built target interaction_summary [0.045 seconds]
+● built target interaction_summary [0.052 seconds]
 ▶ start target species_summary
-● built target species_summary [0.003 seconds]
-▶ end pipeline [0.168 seconds]
+● built target species_summary [0.004 seconds]
+▶ end pipeline [0.191 seconds]
 ```
 
 Let's look at the summary of one of the models:
@@ -226,15 +226,15 @@ First, let's look at the messages provided by `tar_make()`.
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
 ▶ start target models
-● built target models [0.007 seconds]
+● built target models [0.008 seconds]
 ▶ start branch model_summaries_5ad4cec5
-● built branch model_summaries_5ad4cec5 [0.009 seconds]
+● built branch model_summaries_5ad4cec5 [0.01 seconds]
 ▶ start branch model_summaries_c73912d5
 ● built branch model_summaries_c73912d5 [0.004 seconds]
 ▶ start branch model_summaries_91696941
-● built branch model_summaries_91696941 [0.047 seconds]
+● built branch model_summaries_91696941 [0.055 seconds]
 ● built pattern model_summaries
-▶ end pipeline [0.172 seconds]
+▶ end pipeline [0.2 seconds]
 ```
 
 There is a series of smaller targets (branches) that are each named like model_summaries_5ad4cec5, then one overall `model_summaries` target.
@@ -365,13 +365,13 @@ tar_plan(
 ✔ skip target penguins_data
 ✔ skip target models
 ▶ start branch model_summaries_5ad4cec5
-● built branch model_summaries_5ad4cec5 [0.018 seconds]
+● built branch model_summaries_5ad4cec5 [0.022 seconds]
 ▶ start branch model_summaries_c73912d5
-● built branch model_summaries_c73912d5 [0.053 seconds]
+● built branch model_summaries_c73912d5 [0.066 seconds]
 ▶ start branch model_summaries_91696941
-● built branch model_summaries_91696941 [0.005 seconds]
+● built branch model_summaries_91696941 [0.006 seconds]
 ● built pattern model_summaries
-▶ end pipeline [0.18 seconds]
+▶ end pipeline [0.219 seconds]
 ```
 
 And this time, when we load the `model_summaries`, we can tell which model corresponds to which row (you may need to scroll to the right to see it).

files.md

@@ -56,8 +56,8 @@ tar_plan(
 
 ```{.output}
 ▶ start target some_data
-● built target some_data [0.001 seconds]
-▶ end pipeline [0.065 seconds]
+● built target some_data [0 seconds]
+▶ end pipeline [0.071 seconds]
 ```
 
 If we inspect the contents of `some_data` with `tar_read(some_data)`, it will contain the string `"Hello World"` as expected.
@@ -77,7 +77,7 @@ tar_plan(
 
 ```{.output}
 ✔ skip target some_data
-✔ skip pipeline [0.047 seconds]
+✔ skip pipeline [0.052 seconds]
 ```
 
 The target `some_data` was skipped, even though the contents of the file changed.
@@ -100,8 +100,8 @@ tar_plan(
 ▶ start target data_file
 ● built target data_file [0.001 seconds]
 ▶ start target some_data
-● built target some_data [0 seconds]
-▶ end pipeline [0.072 seconds]
+● built target some_data [0.001 seconds]
+▶ end pipeline [0.08 seconds]
 ```
 
 This time we see that `targets` does successfully re-build `some_data` as expected.
@@ -186,10 +186,10 @@ tar_plan(
 ▶ start target penguins_data_raw_file
 ● built target penguins_data_raw_file [0.001 seconds]
 ▶ start target penguins_data_raw
-● built target penguins_data_raw [0.27 seconds]
+● built target penguins_data_raw [0.32 seconds]
 ▶ start target penguins_data
-● built target penguins_data [0.019 seconds]
-▶ end pipeline [0.366 seconds]
+● built target penguins_data [0.023 seconds]
+▶ end pipeline [0.427 seconds]
 ```
 
 ::::::::::::::::::::::::::::::::::
@@ -260,14 +260,14 @@ tar_plan(
 
 ```{.output}
 ▶ start target hello_file
-● built target hello_file [0.001 seconds]
+● built target hello_file [0 seconds]
 ▶ start target hello
-● built target hello [0 seconds]
+● built target hello [0.001 seconds]
 ▶ start target hello_caps
 ● built target hello_caps [0 seconds]
 ▶ start target hello_caps_out
 ● built target hello_caps_out [0.001 seconds]
-▶ end pipeline [0.079 seconds]
+▶ end pipeline [0.09 seconds]
 ```
 
 Take a look at `hello_caps.txt` in the `results` folder and verify it is as you expect.

hpc.md

@@ -0,0 +1,26 @@
+---
+title: 'Deploying Targets on HPC'
+teaching: 10
+exercises: 2
+---
+
+
+sbatch was not detected. Likely Slurm is not installed. Exiting.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

lifecycle.md

@@ -43,7 +43,7 @@ tar_make()
 ✔ skip target penguins_csv_file
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
-✔ skip pipeline [0.063 seconds]
+✔ skip pipeline [0.069 seconds]
 ```
 
 Remember how the first time we ran the pipeline, `targets` printed out a list of each target as it was being built?
@@ -89,7 +89,7 @@ tar_make()
 ✔ skip target penguins_data_raw
 ▶ start target penguins_data
 ● built target penguins_data [0.022 seconds]
-▶ end pipeline [0.112 seconds]
+▶ end pipeline [0.109 seconds]
 ```
 
 What happened?
@@ -259,7 +259,7 @@ tar_make()
 ✔ skip target penguins_csv_file
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
-✔ skip pipeline [0.056 seconds]
+✔ skip pipeline [0.069 seconds]
 ```
 
 Let's invalidate `penguins_data` and run it again:
@@ -275,8 +275,8 @@ tar_make()
 ✔ skip target penguins_csv_file
 ✔ skip target penguins_data_raw
 ▶ start target penguins_data
-● built target penguins_data [0.02 seconds]
-▶ end pipeline [0.101 seconds]
+● built target penguins_data [0.023 seconds]
+▶ end pipeline [0.112 seconds]
 ```
 
 If you want to reset **everything** and start fresh, you can use `tar_invalidate(everything())` (`tar_invalidate()` [accepts `tidyselect` expressions](https://docs.ropensci.org/targets/reference/tar_invalidate.html) to specify target names).

md5sum.txt

@@ -1,21 +1,22 @@
 "file" "checksum" "built" "date"
-"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-07-11"
-"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2023-07-11"
-"config.yaml" "97cf738871f0133f70da7d938c14bfb2" "site/built/config.yaml" "2023-07-11"
-"index.md" "06bbfd5ab0e2353032361b3321342d13" "site/built/index.md" "2023-07-11"
-"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2023-07-11"
-"episodes/introduction.Rmd" "feaacfccab344eb1fa6e702aded97924" "site/built/introduction.md" "2023-07-11"
-"episodes/basic-targets.Rmd" "9a431b9a3596cb55c1f62f905cb808a2" "site/built/basic-targets.md" "2023-07-11"
-"episodes/cache.Rmd" "6395b6d5b81a029daf9d37a2cb56d6d9" "site/built/cache.md" "2023-07-11"
-"episodes/lifecycle.Rmd" "b52fcffdd75504e8579c8a7f1908ade2" "site/built/lifecycle.md" "2023-07-11"
-"episodes/organization.Rmd" "ef33426eed3d4e0784a728b5aa670836" "site/built/organization.md" "2023-07-11"
-"episodes/packages.Rmd" "2812a10b7ae0e8e0b3e000a5b74f939c" "site/built/packages.md" "2023-07-11"
-"episodes/files.Rmd" "f05ed479ce1a0dfdcc14ebcd872c554c" "site/built/files.md" "2023-07-11"
-"episodes/branch.Rmd" "b07912f5d8f14eb0e831a6a081ee99f2" "site/built/branch.md" "2023-07-11"
-"episodes/parallel.Rmd" "69b941c8fd37a23249e6d16636fb645a" "site/built/parallel.md" "2023-07-11"
-"episodes/quarto.Rmd" "a6c2d51f32e4a7e1087b87b211d7a03a" "site/built/quarto.md" "2023-07-11"
-"instructors/instructor-notes.md" "df3784ee5c0436a9e171071f7965d3fc" "site/built/instructor-notes.md" "2023-07-11"
-"learners/reference.md" "3f06251c1f932e767ae8f22db25eb5a2" "site/built/reference.md" "2023-07-11"
-"learners/setup.md" "99a67bca32058e9f70d6d8e405519826" "site/built/setup.md" "2023-07-11"
-"profiles/learner-profiles.md" "44d8b9d8aca7963e6577e8c67d23eac0" "site/built/learner-profiles.md" "2023-07-11"
-"renv/profiles/lesson-requirements/renv.lock" "e4993bea6dd21f86ad9950337f7ec4f0" "site/built/renv.lock" "2023-07-11"
+"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-07-12"
+"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2023-07-12"
+"config.yaml" "5b0ca11806a6d604dd96faa2f669590e" "site/built/config.yaml" "2023-07-12"
+"index.md" "06bbfd5ab0e2353032361b3321342d13" "site/built/index.md" "2023-07-12"
+"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2023-07-12"
+"episodes/introduction.Rmd" "feaacfccab344eb1fa6e702aded97924" "site/built/introduction.md" "2023-07-12"
+"episodes/basic-targets.Rmd" "9a431b9a3596cb55c1f62f905cb808a2" "site/built/basic-targets.md" "2023-07-12"
+"episodes/cache.Rmd" "6395b6d5b81a029daf9d37a2cb56d6d9" "site/built/cache.md" "2023-07-12"
+"episodes/lifecycle.Rmd" "b52fcffdd75504e8579c8a7f1908ade2" "site/built/lifecycle.md" "2023-07-12"
+"episodes/organization.Rmd" "ef33426eed3d4e0784a728b5aa670836" "site/built/organization.md" "2023-07-12"
+"episodes/packages.Rmd" "2812a10b7ae0e8e0b3e000a5b74f939c" "site/built/packages.md" "2023-07-12"
+"episodes/files.Rmd" "f05ed479ce1a0dfdcc14ebcd872c554c" "site/built/files.md" "2023-07-12"
+"episodes/branch.Rmd" "b07912f5d8f14eb0e831a6a081ee99f2" "site/built/branch.md" "2023-07-12"
+"episodes/parallel.Rmd" "69b941c8fd37a23249e6d16636fb645a" "site/built/parallel.md" "2023-07-12"
+"episodes/quarto.Rmd" "a6c2d51f32e4a7e1087b87b211d7a03a" "site/built/quarto.md" "2023-07-12"
+"episodes/hpc.Rmd" "e4dc6ad85746a4b8a147e41ac18ca281" "site/built/hpc.md" "2023-07-12"
+"instructors/instructor-notes.md" "df3784ee5c0436a9e171071f7965d3fc" "site/built/instructor-notes.md" "2023-07-12"
+"learners/reference.md" "3f06251c1f932e767ae8f22db25eb5a2" "site/built/reference.md" "2023-07-12"
+"learners/setup.md" "b4bdd601ab985cf048829f49710df7fc" "site/built/setup.md" "2023-07-12"
+"profiles/learner-profiles.md" "44d8b9d8aca7963e6577e8c67d23eac0" "site/built/learner-profiles.md" "2023-07-12"
+"renv/profiles/lesson-requirements/renv.lock" "0ef31347a5f441da417df76687c654a2" "site/built/renv.lock" "2023-07-12"

packages.md

@@ -71,8 +71,8 @@ tar_plan(
 
 ```{.output}
 ▶ start target adelie_data
-● built target adelie_data [0.028 seconds]
-▶ end pipeline [0.093 seconds]
+● built target adelie_data [0.029 seconds]
+▶ end pipeline [0.1 seconds]
 ```
 
 This method gets around the slow-downs that may sometimes be experienced with Method 1.
@@ -101,7 +101,7 @@ tar_plan(
 ```{.output}
 ▶ start target adelie_data
 ● built target adelie_data [0.028 seconds]
-▶ end pipeline [0.09 seconds]
+▶ end pipeline [0.098 seconds]
 ```
 
 This can be more memory efficient in some cases than loading all packages, since not every target is always made during a typical run of the workflow.
@@ -127,8 +127,8 @@ tar_plan(
 
 ```{.output}
 ▶ start target adelie_data
-● built target adelie_data [0.014 seconds]
-▶ end pipeline [0.078 seconds]
+● built target adelie_data [0.015 seconds]
+▶ end pipeline [0.087 seconds]
 ```
 
 The benefits of this approach are that the origins of all functions is explicit, so you could browse your code (for example, by looking at its source in GitHub), and immediately know where all the functions come from.

setup.md

@@ -31,4 +31,4 @@ install.packages(
 
 There is a [Posit Cloud](https://posit.cloud/) instance with RStudio and all necessary packages pre-installed available, so you don't need to install anything on your own computer. You may need to create an account (free).
 
-Click this link to open: <https://posit.cloud/content/6064275>
+Click this link to open: <https://posit.cloud/content/6064275>