differences for PR #18

Author: actions-user

basic-targets.md

@@ -277,13 +277,13 @@ tar_make()
 
 
 ```{.output}
-• start target penguins_csv_file
-• built target penguins_csv_file [0.002 seconds]
-• start target penguins_data_raw
-• built target penguins_data_raw [0.167 seconds]
-• start target penguins_data
-• built target penguins_data [0.011 seconds]
-• end pipeline [0.277 seconds]
+▶ start target penguins_csv_file
+● built target penguins_csv_file [0.001 seconds]
+▶ start target penguins_data_raw
+● built target penguins_data_raw [0.134 seconds]
+▶ start target penguins_data
+● built target penguins_data [0.01 seconds]
+▶ end pipeline [0.219 seconds]
 ```
 
 Congratulations, you've run your first workflow with `targets`!

branch.md

@@ -78,9 +78,9 @@ tar_plan(
 ✔ skip target penguins_data_raw_file
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
-• start target combined_model
-• built target combined_model [0.036 seconds]
-• end pipeline [0.145 seconds]
+▶ start target combined_model
+● built target combined_model [0.027 seconds]
+▶ end pipeline [0.104 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.
@@ -146,17 +146,17 @@ tar_plan(
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
 ✔ skip target combined_model
-• start target interaction_model
-• built target interaction_model [0.007 seconds]
-• start target species_model
-• built target species_model [0.002 seconds]
-• start target combined_summary
-• built target combined_summary [0.066 seconds]
-• start target interaction_summary
-• built target interaction_summary [0.008 seconds]
-• start target species_summary
-• built target species_summary [0.005 seconds]
-• end pipeline [0.231 seconds]
+▶ start target interaction_model
+● built target interaction_model [0.004 seconds]
+▶ start target species_model
+● built target species_model [0.002 seconds]
+▶ start target combined_summary
+● built target combined_summary [0.008 seconds]
+▶ start target interaction_summary
+● built target interaction_summary [0.048 seconds]
+▶ start target species_summary
+● built target species_summary [0.003 seconds]
+▶ end pipeline [0.163 seconds]
 ```
 
 Let's look at the summary of one of the models:
@@ -225,16 +225,16 @@ First, let's look at the messages provided by `tar_make()`.
 ✔ skip target penguins_data_raw_file
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
-• start target models
-• built target models [0.008 seconds]
-• start branch model_summaries_5ad4cec5
-• built branch model_summaries_5ad4cec5 [0.01 seconds]
-• start branch model_summaries_c73912d5
-• built branch model_summaries_c73912d5 [0.058 seconds]
-• start branch model_summaries_91696941
-• built branch model_summaries_91696941 [0.005 seconds]
-• built pattern model_summaries
-• end pipeline [0.216 seconds]
+▶ start target models
+● built target models [0.007 seconds]
+▶ start branch model_summaries_5ad4cec5
+● built branch model_summaries_5ad4cec5 [0.008 seconds]
+▶ start branch model_summaries_c73912d5
+● built branch model_summaries_c73912d5 [0.003 seconds]
+▶ start branch model_summaries_91696941
+● built branch model_summaries_91696941 [0.048 seconds]
+● built pattern model_summaries
+▶ end pipeline [0.164 seconds]
 ```
 
 There is a series of smaller targets (branches) that are each named like model_summaries_5ad4cec5, then one overall `model_summaries` target.
@@ -364,14 +364,14 @@ tar_plan(
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
 ✔ skip target models
-• start branch model_summaries_5ad4cec5
-• built branch model_summaries_5ad4cec5 [0.019 seconds]
-• start branch model_summaries_c73912d5
-• built branch model_summaries_c73912d5 [0.01 seconds]
-• start branch model_summaries_91696941
-• built branch model_summaries_91696941 [0.007 seconds]
-• built pattern model_summaries
-• end pipeline [0.222 seconds]
+▶ start branch model_summaries_5ad4cec5
+● built branch model_summaries_5ad4cec5 [0.016 seconds]
+▶ start branch model_summaries_c73912d5
+● built branch model_summaries_c73912d5 [0.052 seconds]
+▶ start branch model_summaries_91696941
+● built branch model_summaries_91696941 [0.004 seconds]
+● built pattern model_summaries
+▶ end pipeline [0.168 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).

config.yaml

@@ -55,9 +55,9 @@ tar_plan(
 
 
 ```{.output}
-• start target some_data
-• built target some_data [0.002 seconds]
-• end pipeline [0.077 seconds]
+▶ start target some_data
+● built target some_data [0 seconds]
+▶ end pipeline [0.058 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 [0.057 seconds]
+✔ skip pipeline [0.043 seconds]
 ```
 
 The target `some_data` was skipped, even though the contents of the file changed.
@@ -97,11 +97,11 @@ tar_plan(
 
 
 ```{.output}
-• start target data_file
-• built target data_file [0.001 seconds]
-• start target some_data
-• built target some_data [0.001 seconds]
-• end pipeline [0.092 seconds]
+▶ start target data_file
+● built target data_file [0.001 seconds]
+▶ start target some_data
+● built target some_data [0 seconds]
+▶ end pipeline [0.065 seconds]
 ```
 
 This time we see that `targets` does successfully re-build `some_data` as expected.
@@ -183,13 +183,13 @@ tar_plan(
 
 
 ```{.output}
-• start target penguins_data_raw_file
-• built target penguins_data_raw_file [0.002 seconds]
-• start target penguins_data_raw
-• built target penguins_data_raw [0.358 seconds]
-• start target penguins_data
-• built target penguins_data [0.021 seconds]
-• end pipeline [0.476 seconds]
+▶ 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 [0.275 seconds]
+▶ start target penguins_data
+● built target penguins_data [0.018 seconds]
+▶ end pipeline [0.362 seconds]
 ```
 
 ::::::::::::::::::::::::::::::::::
@@ -259,15 +259,15 @@ tar_plan(
 
 
 ```{.output}
-• start target hello_file
-• built target hello_file [0.002 seconds]
-• start target hello
-• built target hello [0 seconds]
-• start target hello_caps
-• built target hello_caps [0.001 seconds]
-• start target hello_caps_out
-• built target hello_caps_out [0.011 seconds]
-• end pipeline [0.113 seconds]
+▶ start target hello_file
+● built target hello_file [0.001 seconds]
+▶ start target hello
+● 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 seconds]
+▶ end pipeline [0.07 seconds]
 ```
 
 Take a look at `hello_caps.txt` in the `results` folder and verify it is as you expect.

files.md

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

hpc.md

@@ -43,7 +43,7 @@ tar_make()
 ✔ skip target penguins_csv_file
 ✔ skip target penguins_data_raw
 ✔ skip target penguins_data
-✔ skip pipeline [0.079 seconds]
+✔ skip pipeline [0.056 seconds]
 ```
 
 Remember how the first time we ran the pipeline, `targets` printed out a list of each target as it was being built?
@@ -87,9 +87,9 @@ tar_make()
 ```{.output}
 ✔ skip target penguins_csv_file
 ✔ skip target penguins_data_raw
-• start target penguins_data
-• built target penguins_data [0.023 seconds]
-• end pipeline [0.121 seconds]
+▶ start target penguins_data
+● built target penguins_data [0.019 seconds]
+▶ end pipeline [0.092 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 [0.079 seconds]
+✔ skip pipeline [0.059 seconds]
 ```
 
 Let's invalidate `penguins_data` and run it again:
@@ -274,9 +274,9 @@ tar_make()
 ```{.output}
 ✔ skip target penguins_csv_file
 ✔ skip target penguins_data_raw
-• start target penguins_data
-• built target penguins_data [0.026 seconds]
-• end pipeline [0.133 seconds]
+▶ start target penguins_data
+● built target penguins_data [0.02 seconds]
+▶ end pipeline [0.093 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).

lifecycle.md

@@ -1,21 +1,22 @@
 "file" "checksum" "built" "date"
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