From 982e83a9fa44d88cb63b972b165c70cab746c1b0 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 10 Jul 2023 06:03:47 +0000 Subject: [PATCH] differences for PR #18 --- basic-targets.md | 14 +- branch.md | 64 +- config.yaml | 87 --- files.md | 50 +- hpc.md | 26 + lifecycle.md | 16 +- md5sum.txt | 41 +- packages.md | 18 +- renv.lock | 1790 ---------------------------------------------- setup.md | 2 +- 10 files changed, 129 insertions(+), 1979 deletions(-) delete mode 100644 config.yaml create mode 100644 hpc.md delete mode 100644 renv.lock diff --git a/basic-targets.md b/basic-targets.md index 0dab7c12..e8187ea6 100644 --- a/basic-targets.md +++ b/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`! diff --git a/branch.md b/branch.md index aa67199f..9a784c49 100644 --- a/branch.md +++ b/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). diff --git a/config.yaml b/config.yaml deleted file mode 100644 index d7951c6c..00000000 --- a/config.yaml +++ /dev/null @@ -1,87 +0,0 @@ -#------------------------------------------------------------ -# Values for this lesson. -#------------------------------------------------------------ - -# Which carpentry is this (swc, dc, lc, or cp)? -# swc: Software Carpentry -# dc: Data Carpentry -# lc: Library Carpentry -# cp: Carpentries (to use for instructor training for instance) -# incubator: The Carpentries Incubator -carpentry: 'incubator' - -# Overall title for pages. -title: 'Introduction to targets' - -# Date the lesson was created (YYYY-MM-DD, this is empty by default) -created: ~ - -# Comma-separated list of keywords for the lesson -keywords: 'reproducibility, data, targets, R' - -# Life cycle stage of the lesson -# possible values: pre-alpha, alpha, beta, stable -life_cycle: 'pre-alpha' - -# License of the lesson -license: 'CC-BY 4.0' - -# Link to the source repository for this lesson -source: 'https://github.com/joelnitta/targets-workshop' - -# Default branch of your lesson -branch: 'main' - -# Who to contact if there are any issues -contact: 'joelnitta@gmail.com' - -# Navigation ------------------------------------------------ -# -# Use the following menu items to specify the order of -# individual pages in each dropdown section. Leave blank to -# include all pages in the folder. -# -# Example ------------- -# -# episodes: -# - introduction.md -# - first-steps.md -# -# learners: -# - setup.md -# -# instructors: -# - instructor-notes.md -# -# profiles: -# - one-learner.md -# - another-learner.md - -# Order of episodes in your lesson -episodes: -- introduction.Rmd -- basic-targets.Rmd -- cache.Rmd -- lifecycle.Rmd -- organization.Rmd -- packages.Rmd -- files.Rmd -- branch.Rmd -- parallel.Rmd -- quarto.Rmd - -# Information for Learners -learners: - -# Information for Instructors -instructors: - -# Learner Profiles -profiles: - -# Customisation --------------------------------------------- -# -# This space below is where custom yaml items (e.g. pinning -# sandpaper and varnish versions) should live - - diff --git a/files.md b/files.md index 915867b4..cedb4038 100644 --- a/files.md +++ b/files.md @@ -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. diff --git a/hpc.md b/hpc.md new file mode 100644 index 00000000..1d74f607 --- /dev/null +++ b/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. + + + + + + + + + + + + + + + + + + diff --git a/lifecycle.md b/lifecycle.md index 1b9f033a..c952f3e0 100644 --- a/lifecycle.md +++ b/lifecycle.md @@ -43,7 +43,7 @@ tar_make() ✔ skip target penguins_csv_file ✔ skip target penguins_data_raw ✔ skip target penguins_data -✔ skip pipeline [0.079 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). diff --git a/md5sum.txt b/md5sum.txt index c410497a..f29e6a49 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -1,21 +1,22 @@ "file" "checksum" "built" "date" -"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-06-19" -"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2023-06-19" -"config.yaml" "97cf738871f0133f70da7d938c14bfb2" "site/built/config.yaml" "2023-06-19" -"index.md" "06bbfd5ab0e2353032361b3321342d13" "site/built/index.md" "2023-06-19" -"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2023-06-19" -"episodes/introduction.Rmd" "feaacfccab344eb1fa6e702aded97924" "site/built/introduction.md" "2023-06-19" -"episodes/basic-targets.Rmd" "9a431b9a3596cb55c1f62f905cb808a2" "site/built/basic-targets.md" "2023-06-19" -"episodes/cache.Rmd" "6395b6d5b81a029daf9d37a2cb56d6d9" "site/built/cache.md" "2023-06-19" -"episodes/lifecycle.Rmd" "b52fcffdd75504e8579c8a7f1908ade2" "site/built/lifecycle.md" "2023-06-19" -"episodes/organization.Rmd" "ef33426eed3d4e0784a728b5aa670836" "site/built/organization.md" "2023-06-19" -"episodes/packages.Rmd" "2812a10b7ae0e8e0b3e000a5b74f939c" "site/built/packages.md" "2023-06-19" -"episodes/files.Rmd" "f05ed479ce1a0dfdcc14ebcd872c554c" "site/built/files.md" "2023-06-19" -"episodes/branch.Rmd" "b07912f5d8f14eb0e831a6a081ee99f2" "site/built/branch.md" "2023-06-19" -"episodes/parallel.Rmd" "69b941c8fd37a23249e6d16636fb645a" "site/built/parallel.md" "2023-06-19" -"episodes/quarto.Rmd" "a6c2d51f32e4a7e1087b87b211d7a03a" "site/built/quarto.md" "2023-06-19" -"instructors/instructor-notes.md" "df3784ee5c0436a9e171071f7965d3fc" "site/built/instructor-notes.md" "2023-06-19" -"learners/reference.md" "3f06251c1f932e767ae8f22db25eb5a2" "site/built/reference.md" "2023-06-19" -"learners/setup.md" "99a67bca32058e9f70d6d8e405519826" "site/built/setup.md" "2023-06-19" -"profiles/learner-profiles.md" "44d8b9d8aca7963e6577e8c67d23eac0" "site/built/learner-profiles.md" "2023-06-19" -"renv/profiles/lesson-requirements/renv.lock" "28b85c40b8c0d91354d67a70ca6a6005" "site/built/renv.lock" "2023-06-19" +"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-07-10" +"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2023-07-10" +"config.yaml" "5b0ca11806a6d604dd96faa2f669590e" "site/built/config.yaml" "2023-07-10" +"index.md" "06bbfd5ab0e2353032361b3321342d13" "site/built/index.md" "2023-07-10" +"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2023-07-10" +"episodes/introduction.Rmd" "feaacfccab344eb1fa6e702aded97924" "site/built/introduction.md" "2023-07-10" +"episodes/basic-targets.Rmd" "9a431b9a3596cb55c1f62f905cb808a2" "site/built/basic-targets.md" "2023-07-10" +"episodes/cache.Rmd" "6395b6d5b81a029daf9d37a2cb56d6d9" "site/built/cache.md" "2023-07-10" +"episodes/lifecycle.Rmd" "b52fcffdd75504e8579c8a7f1908ade2" "site/built/lifecycle.md" "2023-07-10" +"episodes/organization.Rmd" "ef33426eed3d4e0784a728b5aa670836" "site/built/organization.md" "2023-07-10" +"episodes/packages.Rmd" "2812a10b7ae0e8e0b3e000a5b74f939c" "site/built/packages.md" "2023-07-10" +"episodes/files.Rmd" "f05ed479ce1a0dfdcc14ebcd872c554c" "site/built/files.md" "2023-07-10" +"episodes/branch.Rmd" "b07912f5d8f14eb0e831a6a081ee99f2" "site/built/branch.md" "2023-07-10" +"episodes/parallel.Rmd" "69b941c8fd37a23249e6d16636fb645a" "site/built/parallel.md" "2023-07-10" +"episodes/quarto.Rmd" "a6c2d51f32e4a7e1087b87b211d7a03a" "site/built/quarto.md" "2023-07-10" +"episodes/hpc.Rmd" "1079e743b43d65f0f1c928ed60c44089" "site/built/hpc.md" "2023-07-10" +"instructors/instructor-notes.md" "df3784ee5c0436a9e171071f7965d3fc" "site/built/instructor-notes.md" "2023-07-10" +"learners/reference.md" "3f06251c1f932e767ae8f22db25eb5a2" "site/built/reference.md" "2023-07-10" +"learners/setup.md" "b4bdd601ab985cf048829f49710df7fc" "site/built/setup.md" "2023-07-10" +"profiles/learner-profiles.md" "44d8b9d8aca7963e6577e8c67d23eac0" "site/built/learner-profiles.md" "2023-07-10" +"renv/profiles/lesson-requirements/renv.lock" "68966b476b940ae0fc805b292f4dc109" "site/built/renv.lock" "2023-07-10" diff --git a/packages.md b/packages.md index d0929b3b..86a06a41 100644 --- a/packages.md +++ b/packages.md @@ -70,9 +70,9 @@ tar_plan( ```{.output} -• start target adelie_data -• built target adelie_data [0.03 seconds] -• end pipeline [0.102 seconds] +▶ start target adelie_data +● built target adelie_data [0.024 seconds] +▶ end pipeline [0.082 seconds] ``` This method gets around the slow-downs that may sometimes be experienced with Method 1. @@ -99,9 +99,9 @@ tar_plan( ```{.output} -• start target adelie_data -• built target adelie_data [0.034 seconds] -• end pipeline [0.114 seconds] +▶ start target adelie_data +● built target adelie_data [0.025 seconds] +▶ end pipeline [0.083 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. @@ -126,9 +126,9 @@ tar_plan( ```{.output} -• start target adelie_data -• built target adelie_data [0.017 seconds] -• end pipeline [0.099 seconds] +▶ start target adelie_data +● built target adelie_data [0.012 seconds] +▶ end pipeline [0.07 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. diff --git a/renv.lock b/renv.lock deleted file mode 100644 index e02e82bd..00000000 --- a/renv.lock +++ /dev/null @@ -1,1790 +0,0 @@ -{ - "R": { - "Version": "4.3.0", - "Repositories": [ - { - "Name": "carpentries", - "URL": "https://carpentries.r-universe.dev" - }, - { - "Name": "carpentries_archive", - "URL": "https://carpentries.github.io/drat" - }, - { - "Name": "CRAN", - "URL": "https://cran.rstudio.com" - } - ] - }, - "Packages": { - "DBI": { - "Package": "DBI", - "Version": "1.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "b2866e62bab9378c3cc9476a1954226b" - }, - "MASS": { - "Package": "MASS", - "Version": "7.3-59", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "methods", - "stats", - "utils" - ], - "Hash": "26570ae748e78cb2b0f56019dd2ba354" - }, - "Matrix": { - "Package": "Matrix", - "Version": "1.5-4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "graphics", - "grid", - "lattice", - "methods", - "stats", - "utils" - ], - "Hash": "e779c7d9f35cc364438578f334cffee2" - }, - "R6": { - "Package": "R6", - "Version": "2.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "470851b6d5d0ac559e9d01bb352b4021" - }, - "RColorBrewer": { - "Package": "RColorBrewer", - "Version": "1.1-3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "45f0398006e83a5b10b72a90663d8d8c" - }, - "Rcpp": { - "Package": "Rcpp", - "Version": "1.0.10", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods", - "utils" - ], - "Hash": "e749cae40fa9ef469b6050959517453c" - }, - "askpass": { - "Package": "askpass", - "Version": "1.1", - "Source": "Repository", 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You may need to create an account (free). -Click this link to open: \ No newline at end of file +Click this link to open: