Merge pull request #4 from hschellman/Dec2024

Merge new format changes in.  A few bug fixes as well.

.github/workflows/template.yml

@@ -47,7 +47,7 @@ jobs:
       - name: Set up Ruby
         uses: ruby/setup-ruby@v2
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0'
           bundler-cache: true
 
       - name: Set up Python
@@ -127,19 +127,21 @@ jobs:
         id: check-rmd
         working-directory: lesson
         run: |
-          echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
+          echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT
 
       - name: Set up R
         if: steps.check-rmd.outputs.count != 0
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
-          r-version: 'release'
+          use-public-rspm: true
+          install-r: false
 
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
         run: |
-          packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
-          install.packages(packages, repo="https://cran.rstudio.com/")
+          source('bin/dependencies.R')
+          install_required_packages(.libPaths()[1])
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -149,11 +151,12 @@ jobs:
           source('bin/dependencies.R')
           deps <- identify_dependencies()
           create_description(deps)
+          use_bioc_repos()
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Restore Package Cache
         if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0
         uses: actions/cache@v2
         with:
@@ -172,7 +175,7 @@ jobs:
         run: |
           while read -r cmd
           do
-            eval sudo $cmd
+            eval sudo $cmd || echo "Nothing to update"
           done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
 
       - run: make site

.github/workflows/website.yml

@@ -19,7 +19,7 @@ jobs:
       - name: Set up Ruby
         uses: ruby/setup-ruby@v2
         with:
-          ruby-version: '2.7'
+          ruby-version: '3.0'
           bundler-cache: true
 
       - name: Set up Python
@@ -44,15 +44,16 @@ jobs:
       - name: Look for R-markdown files
         id: check-rmd
         run: |
-          echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
+          echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT
 
       - name: Set up R
         if: steps.check-rmd.outputs.count != 0
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
-          r-version: 'release'
+          use-public-rspm: true
+          install-r: false
 
-      - name: Cache R packages
+      - name: Restore R Cache
         if: steps.check-rmd.outputs.count != 0
         uses: actions/cache@v2
         with:
@@ -63,8 +64,8 @@ jobs:
       - name: Install needed packages
         if: steps.check-rmd.outputs.count != 0
         run: |
-          packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages()))
-          install.packages(packages, repo="https://cran.rstudio.com/")
+          source('bin/dependencies.R')
+          install_required_packages()
         shell: Rscript {0}
 
       - name: Query dependencies
@@ -73,6 +74,7 @@ jobs:
           source('bin/dependencies.R')
           deps <- identify_dependencies()
           create_description(deps)
+          use_bioc_repos()
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
@@ -83,7 +85,7 @@ jobs:
         run: |
           while read -r cmd
           do
-            eval sudo $cmd
+            eval sudo $cmd || echo "Nothing to update"
           done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
 
       - name: Render the markdown and confirm that the site can be built

404.md

@@ -5,12 +5,12 @@ permalink: 404.html
 title: "Page not found"
 ---
 
-# Oops! We can't find that page.
+# Oops! We cannot find that page.
 {: style="text-align: center;"}
 
 > ## Our apologies!
 >
-> We can't seem to find the page you're looking for.
+> We cannot seem to find the page you are looking for.
 > Try going back to the <a href="javascript:history.back()">previous page</a> or
 > navigate to any other page using the navigation bar above
 > {%- if site.kind == "lesson" -%} or the schedule below {%- endif -%}.

LICENSE.md

@@ -5,6 +5,52 @@ root: .
 ---
 ## Instructional Material
 
+All HEP Software Foundation instructional material is
+made available under the [Creative Commons Attribution
+license][cc-by-human]. The following is a human-readable summary of
+(and not a substitute for) the [full legal text of the CC BY 4.0
+license][cc-by-legal].
+
+You are free:
+
+* to **Share**---copy and redistribute the material in any medium or format
+* to **Adapt**---remix, transform, and build upon the material
+
+for any purpose, even commercially.
+
+The licensor cannot revoke these freedoms as long as you follow the
+license terms.
+
+Under the following terms:
+
+* **Attribution**---You must give appropriate credit (mentioning that
+  your work is derived from work that is Copyright © Software
+  Carpentry and, where practical, linking to
+  <http://hepsoftwarefoundation.org/>), provide a [link to the
+  license][cc-by-human], and indicate if changes were made. You may do
+  so in any reasonable manner, but not in any way that suggests the
+  licensor endorses you or your use.
+
+**No additional restrictions**---You may not apply legal terms or
+technological measures that legally restrict others from doing
+anything the license permits.  With the understanding that:
+
+Notices:
+
+* You do not have to comply with the license for elements of the
+  material in the public domain or where your use is permitted by an
+  applicable exception or limitation.
+* No warranties are given. The license may not give you all of the
+  permissions necessary for your intended use. For example, other
+  rights such as publicity, privacy, or moral rights may limit how you
+  use the material.
+
+## Templates and Framework from software carpentries
+
+This lesson is built on a framework developed by Software Carpentry. Below is their license:
+
+### Instructional material
+
 All Software Carpentry, Data Carpentry, and Library Carpentry instructional material is
 made available under the [Creative Commons Attribution
 license][cc-by-human]. The following is a human-readable summary of
@@ -26,7 +72,7 @@ Under the following terms:
 * **Attribution**---You must give appropriate credit (mentioning that
   your work is derived from work that is Copyright © Software
   Carpentry and, where practical, linking to
-  http://software-carpentry.org/), provide a [link to the
+  <http://software-carpentry.org/>), provide a [link to the
   license][cc-by-human], and indicate if changes were made. You may do
   so in any reasonable manner, but not in any way that suggests the
   licensor endorses you or your use.
@@ -45,7 +91,7 @@ Notices:
   rights such as publicity, privacy, or moral rights may limit how you
   use the material.
 
-## Software
+### Software
 
 Except where otherwise noted, the example programs and other software
 provided by Software Carpentry and Data Carpentry are made available under the
@@ -71,7 +117,7 @@ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
-## Trademark
+### Trademark
 
 "Software Carpentry" and "Data Carpentry" and their respective logos
 are registered trademarks of [Community Initiatives][CI].

Makefile

@@ -7,6 +7,9 @@ JEKYLL=bundle config set --local path .vendor/bundle && bundle install && bundle
 PARSER=bin/markdown_ast.rb
 DST=_site
 
+# Find Docker
+DOCKER := $(shell which docker 2>/dev/null)
+
 # Check Python 3 is installed and determine if it's called via python3 or python
 # (https://stackoverflow.com/a/4933395)
 PYTHON3_EXE := $(shell which python3 2>/dev/null)
@@ -41,23 +44,27 @@ endif
 .PHONY: site docker-serve repo-check clean clean-rmd
 
 ## * serve            : render website and run a local server
-serve : lesson-md
+serve : lesson-md index.md
 	${JEKYLL} serve
 
 ## * site             : build website but do not run a server
-site : lesson-md
+site : lesson-md index.md
 	${JEKYLL} build
 
 ## * docker-serve     : use Docker to serve the site
 docker-serve :
-	@docker pull carpentries/lesson-docker:latest
-	@docker run --rm -it \
+ifeq (, $(DOCKER))
+	$(error Your system does not appear to have Docker installed)
+else
+	@$(DOCKER) pull carpentries/lesson-docker:latest
+	@$(DOCKER) run --rm -it \
 		-v $${PWD}:/home/rstudio \
 		-p 4000:4000 \
 		-p 8787:8787 \
 		-e USERID=$$(id -u) \
 		-e GROUPID=$$(id -g) \
 		carpentries/lesson-docker:latest
+endif
 
 ## * repo-check       : check repository settings
 repo-check : python
@@ -172,3 +179,10 @@ ifeq (, $(PYTHON))
 else
 	@:
 endif
+
+index.md :
+ifeq (, $(wildcard index.md))
+	$(error index.md not found)
+else
+	@:
+endif

_config.yml

@@ -7,15 +7,32 @@
 # dc: Data Carpentry
 # lc: Library Carpentry
 # cp: Carpentries (to use for instructor traning for instance)
-carpentry: "incubator"
+# incubator: Carpentries Incubator
+carpentry: "dune"
 
 # Overall title for pages.
-title: "DUNE Computing Training 2024 Online Update" # FIXME
+title: "Computing Basics for DUNE - Late 2024 edition"
 
 # Life cycle stage of the lesson
 # See this page for more details: https://cdh.carpentries.org/the-lesson-life-cycle.html
 # Possible values: "pre-alpha", "alpha", "beta", "stable"
-life_cycle: "beta"
+#
+# Lessons that are going through the transition to the
+# Carpentries Workbench will go through 3 steps:
+# 'transition-step-1': notice indicating a new version
+# 'transition-step-2': notice encouraging to use new version
+# 'transition-step-3': notice indicating the lesson is deprecated,
+#                      with automated redirect
+life_cycle: "pre-alpha"
+
+# For lessons in the life stages in 'transition-step-1' or later:
+# - 'transition_url' holds the URL for the version of the lesson that
+#    uses the Workbench (needed for all 3 steps)
+# - 'transition_date' (in yyyy-mm-dd format) is the date when the lesson
+#    will transition to being deprecated. The date only needs to be decided
+#    when the lesson is in 'transition-step-2'.
+transition_url:
+transition_date:
 
 #------------------------------------------------------------
 # Generic settings (should not need to change).
@@ -30,9 +47,10 @@ kind: "lesson"
 repository: <USERNAME>/<PROJECT>
 
 # Email address, no mailto:
-email: "dune-computing-training@fnal.gov" # FIXME
+email: "dune-computing-training@fnal.gov"
 
 # Sites.
+coc: "https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html"
 amy_site: "https://amy.carpentries.org/"
 carpentries_github: "https://github.com/carpentries"
 carpentries_pages: "https://carpentries.github.io"
@@ -44,18 +62,22 @@ lc_site: "https://librarycarpentry.org/"
 swc_github: "https://github.com/swcarpentry"
 swc_pages: "https://swcarpentry.github.io"
 swc_site: "https://software-carpentry.org"
+dune_site: "https://dunescience.org"
+dune_github: "https://github.com/DUNE"
 template_repo: "https://github.com/carpentries/styles"
 training_site: "https://carpentries.github.io/instructor-training"
 workshop_repo: "https://github.com/carpentries/workshop-template"
 workshop_site: "https://carpentries.github.io/workshop-template"
 cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
 
 # Surveys.
-pre_survey: "https://carpentries.typeform.com/to/wi32rS?slug="
-post_survey: "https://carpentries.typeform.com/to/UgVdRQ?slug="
-instructor_pre_survey: "https://www.surveymonkey.com/r/instructor_training_pre_survey?workshop_id="
-instructor_post_survey: "https://www.surveymonkey.com/r/instructor_training_post_survey?workshop_id="
+pre_survey: "https://carpentries.typeform.com/to/wi32rS#slug="
+post_survey: "https://carpentries.typeform.com/to/UgVdRQ#slug="
+instructor_pre_survey: "https://carpentries.typeform.com/to/QVOarK#slug="
+instructor_post_survey: "https://carpentries.typeform.com/to/cjJ9UP#slug="
 
+# Set to 'true' for instructor training websites only.
+instructor_training: false
 
 # Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
 start_time: 0
@@ -98,8 +120,3 @@ exclude:
 
 # Turn on built-in syntax highlighting.
 highlighter: rouge
-
-
-# Remote theme
-remote_theme: carpentries/carpentries-theme
-#remote_theme: pages-themes/leap-day@v0.2.0

_episodes/02-storage-spaces.md

@@ -204,7 +204,6 @@ The eXtended ROOT daemon is software framework designed for accessing data from
 XRootD is most suitable for read-only data access.
 [XRootD Man pages](https://xrootd.slac.stanford.edu/docs.html)
 
-
 Issue the following command. Please look at the input and output of the command, and recognize that this is a listing of /pnfs/dune/scratch/users/${USER}/DUNE_tutorial_2024. Try and understand how the translation between a NFS path and an xrootd URI could be done by hand if you needed to do so.
 
 ~~~
@@ -290,6 +289,28 @@ xrdfs root://fndca1.fnal.gov:1094/ ls /pnfs/fnal.gov/usr/dune/tape_backed/dunepr
 ~~~
 {: .language-bash}
 
+
+> ## Is my file available or stuck on tape?
+> /tape_backed/ storage at Fermilab is migrated to tape and may not be on disk?
+> You can check this by doing the following **in an AL9 window**
+> ~~~
+> gfal-xattr  <xrootpath> user.status
+> ~~~
+> {: .language-bash}
+> if it is on disk you get
+> ~~~
+> ONLINE
+> ~~~
+> {: .output}
+> if it is only on tape you get
+> ~~~
+> NEARLINE
+> ~~~
+> {: .output}
+>  (This command doesn't work on SL7 so use an AL9 window)
+{: .challenge}
+
+
 ### The df command
 
 To find out what types of volumes are available on a node can be achieved with the command `df`. The `-h` is for _human readable format_. It will list a lot of information about each volume (total size, available size, mount point, device location).