Merge branch 'main' into fix/image_replacements

Author: cmeesters

.github/workflows/announce-release.yml

@@ -23,9 +23,7 @@ jobs:
           message: |
             Beep, Beep - I am your friendly #Snakemake release announcement bot.
             
-            There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is {{ version }}!
-            
-            Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.
+            There is a new release of the #HPC Teaching Material for Snakemake. Its version now is {{ version }}!
             
             If you want to discuss the release, you will find the maintainers here on Mastodon!
             @rupdecat and @[email protected]

.github/workflows/build.yml

@@ -28,10 +28,10 @@ jobs:
 
       - name: LaTeX compile  
         run: |
-          ./render --master-tex Snakemake_HPC_Users.tex --configfile config/config_for_github.yaml ; 
-          ./render --master-tex Snakemake_HPC_Creators.tex --configfile config/config_for_github.yaml
-          ./render --master-tex Snakemake_HPC_User_Creator_Combi.tex --configfile config/config_for_github.yaml
-          ./render --master-tex Snakemake_HPC_Admins.tex --configfile config/config_for_github.yaml ;
+          ./render --master-tex Snakemake_HPC_Users.tex --configfile config/config_for_github.yaml --handout --sample-directory=_; 
+          ./render --master-tex Snakemake_HPC_Creators.tex --configfile config/config_for_github.yaml --handout --sample-directory=_;
+          ./render --master-tex Snakemake_HPC_User_Creator_Combi.tex --configfile config/config_for_github.yaml --handout --sample-directory=_;
+          ./render --master-tex Snakemake_HPC_Admins.tex --configfile config/config_for_github.yaml --handout --sample-directory=_;
       
       - name: Certificate compile
         run: |

CHANGELOG.md

@@ -1,5 +1,56 @@
 # Changelog
 
+## [1.2.0](https://github.com/snakemake/snakemake-hpc-teaching-material/compare/v1.1.2...v1.2.0) (2025-05-25)
+
+
+### Features
+
+* added announcement bot workflow ([034082c](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/034082c6d9ff378dbd886d21b300bc3655f30baa))
+* added announcement bot workflow ([1e95fd1](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/1e95fd1d5812cfc7046d4d51df948ec2342de558))
+* added current paper reference ([e83919e](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/e83919eee6edd6d2c2f2381d5d14828b0fdc92f6))
+* added handout watermark to all slide sets ([aece2e0](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/aece2e032a7eca0097bc2d65170a1719c26cbeb6))
+* added image to illustrate modularization ([8a00753](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/8a0075390a8f3d7fd04fff4a2e37f3d398709fc0))
+* added mastodon shield for release bot ([010a6cc](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/010a6ccd86ba3eb5ecabba3bf226193eb3e29c5a))
+* added section about modularization ([7fb6840](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/7fb6840497fd5d49e9ea2c9122a9205db8fb7be9))
+* added selecting workflows section ([6e0cfad](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/6e0cfadb78208dbf6dcda324fb6ad312a163e543))
+* added up-to-date image ([583df46](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/583df467af91505a3109b8578b90ae39ab0bcca1))
+* added using wrappers section ([35c7f7e](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/35c7f7eee0ef5dc0aa63b5c61919655b80e0577a))
+* added wrapper solution ([e5527d4](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/e5527d46f50755171b4a01fe574cf66c29477a5f))
+* better directory layout shown - added slide about logging functionality with Python ([9c46d72](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/9c46d721fccbdad3fe049118243b42ec4ebba3d1))
+* render script can skip packaging when rendering handouts! ([ceb081b](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/ceb081b0442dfafa59c7f9360150e928d2391b2d))
+* rendering release slides with handout watermark ([a4c63a5](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/a4c63a52e3e5fcfb0f812edfdfe82fac06298ee5))
+* update dresden yaml ([ef2b076](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/ef2b07665614f4231794eee1ac6e8f1aa900ffaf))
+
+
+### Bug Fixes
+
+* accounting for updates in barnard and mamba/conda ([295f959](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/295f9597e2e48210f24f2878bcd1dce636525ffd))
+* added deploy_url ([f1417a2](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/f1417a263101d85d4e8d7b2e4b2dcb7b66ceb783))
+* added missing --sample-directory flag ([5e2e45d](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/5e2e45da667deb27137e5c9abba9a69e161e0b74))
+* added missing quotation marks ([13b31fa](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/13b31fabfac2ec6eb8c8ac0b6a355ce4073887eb))
+* added missing quotation marks! ([0c3d5b4](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/0c3d5b4c2a51b682925a536cb5e43cec63dfc0b5))
+* better handout watermark ([8efad6d](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/8efad6d6f3e89112e56208d8b2047c0f93a837c3))
+* correct directory and suffix for quals plot - on some clusters display of svg files does not work. ([6281807](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/6281807d07b8847357be943ece6400695296057e))
+* corrected title ([f8c6449](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/f8c644981e4ec0bbe350661089fbaa4a7744b0cf))
+* deleted outcommented code ([83c7b15](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/83c7b15db0bf352ef6791b6fc507869c8be5e191))
+* dresden ([f754fc8](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/f754fc899211d7482fa2899413ef2cff6aa2b741))
+* handout production ([79504f0](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/79504f0eb288a0e7f057091473f86368ce6ba3bd))
+* image path ([badf818](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/badf818b64f9478659a644a177c7e697549dd694))
+* introduced skipping producing a zip file ([88fd1ac](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/88fd1ac98849a72932c694e7ecb8e20dccca9b28))
+* minor ([7374ef8](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/7374ef8937f0c6b611cdfb9be17336745001023b))
+* moved reference to bottom in Survey slide ([80e8742](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/80e8742d1f01ff246b346857cecc454f74cadef5))
+* SAMPLES -> samples ([613b926](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/613b926380e6cc965414e454b78b75452cce5b1e))
+* SAMPLES -> samples ([ba73e79](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/ba73e79bd48de8e10eddf37325204bbe7ed3a70b))
+* SAMPLES -> samples ([7b855df](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/7b855df580d801c40ca9e8e50a47f174c31eeb37))
+* superscript without math mode ([01c031d](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/01c031dc94643b28049d3729b092cddc149eb747))
+* tutorial folder renamed to task folder ([46ddabc](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/46ddabcbd37ce2215f6f38668ff93c3fc47cf957))
+* typo ([0bd1454](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/0bd14548239b834e3804aa224e959184a24fde80))
+* update github config yaml ([9350d94](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/9350d941e60928aa46bd5502b95318678922ddee))
+* updated condarc for mogon ([4a99729](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/4a9972987e7ae97ca8c537e587866565c7fddd05))
+* updated plot output path ([cdbd2f6](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/cdbd2f6923520dd1e31af4c663adcf67b74d4ed4))
+* will end if --handout, but not --sample-diretory is given ([6ff800d](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/6ff800d4bbec87566d2ac51e2324ebd0f981ce8c))
+* with the introduction of libmamba in conda, we can savely use conda, too ([111ffbb](https://github.com/snakemake/snakemake-hpc-teaching-material/commit/111ffbbfcced2a71e7dfcb83bd70b8459829bfbd))
+
 ## [1.1.2](https://github.com/snakemake/snakemake-hpc-teaching-material/compare/v1.1.1...v1.1.2) (2025-02-18)
 
 

CITATION.cff

@@ -0,0 +1,32 @@
+cff-version: 1.2.0
+message: "If you use this teaching material, please cite it as below."
+authors:
+- family-names: "Petersen"
+  given-names: "Malte"
+  orcid: "https://orcid.org/0000-0001-7601-9873"
+- family-names: "Hellmann"
+  given-names: "Sören Lukas"
+  orcid: "https://orcid.org/0000-0003-4958-1419"
+- family-names: "Böker"
+  given-names: "Florian"
+  orcid: "https://orcid.org/0000-0002-0732-6914"
+- family-names: "Brand"
+  given-names: "Fabian"
+  orcid: "https://orcid.org/0000-0003-1885-7021"
+- family-names: "Sharma"
+  given-names: "Aasish Kumar"
+  orcid: "https://orcid.org/0000-0002-7514-2340"
+- family-names: "Pleico"
+  given-names: "Martin Leandro"
+  orcid: "https://orcid.org/0000-0002-8427-0221"
+- family-names: "Köster"
+  given-names: "Johannes"
+  orcid: "https://orcid.org/0000-0001-9818-9320"
+- family-names: "Meesters"
+  given-names: "Christian"
+  orcid: "https://orcid.org/0000-0003-2408-7588"
+title: "Teaching Reproducible Data Analysis for HPC Users -- The Snakemake Teaching Alliance "
+version: 1.0
+doi: https://doi.org/10.14279/eceasst.v83.2600 
+date-released: 2025-02-21
+url: "https://github.com/snakemake/snakemake-hpc-teaching-material/"

README.md

@@ -2,6 +2,7 @@
 [![GitHub Workflow Status (with event)](https://img.shields.io/github/actions/workflow/status/snakemake/snakemake-hpc-teaching-material/build.yml?label=tests)](https://github.com/snakemake/snakemake-hpc-teaching-material/actions?query=branch%3Amain++)
 [![Build LaTex sources.](https://github.com/snakemake/snakemake-hpc-teaching-material/actions/workflows/build.yml/badge.svg)](https://github.com/snakemake/snakemake-hpc-teaching-material/actions/workflows/build.yml)
 ![Mastodon Follow](https://img.shields.io/mastodon/follow/109245696038111591?domain=https%3A%2F%2Ffediscience.org&style=flat)
+![Mastodon Follow](https://img.shields.io/mastodon/follow/113407240116926289?domain=fediscience.org&style=flat)
 
 # The Snakemake Teaching Alliance
 

config/config_for_github.yaml

@@ -13,6 +13,7 @@ layout:
   beamercolor_title:      "fg=UniRot"
   beamercolor_title_head: "fg=UniRot"
 
+
   beamercolor_block_title: "bg=UniRot!20,fg=darkred"
   beamercolor_block_body:  "fg=black, bg=plightgrey2"
 
@@ -22,10 +23,11 @@ layout:
 # The configuration for github needs valid file strings!
 
 course:
-  date: "datestring" # maybe: "\today"
+  # sets the slides aspectratio (if outcommented, the default is 43=4:3)
+  aspectratio: 1609 # - 169 = 16:9
+  date: "\today" # maybe: "\today"
   #title: "" # specifiy your title here, else a default is used. 
   #subtitle: "" # specifiy your subtitle here, else a default is used. 
-  question: "yes"
   # Editors recommendations are a matter of taste and technological
   # setups (e.g. on-demand setups). Hence, specify an editor-slide,
   #  here:
@@ -36,7 +38,9 @@ course:
   condarcfile: "common/condarc_mogon.tex"
   # the same for admins:
   condarc_admins_file: "admin/condarc_mogon.tex"
-  # the following path will indicate a sample workflow for the user part
+  # We provide a common software stack to avoid long
+  # installation sessions.
+  softwarepath: "software-stack-path"
   # if it is defined, the slide set will instruct participants to copy
   # it and adapt its configuration and profile.
   pathtoworkflow: "/lustre/project/nhr-workflow/workflow"

render

@@ -183,7 +183,9 @@ def find_and_replace_sections(boundaries, section_estimate, fname):
     if minitocline:
         lower = max((section_estimate - 2), 1)  # lower boundary not lower than 1
         upper = section_estimate + 2
-        upper = upper if upper < boundaries["upper"] else boundaries["upper"] + 1  # upper boundary not higher then upper boundary ;-)
+        upper = (
+            upper if upper < boundaries["upper"] else boundaries["upper"] + 1
+        )  # upper boundary not higher then upper boundary ;-)
         sections = f"{lower}-{upper}"
         lines[minitocline] = (
             "            \\tableofcontents[currentsection, sections={"
@@ -232,7 +234,7 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--sample-directory",
-        help="needed with `--handout` - should indicate directory with script file (cloze and solution)",
+        help="needed with `--handout` - should indicate directory with script files (cloze and solution)",
     )
     args = parser.parse_args()
 
@@ -241,6 +243,7 @@ if __name__ == "__main__":
             "ERROR: must indicate --sample-directory when writing handouts",
             file=sys.stderr,
         )
+        sys.exit(1)
 
     # the master tex needs to be without the 'slides' path, because
     # on the tempfs, the relative path work without
@@ -333,6 +336,9 @@ if __name__ == "__main__":
             ]
             opj = os.path.join
 
+            if args.sample_directory == "_": # will skip producing a zip file
+                sys.exit(0)
+
             for root, dirs, files in os.walk(args.sample_directory):
                 for fname in files:
                     # restrict to sample files, no helper files

setup_creators/condarc_mogon

@@ -1,5 +1,3 @@
-create_default_packages:
-  - setuptools
 channels:
   - conda-forge
   - bioconda

slides/Snakemake_HPC_Admins.tex

@@ -20,6 +20,14 @@
 
 \subtitle{<+++ if course.subtitle is defined +++><++course.subtitle++><+++else+++>Providing DataAnalytics Service<+++endif+++> - <++course.edition++>} 
 
+\ifdefined\ishandout
+\AddToHook{shipout/foreground}{
+	\begin{tikzpicture}[remember picture,overlay]
+		\node[red,rotate=10,scale=1,opacity=0.7] at (current page.center) {\footnotesize Handout from Snakemake Teaching Alliance by <++instructor.name++>}; 
+	\end{tikzpicture}
+}
+\fi
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{document}

slides/Snakemake_HPC_Creators.tex

@@ -20,6 +20,14 @@
 
 \subtitle{<+++ if course.subtitle is defined +++><++course.subtitle++><+++else+++>Programming<+++endif+++> - <++course.edition++>} 
 
+\ifdefined\ishandout
+\AddToHook{shipout/foreground}{
+	\begin{tikzpicture}[remember picture,overlay]
+		\node[red,rotate=10,scale=1,opacity=0.7] at (current page.center) {\footnotesize Handout from Snakemake Teaching Alliance by <++instructor.name++>}; 
+	\end{tikzpicture}
+}
+\fi
+
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

slides/Snakemake_HPC_User_Creator_Combi.tex

@@ -21,15 +21,11 @@
 \subtitle{<+++ if course.subtitle is defined +++><++course.subtitle++><+++else+++>Programming and Deployment<+++endif+++> - <++course.edition++>\newline by <++instructor.name++>} 
 
 \ifdefined\ishandout
-\usepackage{background}
-\backgroundsetup{
-	placement=center,
-	angle=30,
-	scale=1,
-	contents={\footnodesize Handout from Snakemake Teaching Alliance by <++instructor.name++>},
-	opacity=1
+\AddToHook{shipout/foreground}{
+	\begin{tikzpicture}[remember picture,overlay]
+		\node[red,rotate=10,scale=1,opacity=0.7] at (current page.center) {\footnotesize Handout from Snakemake Teaching Alliance by <++instructor.name++>}; 
+	\end{tikzpicture}
 }
-\setbeamertemplate{background}{\BgMaterial}
 \fi
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

slides/Snakemake_HPC_Users.tex

@@ -20,6 +20,14 @@
 
 \subtitle{<+++ if course.subtitle is defined +++><++course.subtitle++><+++else+++>Deployment<+++endif+++> - <++course.edition++>} 
 
+\ifdefined\ishandout
+\AddToHook{shipout/foreground}{
+	\begin{tikzpicture}[remember picture,overlay]
+		\node[red,rotate=10,scale=1,opacity=0.7] at (current page.center) {\footnotesize Handout from Snakemake Teaching Alliance by <++instructor.name++>}; 
+	\end{tikzpicture}
+}
+\fi
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{document}

version.txt

@@ -1 +1 @@
-1.1.2
+1.2.0