Recent Releases of snakemake-hpc-teaching-material
snakemake-hpc-teaching-material - v1.2.0
1.2.0 (2025-05-25)
Features
- added announcement bot workflow (034082c)
- added announcement bot workflow (1e95fd1)
- added current paper reference (e83919e)
- added handout watermark to all slide sets (aece2e0)
- added image to illustrate modularization (8a00753)
- added mastodon shield for release bot (010a6cc)
- added section about modularization (7fb6840)
- added selecting workflows section (6e0cfad)
- added up-to-date image (583df46)
- added using wrappers section (35c7f7e)
- added wrapper solution (e5527d4)
- better directory layout shown - added slide about logging functionality with Python (9c46d72)
- render script can skip packaging when rendering handouts! (ceb081b)
- rendering release slides with handout watermark (a4c63a5)
- update dresden yaml (ef2b076)
Bug Fixes
- accounting for updates in barnard and mamba/conda (295f959)
- added deploy_url (f1417a2)
- added missing --sample-directory flag (5e2e45d)
- added missing quotation marks (13b31fa)
- added missing quotation marks! (0c3d5b4)
- better handout watermark (8efad6d)
- correct directory and suffix for quals plot - on some clusters display of svg files does not work. (6281807)
- corrected title (f8c6449)
- deleted outcommented code (83c7b15)
- dresden (f754fc8)
- handout production (79504f0)
- image path (badf818)
- introduced skipping producing a zip file (88fd1ac)
- minor (7374ef8)
- moved reference to bottom in Survey slide (80e8742)
- SAMPLES -> samples (613b926)
- SAMPLES -> samples (ba73e79)
- SAMPLES -> samples (7b855df)
- superscript without math mode (01c031d)
- tutorial folder renamed to task folder (46ddabc)
- typo (0bd1454)
- update github config yaml (9350d94)
- updated condarc for mogon (4a99729)
- updated plot output path (cdbd2f6)
- will end if --handout, but not --sample-diretory is given (6ff800d)
- with the introduction of libmamba in conda, we can savely use conda, too (111ffbb)
- TeX
Published by github-actions[bot] 9 months ago
snakemake-hpc-teaching-material - v1.1.0
1.1.0 (2025-02-17)
Features
- finally trying slide releases (940a224)
- TeX
Published by github-actions[bot] about 1 year ago
snakemake-hpc-teaching-material - v1.0.0
1.0.0 (2025-02-17)
Features
- #82 update certificat generator (#83) (fddea0a)
- 09 with config read groups (b5a9ebe)
- 10 with log directives (ab0f505)
- adapted configuration template strings to the new scheme (b8f6a35)
- adapted github workflow accordingly (522856e)
- added / adjusted condarc for barnard (e83f939)
- added an enslide figure (de9cdd3)
- added cluster account and partition to config file (f853fdb)
- added collab image (12c7692)
- added combi for users and creators (59b6453)
- added config file to tutorial folder (cad3c22)
- added configuration for github (0605d6c)
- added dummy config template in yaml format (3b409ee)
- added edition strings to configurations (784d49a)
- added first version of a render script reading default from a yaml file (77281df)
- added flavour icon image (48ba3ce)
- added generic config workflow profile (50207fa)
- added image to illustrate workflow deployment (d51f313)
- added new 'report' image (a1cd8d2)
- added NumFocus-relation (#145) (073eb60)
- added slide about course material feedback (3a9e72a)
- added standard pdflatex flags (9bf7d0e)
- added task description to cloze text (bd9cc20)
- Adding slides explaining the setup, usage and creation of snakemake wrappers. (f934787), closes #44
- Adding slides explaining the setup, usage and creation of snakemake wrappers. (1462a6c), closes #44
- adding testing, mastodon badge and license badge (#87) (c505e10)
- adding the need for conventional commits to our CI (263887c)
- admin slideset (#124) (0b2d74f)
- admin talk (#177) (447cffe)
- admin talk (#180) (b2ab5dd)
- allowing for different aspect ratios (configurable) (#172) (90319f6)
- benchmarking slide set with graphical section slide and about slide (35769b5)
- central software path (#138) (e8adf3c)
- cluster name and distro configurable (55e2309)
- completing last slide (b40b80d)
- configurable basic layout (#90) (425cf14)
- copy script sample for ZIH Dresden (db52e27)
- customizable themes (#92) (e320a03)
- deploy (#144) (c86a364)
- describing purpose of input functions and asking for config file benefits (d541e34)
- description of protected funtion (3c19fe2)
- dresden cluster barnard config (05b6a95)
- eval touch (#190) (d1537a2)
- example for new minitoc section start slide (a80c0bc)
- explaining wildcards.sample (5447b5e)
- explicit mention of 06_Snakefile in end of Python slide deck (42e4e9a)
- finished graphical minitoc for Contributing section (8f62989)
- formatting (adc99ee)
- graphical minitoc for contribution section (a79b00a)
- graphical minitor for 'a first workflow' (246ffbc)
- graphical minitor for contribution section (265b9ae)
- graphical minitor for Decoration slide set (269dbe0)
- graphical slide for Python in Snakemake minitoc (ae07bec)
- hello world example for cluster barnard (69b449f)
- intro with shell commands (#157) (6240179)
- introduced configurable edition (59b4958)
- introduced get sample data slide in users (bca0c55)
- introduced slides about actual deployment in 'Selecting_Workflow' slide set (aaa729a)
- login slides (#178) (bcaa68f)
- made all cluster parameters configurable (9b52524)
- mentioning 'snakedeploy' in 'Deployment' slide (e55f012)
- mission statement (#169) (3b6f572)
- mogon ondemand (#142) (0ded6dd)
- new benchmarking file set (c51c7cf)
- new benchmarking file set in SnakemakeHPCCreators.tex master doc (8cb1312)
- new chapter 'About Snakemake' correctly placed (4f879d4)
- new config for ZIH - not ready (50c5f99)
- new mini toc slide (aa86bcd)
- new minitoc for selecting workflows chapters (609ba07)
- new section (3e58945)
- new slide about conda flavours (9e84721)
- new slide in Python section - asking for plot output to be a target, too. (894540f)
- new slide set covering issue #47 (#88) (ddab9c7)
- note on 09 (69d6731)
- optional question time encouragement (#171) (ca629a1)
- optional rendering of slurm account - barndard cluster has default accounts (2752135)
- optional rendering of slurm account - barndard cluster has default accounts - now for all slides using this feature (8b73027)
- pack_release.py does not render handouts any longer (f656e1a)
- parallel execution chapter (#173) (7d4fccc)
- plain text configuration file deleted (e25ee76)
- reflecting latests changes for CI config (3ea9c6d)
- removed mogon referenced, added barnard; more generic (8f37de5)
- render can skip rerun upcon request (will safe devel time) (1cb676e)
- render now counts sections (920e302)
- render script now accepts relative path to master (78b598f)
- render script now has a --handout option (99c29fa)
- rendering minitoc section slides enabled, not yet counting boundaries (8422362)
- rendering of toc slides integrated in (c2e90e9)
- replaced autorelease with releae-please - works well with workflows (bae08ff)
- Reports slide section now with graphical intro slide (cf1d847)
- shorter path to solutions, when all is copied (44fc2f0)
- slides on env creation updated (b2dd4cb)
- solving issue #57 (2d7d9da)
- started slide set for cluster benefits (6c2739b)
- trying autorelease template (e915360)
- updated 06_Snakemake to contain the (mini) task (4f50475)
Bug Fixes
- #80 update teaching elsewhere (#127) (4399be8)
- 04_Snakefile was a) not in sync with the slides and b) not corrected - it was so some time ago - lost in git ... (39da726)
- 05_Snakefile clearer task description (e9db1ab)
- 6->& to show that stdout and -err are combined (aa87d98)
- according to web page (0eeba10)
- added barnard editor file (6459994)
- added chapters to combined part (f409b73)
- added editor section to slide set (a6a92a5)
- added Martin's name - was missing (#74) (6d5d3e1)
- added missing image (55211ce)
- added missing image (0b68e16)
- added missing image to repo (95e8f7a)
- added missing images (9bebb35)
- added missing images (3080dd2)
- added repo name (fd18e97)
- adding include hook that fails when a file is missing. (6287891)
- adjust sample data slide path in slides/SnakemakeHPCCreators.tex (13d481d)
- adjusted for barnard (0acf6e9)
- after merge conflict - working state restored. (0e355f8)
- another attempt (83d3336)
- artifact version (#175) (780bf6a)
- attempt to fix CI dependencies I (36e0823)
- attempt to fix CI dependencies II (143793d)
- attempt to fix CI dependencies III (c065853)
- attempt to fix CI dependencies IV (f6105f9)
- attempt to fix CI dependencies IX (6740188)
- attempt to fix CI dependencies V (67ab95c)
- attempt to fix CI dependencies VI (2f6d5fe)
- attempt to fix CI dependencies VII (446471f)
- attempt to fix CI dependencies VIII - test (3a18956)
- attempt to fix CI dependencies X (12abec5)
- attempt to fix CI dependencies XI (2a4ab69)
- attempt to fix CI dependencies XII (5ded75b)
- attempt to fix CI dependencies XIII - smaller texlive (d96c550)
- attempt to fix CI dependencies XIV - smaller texlive - correction (a5e8ceb)
- attempt to fix CI dependencies XIV - smaller texlive - correction (6478425)
- attempt to fix CI dependencies XV - smaller texlive - correction (09d0147)
- attempt to fix CI dependencies XVI - smaller texlive - correction (03af26b)
- attempt to fix CI dependencies XVII - smaller texlive - correction (e44ae3a)
- attempt to shift upload to build (#140) (a9a3c2a)
- attempt to upload artifacts (#130) (e75b76a)
- attempt to upload slides, too (#96) (82c1c07)
- attempted release-please fix (#91) (9f6e883)
- attempting apt-update prior to install (#159) (63a9f97)
- better grammar (7df70fa)
- better grammar (91ba78e)
- Changed files paths in SnakemakeHPCUsers.tex to existing files. (e00f418)
- ci (#160) (b03cf41)
- ci (#182) (6a4db2d)
- ci (#183) (8eed375)
- ci (#184) (5129fad)
- ci (#185) (4a12006)
- ci (#186) (e2fb606)
- ci (#187) (7c1cd59)
- ci (#188) (ad1b988)
- ci (#189) (27e86bb)
- clarifying mini-task about directory creation (b7b01dd)
- clearer wording for logging change (08e087e)
- complementing task on 07 (e8602a0)
- condensed version of 'A first workflow' and moved to common version (a422f90)
- configurable path to solution for 06 in Fininshing section (d6b8ec1)
- corrected example for config parsing in README (cb72d18)
- corrected figure of Snakemake downloads (b803304)
- corrected path for workflow profile (f2b565f)
- corrected to sdm for envmodules (6589dc3)
- corrected URL in contributions slide (df0896c)
- deleted broken 'optaining workflows' slide (e800648)
- deleted slide for module naming schemes - this is cluster specific (217725e)
- did not help - inserting package name back in (d93b08e)
- different condarcs for barnard and mogon (cb7ce7c)
- forgot to add the install_mamba.sh script (83f8baf)
- formatting (render) (fb42451)
- generalized date string in example log path (a6429d6)
- generalized date string in example log path (4df7fb3)
- gnarf - deleted old toc, apparently in buffer (5b7c10e)
- grammar (fc398da)
- grammar (a46ad62)
- grammar (af60e0d)
- grammar (6e8e9d4)
- grammar (7e6e066)
- handout URL #126 (#136) (4156aa9)
- identation (5b7e313)
- inserted configuration values for exercise 04 (abe8c40)
- inserted configuration values for exercise 05 (4a2c9b0)
- installmicromamba.sh -> installmamba.sh in 'Sample_Data' slide set (f742f78)
- language and parser (448cee7)
- layout (70991f2)
- line break in exercise for 04 (3f4ab2e)
- mentioning 10 in loggin directive task (2844809)
- merge conflict fixed, but needs sorting out (10a191b)
- minitoc section counting now working (dabeee8)
- minor cleanup and reformatting in render script (047a6b9)
- moved Finishing content to Python slide set - it was too short to merit a chapter; erased the Finishing chapter (be0ff81)
- moved sample data retrival to 'Getting Started' (a990212)
- moved sample data slides to common, as some data are just common (67c6fc0)
- no log directive for 08/09 (bdca285)
- no ordering for Python slide set correct (3b23899)
- no underscore escape anymore (adec2d0)
- one slide was doubled (4410b0c)
- order (#161) (a327718)
- outcommented 'package-name' not allowed (#170) (3226f6d)
- outcommented last slide - helping? (c7ab15a)
- overhaul (#155) (aa6722b)
- pipline -> workflow (d890065)
- Preparing to merge wrappers into main. (a73e1e1)
- properly access release please output for artifact upload (#156) (39676e9)
- python (#158) (ae87436)
- re-shuffled slide deck to better introduce the coding scenario and data retrival (#146) (e8a4af8)
- realease artifacts - separate release&build script (#100) (2a458f6)
- realease artifacts (#98) (ab0ce3d)
- realease artifacts (#99) (6f7ab18)
- reflecting mamba and not micromamba support (bf5a550)
- release artifacts - again (#101) (0ffeaef)
- release ci (#176) (ff93dd0)
- release generator 2 (#106) (8af0271)
- release generator 2 (#107) (60ee1e4)
- release generator 2 (#108) (e53fbf7)
- release generator 2 (#109) (d3265c8)
- release generator 2 (#110) (ac680c1)
- release generator 2 (#111) (e311fab)
- release generator 2 (#113) (68148a7)
- release generator 2 (#114) (10ca461)
- release generator 2 (#115) (b7be5fd)
- release generator 2 (#116) (b35a13f)
- release generator 2 (#93) (018b7cf)
- release generator 2 (#94) (0d20b24)
- release generator 3 (#118) (05c7f9e)
- release generator 3 (#119) (63c2b7a)
- release generator 3 (#120) (1086137)
- release generator 3 (#121) (d96f040)
- remotejoblocalstorageprefix for dresden config (e180830)
- removed '-quiet' from render call to pdflatex - option has been removed (d9b4eb3)
- removed benchmarking slides from 'Report' slide set (47a327f)
- removed outaded section adapt script 'adapt_sections.py' (e0521f2)
- removed reference to Mogon (0eccb1c)
- removed specific article from HPC 101 set, to make it more generic (47008d0)
- removed superflous conditional (#154) (c0cbae9)
- removed toc slide in favour of minitoc in Python in Snakemake slideset (de2f77b)
- removed unnecessary extra name (b65ccfd)
- replaced old config reference (188778e)
- resource -> resources (dfadf47)
- semantics in warning slide (6a87af5)
- several minifixes after last course (#181) (433cb6d)
- showcase for mamba install added (1621b72)
- slide order corrected to introduce workflow profiles (f0d1743)
- slide order in Decorating straight (73ace4a)
- Snakemake -> Snakefile (a6b9e71)
- some previous commit did screw the identation of the solution 06 (2d78fc8)
- source code identation (0204a17)
- texfiles in configs, need to be without suffix (dde2c18)
- the 'render' script had a broken logic for minitocs (f76a3b7)
- trying with different name - see https://github.com/orgs/community/discussions/60820 (f9b6ee3)
- two typos (bb62c14)
- typo (51f1fae)
- typo (dc818f9)
- typo S45 in software_environment (6adaab7)
- upload artifact (#131) (1326360)
- various little details (#148) (058e251)
- various2 (#150) (fc01975)
- yet another attempt to upload artifacts (#151) (d8871f1)
- yet another attempt to upload artifacts (#153) (0ac283c)
- TeX
Published by github-actions[bot] about 1 year ago