v1.0.0

1.0.0 (2024-05-15)

Features

• 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 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 the need for conventional commits to our CI (263887c)
• benchmarking slide set with graphical section slide and about slide (35769b5)
• 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)
• describing purpose of input functions and asking for config file benefits (d541e34)
• description of protected funtion (3c19fe2)
• dresden cluster barnard config (05b6a95)
• 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)
• introduced configurable edition (59b4958)
• introduced get sample data slide in users (bca0c55)
• introduced slides about actual deployment in 'Selecting_Workflow' slide set (aaa729a)
• made all cluster parameters configurable (9b52524)
• mentioning 'snakedeploy' in 'Deployment' slide (e55f012)
• new benchmarking file set (c51c7cf)
• new benchmarking file set in Snakemake_HPC_Creators.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)
• note on 09 (69d6731)
• 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)
• 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

• 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)
• added barnard editor file (6459994)
• added chapters to combined part (f409b73)
• added editor section to slide set (a6a92a5)
• 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/Snakemake_HPC_Creators.tex (13d481d)
• adjusted for barnard (0acf6e9)
• 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)
• attempted release-please fix (#91) (9f6e883)
• better grammar (7df70fa)
• better grammar (91ba78e)
• Changed files paths in Snakemake_HPC_Users.tex to existing files. (e00f418)
• 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)
• 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)
• identation (5b7e313)
• inserted configuration values for exercise 04 (abe8c40)
• inserted configuration values for exercise 05 (4a2c9b0)
• install_micromamba.sh -> install_mamba.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)
• outcommented last slide - helping? (c7ab15a)
• pipline -> workflow (d890065)
• Preparing to merge wrappers into main. (a73e1e1)
• reflecting mamba and not micromamba support (bf5a550)
• release generator 2 (#93) (018b7cf)
• release generator 2 (#94) (0d20b24)
• 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 toc slide in favour of minitoc in Python in Snakemake slideset (de2f77b)
• replaced old config reference (188778e)
• resource -> resources (dfadf47)
• semantics in warning slide (6a87af5)
• 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)
• two typos (bb62c14)
• typo (51f1fae)
• typo (dc818f9)
• typo S45 in software_environment (6adaab7)