72 Commits (master)

Author SHA1 Message Date
Taha Ahmed 687379932f Compile only paper or only SI with dynamically set
manuscript filenames and corresponding
LaTeX template files for Markdown.
To avoid having to set overly long command
I have opted to read these values from file.
6 months ago
Taha Ahmed d587da571a New script to compile Markdown manuscript 6 months ago
Taha Ahmed 205c8a8afe Restore thesis.bcf from git commit if modified in workspace
This is a convenience to avoid having to remember to restore
this file after any broken compiles.
8 months ago
Taha Ahmed 5a73e3e49d Fixed a bug: path_thesis should be path_wd.
+ gave the die() function a way to customise the sleep duration
  (allows the clean-up step to terminate immediately without waiting),
  and removed its unused exit-code argument.
9 months ago
Taha Ahmed c965437a0f No more file not found errors during cleanup
Cleanup with "rm $auxfiles" produced error messages for all filetypes
that were not found.
Rewritten as "find ... -exec rm ...",  much neater approach.
9 months ago
Taha Ahmed 51e2ca725b auxiliary file .out is by hyperref (comment) 11 months ago
Taha Ahmed 7ef254dd69 Added minitoc aux files to list of aux files. 12 months ago
Taha Ahmed 688c7404ef Added flag that disables Gotify notification
+ cleaned up help section
+ replaced hard-coded colour codes with dependency on colours script
1 year ago
Taha Ahmed 44ff1cfdc1 Gotify via CURL instead of CLI for better flexibility
(Gotify CLI only works if the CLI is installed on the machine,
whereas POST request via CURL to Gotify server should always work).
1 year ago
Taha Ahmed 296cc79bb9 No need to use "-r .latexmkrc" for latexmk command
because latexmk will use .latexmkrc file in the working directory
without needing to be prompted to do so.
In fact, the "-r" argument was causing latexmk to emit a warning,
so we are better of without it.
2 years ago
Taha Ahmed 2aded2bfc5 Added script that converts git submodules to regular git repos.
Last used on /media/bay/taha/projects/ansible/roles/public
with the script located in the root of that directory,
and invoked as:
./submodule-to-repo.sh tailscale
2 years ago
Taha Ahmed 2db7a877c8 clean *.lol files 3 years ago
Taha Ahmed cab448cfd5 Refactor: improved arg handling, added usage, colors and better messaging.
3 years ago
Taha Ahmed 0534288dcc Fixed two issues: handle spaces in paths, and don't copy assets.external into .lowres tree 3 years ago
Taha Ahmed e467fb74df Improved finding new photos and converting them to lower-res version
Was not working well at all before.
Forums online suggested not using for-loop for this kind of job,
so I've replaced those with find -exec statements. Initial tests
suggest this is much more robust. Also fewer lines.
3 years ago
Taha Ahmed c7d7b1db3c rsync line was using poor syntax. Fixed.
asterisk in rsync source was wrong, removed.
exclude path should not be absolute but relative to source, fixed.
My change of var path_wd to path_thesis was done on a whim, hope it
doesn't make anything worse
3 years ago
Taha Ahmed 021afc363f Wipe now includes minitoc auxiliary files 3 years ago
Taha Ahmed 18e1d82be7 Allow assets.external to copy directories, not just files. 3 years ago
Taha Ahmed 22120b2337 assets.external now supports specifying target subdir
I did this to lessen risk of filename clashes in the thesis/assets/data/
folder. This way, I can easily have a separate subdir for each manuscript.
3 years ago
Taha Ahmed d6866b7832 files in assets/references/ actually need to be overwritten
since they are bibtex libraries which often change on disk
and this copying is how we update the thesis's copy of them
4 years ago
Taha Ahmed 52f8fb5ea8 external assets for thesis now handled more robustly
we can now find all external.assets file in the entire assets/ tree
also copy operation does not overwrite
4 years ago
Taha Ahmed 0109401636 Also match .glstex aux files 4 years ago
Taha Ahmed d2df646a8c Exploded the list of aux filetypes into a list to allow more comments,
and added *.ist to the list.
4 years ago
Taha Ahmed 511fd8cad3 Added push functionality Gotify CLI for longer runs. 4 years ago
Taha Ahmed b000f1b489 Don't clean *.bcf files as they are useful when generating stand-alone bibliographies using biber 4 years ago
Taha Ahmed 0ee110ac18 Excluded *.svg, *.pdf and extensionless files from low-res photos
in the special thesis submodule.
There is no need to convert pdf, svg to jpeg and shrink even in
thesis draft mode.
4 years ago
Taha Ahmed 696c5a2127 Added more filetypes to chertex.sh clean-up <2>. 4 years ago
Taha Ahmed 482ba40ede The current assets.external implementation cannot handle empty lines.
Added a comment to warn about that.
4 years ago
Taha Ahmed 32fa1b848f Fixed low-res photos getting re-created every run.
It was missing a touch to the lastrun file in case of success. Now added.
5 years ago
Taha Ahmed 924ce8de2b env bash is better for portability, I heard. 5 years ago
Taha Ahmed 8152d3de61 Added "list-of-schemes" and "list-of-reactions" to aux files. 5 years ago
Taha Ahmed 10254e0377 Removed extraneous and possibly confusing echo "delay completed". 5 years ago
Taha Ahmed 897293de2c Misplaced cd command caused working directory errors. Fixed. 6 years ago
Taha Ahmed fb97a2acc8 Thesis: create low-res photos on-the-fly from existing photos 6 years ago
Taha Ahmed 93fbb4586f Cosmetic changes, should improve UX a little 6 years ago
Taha Ahmed 1d0d8f3950 chertex.sh now reads and fetches external assets for thesis 6 years ago
Taha Ahmed 67db6ef159 Added a total runtime to script output. 6 years ago
Taha Ahmed 904cdd62a4 Created two new scripts for launching Chrome webapp windows. 6 years ago
Taha Ahmed 2c5b5cd2c3 The "job complete"-block now aligns properly for both summer and wintertime. 6 years ago
Taha Ahmed fdff311703 Changed all absolute paths to so they begin "/media/bay/..." 6 years ago
Taha Ahmed b7d10d9863 Decreased wait (sleep) times for chertex.sh slightly. 6 years ago
Taha Ahmed 1e6ce316f1 Corrected exit statuses in chertex.sh to zero for success and one otherwise. 8 years ago
Taha Ahmed 97e446e480 Completed script that manages and builds jekyll site. 10 years ago
Taha Ahmed ef85917a71 Mainly updates to the way chertex.sh handles Shiny. 10 years ago
Taha Ahmed 4ef82b2e13 chertex.sh now handles sample-matrix jobs only to produce HTML (Shiny) output.
Previously a pdf file was always created as well, but from now on,
sample-matrix will be exclusively used in the Shiny app.
10 years ago
Taha Ahmed c7f5f7e6f8 The integration between chertex.sh and shiny-matrix.sh now works better.
Running chertex.sh on sample-matrix.Rnw kills previous shiny::runApp() instances,
and creates a new and persistent shiny instance using the nohup command.
10 years ago
Taha Ahmed a6daa3aced Added shiny-matrix.sh, and now chertex.sh updates the Shiny matrix. 10 years ago
Taha Ahmed 59e38ea466 Added date information to end of chertex.sh output. 10 years ago
Taha Ahmed 95164fa0a3 Added support for knitr jobs as well.
chertex.sh will use knitr instead of pgfSweave if it detects a file name ".knitme"
in the directory of the current job. Crude solution, but it should work.
12 years ago
Taha Ahmed 724ebff898 Added support for new sample-matrix markdown source files. 12 years ago