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.
1 year ago
Taha Ahmed
d587da571a
New script to compile Markdown manuscript
1 year ago
Taha Ahmed
205c8a8afe
Restore thesis.bcf from git commit if modified in workspace
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This is a convenience to avoid having to remember to restore
this file after any broken compiles.
2 years 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.
2 years 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.
2 years ago
Taha Ahmed
51e2ca725b
auxiliary file .out is by hyperref (comment)
2 years ago
Taha Ahmed
7ef254dd69
Added minitoc aux files to list of aux files.
2 years ago
Taha Ahmed
688c7404ef
Added flag that disables Gotify notification
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+ cleaned up help section
+ replaced hard-coded colour codes with dependency on colours script
2 years 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).
2 years 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.
3 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
```
3 years ago
Taha Ahmed
2db7a877c8
clean *.lol files
4 years ago
Taha Ahmed
cab448cfd5
Refactor: improved arg handling, added usage, colors and better messaging.
...
https://betterdev.blog/minimal-safe-bash-script-template/
4 years ago
Taha Ahmed
0534288dcc
Fixed two issues: handle spaces in paths, and don't copy assets.external into .lowres tree
4 years ago
Taha Ahmed
e467fb74df
Improved finding new photos and converting them to lower-res version
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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.
4 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
4 years ago
Taha Ahmed
021afc363f
Wipe now includes minitoc auxiliary files
4 years ago
Taha Ahmed
18e1d82be7
Allow assets.external to copy directories, not just files.
4 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.
4 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
5 years ago
Taha Ahmed
d2df646a8c
Exploded the list of aux filetypes into a list to allow more comments,
...
and added *.ist to the list.
5 years ago
Taha Ahmed
511fd8cad3
Added push functionality Gotify CLI for longer runs.
5 years ago
Taha Ahmed
b000f1b489
Don't clean *.bcf files as they are useful when generating stand-alone bibliographies using biber
5 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.
5 years ago
Taha Ahmed
696c5a2127
Added more filetypes to chertex.sh clean-up <2>.
5 years ago
Taha Ahmed
482ba40ede
The current assets.external implementation cannot handle empty lines.
...
Added a comment to warn about that.
5 years ago
Taha Ahmed
32fa1b848f
Fixed low-res photos getting re-created every run.
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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.
6 years ago
Taha Ahmed
10254e0377
Removed extraneous and possibly confusing echo "delay completed".
6 years ago
Taha Ahmed
897293de2c
Misplaced cd command caused working directory errors. Fixed.
6 years ago
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
7 years ago
Taha Ahmed
1d0d8f3950
chertex.sh now reads and fetches external assets for thesis
7 years ago
Taha Ahmed
67db6ef159
Added a total runtime to script output.
7 years ago
Taha Ahmed
904cdd62a4
Created two new scripts for launching Chrome webapp windows.
7 years ago
Taha Ahmed
2c5b5cd2c3
The "job complete"-block now aligns properly for both summer and wintertime.
7 years ago
Taha Ahmed
fdff311703
Changed all absolute paths to so they begin "/media/bay/..."
7 years ago
Taha Ahmed
b7d10d9863
Decreased wait (sleep) times for chertex.sh slightly.
7 years ago
1e6ce316f1
Corrected exit statuses in chertex.sh to zero for success and one otherwise.
9 years ago
97e446e480
Completed script that manages and builds jekyll site.
10 years ago
Taha Ahmed
ef85917a71
Mainly updates to the way chertex.sh handles Shiny.
11 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.
11 years ago
c7f5f7e6f8
The integration between chertex.sh and shiny-matrix.sh now works better.
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Running chertex.sh on sample-matrix.Rnw kills previous shiny::runApp() instances,
and creates a new and persistent shiny instance using the nohup command.
11 years ago
a6daa3aced
Added shiny-matrix.sh, and now chertex.sh updates the Shiny matrix.
11 years ago
Taha Ahmed
59e38ea466
Added date information to end of chertex.sh output.
11 years ago
95164fa0a3
Added support for knitr jobs as well.
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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
724ebff898
Added support for new sample-matrix markdown source files.
12 years ago
Taha Ahmed
Taha Ahmed