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57 Commits (c7d7b1db3c9092e8d848642dab7b4760ed2e1bd5)
 

Author SHA1 Message Date
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. 
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
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 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
Taha Ahmed 1e6ce316f1 Corrected exit statuses in chertex.sh to zero for success and one otherwise. 9 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. 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
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.
 11 years ago
Taha Ahmed 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
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
Taha Ahmed 8f939e4d83 Added *.Rmd files to the set of returned files after directory wipe (option 3). 12 years ago
Taha Ahmed f4252bf9c2 Added conversion of png to low-res png (25% of original size). 13 years ago
Taha Ahmed f6af643df4 Added *.fls to list of aux file types (used for clean-up option). 13 years ago
Taha Ahmed 4be1505333 Added a check for *.rda files after directory wiping. 13 years ago
Taha Ahmed 8082ea3039 The check for Rproj files now fixed and works properly. 
An answer on stackoverflow provided by the basis for the code.
 13 years ago
Taha Ahmed 4b224b0c01 Now checks if Rproj exists before attempting to copy it. 
Embarrasing oversight. Rproj file may not always exist (only created if an Rstudio project has been created in that directory).
 13 years ago
Taha Ahmed 8f8b07a485 chertex.sh now keeps *.Rproj files after wiping a directory. This is necessary for RStudio's project system. 13 years ago
Taha Ahmed 1c67e1b2c6 Added support for makeglossaries to .latexmkrc 
Incorporated the contents of previous ltxmkshellescape.rc
into the new .latexmkrc.
Updated chertex.sh to reflect the new rc file structure.
 13 years ago
Taha Ahmed 710b12deaa Added a timestamp to the dirname in the tmp directory. This ensures uniqueness. 13 years ago
Taha Ahmed 07ce71f33f Added an option to wipe the current directory. 
Crude implementation currently, but it appears to work. Good enough.
 13 years ago
Taha Ahmed 1b13d6e27d Added explanatory comment. 14 years ago
Taha Ahmed 7d88ea27cc TIFF conversion to PNG and aggregated PDF combined in semtiffconv.sh. 
For use with new SEM images.
Just run the command once, and PNG files and one PDF will be created in
working directory where semtiffconv.sh is called.
 14 years ago
Taha Ahmed 74182ae148 Added *.lof and *.tdo to clean-up. 14 years ago
Taha Ahmed d168eab7b9 Changed "require" to "request" in user info message. 14 years ago
Taha Ahmed 710955d247 Added support for latexmk shell escape in chertex.sh. Added clean-up option. 14 years ago