Some emacs lisp utilities of mine, that have been useful for me.

Several utilities to ease the pain of working with a  single monitor

Working on a small monitor, like a laptop screen, can be a strain.  To make this easier, I wrote some utilities in emacs lisp.  Another one was written by someone named "Gildea" on a mailing list.  They have been useful to me; perhaps they will be useful to others.  They are simple, and certainly could be improved upon. 

 

First open a second window, horizontally (\C-x3).  Then use the first functoin to enlarge one of the windows horizontally.  It is hardwired to enlarge, horizontally, by 20 character widths, which can be changed. One can just as easily change the sizes of windows by dragging with a mouse.

 

I.   Enlarge one of two horizontally split windows

(defun enlarge-window-very-horizontally ()
  "Enlarge this window horizontally."
  (interactive)
  (enlarge-window-horizontally 20))

 

II.  Flip flop: Move to other window and swap widths.

This utility does two things: it moves the cursor to the other window; and it swaps the sizes of the two windows.    

 

(defun flip-flop-and-change-horizontal-windows ()
  "Swap HORIZONTAL window sizes; move into the other window.  This function
enables one to have two windows visible, but with one very narrow."
   (interactive)
   (let ((current-window-width (window-width)) 
     (new-window-width nil)
     (delta-window-width nil))
     (other-window 1)
     (setq new-window-width (window-width))
     (setq delta-window-width (- current-window-width new-window-width))
     (enlarge-window-horizontally delta-window-width)))

 

 III.  Flip flop vertically (like the above)

This version works with vertically split windows.  This might work better in some cases.  These utilities are minimal, written by a naive emacs user.  I feel certain they can be modified and improved in various ways.  I would like to find a way that the tool above, for horizontally split windows, can move back and forth, even when either or both sides is split into two or more windows vertically.  They sky's the limit, but these utilities are simple, and therefore easy to use and remember.

 

(defun flip-flop-and-change-windows ()
  "Swap window sizes; move into the other window.  This function
enables one to have two windows visible, but with one reduced to two lines."
   (interactive)
   (let ((current-window-height (window-height)) 
     (new-window-height nil)
     (delta-window-height nil))
     (other-window 1)
     (setq new-window-height (window-height))
     (setq delta-window-height (- current-window-height new-window-height))
     (enlarge-window delta-window-height)))

 

IV.  Swap positions of two windows with contents. 

 Another tool was written by a "Gildea" on a mailing list in 1988, possibly in answer to a query of mine.  It enables one to just swap the positions of two whole windows. 

 

 (defun swap-window-positions ()
  "Swap the positions of this window and the next one.
(credit to gildea Nov 88)"
  (interactive)
  (let ((other-window (next-window (selected-window) 'no-minibuf)))
    (let ((other-window-buffer (window-buffer other-window))
      (other-window-hscroll (window-hscroll other-window))
      (other-window-point (window-point other-window))
      (other-window-start (window-start other-window)))
      (set-window-buffer other-window (current-buffer))
      (set-window-hscroll other-window (window-hscroll (selected-window)))
      (set-window-point other-window (point))
      (set-window-start other-window (window-start (selected-window)))
      (set-window-buffer (selected-window) other-window-buffer)
      (set-window-hscroll (selected-window) other-window-hscroll)
      (set-window-point (selected-window) other-window-point)
      (set-window-start (selected-window) other-window-start))
    (select-window other-window)))

 I hope these are useful, as they have been useful to me.

CachyOS

 At this time I would just like to note that I have been using CachyOS exclusively for a couple of months.  An earlier iteration didn't work for me, at the time of the great Archlinux Nvidia debacle that made it functionally impossible for someone with my limited expertise to use my GTX 1050 card.  Too old.  It works, but no longer supported.  

 

As of earlier this year, however, CachyOS automatically chooses the correct older driver version to run this card.  No wonder it climbed up to the top of the hit list on DistroWatch.  I think deservedly so.  I understand that it will also run other cards---the 1650 series-albeit with some manual intervention.  I hate that term, but I would love to have one of those.  My system works quite well, and I was grateful that an NVIDIA card had drivers, even proprietary, that work really well.  I am opposed to proprietary drivers, but I admit I have been using several for years, because I cannot just go and change my hardware choices every time I would like.  I home built, on the cheap, with a nice CPU, some good amount of RAM, good storage, and at least some kind of affordable video card.  It hurts that companies can just decide it's not worth it to support hardware that's little more than 10 years old.  IMO, it's criminal.  PT Barnum had something to say about this.  Basically we are the suckers.  Next time, will there ever be a next time, I will probably go with AMD.  Corporate decisions don't work out for the consumer.  

 

That said, this old card is doing its job.  -

 

-----------------------

 

It's been a few months since I wrote the above.  The system is still running nicely.   I have noticed one thing: updates, which I like to run every so often, take quite long on this system, as opposed to my Thinkpad with it's Intel graphics, because the kernel must be compiled together with the Nvidia bits, on every update.  Even with a 26 core Intel i7, this takes a good long time.  It's worth the wait.  

 

 

  

How I got into Emacs (and Free Software)

This is a long tale, not confined to Emacs alone. This is, indeed, a story about why I am a confirmed Free Software advocate. This has been a rocky road. For this chapter, I'll try my best to restrict my discussion to Emacs; but that's impossible. In the late 80s and early 90s, I was living in Chuuk Lagoon, Micronesia. Graduate work at the University of Guam (UOG) marine lab had been interrupted, at the outset of my third year; in Chuuk, my wife was preparing to give birth to our first son.

In my letter of intent for my application to the graduate program at UOG Marine Lab, in 1984, I had written that my first order of business was to learn the marine fauna  of Micronesia, to prepare for future study of traditional marine biological knowledge. A lexicon of marine life would be required. After  two years of classwork, with a working  knowledge of the fauna, in late 1986 I hit the ground running, collecting notes on the names and knowledge of marine animals. 

As  notes piled up, I would obviously need a PC to compile, sort, and analyze the burgeoning information. I had a working knowledge of computers, and had used some of the earliest PCs---IBM XT and IBM AT--- at the Marine Lab. Somehow I acquired a PC, and started messing around with typing in  names, and organizing the data.  I  purchased a copy of SNOBOL4, and began to study it, and SPITBOL, hopeful it would be helpful for string manipulation.   I tried Borland Paradox.   Progress was minimal. 

 

In 1990 and 1991, my life in turmoil I moved to another island, nearby. My Mother came to the rescue, gifting me a Toshiba laptop. I soon  realized it came with no software, not even a word processor.  I made do for a while.  I remember using 4Dos.  

 In  1991, I had remarried, moved again, and had a new teaching job. With a 10W solar panel, the laptop could be used,  and I tried various editors to develop a simple database---a list of animal names with descriptive text.   I needed a programmer's editor that did not mangle the text with control codes.  A linguist from the University of Hawaii sent a demonstration copy of MultiEdit, which did some of what I wanted. But to learn how to type diacritics, I would need to purchase the manual, for over 300.00. On my teacher's salary, this was impossible.  

 At the time, I had been reading Infoworld, and , ran across  a short article buried a few pages in, about the Free Software Foundation. I knew nothing about this, or about Free Software, but the name said it all. I wrote a letter to the FSF explaining my project, and asking for help for an editor. A few weeks later, I received a package with about 13 3-1/2" diskettes, a package that would change my life.  (Whom should I thank?)  On one disk was "Demacs," an implementation of Emacs for the Windows ecosystem, in addition to a number of Unix text tools ported to Windows, by Cygwin, and Unix Text Tools---sort, ptx, grep, find, and other---ported for Windows 3.0.   

 Demacs was a well-functioning port of Emacs to Windows. One of the first things I noticed was the existence of a Tutorial, a genius introduction.  And this was the "self documenting text editor."  Within minutes I was sufficiently able to navigate the interface and to work with text.  I developed a crude understanding of Emacs Lisp, and wrote several low level helper functions for my needs. This software was beyond any dream. 

  Shockingly, in this age of continual modernization, most of the tweaks I developed to my first emacs files still function on today's Emacs 30+, in 2026, not the case for files written on early windows Word versions.  Happily, over the next couple of years, the Gnus Bull, the bulletin of the Free Software Foundation arrived every so often in my post office box. In one of these bulletins, fascinating reading for me at the time, was an article about Unix work-alike operating systems, Linux and FreeBSD.  Later on, on an extended medical visit to Guam, I was able, through generous assistance of the owners of the ISP Kuentos Communications, I was enabled to download Slackware and install it on my Toshiba Laptop.

This meant I could install Emacs directly. The Unix text tools were available directly as well.  My needs are simple, compared to many---if not most---Emacs users, many of whom are programmers comfortable with generating elaborate and extensive code. As my project grew, Emacs was the essential ingredient. Later on I learned of the existence of LaTeX. Eventually, my lexicon was published from camera ready copy generated by LaTeX in the journal Micronesica.  With the help of a programmer at the University of Hawaii Linguistics Department, an Emacs guru, I was able to write an emacs lisp program to "alphabetize" Chuukese in an arbitrary order.  Many other scholars and programmers have helped along the way, on mailing lists, or through lengthy correspondences.   Early on, Professor Hsu at UH mentioned the Band Format---a free form database used by linguists for lexical data.  I could not afford the tools he offered, but I was able to mimic some of the needed facility using Emacs lisp.  

 I was able to implement a tool to convert each record of the band format database into LaTeX code for a single entry, that was typeset as camera ready copy for the ultimate publication.   

 For this carnival, the take home messages for Newbies and scholars was that the Tutorial can provide, in an hour or two, a tremendous introduction to the keyboard use for Emacs.  And secondly, I think it's important to recognize the number of Emacs experts who are willing to assist in such an endeavor as mine.  I have not resorted to a starter kit.   

Setting file times in Emacs from Time-stamps in file, or "Created " at start of a file: Generated through Google AI Summary

AI is problematic, but the sheer convenience of it has grabbed my attention.  For tweaking my GNU/Linux system, AI summaries of Google searches come in a few seconds, and they sometimes save hours of research.  It is helpful that low grade links to sources are often provided.  I balk, however, at the damaging infrastructure involved.   

 A recent adventure has been developing a useful emacs lisp tool to change the metadata time stamps of a file from emacs' Time-stamps, when they exist.   

Today I realized I had copied files from another system without specifying to save file metadata.  Could I set the file times of files with timestamps using the "Time-stamp: < >" utility in Emacs?   I searched, and, I must freely admit, I asked for more info from the AI helper of Google Search.  After about 7 or more rounds of providing feedback about  a regular expression that did not work, these functions were provided.  Wow.   The last two of these is probably sufficient for my needs.  I will change the names.

 

(defun my/set-file-time-final ()
  "Sets file time by finding 'Time-stamp' and extracting only the date/time.  From Google AI."
  (interactive)
  (save-excursion
    (goto-char (point-min))
    ;; 1. Find the literal word "Time-stamp" anywhere (ignores #, brackets, etc.)
    (if (re-search-forward "Time-stamp" nil t)
        ;; 2. Look for the first date pattern (YYYY-MM-DD HH:MM:SS) that follows it
        (if (re-search-forward "\\([0-9]\\{4\\}-[0-9]\\{2\\}-[0-9]\\{2\\}[ T][0-9]\\{2\\}:[0-9]\\{2\\}:[0-9]\\{2\\}\\)" nil t)
            (let* ((ts-string (match-string 1))
                   (parsed (parse-time-string ts-string))
                   (lisp-time (when parsed (encode-time parsed))))
              (if (and (buffer-file-name) lisp-time)
                  (progn
                    (set-file-times (buffer-file-name) lisp-time)
                    (message "Success! Mtime set to %s (Username ignored)" ts-string))
                (error "Parsed '%s' but system couldn't use it" ts-string)))
          (error "Found 'Time-stamp' but no YYYY-MM-DD HH:MM:SS format found after it"))
      (error "The word 'Time-stamp' is missing from this file"))))

(defun my/dired-set-times-from-stamps ()
  "In Dired, run 'my/set-file-time-final' on all marked files. From Google AI."
  (interactive)
  (let ((files (dired-get-marked-files)))
    (dolist (file files)
      (with-current-buffer (find-file-noselect file)
        (condition-case err
            (progn
              (my/set-file-time-final)
              (save-buffer))
          (error (message "Skipping %s: %s" file (error-message-string err))))))
    (revert-buffer) ; Refresh the Dired buffer to show the new times
    (message "Done processing marked files.")))

(defun my/dired-set-times-from-stamps ()
  "In Dired, sync system times for marked files. Files without stamps are ignored."
  (interactive)
  (let ((files (dired-get-marked-files))
        (skipped 0)
        (updated 0))
    (dolist (file files)
      (with-current-buffer (find-file-noselect file)
        ;; Use condition-case to catch files that don't have the stamp
        (condition-case nil
            (progn
              (my/set-file-time-final)
              (save-buffer)
              (setq updated (1+ updated)))
          (error (setq skipped (1+ skipped))))))
    (revert-buffer)
    (message "Done! Updated: %d | Skipped (no stamp): %d" updated skipped)))

(defun my/set-file-time-final ()
  "From Google AI summary session after Google search.  Sets file time from header. Handles: Created YYYY-MM-DD Day HH:MM:"
  (interactive)
  (save-excursion
    (goto-char (point-min))
    ;; 1. Search for 'Time-stamp' or 'Created'
    (if (re-search-forward "\\(Time-stamp\\|Created\\):?" nil t)
        ;; 2. Match the date (YYYY-MM-DD) 
        ;;    Then skip any day-of-week (like Tue)
        ;;    Then grab the time (HH:MM or HH:MM:SS)
        (if (re-search-forward "\\([0-9]\\{4\\}-[0-9]\\{2\\}-[0-9]\\{2\\}\\)[^0-9]*\\([0-9]\\{2\\}:[0-9]\\{2\\}\\(?::[0-9]\\{2\\}\\)?\\)" nil t)
            (let* ((date-part (match-string 1))
                   (time-part (match-string 2))
                   (ts-string (concat date-part " " time-part))
                   (parsed (parse-time-string ts-string))
                   (lisp-time (when parsed (encode-time parsed))))
              (if (and (buffer-file-name) lisp-time)
                  (progn
                    (set-file-times (buffer-file-name) lisp-time)
                    (message "Success! Mtime set to %s" ts-string))
                (error "Parsed '%s' but couldn't use it" ts-string)))
          (error "Found keyword but date/time format was unexpected"))
      (error "No 'Time-stamp' or 'Created' header found"))))

(defun my/dired-set-times-from-stamps ()
  "From Google AI summary session.  This calls the function my/set-file-time-final.  In Dired, sync system modification times for all marked files
based on the 'Created' or 'Time-stamp' lines inside them."
  (interactive)
  (let ((files (dired-get-marked-files))
        (updated 0)
        (skipped 0))
    (dolist (file files)
      ;; Open the file in a buffer without switching to it
      (with-current-buffer (find-file-noselect file)
        (condition-case nil
            (progn
              ;; Call your working 'within-the-file' function
              (my/set-file-time-final)
              ;; Save the buffer to ensure metadata is flushed to disk
              (save-buffer)
              (setq updated (1+ updated)))
          (error 
           (setq skipped (1+ skipped))))))
    ;; Refresh the Dired buffer so you see the new dates immediately
    (revert-buffer)
    (message "Batch complete: %d updated, %d skipped (no stamp found)." updated skipped)))

(with-eval-after-load 'dired
  (define-key dired-mode-map (kbd "T") 'my/dired-set-times-from-stamps))

Shinestacker for focus stacking: Hurray!!

 This is the first image I processed using Shinestacker.  It's a remarkable and technically advanced piece of open source software.    This software is beyond my skill level, but works incredibly well with defaults.  

 

Sufficeth to say it was very simple, after a somewhat convoluted---but not difficult---installation on CachyOS, to process this stack of 40 images.  I have a CPU with 27 or 28 processors; and this software even took advantage of my aging Nvidia GTX-1050 video card with a mere 3GB of video ram.  25X objective, mounted in UV-curing glass glue from a hardware store.  Too bad about the detritus.  Processing took a few seconds.  

 

Ossicles of sea cucumber Holothuria atra, mounted in UV-curing glass glue.

 UPDATE (2026 May 18)

  Updated Shinestacker this week,  Incredibly, it can accept Canon EOS *.cr3 raw files.  Neither Fiji (unless by trickery), or Helicon Focus can open these files.  The developer of Shinestacker stated that tiff files work better on SS, which apparentely was a major impetus for accepting cr3 files.  It works well, but required more resources.  My 26 core intel i7 cpu, with 32G of ram, and 128G of swap space, works well; shinestacker utilizes all cores, I believe.

 

Some images have shown blotchiness.  In one case, even using .cr3 files did not solve this.  These are microscope images, which may be a factor.  The focus stack of images of ossicles, above, used very few shots, a rather coarse Z sampling.  

The ease of using this software is a huge upside.   Some experimentation will be required to figure out advanced settings, ie, what kind of images do well with pyramid stacking, and which work best with depth masks.  I had some problems on some images; it seemed, perhaps, that turning off balancing may have helped.  These images are fairly consistent in illumination.

 

Hurray for  this software!!! 

 

 

Actually, Wayland is usable. I am leaning on Sway on my laptop.

 Just to bring the conversation up to date.  It is easier to use sway on this laptop---a Lenovo X1 Carbon gen. 9---because it has a HiDPI display.  I3/X11 are problematic, requiring numerous configuration tweaks.  Hyprland is easier, but less compatible.  

 

My personal customizations for i3 are not completely compatible with Sway.  For one thing, I have adopted dropdown windows for a number of applications on i3, which is sometimes problematic, but usually works.  Kitty works ok in this way on Sway.  Emacs, not so much.  The following applications have bindings in my i3 configuration, and work well: orage (calendar); xephem; R).  Emacs is ok, but tricky.  Kitty too can be tricky.  This manner of using i3wm is fantastic for my workflow.  I also have had kmag on a dropdown keybinding, which is useful.   

 I have, as of May, 2026, not made much effort to get all of these utilities working on Sway.  Dropbox's hot icon does not work on i3, so far, for me; on Sway it does work with swaybar, an excellent bar.  

 Tiling WMs work for me.  I3 is easy to configure.  Sway can run ok using the i3 config files, except for edge cases.

 

 

 

A 

 

 

 

 

 

 

Trying out Sway, an i3wm workalike for Wayland

 A good move I recently made was to sell my MacBook Pro, M2; and purchase a Lenovo Thinkpad X1 Carbon, several years old.  One of the best features of this new laptop is a HiDPI (High Dots Per Inch) screen with a resolution of something like  3200x1800.  It's a remarkable display for other reasons, which I will not go into here.  The blacks are incredible.  

 With my usual Manjaro i3wm, this means that the type is almost unreadable.  With the guidance of several source on the Internet, I was able to cajol the system into somewhat useful settings that most software works fine with.  Along they way, several references passed me by about Wayland, a newer graphical setup that X11.  

 

I am reluctant to make huge changes to a long time stalwart system, but finally I have begun to experiment with Sway, a workalike system to i3, and Hyprland, a fancier tiling window manager, working on top of Wayland.  Both, I am happy to report, work nicely with this  HiDPI screen.  

 

So I installed Manjaro's Sway edition.  So far, so good.  Now I'm at the point of trying to configure pop-up/drop-down floating windows for Kitty, Emacs, R, orage (probably impossible, but this is the best little calendar app I have found.  Once I have set the month, and popped it back up, the same month is show.  Very useful for calendar work), and a ham radio clock, that is actually of little use.  

HiDPI is not a problem.  

 

When I install a new distro, one of the first things I do  is set the user id to "1004", as well as the groupid.  Consequently, the home directory of my previous setup and user are completely accessible, because this was the case for the previous login as well.  I never duplicate the login, out of worry that the dot file tweaks will be incompatible with anything different.  

 

So far, so good.

 

Tools of Excellence: Cb2bib, Yazi, Sioyek, Entangle, XnViewMP, Emacs,...: WOW!

In the summer of either 1982 or 1983, I enrolled in a summer school class at UCSB offered by the College of Engineering on Computer Architecture.  At about this time two of my regular classes required the use of Wordstar, on a mainframe terminal.  I had been required to write a program in Fortran for a math course; now, in this Computer Architecture class, I wrote some minimal code in PDP-1170 Assembly Language.   Intel's early microprocessors---the engines that  would spark a revolution in Personal Computing---had come into being.   I had enrolled on a Pass/Fail basis, fearing that it would be a technical challenge.  I had enrolled later in an amazing  Invertebrate  Paleontology course, also Pass/Fail.  Both times, I would have earned an honest "A."         Yet another Lesson learned.  

 The theory behind digital computers, as it turns out, is straightforward and fascinating, logical and understandable.  I later came to realize that these systems, invented  by humans, reflected human logic; they are non-complex, a fact I understood more fully after being introduced to Molecular Biology and Genetics, and the extreme complexity of the Central Dogma  By the end of the short summer session, I had a tentative grasp of the nature of digital computers.  The graduate student instructor took me aside and advised that the knowledge I had gained in this brief introduction would be valuable in the future, and I would be able to advise others about what computers can do.  

 This advice could not have been more applicable when I moved to Chuuk Lagoon, and started a project collecting animal names in local dialects of the islands.  At the University of Guam Marine Lab, I was exposed to early Personal Computers, the IBM XT and IBM AT.  My basic knowledge of the workings of computing systems provided useful perspective for solving problems.  I eschewed the commercial/proprietary solutions, the high priced computer programs that would make the entrepreneurs wealthy.  

 I learned what I could and scrounged software of many kinds.  Except the big brands.  There are always other solutions that work better; those behemoths aren't worth the cost to society.  I believed this then, and I believe it even more today.  

 My Toolbox

Previously, I have written a little about Yazi and Sioyek.   They, like Cb2Bib and Entangle, are functionally remarkable tools.   Among Free Software users, they are not the most popular.  I also rely upon the highly functional, low overhead foundation, the i3 tiling window manager.  Emacs is a mainstay; like these other tools, the simplicity and functional design of Emacs makes it run circles around most proprietary software.  Windows is dumbed down; the stress of using such a dysfunctional tool might be likened to trying to build a cabinet using a jackhammer; a poorly made jackhammer at that.   I use LibreOffice from time to time, and some other more mainstream tools.  They are fine; but the workhorses in my toolbox are more special. The packages I am writing about today are truly special, and enabling. 

 

I as initially attracted to Free Software for financial reasons.  The story is too long to recount here.  But as I have come to understand the GNU Project, and the grass-roots nature of the development of these tools, it became clear to me that the Free in Free Software actually refers to freedom, not free beer.   

 

Sioyek

The PDF reader Sioyek caught my attention relatively recently, with its plain exterior, focus on research, and its  hidden gems.  For a couple of days, I returned to sioyek, after setting it aside a while; a closer reading of the documentation has given me a new appreciation of it's wonders.  And today, after some digging, I was able to configure yazi to open files in Sioyek, or Evince, at will.  Gradually, the levers and buttons of sioyek are revealed.

 

The documentation is relatively straightforward.   But I struggled with configuration.  Later for that.  PrintHere are some of the more interesting features:

• A keystroke sends the text at the cursor to Google Scholar (GS), or another tool I am unfamilar with.  A browser opens, Google Chrome.  Keystrokes are available, either standard or by a plugin, to download the pdf from GS.  
• Sioyek remembers bookmarks of two or three kinds.  A keystroke causes display of a list of bookmarks in either the current file, or all pdfs sioyek knows about.  
• One of these "bookmark" functionalites is called "highlighting."  Selected text may be highlighted.  The keystroke for highlighting must be followed by a single key, which represents the type of material.  So someone like me, whose mind travels in so many directions, can keep track of various threads of interest.  If several files are highlighted in this way, retrieval of highlights can optionally display all highlights of a given type in all files (globally).  
• The Global retrieval feature holds for bookmarks as well.  So if I am reading four PDFs that relate to each other, I can bounce around.  And selections can be copied to the system clipboard.  You know where this is going.
• Portals are something I don't yet understand.  I position may be set as a target for a portal, so as I'm reading I can refer back to a certain specific piece of text, diagram, table, whatever.  Backspace brings me home.
•  I was able to print.
• Sioyek is mainly keyboard driven; but scrolling with a mouse is possible.
• A "visual mark" (or whatever it's called) underlines current text if that is wanted; and this mark can be manipulated in various ways.  More to learn hear.
• Zooming is great.
• In PDFs text can be selected and various functions are possible.  A click on a figure number will take me directly to that figure.  This built-in feature seems almost intelligent, and it reminds me of snarfing references in Cb2Bib, a remarkable feature.  
• Synctex mode allows the latex source to be opened and followed when reading a pdf.  Wow.

Some thought went into this tool.  

 

Yazi 

Yazi is a console based file manager with superpowers.  I have gotten into the configuration details far enough to make it possible to choose which pdf viewer is desired.  Sometimes, I think sioyek may be too far out, for some things; so I set up to be able to open in either  evince or sioyek.  Shift-O opens a minimal menu; included here is a button to open it in a folder.  I think some more tweaking is needed to identify low-overhead tools like qutebrowser for Google Scholar searches, and a minimal Graphical File Manager with lower overhead.  My laptop lags seriously, but it's a very old laptop.

 

Yazi works swell with kitty.  Previews of jpegs and pngs, and possibly tiffs (with some tweaking) is extremely fast, and a plugin "zoom" feature enables the image to zoom to the full height of the window.  Image and PDF previews are useful.  

 

Bunny is an amazing bookmarking tool.  

 

A tweak in .bashrc (or .zshrc) makes it possible to open yazi by typing 'y'.  As a bonus feature, when one changes directory, then types "q" to quit, yazi leaves the console in the last folder visited.  

 

This tool is undergoing rapid development, and plugins have been known to fail after updating.  

 

I use this for editing filenames, with tags.  A filter function ("f") then makes possible isolating files with a specific tag, marking them all, creating a directory, and dumping all these into a directory.   

 

Cb2Bib

 

This is an extremely useful tool, to me.  I think I'm the only one who uses it in the way I do, to write annotations to records in my bibtex database, and print out annotated bibliographies on demand.  I write, for example, a call number of a book, and notes on pages, compile it into LaTeX, and print.  Very convenient.  The developer was kind enough to explain how to modify the code to incorporate an "annotate" field in the bibtex entry, and also modify the tools that generate a pdf, so an annotation is formated together with the citation.  

 

In this space, I hope to present instructions for the benefit of others.  

Cb2Bib also automatically picks up citations that are highlighted in other programs.  Also, one can copy a bibtex citation from Google Scholar, that is instantly picked up and incorporated into the database associated with the program.  

This program does much more than I am able to understand, but what I can understand, and do---with the help of Pere Constans---is amazing.  

 

This is another reason I don't stick to the commercial / proprietary software packages.

 

Entangle

 

More to follow. 

 

 

sioyek and yazi

I have set Sioyek as the default pdf viewer for Yazi; actually, probably for the entire system.  

 It was *relatively* simple to do this, after installing xdg-utils-mimeo.  I will not go back through that here, but it's not hard.  

 Sioyek has no native capacity to print.  This is a potential show stopper.  I have attempted to set this up from instructions from some random internet post.  The location of the user config files is in doubt, however.  By "reports," config files should be found in ~/.config/sioyek; however, other reports indicate .local/share/sioyek.  I did install a rather decrepid tool, a gtk-print tool (name?).  My config does not work yet.

Another potential downside relates to the use case for Sioyek, as a pdf annotation tool for research.  When a file is opened for the first time, sioyek indexes the file; this makes searches incredibly quick and useful.  Will this result in cluttering the system after a large number of pdfs are opened?  Probably another lightweight pdf viewer should be established as the default, to streamline the process of reviewing random files on the fly.  

Sioyek is uncluttered, as far as GUI.  There hardly is any GUI.  A fairly extensive set of utilities is tied to keystrokes.  Some of them are not exactly intuitive, at least to me.  

Some facilities:

• Bookmarking
• Search in google scholar (may not work right)
• gg -> go to page 1
• G -> go to last page
• rt click -> mark line (not sure this is working with a track pad)
• highlighting in various colors
• search highlights
• "Smart Jumps" to figures or references, with or without links: this didn't work out of the box, for me.
• mark a location, give character as a name for the mark.

 

Yazi is turning out to be extremely useful.  I use it multiple times a day.  Some useful tweaks:

• set a much larger preview size, then
• install a preview to Toggle full view of the preview
• somehow a special tweak was needed to view tiffs (this wasn't the case when I first tried yazi)
• bookmarks.  yabm (Yet Another Book Mark) is great.  Another one was incompatible, AFAICT.
• Zoom plugin
• In a tips section of the web site, is recommended to install some code in the rc file of the shell, which allows to start with "y" and that leaves the terminal in the last used directory, when quit with "q".  Extremely useful.

A problem: not really a big one: yazi is undergoing rapid and intense development, so incomptibilities arise frequently.   Especially with plugins.

 

 

Some recent useful software additions

 A brief list for now:

• dysk : concise "df" and graphic
• sioyek: interesting  document reader.  Keyboard driven, mostly, maybe. Designed for academic papers and textbooks.  
•  bpytop: A feature-ful process/memory/cpu monitor, text based; similar to top or htop.
  
•  

Notes on Yazi

 Yazi is good.  Real good.  I used it over ssh to cull a directory on my second system; it worked as I had hoped, except, perhaps, for color theming.

 Knock on Wood.

 Viewing/reviewing

One of the needs that yazi has fulfilled for me is rapid viewing.  I can only imagine that should I ever be able to upgrade my current machines (RAM and CPU, as well as Storage), viewing would be even more friendly, especially for images.  The ability to flip through a directory of images, mark, and move, copy, or delete marked files, has made a huge difference to my workflow.  The only other tool that is useful in this regard is xnviewmp.  I use a fairly simple set of commands; probably if I mastered tabs and other complexities and plugins, yazi would be even more helpful.

 

By the way, the terminal "kitty" has wonderful facilities built in to work well for viewing images.   I prefer the black background and contrasty color scheme to any other.

 Ranger was good enough, until it wasn't.

Copy, Paste and move and Notes on plugins.

 [Cautionary note: I have lost files through carelessness here, and yazi has some gotchas to be navigated around.]

This is pretty much self-explanatory.  I will try to address this topic in detail at some future time.  For now, I'll mention a plugin that has helped speed these processes: 

• yamb is a bookmarking plugin that works well.  In the absence of a much needed multi-step backup command, this does a good job when sorting through files and moving or copying them to another directory.  I have gotten around the mentioned limitation by defining  bookmarks for the current from directory, and the currently interesting goto directory,  I define a set of book marks to frequently used directories, as well.  This is an easy tool to master.  Like other plugins, issues have been experienced after updating yazi (it is under fairly intense development).  

• toggle-pane: This helps when viewing both pdfs and images.  It is possible to configure the mazimum size of displayed images (I'm not certain whether this works for pdfs) by putting this code into ~?.config/yazi/yazi.toml:

                       [preview]

                      # Change them to your desired values
                      max_width  = 1800
                      max_height = 1800
  

       Plugins are found on a resources link on yazi's web pages.  Other sites exist with plubins.

 

Filtering

Filtering is a wonderful way to sort.  It has been even more useful to me, because of a filenaming scheme I have adopted.  I stole this idea from Protesilaos's Denote system.  I have not found denote very useful, but the concept of tags at the end of the filename, before the extension has become a useful tool allowing me to sort files more rapidly.  Here is an example.

    Jones--2060--JargonInBiology__taxonomy_nomenclature_zoology.pdf

I have started avoiding underscores in filenames ("_") in favor of using them in tags.  Interestingly, I saw a web page or thread somewhere about tagging styles, and this is one of several.  I used to use a 10 (or so) character at the beginning of lines in a bibliography, where each position had a meaning.  So anything related to crabs would have "c" in the third position (12ctx8urt-Anon-Crabs of the world) would be sorteable by sorting by the third position.  The Unix (GNU/Linux) sort command worked excellently.  

 With filtering  in yazi, one can narrow down a large folder/directory with pdfs about taxonomy: "_taxonom".  Prot has demonstrated the use of regular expressions to sort even more specifically in, I think emacs dired.  To avoid filtering for "_" in filenames, one would theoretically use a regular expression requiring a "__" (double underscore) somewhere before the "_:" single underscore.  This is probably easy.  Filtering is easier, I think.  It may be that emacs would be better, but so far, aside from a couple of learning experiences, Yazi is working well.

Moving around 

In either the getting started or tips section of the yazi main web pages, is a suggestion that makes yazi more useful.  

Inserting this code into .bashrc (and I think .zshrc as well) makes things easy.

 function y() {
    local tmp="$(mktemp -t "yazi-cwd.XXXXXX")" cwd
    yazi "$@" --cwd-file="$tmp"
    if cwd="$(command cat -- "$tmp")" && [ -n "$cwd" ] && [ "$cwd" != "$PWD" ]; then
        builtin cd -- "$cwd"
    fi
    rm -f -- "$tmp"
}

Then, when in a terminal, type "y" to start yazi.  After moving to another directly, quitting with "q" leaves the terminal in this new directory.

 

A Caution or Two 

 Plugins are often not mutually compatible.  I have tried several others, but some collided with these few i do use.  

Some plugins iexplicably use keybindings that are assigned to other functions by default, and it is not always apparently what key bindings may be used.  <F1> may display a help screen, which may be filtered.  Filtering rocks.  Bookmarks rock.

 

2025 May 19