Friday, July 25, 2025

Tangled in Entangle: resignation to flatpak

Entangle is a wonderful program, an elegant tool---elegant in the sense of efficiency and design for function.   Daniel BerrangĂ©  has written other uncommonly interesting  software as well.  This tool, which I run on GNU/Linux, flawlessly connects to my Canon DSLR cameras; I use it primarily for photomicrography.  What it lacks is documentation.  The GUI is not super shiny, but adequate.  

I have taken Entangle for granted for many years; it has installed easily on GNU/Linux Arch-based systems---via the AUR repository---and also on Ubuntu, as I recently learned.  However, for several months it has been a struggle.  On Manjaro GNU/Linux, my goto distribution for over a decade, building has been impossible, for me.  Because Entangle is so important to me, I moved to EndeavourOS, a distribution that otherwise is not my favorite; Entangle did build fine on EndeavourOS, however.  But recently, other issues plagued my EndeavourOS experience, initiating a devastating avalanche: my desperate flailings led to the loss of a 600GB partition, that had not been backed up except in some bits and pieces, with decades worth of work, now completely unrecoverable.  

Monofilament fishing line sucks.  Google's AI suggest some terms for  snarls of monofilament on a reel: backlash, bird's nest, webbing, or wind knot.  I have forgotten the more colorful term I knew long ago---explosion?  I had to cut the mono off of the reel.  (I no longer fish, out of concern for the health of the ocean, and overfishing).  This week's avalanche is another lesson, because the entire journey was unnecessary, had I but taken heed of the notice on the web page of Entangle: flatpak is the method of choice for installing Entangle:

 



At least I can now report that I am back to Manjaro.  Each of the other distros had other shortcomings; so does Manjaro, but in the main, it is most comfortable.
 

EndeavourOS

As a firmly committed user of the tiling i3wm, this distribution is clearly out of bounds.  I3 has been over-riced and the keybindings are out of sync with any others I have seen.  As one reviewer remarked, Endeavour''s setup seems more like a single user's custom setup than to reflect any functional vision.  I love it uses Archlinux's upstream repos (this is the most serious issue I have with Manjaro).  I can tweak it to my satisfaction, but the theming is garish and overdone.
 
Later this week, I attempted to install EndeavourOS again.  But the web site is down, and I was unable to download the install image any longer, or find the wiki or forum.  I think this is the death  knell for EndeavourOS.  It "couldn't have happened to a nicer distro," but it's sad that the reason turned out to be inability to pay hosting fees.  
 
Don't get me started about Capitalism. 
 

CachyOS

On Distrowatch CachyOS---a newer Arch-based distro---has snuck into first place, quick swiftly.  Reviews are quite positive.  The vision is amazing; a breath of fresh air.   I took the bait, and grabbed an iso.  The installation went well, or so I thought.  I even let out a joyous laugh, while installing it.  (Someday, this will be my fave.)  This is the ultimate functional distribution, even including a stress testing facility on the installation medium.  But when I booted the installed setup... crickets.  Black, blank screens.  After too much sleuthing---this past week has been all about too much sleuthing, no working---I found a plethora of complaints about this issue, on Nvidia GPUs.  The issue for me, as it took days to figure out, is that the GTX 1050 of mine is no longer supported by Nvidia; but it works on all other distros.  CachyOS has favored a newer open source driver (which I'm all about, but this new open source driver is not Neuveau.  It's apparently an officially sanctioned open source driver, but older hardware is still closed source, so are not supported.  
 
Curiously, once, after I yanked the HDMI cable to one of my monitors, test output appeared on the other monitor, connected by display port.  I noted a single mention, during my sleuthing, of the issue with HDMI.  
 
For now, this is the GPU I have  So no more CachyOS.  Too bad.  It was a real thrill to install something so fresh and cool.  I tried Manjaro again, but no luck with Entangle---and the module/drivers for my USB Wifi Dongle was not included with the 6.12 kernels, so I tried something new.  Or old.  The hard way. 
 
 

The Semi-Hard Way: Installing Archlinux

All of these "Arch-based" distros are fed by Archlinux itself.  I have installed Arch a bunch of times; and used various short-cut scripts and (of course) the arch-based easy way distros, like Manjaro, Antergos, and others.  I have done it enough times, the hard way.  On the forums, developers of Arch make much ado about the need to install the hard way as a way to learn GNU/Linux; but enough is enough.  The General Purpose Computer is a tool; I want to understand this tool, sure, but that is not my raison d' etre.   
 
Anyway, at this point in the trip down the abyss, I thought, well, why not go ahead and reach for the progenitor of these others, settle down, and bite the bullet.  I used the "somewhat hard" way.
 
Arch's installation iso images now include a script called Archinstall (or so), that is intended to make it easier to install.  I experienced a disaster of untellable proportions while using this script.  I had forgotten this, but some years ago, apparently, I had attempted to use the script, and had been stymied by the disk partitioning module.  Once something has been typed in to the widgets, indicating mount points, it is difficult, or sometimes impossible, to back out of it.  In this instance, I encountered other problems with the partitioning component of this script: I had mostly figured out the correct paritioning scheme, and eventually had them all in place, but once I had typed something into the wrong partition, it was impossible to back out, so I typed "/extra".  Who knows whether that affected our issue. 
 
The notice escaped me during the process that the partitions that were selected for the install would be wiped.   Somehow, it occurs to me that this notice should not be a subtle one.  I cannot think of another distro's install that does not take extra care to explain the consequences of similar actions.  
 
Not only that, there is a button, not clearly defined or marked, for each partition defined, to change the formatting status (ie, format as opposed to keep).  It is not only poorly marked: when I tried to install again using this script, it was clear that this button only switches to "format" and does not seem to convert back to a "keep" state.  The wording was difficult to understand, for me.  This, I think, is a bug.
 
Immediately after I clicked "install"  I saw the words "partition deleted"; I killed the install at this point.  Once I had taken a look at the system, using gparted, it was clear that this partition had been deleted and wiped.  Nothing I could do could possibly recover my data.  This only reinforces my sense that this script reflects a disdain for the user, so, arguable, it is a bug.
 
At this point I decided  to install Ubuntu.  I have had several problems with Ubuntu in the past.  Installs that led to blank screens on laptops.  But it's been some time.
 

Ubuntu

Ubuntu installed nicely.  It was a breath of fresh air.  But it's tedious to maintain and set up.  Many of the packages I install routinely on Manjaro are difficult on Ubuntu.  Entangle did install nicely.  
 

Final Chapters

At this point, perhaps four days into this waste of time, it occurred to me that maybe a binary package was available on the Manjaro web site.  What I found was the notice, above, that the canonical way of installation would be flatpak.  
 
Back to Manjaro.  What's to complain about?  It worked.
 

In Praise of Manjaro

 The issue with Entangle was a mirage; it does work, but requires installation as a flatpak.  I don't like this; hopefully in the future a new version will be released (it's been a long while) that will compile on today's systems.  But I can think of few or no issues over at least 15 years since I started using Manjaro.  
 
One think points to a high level of knowledge among the developers of Manjaro.  I have made it a habit to keep a separate /home directory and even /usr/local---for self-compiled software---so that if an issue does creep in, a quick installation of Manjaro to a different root partition will solve the problem.  Grub uses os-prober to locate other installed GNU/Linux sets on the same machine, and configure the grub startup screen to offer choices.  Only in Manjaro, once I have chosen a different partition to start up, does Grub remember.  This is not a unique deal; Grub makes this possible with a simple configuration tweak.   But this points to a level of attention to detail that is lacking elsewhere.
 
I might also mention i3wm.  I have a 2014 Thinkpad that still is a bit spunky, when not held back by an excessive amount of overhead from, say, KDE, Gnome, or even XFCE4.  It's a big deal.  My desktop is getting along in years as well; I think without i3 (or some other super lightweight window manager) I would have felt bogged down.  Not only that, i3wm is functional.  All of the ricing, all of the beautiful desktop tweaks and wallpapers, cannot compete with the beauty of a smoothly functioning machine. Also, i3wm is easy to configure, and some experts have provided great tweaks.  I have configured popups for R, emacs, kitty (terminal), and other tools.  Wonderful.
 
Manjaro, as an Arch-derivative, comes configured to take advantage of the AUR: Arch User Repository.  Using the tool "yay" (replacement for pacman), there are few packages that are not installable out of the box.   AUR packages compile programs from source, downloaded from git.  This is consistent with my inclination toward using programs in the manner in which they were written; Debian and Ubuntu, for example, provide patches for almost every package that alters the software in various---usually innocuous---ways.  
 
And Manjaro comes, out of the box, with development tools installed, so that for many programs, compiling from source is accomodated.  
 
I am pleased that I can now run Entangle, even if I must (drat!) resort to a flatpak.
 
One thing I do not like about Manjaro: the "repostories" lag behind those of Archlinux, the canonical upstream source repository, in the supposed name of security.  I like to run either the Testing or Unstable branch of Manjaro (I think one of them may not longer be supported), which is one step more up-to-date with Arch.  I blamed this for Entangle not compiling, but it appears I was mistaken.  
 
 

  

Saturday, July 12, 2025

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.
  •  

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 Architec...