31.0.50; Org Persist file formatting

31.0.50; Org Persist file formatting

[Michael Mauger]

This bug has been difficult to reproduce but several people have
encountered it, or symptoms of it. Most recently, there has been this
thread on Reddit:
https://www.reddit.com/r/emacs/comments/1drxsz6/tangled_0_code_blocks_from_filename_problem/

Unfortunately, replicating on emacs -Q has proven impossible since -Q
disables some of the implicated features. My Emacs config is contained 
in Org Babel files that are invoked with `org-babel-tangle-file' and have
demonstrated the error multiple times.

After some poking around I started getting failure when I tried to
reopen an Org file or ran `normal-mode' on it. Shutting down emacs and
restarting cleared the issue. When the issue arose when reopening the
file within a session, the backtrace was pointing to `plistp' failing in
`org-persist-read'. When I looked at the persist index there were
entries like:

     (:container
      ((elisp org-element--headline-cache) (elisp org-element--cache)
       (version "2.3"))
      :persist-file "49/605653-361a-49a4-a000-47db8d522096" :associated
      (:hash "aa1176747642fdac45aaf96095a88367" :file
    	 "/home/michael/Projects/my-config/emacs/my-org.org" :inode
    	 2554490)
      :expiry 30 :last-access 1719791738.4428508 :last-access-hr
      "2024-06-30T19:55:38-0400" ...)

(Note: the "..." in the last entry; sometimes it showed up as "\...".)

The failure during tangling occurred with `org-get-heading' expecting
`stringp' but getting `nil'. That seemed to be tracked down to
`org-complex-heading-regexp' not being set yet. If an error had aborted
out of the `org-persist-read' it appears we could have half of org-mode
up but not everything properly initialized.

Looking at the code in `org-persist.el' in
`org-persist--write-elisp-file (file data &optional no-circular pp)'
around line 486 it handles calling `pp' or `prin1'. The code for `pp'
uses `pp-use-max-width' (as part of a bug fix #58687) which has since
been superseded in Emacs 30.

It looks like the `org-persist-write' code ought to be updated and the
`org-persist-read' code made more robust so that it does not just shut
down processing of Org files entirely. That is if the entry is not a
plist, act as though no entry exists and proceed as if it were a new
org file. 

By deleting the persist index file, the calls to `org-babel-tangle-file'
succeed and I proceed without error. If an entry in the persist index
has the elided entries, then the tangling fails.

I'm not entirely sure that this is the recipe but I have seen some 
weirdness around the `org-persist' feature but fixes other than deleting
persistent storage seem to be inconsistent.

Please feel free to reach out if you'd like me to verify or try some other 
recipe.

In GNU Emacs 31.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version
 3.24.42, cairo version 1.18.0) of 2024-06-29 built on michael-laptop
Repository revision: fcd6403d8ebf7ce6e61ba17971d4fdaaaaecf06c
Repository branch: master
System Description: Fedora Linux 40 (Workstation Edition)
Package: Org mode version 9.7.5 (release_9.7.5-9-ga091ca @ /usr/local/share/emacs/31.0.50/lisp/org/)

Configured using:
 'configure --with-pgtk --with-native-compilation
 --with-file-notification=yes --with-wide-int --with-tree-sitter
 --with-mailutils 'CFLAGS= -O0 -g''

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-- 
MICHAEL@MAUGER.COM // FSF and SFConservancy member // GNU Emacs sql.el maintainer

Re: 31.0.50; Org Persist file formatting

[Ihor Radchenko]

Michael Mauger <michael.mauger@protonmail.com> writes:

> This bug has been difficult to reproduce but several people have
> encountered it, or symptoms of it. Most recently, there has been this
> thread on Reddit:
> https://www.reddit.com/r/emacs/comments/1drxsz6/tangled_0_code_blocks_from_filename_problem/
>
> Unfortunately, replicating on emacs -Q has proven impossible since -Q
> disables some of the implicated features. My Emacs config is contained 
> in Org Babel files that are invoked with `org-babel-tangle-file' and have
> demonstrated the error multiple times.

Thanks for reporting!

> After some poking around I started getting failure when I tried to
> reopen an Org file or ran `normal-mode' on it. Shutting down emacs and
> restarting cleared the issue. When the issue arose when reopening the
> file within a session, the backtrace was pointing to `plistp' failing in
> `org-persist-read'. When I looked at the persist index there were
> entries like:
>
>      (:container
>       ((elisp org-element--headline-cache) (elisp org-element--cache)
>        (version "2.3"))
>       :persist-file "49/605653-361a-49a4-a000-47db8d522096" :associated
>       (:hash "aa1176747642fdac45aaf96095a88367" :file
>     	 "/home/michael/Projects/my-config/emacs/my-org.org" :inode
>     	 2554490)
>       :expiry 30 :last-access 1719791738.4428508 :last-access-hr
>       "2024-06-30T19:55:38-0400" ...)
>
> (Note: the "..." in the last entry; sometimes it showed up as "\...".)

This is curious. May it be that you have non-default value of
`pp-default-function'?

> The failure during tangling occurred with `org-get-heading' expecting
> `stringp' but getting `nil'. That seemed to be tracked down to
> `org-complex-heading-regexp' not being set yet. If an error had aborted
> out of the `org-persist-read' it appears we could have half of org-mode
> up but not everything properly initialized.

Sounds right.

> Looking at the code in `org-persist.el' in
> `org-persist--write-elisp-file (file data &optional no-circular pp)'
> around line 486 it handles calling `pp' or `prin1'. The code for `pp'
> uses `pp-use-max-width' (as part of a bug fix #58687) which has since
> been superseded in Emacs 30.

Yes, it should be fixed. I did not know that they quickly obsoleted that
variable.

> It looks like the `org-persist-write' code ought to be updated and the
> `org-persist-read' code made more robust so that it does not just shut
> down processing of Org files entirely. That is if the entry is not a
> plist, act as though no entry exists and proceed as if it were a new
> org file. 

Yes. The case when the contents of index file is a valid Elisp data, but
not the data we expect is currently not covered. It should be.

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: 31.0.50; Org Persist file formatting

[Michael Mauger]

On Monday, July 8th, 2024 at 11:45 AM, Ihor Radchenko <yantar92@posteo.net> wrote:

> Michael Mauger michael.mauger@protonmail.com writes:
> 
> > This bug has been difficult to reproduce but several people have
> > encountered it, or symptoms of it. Most recently, there has been this
> > thread on Reddit:
> > https://www.reddit.com/r/emacs/comments/1drxsz6/tangled_0_code_blocks_from_filename_problem/
> > 

Just encountered it again. :( The recipe is still not obvious but I'm trying to find one... 
(This time got the "\..." version)

> > After some poking around I started getting failure when I tried to
> > reopen an Org file or ran `normal-mode' on it. Shutting down emacs 
> > and restarting cleared the issue. When the issue arose when reopening 
> > the file within a session, the backtrace was pointing to` plistp' failing in
> > `org-persist-read'. When I looked at the persist index there were
> > entries like:
> > 
> > (:container
> > ((elisp org-element--headline-cache) (elisp org-element--cache)
> > (version "2.3"))
> > :persist-file "49/605653-361a-49a4-a000-47db8d522096" :associated
> > (:hash "aa1176747642fdac45aaf96095a88367" :file
> > "/home/michael/Projects/my-config/emacs/my-org.org" :inode
> > 2554490)
> > :expiry 30 :last-access 1719791738.4428508 :last-access-hr
> > "2024-06-30T19:55:38-0400" ...)
> > 
> > (Note: the "..." in the last entry; sometimes it showed up as "\...".)
> 
> 
> This is curious. May it be that you have non-default value of
> `pp-default-function'?
> 

I don't touch `pp-default-function' and I've confirmed that it is 
set to `pp-fill' in my instance.

> --
> Ihor Radchenko // yantar92,
> Org mode contributor,

Thanks for your attention.

Re: 31.0.50; Org Persist file formatting

[Ihor Radchenko]

Michael Mauger <michael.mauger@protonmail.com> writes:

>> > (Note: the "..." in the last entry; sometimes it showed up as "\...".)
>> 
>> 
>> This is curious. May it be that you have non-default value of
>> `pp-default-function'?
>> 
>
> I don't touch `pp-default-function' and I've confirmed that it is 
> set to `pp-fill' in my instance.

Then, what if you re-define `org-persist-write:index' to

(defun org-persist-write:index (container _)
  "Write index CONTAINER."
  (org-persist--get-collection container)
  (unless (file-exists-p org-persist-directory)
    (condition-case nil
        (make-directory org-persist-directory 'parent)
      (t
       (warn "Failed to create org-persist storage in %s."
             org-persist-directory)
       (org-persist--check-write-access org-persist-directory))))
  (when (file-exists-p org-persist-directory)
    (let ((index-file
           (org-file-name-concat org-persist-directory org-persist-index-file)))
      (org-persist--merge-index-with-disk)
      ;; CHANGED: disable pretty-printing
      (org-persist--write-elisp-file index-file org-persist--index t nil)
      (setq org-persist--index-age
            (file-attribute-modification-time (file-attributes index-file)))
      index-file)))

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: 31.0.50; Org Persist file formatting

[Michael Mauger]

Sorry for not getting back to you sooner. This change has seemed to work, but I haven't been playing with my Org Babel config much lately. I'll let you know if I see it again.

Thanks for your help.

--
MICHAEL@MAUGER.COM // FSF and SFConservancy member // GNU Emacs sql.el maintainer


On Monday, July 8th, 2024 at 1:39 PM, Ihor Radchenko <yantar92@posteo.net> wrote:

> Michael Mauger michael.mauger@protonmail.com writes:
> 
> > > > (Note: the "..." in the last entry; sometimes it showed up as "\...".)
> > > 
> > > This is curious. May it be that you have non-default value of
> > > `pp-default-function'?
> > 
> > I don't touch `pp-default-function' and I've confirmed that it is set to` pp-fill' in my instance.
> 
> 
> Then, what if you re-define `org-persist-write:index' to
> 
> (defun org-persist-write:index (container _)
> "Write index CONTAINER."
> (org-persist--get-collection container)
> (unless (file-exists-p org-persist-directory)
> (condition-case nil
> (make-directory org-persist-directory 'parent)
> (t
> (warn "Failed to create org-persist storage in %s."
> org-persist-directory)
> (org-persist--check-write-access org-persist-directory))))
> (when (file-exists-p org-persist-directory)
> (let ((index-file
> (org-file-name-concat org-persist-directory org-persist-index-file)))
> (org-persist--merge-index-with-disk)
> ;; CHANGED: disable pretty-printing
> (org-persist--write-elisp-file index-file org-persist--index t nil)
> (setq org-persist--index-age
> (file-attribute-modification-time (file-attributes index-file)))
> index-file)))
> 
> --
> Ihor Radchenko // yantar92,
> Org mode contributor,
> Learn more about Org mode at https://orgmode.org/.
> 
> Support Org development at https://liberapay.com/org-mode,
> 
> or support my work at https://liberapay.com/yantar92

Re: 31.0.50; Org Persist file formatting

[Ihor Radchenko]

Michael Mauger <michael.mauger@protonmail.com> writes:

> Sorry for not getting back to you sooner. This change has seemed to work, but I haven't been playing with my Org Babel config much lately. I'll let you know if I see it again.

FYI, we have disabled pretty printing for performance reasons. So, the
suggested change you may be testing is already included in Org 9.7.10
https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?h=bugfix&id=f9351456e70ad08dea74525e4a7d4bd29f98176d

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: 31.0.50; Org Persist file formatting

[Michael Mauger]

On Sunday, August 25th, 2024 at 3:31 AM, Ihor Radchenko <yantar92@posteo.net> wrote:

> Michael Mauger michael.mauger@protonmail.com writes:
> 
> > Sorry for not getting back to you sooner. This change has seemed to work, but I haven't been playing with my Org Babel config much lately. I'll let you know if I see it again.
> 
> 
> FYI, we have disabled pretty printing for performance reasons. So, the
> suggested change you may be testing is already included in Org 9.7.10
> https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?h=bugfix&id=f9351456e70ad08dea74525e4a7d4bd29f98176d
> 

Bad news :(  I do not have a reproducible set of steps, but I'll start looking for one. I am not using the fix you sent and am using the latest master of Emacs 30.0.50 and Org 9.7.10

My init is a set of Org Babel scripts (4.5K org lines; 2.8K el lines) which is the latest incarnation of 30+ years of Emacs. Since this problem started, I start Emacs by first removing the org-persist files and the .el files, so that all the babel code is tangled. After a bunch of debugging and edits to the org files, I saved and went to start Emacs again with a clean slate.

Unfortunately, the `index.eld' file had the following (note the "..." in the file contents):

    ((:container ((elisp org-element--headline-cache) (elisp org-element--cache) (version "2.3")) :persist-file "ad/c72d74-f821-4190-97c8-41feb7dc8128" :associated (:hash "a82d8fdcbf03df59c72ca1df20680b3a" :file "/home/michael/Projects/my-config/emacs/my-config.org" :inode 2975404) :expiry 30 :last-access 1724901536.6903014 ...) (:container ((elisp org-element--headline-cache) (elisp org-element--cache) (version "2.3")) :persist-file "a6/436395-1c62-4060-8afc-53893e044fd9" :associated (:hash "8a94101fb7eb8f1f6b6a4ba89f5405e3" :file "/home/michael/Projects/my-config/emacs/my-location.org" :inode 2974753) :expiry 30 :last-access 1724809178.237551 ...) (:container ((elisp org-element--headline-cache) (elisp org-element--cache) (version "2.3")) :persist-file "00/1fd972-5079-4495-ab04-88db0f0a0e6c" :associated (:hash "feb07f13f10cab551dc03089e1919594" :file "/home/michael/Projects/my-config/emacs/my-eshell.org" :inode 2979957) :expiry 30 :last-access 1724805634.696495 ...) (:container ((elisp org-element--headline-cache) (elisp org-element--cache) (version "2.3")) :persist-file "be/57de97-a696-43b4-964c-d9817a54ba0f" :associated (:hash "981e2ee1ce9a79044fe39e31e865ff78" :file "/home/michael/Projects/my-config/emacs/my-org.org" :inode 2974714) :expiry 30 :last-access 1724805423.0839553 ...) (:container ((elisp org-element--headline-cache) (elisp org-element--cache) (version "2.3")) :persist-file "be/052624-e6cf-4034-b29a-dd0d589fec21" :associated (:hash "c9f58d9d1fd1f7f289d35af18aadcbd8" :file "/home/michael/Projects/my-config/emacs/my-library-of-babel.org" :inode 2974478) :expiry 30 :last-access 1724805419.3735616 ...) (:container ((index "3.2")) :persist-file "63/45cf0a-1428-489e-b247-a4e501140c2c" :associated nil :expiry never :last-access 1724908792.4755692 ...))

So it was the process of editing the SRC blocks and executing the elisp code to test that resulted in the bad persist file. I'm thinking I may add some code to see if the elisp variable is corrupt or it's just happening on output. My sense is this may be a core bug but I'll see what I can find.

> --
> Ihor Radchenko // yantar92,
> Org mode contributor,

Re: 31.0.50; Org Persist file formatting

[Ihor Radchenko]

Michael Mauger <michael.mauger@protonmail.com> writes:

> Bad news :(  I do not have a reproducible set of steps, but I'll start looking for one. I am not using the fix you sent and am using the latest master of Emacs 30.0.50 and Org 9.7.10
>
> My init is a set of Org Babel scripts (4.5K org lines; 2.8K el lines) which is the latest incarnation of 30+ years of Emacs. Since this problem started, I start Emacs by first removing the org-persist files and the .el files, so that all the babel code is tangled. After a bunch of debugging and edits to the org files, I saved and went to start Emacs again with a clean slate.
>
> Unfortunately, the `index.eld' file had the following (note the "..." in the file contents):
> ...
> So it was the process of editing the SRC blocks and executing the elisp code to test that resulted in the bad persist file. I'm thinking I may add some code to see if the elisp variable is corrupt or it's just happening on output. My sense is this may be a core bug but I'll see what I can find.

Maybe something is setting `print-level' per-buffer?

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: 31.0.50; Org Persist file formatting

[Michael Mauger]

-------- Original Message --------
On 8/31/24 10:43 AM, Ihor Radchenko <yantar92@posteo.net> wrote:

>  Michael Mauger <michael.mauger@protonmail.com> writes:
>  
>  > Bad news :(  I do not have a reproducible set of steps, but I'll start looking for one. I am not using the fix you sent and am using the latest master of Emacs 30.0.50 and Org 9.7.10

>  Maybe something is setting `print-level' per-buffer?
>  

(Don't have access rn; Holiday weekend here…) 

I will check but I don't set `print-level' anywhere in my code and it's `let' bound in the org-persist code. I'll do some digging on where things go bad when I get home. My gut feeling is that the damage is done elsewhere and doesn't manifest itself until it's persisted.

>  --
>  Ihor Radchenko // yantar92,
>  Org mode contributor,
>  Learn more about Org mode at <https://orgmode.org/>.
>  Support Org development at <https://liberapay.com/org-mode>,
>  or support my work at <https://liberapay.com/yantar92>
>