bug#59722: 30.0.50; project-find-regexp searches project-ignored files

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Rudolf Adamkovič via Bug reports for GNU Emacs, the Swiss army knife of text editors]

I have the following `project.el' configuration:

  (setq xref-search-program 'ripgrep)

and the following `.dir-locals.el' file in a project:

  ((nil . ((project-ignores . ("apps/**/*.scm")))))

As expected, e.g. `project-find-file' ignores all `.scm' files in the
`apps' subdirectory of the project, however `project-find-regexp' does
not ignore them.  TL;DR,

Expected:

  `project-find-regexp' honors `project-ignores'

Rudy


In GNU Emacs 30.0.50 (build 2, aarch64-apple-darwin22.1.0, NS
 appkit-2299.00 Version 13.0.1 (Build 22A400)) of 2022-11-30 built on
 Rudolfs-MacBook-Air.local
Repository revision: 7939184f8e0370e7a3397d492812c6d202c2a193
Repository branch: master
Windowing system distributor 'Apple', version 10.3.2299
System Description:  macOS 13.0.1

Configured using:
 'configure --with-json --with-tree-sitter'

Configured features:
ACL GLIB GNUTLS JSON LCMS2 LIBXML2 MODULES NOTIFY KQUEUE NS PDUMPER PNG
RSVG SQLITE3 THREADS TOOLKIT_SCROLL_BARS TREE_SITTER WEBP XIM ZLIB

Important settings:
  value of $LC_ALL: en_US.UTF-8
  locale-coding-system: utf-8-unix

Major mode: Org

Minor modes in effect:
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  flyspell-mode: t
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  line-number-mode: t
  transient-mark-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t

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Features:
(shadow sort notmuch notmuch-tree notmuch-jump notmuch-hello
notmuch-show notmuch-print notmuch-crypto notmuch-mua notmuch-message
notmuch-draft notmuch-maildir-fcc notmuch-address notmuch-company
notmuch-parser notmuch-wash coolj icalendar diary-lib diary-loaddefs
notmuch-tag notmuch-lib notmuch-version notmuch-compat mail-extr
emacsbug sh-script treesit executable ruby-mode smie ebnf-mode pulse
color misearch multi-isearch hl-line grep cape geiser-mode geiser-xref
geiser-compile geiser-guile info-look transient geiser-debug geiser-repl
geiser-image geiser-capf geiser-doc geiser-menu geiser-autodoc
geiser-edit geiser-completion geiser-eval geiser-connection tq
geiser-syntax geiser-log geiser-popup view scheme vc-hg vc-bzr vc-src
vc-sccs vc-svn vc-cvs vc-rcs log-view pcvs-util char-fold orderless rect
cursor-sensor imenu ess-r-mode ess-r-flymake ess-r-xref ess-trns
ess-r-package ess-r-completion ess-roxy ess-r-syntax ess-rd hideshow
ess-s-lang ess-help ess-mode ess-inf ess-tracebug tramp tramp-loaddefs
trampver tramp-integration files-x tramp-compat ess ess-utils ess-custom
citar-org oc-basic citar citar-file citar-cache citar-format preview
reftex-dcr reftex reftex-loaddefs reftex-vars font-latex latex
latex-flymake tex-ispell tex-style tex crm texmathp tex-mode vc-git
diff-mode tempo image-file image-converter disp-table ol-eww eww
url-queue mm-url ol-rmail ol-mhe ol-irc ol-info ol-gnus nnselect
gnus-art mm-uu mml2015 mm-view mml-smime smime gnutls dig gnus-sum shr
pixel-fill kinsoku url-file svg dom gnus-group gnus-undo gnus-start
gnus-dbus dbus xml gnus-cloud nnimap nnmail mail-source utf7 nnoo
gnus-spec gnus-int gnus-range message sendmail yank-media puny rfc822
mml mml-sec epa epg rfc6068 epg-config mm-decode mm-bodies mm-encode
mail-parse rfc2231 rfc2047 rfc2045 ietf-drums mailabbrev gmm-utils
mailheader gnus-win gnus nnheader gnus-util mail-utils range mm-util
mail-prsvr ol-docview doc-view image-mode exif cus-start ls-lisp dired
dired-loaddefs ol-bbdb ol-w3m ol-doi org-link-doi paredit edmacro kmacro
flyspell ispell flimenu hl-todo compat compat-macs modus-operandi-theme
modus-themes pdf-loader package-vc vc vc-dispatcher lisp-mnt finder-inf
ox-texinfo ox-md oc-csl citeproc citeproc-itemgetters citeproc-biblatex
parse-time citeproc-bibtex parsebib ol-bibtex citeproc-cite
citeproc-subbibs citeproc-sort citeproc-name citeproc-formatters
citeproc-number rst citeproc-proc citeproc-disamb citeproc-itemdata
citeproc-generic-elements citeproc-macro citeproc-choose citeproc-date
citeproc-context citeproc-prange citeproc-style citeproc-locale
citeproc-term f f-shortdoc shortdoc citeproc-rt citeproc-lib citeproc-s
s let-alist queue dash bibtex iso8601 ox-odt rng-loc rng-uri rng-parse
rng-match rng-dt rng-util rng-pttrn nxml-parse nxml-ns nxml-enc xmltok
nxml-util ox-latex ox-icalendar org-habit org-agenda ox-html table
ox-ascii ox-publish ox org-element org-persist xdg org-id org-refile
avl-tree org-clock ob-lisp ob-makefile ob-latex ob-scheme geiser ob-dot
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-- 
"'Contrariwise,' continued Tweedledee, 'if it was so, it might be; and
if it were so, it would be; but as it isn't, it ain't.  That's logic.'"
-- Lewis Carroll, Through the Looking Glass, 1871/1872

Rudolf Adamkovič <salutis@me.com> [he/him]
Studenohorská 25
84103 Bratislava
Slovakia

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Dmitry Gutov]

On 30/11/2022 16:35, Rudolf Adamkovič via Bug reports for GNU Emacs, the 
Swiss army knife of text editors wrote:
> 
> I have the following `project.el' configuration:
> 
>    (setq xref-search-program 'ripgrep)
> 
> and the following `.dir-locals.el' file in a project:
> 
>    ((nil . ((project-ignores . ("apps/**/*.scm")))))
> 
> As expected, e.g. `project-find-file' ignores all `.scm' files in the
> `apps' subdirectory of the project, however `project-find-regexp' does
> not ignore them.  TL;DR,
> 
> Expected:
> 
>    `project-find-regexp' honors `project-ignores'

Hi! 'project-ignores' is not a variable, it's a generic function.

What backend are you using? If it's (most likely) project-vc, then the 
variable you must be looking for is 'project-vc-ignores'.

To answer the "what backend" question, you can evaluate (project-current).

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Rudolf Adamkovič via Bug reports for GNU Emacs, the Swiss army knife of text editors]

Dmitry Gutov <dgutov@yandex.ru> writes:

> Hi! 'project-ignores' is not a variable, it's a generic function.

Oops!  Correct.

> What backend are you using? If it's (most likely) project-vc, then the
> variable you must be looking for is 'project-vc-ignores'.

I do use the Git (VC) backend.  Correction:

When I set the dir locals file to

    ((nil . ((project-vc-ignores . ("apps/**/*.scm")))))

I face the problem where C-x p f ignores the files in the "apps"
directory, as expected, but C-x p g does not.

[The "apps" directory in question contains symbolic links that make
Ripgrep, invoked via C-x p g, see various files multiple times,
resulting in what looks like "chaos".]

I apologize for the confusion!

Rudy
-- 
"The introduction of suitable abstractions is our only mental aid to
organize and master complexity."
-- Edsger Wybe Dijkstra, 1930-2002

Rudolf Adamkovič <salutis@me.com> [he/him]
Studenohorská 25
84103 Bratislava
Slovakia

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Dmitry Gutov]

On 01/12/2022 01:20, Rudolf Adamkovič via Bug reports for GNU Emacs, the 
Swiss army knife of text editors wrote:

>> What backend are you using? If it's (most likely) project-vc, then the
>> variable you must be looking for is 'project-vc-ignores'.
> 
> I do use the Git (VC) backend.  Correction:
> 
> When I set the dir locals file to
> 
>      ((nil . ((project-vc-ignores . ("apps/**/*.scm")))))
> 
> I face the problem where C-x p f ignores the files in the "apps"
> directory, as expected, but C-x p g does not.

Okay.

I wonder how that could be possible: project-find-regexp (that if what 
you have 'C-x p g' bound to, right?) does the search across the files 
returned by 'project-files'. So there is just one place that interprets 
the ignores' list and produces the list of files, and both 
project-find-file and project-find-regexp consume the result.

Can you step through 'project-find-regexp' with edebug? Does the return 
value of 'project-files' (saved to 'files') contain the extra entries?

Or are you calling 'project-find-regexp' with a prefix, which switches 
it to a different mode (the 'project--files-in-directory' branch)?

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Rudolf Adamkovič via Bug reports for GNU Emacs, the Swiss army knife of text editors]

Dmitry Gutov <dgutov@yandex.ru> writes:

> Okay.

Thank you for your time, Dmitry!

> I wonder how that could be possible: project-find-regexp (that if what
> you have 'C-x p g' bound to, right?) does the search across the files
> returned by 'project-files'. So there is just one place that
> interprets the ignores' list and produces the list of files, and both
> project-find-file and project-find-regexp consume the result.

I provide a hypothesis about how that could happen below.

> Can you step through 'project-find-regexp' with edebug? Does the
> return value of 'project-files' (saved to 'files') contain the extra
> entries?

So, I debugged the problem.

FINDING 1:

The first finding may explain why I see the ignored files in C-x p g.

For my dir-local ignore pattern

  ((nil . ((project-ignores . ("apps/**/*.scm")))))

Emacs ends up calling

  git ls-files -z -c --exclude-standard \
    --no-empty-directory -o -- :(exclude,glob,top)apps/**/*.scm

which gives a listing that DOES NOT contain (as expected) any '*.scm'
files in the 'apps' directory, such as

  apps/lib-app-core/src/main/assets/app/atrium.scm
  apps/lib-app-core/src/main/assets/app/database.scm
  ...

but it still DOES contain "logically empty" parent directories (as not
expected, perhaps) that would have contained the ignored files if not
ignored, such as

  apps/lib-app-core/src/main/assets/app

My interpretation:

git ls-files does not output just files, as one would expect, but also
directories with no matching files.  grep then gets a list of files and
possibly also directories, and searches through it all.

FINDING 2:

Given the configuration

  (setq project-switch-use-entire-map t
        project-switch-commands '((nil "C-x p")))

when I type

  C-x p p <...project...> g

then Emacs uses the global project ignores and not the ones defined in
the directory-local file.  However,

  C-x p g

inside of any project buffer works OK.

Notes:

While probably not the root cause, this bug made debugging much harder,
until I realized it exists, so I report this finding as well.

Rudy
-- 
"One can begin to reason only when a clear picture has been formed in
the imagination."
-- Walter Warwick Sawyer, Mathematician's Delight, 1943

Rudolf Adamkovič <salutis@me.com> [he/him]
Studenohorská 25
84103 Bratislava
Slovakia

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Dmitry Gutov]

On 05/12/2022 01:36, Rudolf Adamkovič via Bug reports for GNU Emacs, the 
Swiss army knife of text editors wrote:

>> Can you step through 'project-find-regexp' with edebug? Does the
>> return value of 'project-files' (saved to 'files') contain the extra
>> entries?
> 
> So, I debugged the problem.

Thanks!

> FINDING 1:
> 
> The first finding may explain why I see the ignored files in C-x p g.
> 
> For my dir-local ignore pattern
> 
>    ((nil . ((project-ignores . ("apps/**/*.scm")))))

project-vc-ignores, you mean.

> Emacs ends up calling
> 
>    git ls-files -z -c --exclude-standard \
>      --no-empty-directory -o -- :(exclude,glob,top)apps/**/*.scm
> 
> which gives a listing that DOES NOT contain (as expected) any '*.scm'
> files in the 'apps' directory, such as
> 
>    apps/lib-app-core/src/main/assets/app/atrium.scm
>    apps/lib-app-core/src/main/assets/app/database.scm
>    ...
> 
> but it still DOES contain "logically empty" parent directories (as not
> expected, perhaps) that would have contained the ignored files if not
> ignored, such as
> 
>    apps/lib-app-core/src/main/assets/app

Huh, interesting. Could you try to show a similar command invocation 
which would make Git output include a "logically empty" directory for 
the Emacs repo? So that we have a common public project to compare.

Or alternatively a project-vc-ignores value which, when put in 
.dir-locals.el at the top, produces such effect on the return value of 
(project-files (project-current)).

As a counter-example, if I add

   (project-vc-ignores . ("./doc/emacs/*"))

there, 'project-files' does not include 'doc/emacs/' at all. Not files 
in it, not it separately as a directory.

> My interpretation:
> 
> git ls-files does not output just files, as one would expect, but also
> directories with no matching files.  grep then gets a list of files and
> possibly also directories, and searches through it all.

That would make sense, if it's indeed what happens. Perhaps it's a bug 
in our code, or this behavior is specific to certain versions of Git.

I currently have Git 2.37.2 installed.

> FINDING 2:
> 
> Given the configuration
> 
>    (setq project-switch-use-entire-map t
>          project-switch-commands '((nil "C-x p")))
> 
> when I type
> 
>    C-x p p <...project...> g
> 
> then Emacs uses the global project ignores and not the ones defined in
> the directory-local file.  However,
> 
>    C-x p g
> 
> inside of any project buffer works OK.

And that one is probably a regression from 2389158a31b4a.

It won't revert cleanly now, unfortunately. Here's a quick patch which 
should fix project-switch-project (but not any other potential uses of 
project-vc values outside of the associated directory):

diff --git a/lisp/progmodes/project.el b/lisp/progmodes/project.el
index 3f4a5fb04b..c7fb39b0fb 100644
--- a/lisp/progmodes/project.el
+++ b/lisp/progmodes/project.el
@@ -1770,7 +1770,11 @@ project-switch-project
                       project-switch-commands
                     (project--switch-project-command))))
      (let ((project-current-directory-override dir))
-      (call-interactively command))))
+      (with-temp-buffer
+        (let ((default-directory dir)
+              (enable-local-variables :all))
+          (hack-dir-local-variables-non-file-buffer))
+        (call-interactively command)))))

  (provide 'project)
  ;;; project.el ends here

It's mostly to help with your debugging, since it breaks the default 
prompt for 'project-find-regexp' called from 'C-x p p' as well.

I'll have to think of the best way to resolve this: revert said commit 
outright (with updates for the new code), or do it with certain tweaks.

> Notes:
> 
> While probably not the root cause, this bug made debugging much harder,
> until I realized it exists, so I report this finding as well.

Thank you.

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Dmitry Gutov]

Hi Rudolf,

On 05/12/2022 02:43, Dmitry Gutov wrote:
> I'll have to think of the best way to resolve this: revert said commit 
> outright (with updates for the new code), or do it with certain tweaks.

I have pushed a fix for this to emacs-29 (commit d268ab1c5d).

Please check whether the original problem remains.

Did you have any luck with further debugging the situation with 'git 
ls-files'?

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Rudolf Adamkovič via Bug reports for GNU Emacs, the Swiss army knife of text editors]

Dmitry Gutov <dgutov@yandex.ru> writes:

>>    ((nil . ((project-ignores . ("apps/**/*.scm")))))
>
> project-vc-ignores, you mean.

Correct.  Dmitry, I apologize for causing confusion!

>> Emacs ends up calling
>> 
>>    git ls-files -z -c --exclude-standard \
>>      --no-empty-directory -o -- :(exclude,glob,top)apps/**/*.scm
>> 
>> [...]
>
> Huh, interesting. Could you try to show a similar command invocation 
> which would make Git output include a "logically empty" directory for 
> the Emacs repo? So that we have a common public project to compare.

I could not reproduce the problem with the Emacs source directory, but I
did not give up!  And, after a whole lot of head-scratching, I found the
root cause of the problem:

When `git ls-files' finds a symlink that points to a directory, it does
*not* follow it.  Instead, it lists it in the output.  In my case, the
symlink pointed to a directory with all of its files ignored.  However,
and importantly, upon further testing, I found that ignores do *not*
matter.

In summary, any symlinks to directories shallow-appear in `git ls-files'
outputs.  Emacs hands the list to Ripgrep, and Ripgrep follows symlinks,
possibly searching through ignored directories, effectively ignoring
`project-vc-ignores' from the point of view of the user.

Phew!

Rudy
-- 
"The introduction of suitable abstractions is our only mental aid to
organize and master complexity."
-- Edsger Wybe Dijkstra, 1930-2002

Rudolf Adamkovič <salutis@me.com> [he/him]
Studenohorská 25
84103 Bratislava
Slovakia

bug#59722: 30.0.50; project-find-regexp searches project-ignored files

[Dmitry Gutov]

On 11/12/2022 14:38, Rudolf Adamkovič via Bug reports for GNU Emacs, the 
Swiss army knife of text editors wrote:
> Dmitry Gutov <dgutov@yandex.ru> writes:
> 
>>>     ((nil . ((project-ignores . ("apps/**/*.scm")))))
>>
>> project-vc-ignores, you mean.
> 
> Correct.  Dmitry, I apologize for causing confusion!

No problem. I just wanted to make double-sure that the typo is not the 
cause of the issue.

>>> Emacs ends up calling
>>>
>>>     git ls-files -z -c --exclude-standard \
>>>       --no-empty-directory -o -- :(exclude,glob,top)apps/**/*.scm
>>>
>>> [...]
>>
>> Huh, interesting. Could you try to show a similar command invocation
>> which would make Git output include a "logically empty" directory for
>> the Emacs repo? So that we have a common public project to compare.
> 
> I could not reproduce the problem with the Emacs source directory, but I
> did not give up!  And, after a whole lot of head-scratching, I found the
> root cause of the problem:
> 
> When `git ls-files' finds a symlink that points to a directory, it does
> *not* follow it.  Instead, it lists it in the output.  In my case, the
> symlink pointed to a directory with all of its files ignored.  However,
> and importantly, upon further testing, I found that ignores do *not*
> matter.

Okay, yes, that seems to be the case. And there seems to be no way to 
have 'git ls-files' include symlinks in the output.

I can suggest two options here, both non-ideal:

- Ignore the whole symlinked directories by adding ignore entries that 
match their symlink files, rather than directories. For example, by 
setting project-vc-ignores to '("apps/*") or '("apps/**"), or with 
individual entries for each of them. That is, if you want them ignored 
whole.

- Here's what seems to be a (Linux-only) way to have Git follow 
symlinks: https://github.com/Alcaro/GitBSLR (found at 
https://stackoverflow.com/a/49138555/615245).

Another automatic approach would be to add a new value in 
xref-search-program-alist that would first pipe through a 
non-symlink-ness checker. Or modify the existing values.

But I'm yet to write a suitable command or pipeline (help welcome!), so 
I'm not sure how practical that is, and what's the average overhead.

The obvious choice of (seq-filter #'file-regular-p (project-files 
(project-current))) creates a large overhead (takes about x3 time here 
as just listing the files). That too much, I think.