[BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]

[BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]

[Paul Stansell]

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Hello,

The attached file is an example of how tangle wraps the Fortran module in

  program main
  end program main

which prevents the code from compiling.

There are more instructions on how to reproduce the bug in the attached
bug.org file.

Paul



Emacs  : GNU Emacs 28.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version
3.24.37, cairo version 1.16.0)
 of 2023-03-16, modified by Debian
Package: Org mode version 9.7-pre (release_9.6.7-581-gd38ca5 @
/home/ps/.emacs.d_Kubuntu-23.04/org-mode-git/lisp/)

current state:
==============
(setq
 org-link-elisp-confirm-function 'yes-or-no-p
 org-bibtex-headline-format-function 'org-bibtex-headline-format-default
 org-log-done 'time
 org-fontify-done-headline nil
 org-log-into-drawer t
 org-startup-folded t
 org-persist-after-read-hook '(org-element--cache-persist-after-read)
 org-format-latex-options '(:foreground "Yellow" :background default :scale
1.2
                            :html-foreground "Black" :html-background
"Transparent"
                            :html-scale 1.07 :matchers ("begin" "$1" "$"
"$$" "\\(" "\\["))
 org-export-before-parsing-hook '(org-attach-expand-links)
 org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-file-apps '((auto-mode . emacs) ("\\.odt\\'" . "libreoffice %s")
                 ("\\.docx\\'" . "libreoffice %s") ("\\.xlsx\\'" .
"libreoffice %s")
                 ("\\.png\\'" . "xv %s") ("\\.jpg\\'" . "xv %s")
("\\.jpeg\\'" . "xv %s")
                 ("\\.webp\\'" . "xv %s") ("\\.pdf\\'" . "okular \"%s\"")
                 ("\\.xoj" . "xournal %s") ("\\.xopp" . "xournalpp %s"))
 org-odt-format-inlinetask-function
'org-odt-format-inlinetask-default-function
 org-ascii-format-drawer-function #[771 " \207" [] 4 "\n\n(fn NAME CONTENTS
WIDTH)"]
 org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-show-empty-lines
                  org-cycle-optimize-window-after-visibility-change
                  org-cycle-display-inline-images)
 org-persist-before-read-hook '(org-element--cache-persist-before-read)
 org-mode-hook '(#[0 "\300\301\302\303\304$\207"
                   [add-hook change-major-mode-hook org-fold-show-all
append local] 5]
                 #[0 "\300\301\302\303\304$\207"
                   [add-hook change-major-mode-hook
org-babel-show-result-all append local]
                   5]
                 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-babel-load-languages '((R . t) (emacs-lisp . t) (gnuplot . t) (octave
. t) (python . t)
                            (fortran . t) (sql . t) (ditaa . t) (dot . t)
(shell . t))
 org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn _ CONTENTS)"]
 org-latex-format-headline-function
'org-latex-format-headline-default-function
 org-confirm-shell-link-function 'yes-or-no-p
 org-adapt-indentation t
 org-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 outline-isearch-open-invisible-function 'outline-isearch-open-invisible
 org-highlight-latex-and-related '(latex)
 org-odt-format-headline-function 'org-odt-format-headline-default-function
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-babel-tangle-lang-exts '(("fortran" . "F90") ("python" . "py")
("emacs-lisp" . "el")
                              ("elisp" . "el"))
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-clock-out-remove-zero-time-clocks t
 org-hide-leading-stars t
 org-todo-keywords '((sequence "TODO(t!)" "MAYBE(m!)" "STARTED(s!)"
"WAITING(w@/!)" "|"
                      "DONE(d)" "INFO(i!)" "CANCELLED(c@)" "UNFINISHED(u@)"
"ABANDONED(a@)")
                     )
 org-id-link-to-org-use-id t
 org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
 org-html-format-inlinetask-function
'org-html-format-inlinetask-default-function
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-confirm-babel-evaluate nil
 org-fold-core-isearch-open-function 'org-fold--isearch-reveal
 org-clock-in-switch-to-state "STARTED"
 org-clock-persist 'history
 org-latex-format-inlinetask-function
'org-latex-format-inlinetask-default-function
 org-persist-before-write-hook '(org-element--cache-persist-before-write)
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
 org-link-shell-confirm-function 'yes-or-no-p
 org-babel-pre-tangle-hook '(save-buffer)
 org-clock-display-default-range 'untilnow
 org-agenda-loop-over-headlines-in-active-region nil
 org-todo-keyword-faces '(("TODO" :foreground "light pink" :weight bold)
                          ("MAYBE" :foreground "light pink" :weight bold)
                          ("STARTED" :foreground "gold" :weight bold)
                          ("DONE" :foreground "light green" :weight bold)
                          ("WAITING" :foreground "gold" :weight bold)
                          ("CANCELLED" :foreground "light green" :weight
bold)
                          ("UNFINISHED" :foreground "light green" :weight
bold)
                          ("ABANDONED" :foreground "light green" :weight
bold))
 org-occur-hook '(org-first-headline-recenter)
 org-export-with-drawers '("LATEX_DRAW")
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-link-parameters '(("attachment" :follow org-attach-follow :complete
                        org-attach-complete-link)
                       ("eww" :follow org-eww-open :store
org-eww-store-link)
                       ("rmail" :follow org-rmail-open :store
org-rmail-store-link)
                       ("mhe" :follow org-mhe-open :store
org-mhe-store-link)
                       ("irc" :follow org-irc-visit :store
org-irc-store-link :export
                        org-irc-export)
                       ("info" :follow org-info-open :export
org-info-export :store
                        org-info-store-link :insert-description
                        org-info-description-as-command)
                       ("gnus" :follow org-gnus-open :store
org-gnus-store-link)
                       ("docview" :follow org-docview-open :export
org-docview-export :store
                        org-docview-store-link)
                       ("bibtex" :follow org-bibtex-open :store
org-bibtex-store-link)
                       ("bbdb" :follow org-bbdb-open :export
org-bbdb-export :complete
                        org-bbdb-complete-link :store org-bbdb-store-link)
                       ("w3m" :store org-w3m-store-link)
                       ("doi" :follow org-link-doi-open :export
org-link-doi-export)
                       ("id" :follow org-id-open) ("file+sys")
("file+emacs")
                       ("shell" :follow org-link--open-shell)
                       ("news" :follow
                        #[514 "\301\300\302 Q \"\207" ["news" browse-url
":"] 6
                          "\n\n(fn URL ARG)"]
                        )
                       ("mailto" :follow
                        #[514 "\301\300\302 Q \"\207" ["mailto" browse-url
":"] 6
                          "\n\n(fn URL ARG)"]
                        )
                       ("https" :follow
                        #[514 "\301\300\302 Q \"\207" ["https" browse-url
":"] 6
                          "\n\n(fn URL ARG)"]
                        )
                       ("http" :follow
                        #[514 "\301\300\302 Q \"\207" ["http" browse-url
":"] 6
                          "\n\n(fn URL ARG)"]
                        )
                       ("ftp" :follow
                        #[514 "\301\300\302 Q \"\207" ["ftp" browse-url
":"] 6
                          "\n\n(fn URL ARG)"]
                        )
                       ("help" :follow org-link--open-help :store
org-link--store-help)
                       ("file" :complete org-link-complete-file)
                       ("elisp" :follow org-link--open-elisp))
 org-html-format-headline-function
'org-html-format-headline-default-function
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-clock-history-length 28
 org-clock-into-drawer "CLOCK"
 )

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[-- Attachment #2: bug.org --]
[-- Type: text/org, Size: 1628 bytes --]

Run with

  /usr/bin/emacs -Q -l init.el bug.org

One should be able to click on the following link
- elisp:org-babel-tangle
to tangle (export) the code blocks in this org file.

Then one should be able to execute the code block
- [[code_block_to_execute]]
by using C-c C-c in code block.

However, it does not work because the tangle stage wraps the fortran
module in

  program main

  end program main

which prevents the code from compiling.



#+BEGIN_SRC fortran :tangle circle.f90
  MODULE Circle
        implicit None
        public :: area
  contains
        function area(r) 
        implicit none
        real, intent(in) :: r
        real :: area
        area = 3.14159 * r**2
        return
        end function area
  END MODULE Circle
#+END_SRC


#+BEGIN_SRC fortran :tangle main.f90
  program main

  use circle, only: area

  implicit none
  integer :: i
  REAL, DIMENSION(5) :: R
  R = (/1.0, 2.0, 3.0, 4.0, 5.0 /)

  print *, "#+tblname: circle-area"
  do i = 1, 5
     print *, "|", R(i), "|", area(R(i)), "|"
  end do

  end program main
#+END_SRC


#+BEGIN_SRC makefile :tangle makefile-main
  circle:
  	@gfortran -c circle.f90

  main: circle
  	@gfortran -c main.f90
  	@gfortran circle.o main.o -o main

  clean:
  	@rm -f *.o main
#+END_SRC

<<code_block_to_execute>>
#+BEGIN_SRC sh :results raw replace
  make -f makefile-main clean main
  ./main
#+END_SRC

#+RESULTS:
 #+tblname: circle-area
 |   1.00000000     |   3.14159012     |
 |   2.00000000     |   12.5663605     |
 |   3.00000000     |   28.2743111     |
 |   4.00000000     |   50.2654419     |
 |   5.00000000     |   78.5397491     |



[-- Attachment #3: init.el --]
[-- Type: text/x-emacs-lisp, Size: 122 bytes --]

(org-babel-do-load-languages
     'org-babel-load-languages
     '((fortran . t)))

(setq org-confirm-babel-evaluate nil)

Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]

[Ihor Radchenko]

Paul Stansell <paulstansell@gmail.com> writes:

> The attached file is an example of how tangle wraps the Fortran module in
>
>   program main
>   end program main
>
> which prevents the code from compiling.
>
> There are more instructions on how to reproduce the bug in the attached
> bug.org file.

I opened the latest Org git repo, ran make repro, opened the file,
clicked on "tangle" link, moved to the linked source code, and executed
it. It worked.

So, I am unable to reproduce the problem on my system.

-- 
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: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]

[Paul Stansell]

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>
> I opened the latest Org git repo, ran make repro, opened the file,
> clicked on "tangle" link, moved to the linked source code, and executed
> it. It worked.
>
> So, I am unable to reproduce the problem on my system.
>

Hello Ihor,

Thanks for investigating.  Can you please post your tangled file named
circle.f90.

Mine looks like this

    program main
    MODULE Circle
          implicit None
          public :: area
    contains
          function area(r)
          implicit none
          real, intent(in) :: r
          real :: area
          area = 3.14159 * r**2
          return
          end function area
    END MODULE Circle
    end program main

which is broken because org/babel has added the first and last lines.

Thanks,

Paul

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Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]

[Ihor Radchenko]

Paul Stansell <paulstansell@gmail.com> writes:

>>
>> I opened the latest Org git repo, ran make repro, opened the file,
>> clicked on "tangle" link, moved to the linked source code, and executed
>> it. It worked.
>>
>> So, I am unable to reproduce the problem on my system.
>>
>
> Thanks for investigating.  Can you please post your tangled file named
> circle.f90.
>
> Mine looks like this
>
>     program main

Never mind my previous message. I forgot the provided init.el file,
which makes all the difference.

Confirmed.

By default, ob-fortran (and at least ob-C) wrap the src block body to
become a standalone function unless you put :main no header argument.

The default behaviour is mostly useful during execution, but not when
tangling.

I will need to think about the best way to approach this. A tentative
fix would be handling :main header argument only during block evaluation.

Meanwhile, you can set :main no as default header argument for fortran.

-- 
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: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]

[Paul Stansell]

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>
> Meanwhile, you can set :main no as default header argument for fortran.
>

Thanks for taking another look.  I was not aware of ":main no", but it's a
perfectly good fix for my problem.

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Re: [BUG] tangle breaks fortran modules [9.7-pre (release_9.6.7-581-gd38ca5)]

[Ihor Radchenko]

Paul Stansell <paulstansell@gmail.com> writes:

> ...  I was not aware of ":main no"

Yeah. We don't have any documentation for ob-fortran, unfortunately.

-- 
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>