Bug: COMMENT and noweb-ref

Bug: COMMENT and noweb-ref

[Sebastian Miele]

org-babel-tangle on

  * A

    #+BEGIN_SRC elisp :tangle yes :noweb yes
    ;; A
    <<B>>
    #+END_SRC

  * COMMENT B

    #+BEGIN_SRC elisp :noweb-ref B
    ;; B
    #+END_SRC

  * COMMENT C

    #+BEGIN_SRC elisp :tangle yes
    ;; C
    #+END_SRC

produces a file with A and B in it. Expected: Just A. Changing

    #+BEGIN_SRC elisp :noweb-ref B
    ;; B
    #+END_SRC

to

    # #+BEGIN_SRC elisp :noweb-ref B
    # ;; B
    # #+END_SRC

does yield the expected result.

Re: Bug: COMMENT and noweb-ref

[Sebastian Miele]

GNU Emacs 26.3 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.10) of 2019-08-29
Org mode version 9.2.6 (release_9.2.6-538-g23113f @ /home/w/borg/emacs/org/lisp/)

Re: Bug: COMMENT and noweb-ref

[Sebastian Miele]

In the following days I will try to fix it and write a regression test.

However, in the unlikely case that this is a feature and not a bug,
please let me know. Please also let me know, if anyone is already on it.

Sebastian Miele <sebastian.miele@gmail.com> writes:

> org-babel-tangle on
>
>   * A
>
>     #+BEGIN_SRC elisp :tangle yes :noweb yes
>     ;; A
>     <<B>>
>     #+END_SRC
>
>   * COMMENT B
>
>     #+BEGIN_SRC elisp :noweb-ref B
>     ;; B
>     #+END_SRC
>
>   * COMMENT C
>
>     #+BEGIN_SRC elisp :tangle yes
>     ;; C
>     #+END_SRC
>
> produces a file with A and B in it. Expected: Just A. Changing
>
>     #+BEGIN_SRC elisp :noweb-ref B
>     ;; B
>     #+END_SRC
>
> to
>
>     # #+BEGIN_SRC elisp :noweb-ref B
>     # ;; B
>     # #+END_SRC
>
> does yield the expected result.

Re: Bug: COMMENT and noweb-ref

[Marco Wahl]

Sebastian Miele <sebastian.miele@gmail.com> writes:

> In the following days I will try to fix it and write a regression test.
>
> However, in the unlikely case that this is a feature and not a bug,
> please let me know. Please also let me know, if anyone is already on it.
>
> Sebastian Miele <sebastian.miele@gmail.com> writes:
>
>> org-babel-tangle on
>>
>>   * A
>>
>>     #+BEGIN_SRC elisp :tangle yes :noweb yes
>>     ;; A
>>     <<B>>
>>     #+END_SRC
>>
>>   * COMMENT B
>>
>>     #+BEGIN_SRC elisp :noweb-ref B
>>     ;; B
>>     #+END_SRC

>> [...]

>>
>> produces a file with A and B in it. Expected: Just A. Changing
>>
>>     #+BEGIN_SRC elisp :noweb-ref B
>>     ;; B
>>     #+END_SRC
>>
>> to
>>
>>     # #+BEGIN_SRC elisp :noweb-ref B
>>     # ;; B
>>     # #+END_SRC
>>
>> does yield the expected result.

Your expectation looks right to me.  I guess nobody thought about this
case before.


Happy hacking,
-- 
Marco

Re: Bug: COMMENT and noweb-ref

[Sebastian Miele]

[-- Attachment #1: Type: text/plain, Size: 79 bytes --]

First, here is a patch introducing tests concerning Org comments and
tangling.

[-- Attachment #2: 0001-ob-tangle-Add-tests.patch --]
[-- Type: text/plain, Size: 2359 bytes --]

From c769435b9ab11f7a3b5ff5f1ec2df95ae2c6aa32 Mon Sep 17 00:00:00 2001
From: Sebastian Miele <sebastian.miele@gmail.com>
Date: Wed, 2 Oct 2019 13:02:46 +0000
Subject: [PATCH] ob-tangle: Add tests

* testing/lisp/test-ob-tangle.el (ob-tangle/commented-src-blocks):
  (ob-tangle/commented-src-blocks-with-nowebref): Add tests.
---
 testing/lisp/test-ob-tangle.el | 85 ++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)

diff --git a/testing/lisp/test-ob-tangle.el b/testing/lisp/test-ob-tangle.el
index 47c31dff5..675f0714b 100644
--- a/testing/lisp/test-ob-tangle.el
+++ b/testing/lisp/test-ob-tangle.el
@@ -296,6 +296,91 @@ another block
 		    (org-split-string (buffer-string))))
 	      (delete-file file))))))
 
+(ert-deftest ob-tangle/commented-src-blocks ()
+  "Test omission of commented src blocks."
+  (should
+   (equal '("A")
+	  (let ((file (make-temp-file "org-tangle-")))
+	    (unwind-protect
+		(progn
+		  (org-test-with-temp-text-in-file
+		      (format "#+property: header-args :tangle %S
+* A
+
+  #+BEGIN_SRC emacs-lisp
+  A
+  #+END_SRC
+
+* COMMENT B
+
+  #+BEGIN_SRC emacs-lisp
+  B
+  #+END_SRC
+
+* C
+
+  # #+BEGIN_SRC emacs-lisp
+  # C
+  # #+END_SRC
+
+* D
+
+  #+BEGIN_COMMENT
+  #+BEGIN_SRC emacs-lisp
+  D
+  #+END_SRC
+  #+END_COMMENT"
+			      file)
+		    (org-babel-tangle))
+		  (with-temp-buffer
+		    (insert-file-contents file)
+		    (org-split-string (buffer-string))))
+	      (delete-file file))))))
+
+(ert-deftest ob-tangle/commented-src-blocks-with-nowebref ()
+  "Test omission of commented src blocks with nowebref."
+  (should
+   (equal '("A")
+	  (let ((file (make-temp-file "org-tangle-")))
+	    (unwind-protect
+		(progn
+		  (org-test-with-temp-text-in-file
+		      (format "#+property: header-args :tangle %S
+* A
+
+  #+BEGIN_SRC elisp :noweb yes
+  A
+  <<B>>
+  <<C>>
+  <<D>>
+  #+END_SRC
+
+* COMMENT B
+
+  #+BEGIN_SRC elisp :noweb-ref B
+  B
+  #+END_SRC
+
+* C
+
+  # #+BEGIN_SRC elisp :noweb-ref C
+  # C
+  # #+END_SRC
+
+* D
+
+  #+BEGIN_COMMENT
+  #+BEGIN_SRC elisp :noweb-ref D
+  D
+  #+END_SRC
+  #+END_COMMENT"
+			      file)
+		    (org-babel-tangle))
+		  (with-temp-buffer
+		    (insert-file-contents file)
+		    (org-split-string (buffer-string))))
+	      (delete-file file))))))
+
 (provide 'test-ob-tangle)
 
 ;;; test-ob-tangle.el ends here
-- 
2.23.0

Re: Bug: COMMENT and noweb-ref

[Sebastian Miele]

I wrote:

> I wrote:
>
>> org-babel-tangle on
>>
>>   * A
>>
>>     #+BEGIN_SRC elisp :tangle yes :noweb yes
>>     ;; A
>>     <<B>>
>>     #+END_SRC
>>
>>   * COMMENT B
>>
>>     #+BEGIN_SRC elisp :noweb-ref B
>>     ;; B
>>     #+END_SRC
>>
>>   * COMMENT C
>>
>>     #+BEGIN_SRC elisp :tangle yes
>>     ;; C
>>     #+END_SRC
>>
>> produces a file with A and B in it. Expected: Just A. Changing
>>
>>     #+BEGIN_SRC elisp :noweb-ref B
>>     ;; B
>>     #+END_SRC
>>
>> to
>>
>>     # #+BEGIN_SRC elisp :noweb-ref B
>>     # ;; B
>>     # #+END_SRC
>>
>> does yield the expected result.
>
> In the following days I will try to fix it and write a regression test.

I wanted to mention that this is still on my agenda. But it will take a
while. Among other things, I have to learn the formal syntax and the
element api of Org, before I can satisfactorily dive into ob-tangle.el.
Apart from that I had to seriously limit my Emacs time per day.

It may take several weeks. But it will happen.

Best wishes
Sebastian

[PATCH] COMMENT and noweb-ref

[Sebastian Miele]

[-- Attachment #1: 0001-ob-core-Respect-COMMENTed-headlines-when-expanding-n.patch --]
[-- Type: text/plain, Size: 2047 bytes --]

From ddf0b6d89d30766158311c047d6de10091cb0377 Mon Sep 17 00:00:00 2001
From: Sebastian Miele <sebastian.miele@gmail.com>
Date: Sun, 20 Oct 2019 21:34:02 +0000
Subject: [PATCH 1/2] ob-core: Respect COMMENTed headlines when expanding noweb
 references

* lisp/ob-core.el (org-babel-expand-noweb-references): Add calls to
org-in-commented-heading-p where appropriate.
---
 lisp/ob-core.el | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 572f97919..b99545ab5 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -2780,7 +2780,8 @@ block but are passed literally to the \"example-block\"."
 				    (concat (funcall c-wrap (car cs)) "\n"
 					    b "\n"
 					    (funcall c-wrap (cadr cs)))))))))
-		      (if (re-search-forward name-regexp nil t)
+		      (if (and (re-search-forward name-regexp nil t)
+			       (not (org-in-commented-heading-p)))
 			  ;; Found a source block named SOURCE-NAME.
 			  ;; Assume it is unique; do not look after
 			  ;; `:noweb-ref' header argument.
@@ -2791,14 +2792,16 @@ block but are passed literally to the \"example-block\"."
 			;; those with a matching Noweb reference.
 			(let ((expansion nil))
 			  (org-babel-map-src-blocks nil
-			    (let* ((info (org-babel-get-src-block-info 'light))
-				   (parameters (nth 2 info)))
-			      (when (equal source-name
-					   (cdr (assq :noweb-ref parameters)))
-				(push (funcall expand-body info) expansion)
-				(push (or (cdr (assq :noweb-sep parameters))
-					  "\n")
-				      expansion))))
+			    (unless (org-in-commented-heading-p)
+			      (let* ((info
+				      (org-babel-get-src-block-info 'light))
+				     (parameters (nth 2 info)))
+				(when (equal source-name
+					     (cdr (assq :noweb-ref parameters)))
+				  (push (funcall expand-body info) expansion)
+				  (push (or (cdr (assq :noweb-sep parameters))
+					    "\n")
+					expansion)))))
 			  (when expansion
 			    (mapconcat #'identity
 				       (nreverse (cdr expansion))
-- 
2.23.0


[-- Attachment #2: 0002-Add-tests-about-omission-of-commented-src-blocks-whe.patch --]
[-- Type: text/plain, Size: 3127 bytes --]

From 66c7904298a33900e389acb184fbe7511960b34d Mon Sep 17 00:00:00 2001
From: Sebastian Miele <sebastian.miele@gmail.com>
Date: Sun, 20 Oct 2019 21:38:03 +0000
Subject: [PATCH 2/2] Add tests about omission of commented src blocks when
 e.g. tangling

* testing/lisp/test-ob.el (test-ob/noweb-expansion): Add clause to
test.
* testing/lisp/test-ob-tangle.el (ob-tangle/commented-src-blocks): Add
test.
---
 testing/lisp/test-ob-tangle.el | 84 ++++++++++++++++++++++++++++++++++
 testing/lisp/test-ob.el        | 24 ++++++++++
 2 files changed, 108 insertions(+)

diff --git a/testing/lisp/test-ob-tangle.el b/testing/lisp/test-ob-tangle.el
index 47c31dff5..301f7aff7 100644
--- a/testing/lisp/test-ob-tangle.el
+++ b/testing/lisp/test-ob-tangle.el
@@ -296,6 +296,90 @@ another block
 		    (org-split-string (buffer-string))))
 	      (delete-file file))))))
 
+(ert-deftest ob-tangle/commented-src-blocks ()
+  "Test omission of commented src blocks."
+  (should
+   (equal '("A")
+	  (let ((file (make-temp-file "org-tangle-")))
+	    (unwind-protect
+		(progn
+		  (org-test-with-temp-text-in-file
+		      (format "#+property: header-args :tangle %S
+* A
+
+  #+begin_src emacs-lisp
+  A
+  #+end_src
+
+* COMMENT B
+
+  #+begin_src emacs-lisp
+  B
+  #+end_src
+
+* C
+
+  # #+begin_src emacs-lisp
+  # C
+  # #+end_src
+
+* D
+
+  #+begin_comment
+  #+begin_src emacs-lisp
+  D
+  #+end_src
+  #+end_comment"
+			      file)
+		    (org-babel-tangle))
+		  (with-temp-buffer
+		    (insert-file-contents file)
+		    (org-split-string (buffer-string))))
+	      (delete-file file)))))
+  (should
+   (equal '("A")
+	  (let ((file (make-temp-file "org-tangle-")))
+	    (unwind-protect
+		(progn
+		  (org-test-with-temp-text-in-file
+		      (format "#+property: header-args :tangle %S
+* A
+
+  #+begin_src elisp :noweb yes
+  A
+  <<B>>
+  <<C>>
+  <<D>>
+  #+end_src
+
+* COMMENT B
+
+  #+begin_src elisp :noweb-ref B
+  B
+  #+end_src
+
+* C
+
+  # #+begin_src elisp :noweb-ref C
+  # C
+  # #+end_src
+
+* D
+
+  #+begin_comment
+  #+begin_src elisp :noweb-ref D
+  D
+  #+end_src
+  #+end_comment"
+			      file)
+		    (let (org-babel-noweb-error-all-langs
+			  org-babel-noweb-error-langs)
+		      (org-babel-tangle)))
+		  (with-temp-buffer
+		    (insert-file-contents file)
+		    (org-split-string (buffer-string))))
+	      (delete-file file))))))
+
 (provide 'test-ob-tangle)
 
 ;;; test-ob-tangle.el ends here
diff --git a/testing/lisp/test-ob.el b/testing/lisp/test-ob.el
index 367c70f83..681f3403e 100644
--- a/testing/lisp/test-ob.el
+++ b/testing/lisp/test-ob.el
@@ -758,6 +758,30 @@ x
 #+name: bar
 #+begin_src emacs-lisp
   baz
+#+end_src"
+	    (org-babel-expand-noweb-references))))
+  ;; Respect COMMENT headlines
+  (should
+   (equal "C"
+	  (org-test-with-temp-text "
+#+begin_src emacs-lisp :noweb yes<point>
+  <<foo>>
+#+end_src
+
+* COMMENT A
+#+name: foo
+#+begin_src emacs-lisp
+  A
+#+end_src
+
+* COMMENT B
+#+begin_src emacs-lisp :noweb-ref foo
+  B
+#+end_src
+
+* C
+#+begin_src emacs-lisp :noweb-ref foo
+  C
 #+end_src"
 	    (org-babel-expand-noweb-references)))))
 
-- 
2.23.0


[-- Attachment #3: Type: text/plain, Size: 856 bytes --]

I wrote:

> org-babel-tangle on
>
>   * A
>
>     #+BEGIN_SRC elisp :tangle yes :noweb yes
>     ;; A
>     <<B>>
>     #+END_SRC
>
>   * COMMENT B
>
>     #+BEGIN_SRC elisp :noweb-ref B
>     ;; B
>     #+END_SRC
>
>   * COMMENT C
>
>     #+BEGIN_SRC elisp :tangle yes
>     ;; C
>     #+END_SRC
>
> produces a file with A and B in it. Expected: Just A. Changing
>
>     #+BEGIN_SRC elisp :noweb-ref B
>     ;; B
>     #+END_SRC
>
> to
>
>     # #+BEGIN_SRC elisp :noweb-ref B
>     # ;; B
>     # #+END_SRC
>
> does yield the expected result.

Attached is a patch that fixes the problem.

A second patch is attached that contains tests about this and related
stuff. It is an updated version of an unapplied patch that I
sent to this list earlier this month
(https://lists.gnu.org/archive/html/emacs-orgmode/2019-10/msg00013.html).

Best wishes
Sebastian

[PATCH] COMMENT and noweb-ref

[Sebastian Miele]

[-- Attachment #1: Type: text/plain, Size: 913 bytes --]

Sorry. I messed up the previous mail. Please ignore it.

I wrote:

> org-babel-tangle on
>
>   * A
>
>     #+BEGIN_SRC elisp :tangle yes :noweb yes
>     ;; A
>     <<B>>
>     #+END_SRC
>
>   * COMMENT B
>
>     #+BEGIN_SRC elisp :noweb-ref B
>     ;; B
>     #+END_SRC
>
>   * COMMENT C
>
>     #+BEGIN_SRC elisp :tangle yes
>     ;; C
>     #+END_SRC
>
> produces a file with A and B in it. Expected: Just A. Changing
>
>     #+BEGIN_SRC elisp :noweb-ref B
>     ;; B
>     #+END_SRC
>
> to
>
>     # #+BEGIN_SRC elisp :noweb-ref B
>     # ;; B
>     # #+END_SRC
>
> does yield the expected result.

Attached is a patch that fixes the problem.

A second patch is attached that contains tests about this and related
stuff. It is an updated version of an unapplied patch that I
sent to this list earlier this month
(https://lists.gnu.org/archive/html/emacs-orgmode/2019-10/msg00013.html).

Best wishes
Sebastian

[-- Attachment #2: 0001-ob-core-Respect-COMMENTed-headlines-when-expanding-n.patch --]
[-- Type: text/plain, Size: 2047 bytes --]

From ddf0b6d89d30766158311c047d6de10091cb0377 Mon Sep 17 00:00:00 2001
From: Sebastian Miele <sebastian.miele@gmail.com>
Date: Sun, 20 Oct 2019 21:34:02 +0000
Subject: [PATCH 1/2] ob-core: Respect COMMENTed headlines when expanding noweb
 references

* lisp/ob-core.el (org-babel-expand-noweb-references): Add calls to
org-in-commented-heading-p where appropriate.
---
 lisp/ob-core.el | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/lisp/ob-core.el b/lisp/ob-core.el
index 572f97919..b99545ab5 100644
--- a/lisp/ob-core.el
+++ b/lisp/ob-core.el
@@ -2780,7 +2780,8 @@ block but are passed literally to the \"example-block\"."
 				    (concat (funcall c-wrap (car cs)) "\n"
 					    b "\n"
 					    (funcall c-wrap (cadr cs)))))))))
-		      (if (re-search-forward name-regexp nil t)
+		      (if (and (re-search-forward name-regexp nil t)
+			       (not (org-in-commented-heading-p)))
 			  ;; Found a source block named SOURCE-NAME.
 			  ;; Assume it is unique; do not look after
 			  ;; `:noweb-ref' header argument.
@@ -2791,14 +2792,16 @@ block but are passed literally to the \"example-block\"."
 			;; those with a matching Noweb reference.
 			(let ((expansion nil))
 			  (org-babel-map-src-blocks nil
-			    (let* ((info (org-babel-get-src-block-info 'light))
-				   (parameters (nth 2 info)))
-			      (when (equal source-name
-					   (cdr (assq :noweb-ref parameters)))
-				(push (funcall expand-body info) expansion)
-				(push (or (cdr (assq :noweb-sep parameters))
-					  "\n")
-				      expansion))))
+			    (unless (org-in-commented-heading-p)
+			      (let* ((info
+				      (org-babel-get-src-block-info 'light))
+				     (parameters (nth 2 info)))
+				(when (equal source-name
+					     (cdr (assq :noweb-ref parameters)))
+				  (push (funcall expand-body info) expansion)
+				  (push (or (cdr (assq :noweb-sep parameters))
+					    "\n")
+					expansion)))))
 			  (when expansion
 			    (mapconcat #'identity
 				       (nreverse (cdr expansion))
-- 
2.23.0


[-- Attachment #3: 0002-Add-tests-about-omission-of-commented-src-blocks-whe.patch --]
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From 66c7904298a33900e389acb184fbe7511960b34d Mon Sep 17 00:00:00 2001
From: Sebastian Miele <sebastian.miele@gmail.com>
Date: Sun, 20 Oct 2019 21:38:03 +0000
Subject: [PATCH 2/2] Add tests about omission of commented src blocks when
 e.g. tangling

* testing/lisp/test-ob.el (test-ob/noweb-expansion): Add clause to
test.
* testing/lisp/test-ob-tangle.el (ob-tangle/commented-src-blocks): Add
test.
---
 testing/lisp/test-ob-tangle.el | 84 ++++++++++++++++++++++++++++++++++
 testing/lisp/test-ob.el        | 24 ++++++++++
 2 files changed, 108 insertions(+)

diff --git a/testing/lisp/test-ob-tangle.el b/testing/lisp/test-ob-tangle.el
index 47c31dff5..301f7aff7 100644
--- a/testing/lisp/test-ob-tangle.el
+++ b/testing/lisp/test-ob-tangle.el
@@ -296,6 +296,90 @@ another block
 		    (org-split-string (buffer-string))))
 	      (delete-file file))))))
 
+(ert-deftest ob-tangle/commented-src-blocks ()
+  "Test omission of commented src blocks."
+  (should
+   (equal '("A")
+	  (let ((file (make-temp-file "org-tangle-")))
+	    (unwind-protect
+		(progn
+		  (org-test-with-temp-text-in-file
+		      (format "#+property: header-args :tangle %S
+* A
+
+  #+begin_src emacs-lisp
+  A
+  #+end_src
+
+* COMMENT B
+
+  #+begin_src emacs-lisp
+  B
+  #+end_src
+
+* C
+
+  # #+begin_src emacs-lisp
+  # C
+  # #+end_src
+
+* D
+
+  #+begin_comment
+  #+begin_src emacs-lisp
+  D
+  #+end_src
+  #+end_comment"
+			      file)
+		    (org-babel-tangle))
+		  (with-temp-buffer
+		    (insert-file-contents file)
+		    (org-split-string (buffer-string))))
+	      (delete-file file)))))
+  (should
+   (equal '("A")
+	  (let ((file (make-temp-file "org-tangle-")))
+	    (unwind-protect
+		(progn
+		  (org-test-with-temp-text-in-file
+		      (format "#+property: header-args :tangle %S
+* A
+
+  #+begin_src elisp :noweb yes
+  A
+  <<B>>
+  <<C>>
+  <<D>>
+  #+end_src
+
+* COMMENT B
+
+  #+begin_src elisp :noweb-ref B
+  B
+  #+end_src
+
+* C
+
+  # #+begin_src elisp :noweb-ref C
+  # C
+  # #+end_src
+
+* D
+
+  #+begin_comment
+  #+begin_src elisp :noweb-ref D
+  D
+  #+end_src
+  #+end_comment"
+			      file)
+		    (let (org-babel-noweb-error-all-langs
+			  org-babel-noweb-error-langs)
+		      (org-babel-tangle)))
+		  (with-temp-buffer
+		    (insert-file-contents file)
+		    (org-split-string (buffer-string))))
+	      (delete-file file))))))
+
 (provide 'test-ob-tangle)
 
 ;;; test-ob-tangle.el ends here
diff --git a/testing/lisp/test-ob.el b/testing/lisp/test-ob.el
index 367c70f83..681f3403e 100644
--- a/testing/lisp/test-ob.el
+++ b/testing/lisp/test-ob.el
@@ -758,6 +758,30 @@ x
 #+name: bar
 #+begin_src emacs-lisp
   baz
+#+end_src"
+	    (org-babel-expand-noweb-references))))
+  ;; Respect COMMENT headlines
+  (should
+   (equal "C"
+	  (org-test-with-temp-text "
+#+begin_src emacs-lisp :noweb yes<point>
+  <<foo>>
+#+end_src
+
+* COMMENT A
+#+name: foo
+#+begin_src emacs-lisp
+  A
+#+end_src
+
+* COMMENT B
+#+begin_src emacs-lisp :noweb-ref foo
+  B
+#+end_src
+
+* C
+#+begin_src emacs-lisp :noweb-ref foo
+  C
 #+end_src"
 	    (org-babel-expand-noweb-references)))))
 
-- 
2.23.0

Re: [PATCH] COMMENT and noweb-ref

[Nicolas Goaziou]

Hello,

Sebastian Miele <sebastian.miele@gmail.com> writes:

> Sorry. I messed up the previous mail. Please ignore it.

Applied. Thank you.

Regards,

-- 
Nicolas Goaziou