Problem with references to babel source blocks (possible bug).

Problem with references to babel source blocks (possible bug).

[Emmanuel Charpentier]

[-- Attachment #1: Type: text/plain, Size: 1994 bytes --]

I wish to be able to reference (i. e cross-references, lists) both some
tables or figures AND the code producing the objects.

To this effect, I added (distinct) #+caption:s to the source blocks AND
to the results, adorned with (distinct) org-ref's labels. An example is
included in the enclosed file Min-Ref.org.

The comparison of this source, the LaTeX code obtained by org-latex
export-to latex (Min-Ref.tex) and the resultant PDF (Min-Ref exported
by org-latex-export-to-pdf.pdf) show that the labels attributed to
source blocks are mislabeled as figures. Furthermore, while the org
source requests a list of figure, a list of table and a list of
listings (in that order), the list of figures appears *after* the list
of tables.

I am tempted to conclude that there is some confusion between figures
and listings. Further attempts tend to show that the problem may live n
the core org's code, rather than any specific exporter :

The ODT "native" exporter (org-odt-export-to-odt) is much less capable,
as shown in Min-Ref exported by org-odt-export-to-odt.odt.

Attempts to export via Pandoc to PDF (Min-Ref exported by org-pandoc-
export-to-latex-pdf.pdf), ODT (Min-Ref exported by org-pandoc-export-
to-odt.odt) and DOCX (Min-Ref.docx) show that these exporters may need
some specific configurations in order to be even vaguely usable.

Previous trials, using #+names: rather than org-ref's labels, gave
similar failures. If needed, I can reproduce these trials.

So I have a couple questions :

1) Is the confusion of source blocks and figures a bug, or do I miss a
subtle point ?

2) Is there some introductory material to the care and feeding of ox-
pandoc demonstrating the use of this exporter's options to enable the
addition of the needed features (figure inclusion, tables of tables /
figures / listings, etc...) ? The "manual" available as a README i way
too terse to be usable without diving in the source code and pandoc's
documentation.

Sincerely,

--
Emmanuel Charpentier


[-- Attachment #2: Min-Ref.docx --]
[-- Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document, Size: 10789 bytes --]

[-- Attachment #3: Min-Ref.org --]
[-- Type: text/plain, Size: 1645 bytes --]


#+options: toc:nil
#+property: header-args:python :session
#+language: fr

#+title: What's up with references ?
#+author:
#+date: December 2018

#+toc: headlines
#+toc: figures
#+toc: tables
#+toc: listings

* Some reference samples

This is created using =org-ref= 's =label= 's and =ref= 's.

** A reference...

... to cite:gelmanBayesianDataAnalysis2013 ,a /good/ textbook.

** A table

A Python block producing a (silly) table.

#+caption: A (silly) Python block. label:lst:Python1
#+BEGIN_SRC python :results table :exports both
[[u+str(v) for v in range(1,4)] for u in ["a", "b"]]
#+END_SRC

#+caption: A (silly) Python table. label:tab:Python1
#+RESULTS:
| a1 | a2 | a3 |
| b1 | b2 | b3 |

The table ref:tab:Python1 is produced by the code ref:lst:Python1.

** A figure

A Python block producing a figure.

#+caption: A Python block producing a figure. label:lst:Python2
#+BEGIN_SRC python :results file :exports both
import matplotlib.pyplot as plt, numpy as np
from sympy import *
x=symbols("x")
f=lambda x:sin(x)/x
t=np.arange(-6*np.pi,6*np.pi, 0.1)
ft=[f(u) for u in t]
fig=plt.figure(figsize=(3,2))
plt.plot(t, ft, "b-")
fig.tight_layout()
plt.savefig("tstfig.pdf")
"tstfig.pdf"
#+END_SRC

#+caption: A (not so silly) figure produced by Python. label:fig:Python2
#+RESULTS:
[[file:tstfig.pdf]]

The figure ref:fig:Python2 is produced by the code ref:lst:Python2.

[[bibliographystyle:vancouver]]
[[bibliography:Minimal.bib]]

# Local Variables:
# org-latex-packages-alist: (("AUTO" "babel" t ("pdflatex")) ("AUTO" "polyglossia" t ("xelatex" "lualatex")))
# org-latex-pdf-process: ("latexmk -shell-escape -bibtex -f -pdf %f")
# End:

[-- Attachment #4: Min-Ref.tex --]
[-- Type: text/x-tex, Size: 2236 bytes --]

% Created 2018-12-17 lun. 15:49
% Intended LaTeX compiler: pdflatex
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\usepackage[frenchb]{babel}
\date{December 2018}
\title{What's up with references ?}
\hypersetup{
 pdfauthor={},
 pdftitle={What's up with references ?},
 pdfkeywords={},
 pdfsubject={},
 pdfcreator={Emacs 27.0.50 (Org mode 9.1.14)}, 
 pdflang={Frenchb}}
\begin{document}

\maketitle
\tableofcontents
\listoftables
\listoffigures

\section{Some reference samples}
\label{sec:orgfe4b8ad}

This is created using \texttt{org-ref} 's \texttt{label} 's and \texttt{ref} 's.

\subsection{A reference\ldots{}}
\label{sec:org22891f6}

\ldots{} to \cite{gelmanBayesianDataAnalysis2013} ,a \emph{good} textbook.

\subsection{A table}
\label{sec:org844d514}

A Python block producing a (silly) table.

\begin{verbatim}
[[u+str(v) for v in range(1,4)] for u in ["a", "b"]]
\end{verbatim}
\captionof{figure}{A (silly) Python block. \label{lst:Python1}}

\begin{table}[htbp]
\caption{A (silly) Python table. \label{tab:Python1}}
\centering
\begin{tabular}{lll}
a1 & a2 & a3\\
b1 & b2 & b3\\
\end{tabular}
\end{table}

The table \ref{tab:Python1} is produced by the code \ref{lst:Python1}.

\subsection{A figure}
\label{sec:orgf75a27d}

A Python block producing a figure.

\begin{verbatim}
import matplotlib.pyplot as plt, numpy as np
from sympy import *
x=symbols("x")
f=lambda x:sin(x)/x
t=np.arange(-6*np.pi,6*np.pi, 0.1)
ft=[f(u) for u in t]
fig=plt.figure(figsize=(3,2))
plt.plot(t, ft, "b-")
fig.tight_layout()
plt.savefig("tstfig.pdf")
"tstfig.pdf"
\end{verbatim}
\captionof{figure}{A Python block producing a figure. \label{lst:Python2}}

\begin{figure}[htbp]
\centering
\includegraphics[width=.9\linewidth]{tstfig.pdf}
\caption{A (not so silly) figure produced by Python. \label{fig:Python2}}
\end{figure}

The figure \ref{fig:Python2} is produced by the code \ref{lst:Python2}.

\bibliographystyle{vancouver}
\bibliography{Minimal}
\end{document}

[-- Attachment #5: Min-Ref exported by org-latex-export-to-pdf.pdf --]
[-- Type: application/pdf, Size: 143423 bytes --]

[-- Attachment #6: Min-Ref exported by org-odt-export-to-odt.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 18946 bytes --]

[-- Attachment #7: Min-Ref exported by org-pandoc-export-to-latex-pdf.pdf --]
[-- Type: application/pdf, Size: 202284 bytes --]

[-- Attachment #8: Min-Ref exported by org-pandoc-export-to-odt.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 17044 bytes --]

Problem with references to babel source blocks (possible bug).

[emm.charpentier]

[-- Attachment #1: Type: text/plain, Size: 1994 bytes --]

I wish to be able to reference (i. e cross-references, lists) both some
tables or figures AND the code producing the objects.

To this effect, I added (distinct) #+caption:s to the source blocks AND
to the results, adorned with (distinct) org-ref's labels. An example is
included in the enclosed file Min-Ref.org.

The comparison of this source, the LaTeX code obtained by org-latex
export-to latex (Min-Ref.tex) and the resultant PDF (Min-Ref exported
by org-latex-export-to-pdf.pdf) show that the labels attributed to
source blocks are mislabeled as figures. Furthermore, while the org
source requests a list of figure, a list of table and a list of
listings (in that order), the list of figures appears *after* the list
of tables.

I am tempted to conclude that there is some confusion between figures
and listings. Further attempts tend to show that the problem may live n
the core org's code, rather than any specific exporter :

The ODT "native" exporter (org-odt-export-to-odt) is much less capable,
as shown in Min-Ref exported by org-odt-export-to-odt.odt.

Attempts to export via Pandoc to PDF (Min-Ref exported by org-pandoc-
export-to-latex-pdf.pdf), ODT (Min-Ref exported by org-pandoc-export-
to-odt.odt) and DOCX (Min-Ref.docx) show that these exporters may need
some specific configurations in order to be even vaguely usable.

Previous trials, using #+names: rather than org-ref's labels, gave
similar failures. If needed, I can reproduce these trials.

So I have a couple questions :

1) Is the confusion of source blocks and figures a bug, or do I miss a
subtle point ?

2) Is there some introductory material to the care and feeding of ox-
pandoc demonstrating the use of this exporter's options to enable the
addition of the needed features (figure inclusion, tables of tables /
figures / listings, etc...) ? The "manual" available as a README is way
too terse to be usable without diving in the source code and pandoc's
documentation.

Sincerely,

--
Emmanuel Charpentier

[-- Attachment #2: Min-Ref.docx --]
[-- Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document, Size: 10789 bytes --]

[-- Attachment #3: Min-Ref.org --]
[-- Type: application/octet-stream, Size: 1645 bytes --]


#+options: toc:nil
#+property: header-args:python :session
#+language: fr

#+title: What's up with references ?
#+author:
#+date: December 2018

#+toc: headlines
#+toc: figures
#+toc: tables
#+toc: listings

* Some reference samples

This is created using =org-ref= 's =label= 's and =ref= 's.

** A reference...

... to cite:gelmanBayesianDataAnalysis2013 ,a /good/ textbook.

** A table

A Python block producing a (silly) table.

#+caption: A (silly) Python block. label:lst:Python1
#+BEGIN_SRC python :results table :exports both
[[u+str(v) for v in range(1,4)] for u in ["a", "b"]]
#+END_SRC

#+caption: A (silly) Python table. label:tab:Python1
#+RESULTS:
| a1 | a2 | a3 |
| b1 | b2 | b3 |

The table ref:tab:Python1 is produced by the code ref:lst:Python1.

** A figure

A Python block producing a figure.

#+caption: A Python block producing a figure. label:lst:Python2
#+BEGIN_SRC python :results file :exports both
import matplotlib.pyplot as plt, numpy as np
from sympy import *
x=symbols("x")
f=lambda x:sin(x)/x
t=np.arange(-6*np.pi,6*np.pi, 0.1)
ft=[f(u) for u in t]
fig=plt.figure(figsize=(3,2))
plt.plot(t, ft, "b-")
fig.tight_layout()
plt.savefig("tstfig.pdf")
"tstfig.pdf"
#+END_SRC

#+caption: A (not so silly) figure produced by Python. label:fig:Python2
#+RESULTS:
[[file:tstfig.pdf]]

The figure ref:fig:Python2 is produced by the code ref:lst:Python2.

[[bibliographystyle:vancouver]]
[[bibliography:Minimal.bib]]

# Local Variables:
# org-latex-packages-alist: (("AUTO" "babel" t ("pdflatex")) ("AUTO" "polyglossia" t ("xelatex" "lualatex")))
# org-latex-pdf-process: ("latexmk -shell-escape -bibtex -f -pdf %f")
# End:

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #4: Min-Ref.tex --]
[-- Type: text/x-tex; name=Min-Ref.tex, Size: 2236 bytes --]

% Created 2018-12-17 lun. 15:49
% Intended LaTeX compiler: pdflatex
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\usepackage[frenchb]{babel}
\date{December 2018}
\title{What's up with references ?}
\hypersetup{
 pdfauthor={},
 pdftitle={What's up with references ?},
 pdfkeywords={},
 pdfsubject={},
 pdfcreator={Emacs 27.0.50 (Org mode 9.1.14)}, 
 pdflang={Frenchb}}
\begin{document}

\maketitle
\tableofcontents
\listoftables
\listoffigures

\section{Some reference samples}
\label{sec:orgfe4b8ad}

This is created using \texttt{org-ref} 's \texttt{label} 's and \texttt{ref} 's.

\subsection{A reference\ldots{}}
\label{sec:org22891f6}

\ldots{} to \cite{gelmanBayesianDataAnalysis2013} ,a \emph{good} textbook.

\subsection{A table}
\label{sec:org844d514}

A Python block producing a (silly) table.

\begin{verbatim}
[[u+str(v) for v in range(1,4)] for u in ["a", "b"]]
\end{verbatim}
\captionof{figure}{A (silly) Python block. \label{lst:Python1}}

\begin{table}[htbp]
\caption{A (silly) Python table. \label{tab:Python1}}
\centering
\begin{tabular}{lll}
a1 & a2 & a3\\
b1 & b2 & b3\\
\end{tabular}
\end{table}

The table \ref{tab:Python1} is produced by the code \ref{lst:Python1}.

\subsection{A figure}
\label{sec:orgf75a27d}

A Python block producing a figure.

\begin{verbatim}
import matplotlib.pyplot as plt, numpy as np
from sympy import *
x=symbols("x")
f=lambda x:sin(x)/x
t=np.arange(-6*np.pi,6*np.pi, 0.1)
ft=[f(u) for u in t]
fig=plt.figure(figsize=(3,2))
plt.plot(t, ft, "b-")
fig.tight_layout()
plt.savefig("tstfig.pdf")
"tstfig.pdf"
\end{verbatim}
\captionof{figure}{A Python block producing a figure. \label{lst:Python2}}

\begin{figure}[htbp]
\centering
\includegraphics[width=.9\linewidth]{tstfig.pdf}
\caption{A (not so silly) figure produced by Python. \label{fig:Python2}}
\end{figure}

The figure \ref{fig:Python2} is produced by the code \ref{lst:Python2}.

\bibliographystyle{vancouver}
\bibliography{Minimal}
\end{document}

[-- Attachment #5: Min-Ref exported by org-latex-export-to-pdf.pdf --]
[-- Type: application/pdf, Size: 143423 bytes --]

[-- Attachment #6: Min-Ref exported by org-odt-export-to-odt.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 18946 bytes --]

[-- Attachment #7: Min-Ref exported by org-pandoc-export-to-latex-pdf.pdf --]
[-- Type: application/pdf, Size: 202284 bytes --]

[-- Attachment #8: Min-Ref exported by org-pandoc-export-to-odt.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 17044 bytes --]

Problem with references to babel source blocks (possible bug).

[Emmanuel Charpentier]

[-- Attachment #1: Type: text/plain, Size: 2136 bytes --]

[ Third attempt to send this mail to the emacs-orgmode list, > 24 hours
after second attempt. Nicolas, could you forward it if necessary ? ]

I wish to be able to reference (i. e cross-references, lists) both some
tables or figures AND the code producing the objects.

To this effect, I added (distinct) #+caption:s to the source blocks AND
to the results, adorned with (distinct) org-ref's labels. An example is
included in the enclosed file Min-Ref.org.

The comparison of this source, the LaTeX code obtained by org-latex
export-to latex (Min-Ref.tex) and the resultant PDF (Min-Ref exported
by org-latex-export-to-pdf.pdf) show that the labels attributed to
source blocks are mislabeled as figures. Furthermore, while the org
source requests a list of figure, a list of table and a list of
listings (in that order), the list of figures appears *after* the list
of tables.

I am tempted to conclude that there is some confusion between figures
and listings. Further attempts tend to show that the problem may live n
the core org's code, rather than any specific exporter :

The ODT "native" exporter (org-odt-export-to-odt) is much less capable,
as shown in Min-Ref exported by org-odt-export-to-odt.odt.

Attempts to export via Pandoc to PDF (Min-Ref exported by org-pandoc-
export-to-latex-pdf.pdf), ODT (Min-Ref exported by org-pandoc-export-
to-odt.odt) and DOCX (Min-Ref.docx) show that these exporters may need
some specific configurations in order to be even vaguely usable.

Previous trials, using #+names: rather than org-ref's labels, gave
similar failures. If needed, I can reproduce these trials.

So I have a couple questions :

1) Is the confusion of source blocks and figures a bug, or do I miss a
subtle point ?

2) Is there some introductory material to the care and feeding of ox-
pandoc demonstrating the use of this exporter's options to enable the
addition of the needed features (figure inclusion, tables of tables /
figures / listings, etc...) ? The "manual" available as a README is way
too terse to be usable without diving in the source code and pandoc's
documentation.

Sincerely,

--
Emmanuel Charpentier

[-- Attachment #2: Min-Ref.docx --]
[-- Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document, Size: 10789 bytes --]

[-- Attachment #3: Min-Ref.org --]
[-- Type: application/octet-stream, Size: 1645 bytes --]


#+options: toc:nil
#+property: header-args:python :session
#+language: fr

#+title: What's up with references ?
#+author:
#+date: December 2018

#+toc: headlines
#+toc: figures
#+toc: tables
#+toc: listings

* Some reference samples

This is created using =org-ref= 's =label= 's and =ref= 's.

** A reference...

... to cite:gelmanBayesianDataAnalysis2013 ,a /good/ textbook.

** A table

A Python block producing a (silly) table.

#+caption: A (silly) Python block. label:lst:Python1
#+BEGIN_SRC python :results table :exports both
[[u+str(v) for v in range(1,4)] for u in ["a", "b"]]
#+END_SRC

#+caption: A (silly) Python table. label:tab:Python1
#+RESULTS:
| a1 | a2 | a3 |
| b1 | b2 | b3 |

The table ref:tab:Python1 is produced by the code ref:lst:Python1.

** A figure

A Python block producing a figure.

#+caption: A Python block producing a figure. label:lst:Python2
#+BEGIN_SRC python :results file :exports both
import matplotlib.pyplot as plt, numpy as np
from sympy import *
x=symbols("x")
f=lambda x:sin(x)/x
t=np.arange(-6*np.pi,6*np.pi, 0.1)
ft=[f(u) for u in t]
fig=plt.figure(figsize=(3,2))
plt.plot(t, ft, "b-")
fig.tight_layout()
plt.savefig("tstfig.pdf")
"tstfig.pdf"
#+END_SRC

#+caption: A (not so silly) figure produced by Python. label:fig:Python2
#+RESULTS:
[[file:tstfig.pdf]]

The figure ref:fig:Python2 is produced by the code ref:lst:Python2.

[[bibliographystyle:vancouver]]
[[bibliography:Minimal.bib]]

# Local Variables:
# org-latex-packages-alist: (("AUTO" "babel" t ("pdflatex")) ("AUTO" "polyglossia" t ("xelatex" "lualatex")))
# org-latex-pdf-process: ("latexmk -shell-escape -bibtex -f -pdf %f")
# End:

[-- Attachment #4: Min-Ref.tex --]
[-- Type: text/x-tex, Size: 2236 bytes --]

% Created 2018-12-17 lun. 15:49
% Intended LaTeX compiler: pdflatex
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\usepackage[frenchb]{babel}
\date{December 2018}
\title{What's up with references ?}
\hypersetup{
 pdfauthor={},
 pdftitle={What's up with references ?},
 pdfkeywords={},
 pdfsubject={},
 pdfcreator={Emacs 27.0.50 (Org mode 9.1.14)}, 
 pdflang={Frenchb}}
\begin{document}

\maketitle
\tableofcontents
\listoftables
\listoffigures

\section{Some reference samples}
\label{sec:orgfe4b8ad}

This is created using \texttt{org-ref} 's \texttt{label} 's and \texttt{ref} 's.

\subsection{A reference\ldots{}}
\label{sec:org22891f6}

\ldots{} to \cite{gelmanBayesianDataAnalysis2013} ,a \emph{good} textbook.

\subsection{A table}
\label{sec:org844d514}

A Python block producing a (silly) table.

\begin{verbatim}
[[u+str(v) for v in range(1,4)] for u in ["a", "b"]]
\end{verbatim}
\captionof{figure}{A (silly) Python block. \label{lst:Python1}}

\begin{table}[htbp]
\caption{A (silly) Python table. \label{tab:Python1}}
\centering
\begin{tabular}{lll}
a1 & a2 & a3\\
b1 & b2 & b3\\
\end{tabular}
\end{table}

The table \ref{tab:Python1} is produced by the code \ref{lst:Python1}.

\subsection{A figure}
\label{sec:orgf75a27d}

A Python block producing a figure.

\begin{verbatim}
import matplotlib.pyplot as plt, numpy as np
from sympy import *
x=symbols("x")
f=lambda x:sin(x)/x
t=np.arange(-6*np.pi,6*np.pi, 0.1)
ft=[f(u) for u in t]
fig=plt.figure(figsize=(3,2))
plt.plot(t, ft, "b-")
fig.tight_layout()
plt.savefig("tstfig.pdf")
"tstfig.pdf"
\end{verbatim}
\captionof{figure}{A Python block producing a figure. \label{lst:Python2}}

\begin{figure}[htbp]
\centering
\includegraphics[width=.9\linewidth]{tstfig.pdf}
\caption{A (not so silly) figure produced by Python. \label{fig:Python2}}
\end{figure}

The figure \ref{fig:Python2} is produced by the code \ref{lst:Python2}.

\bibliographystyle{vancouver}
\bibliography{Minimal}
\end{document}

[-- Attachment #5: Min-Ref exported by org-latex-export-to-pdf.pdf --]
[-- Type: application/pdf, Size: 143423 bytes --]

[-- Attachment #6: Min-Ref exported by org-odt-export-to-odt.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 18946 bytes --]

[-- Attachment #7: Min-Ref exported by org-pandoc-export-to-latex-pdf.pdf --]
[-- Type: application/pdf, Size: 202284 bytes --]

[-- Attachment #8: Min-Ref exported by org-pandoc-export-to-odt.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 17044 bytes --]

Problem with references to babel source blocks (possible bug).

[Emmanuel Charpentier]

[-- Attachment #1.1: Type: text/plain, Size: 2094 bytes --]

[ Sixth '!) attempt to send this question to emacs-orgmode. Sorry for the
possible duplicates... ]

I wish to be able to reference (i. e cross-references, lists) both some
tables or figures AND the code producing the objects.

To this effect, I added (distinct) #+caption:s to the source blocks AND
to the results, adorned with (distinct) org-ref's labels. An example is
included in the enclosed file Min-Ref.org.

The comparison of this source, the LaTeX code obtained by org-latex
export-to latex (Min-Ref.tex) and the resultant PDF (Min-Ref exported
by org-latex-export-to-pdf.pdf) show that the labels attributed to
source blocks are mislabeled as figures. Furthermore, while the org
source requests a list of figure, a list of table and a list of
listings (in that order), the list of figures appears *after* the list
of tables.

I am tempted to conclude that there is some confusion between figures
and listings. Further attempts tend to show that the problem may live n
the core org's code, rather than any specific exporter :

The ODT "native" exporter (org-odt-export-to-odt) is much less capable,
as shown in Min-Ref exported by org-odt-export-to-odt.odt.

Attempts to export via Pandoc to PDF (Min-Ref exported by org-pandoc-
export-to-latex-pdf.pdf), ODT (Min-Ref exported by org-pandoc-export-
to-odt.odt) and DOCX (Min-Ref.docx) show that these exporters may need
some specific configurations in order to be even vaguely usable.

Previous trials, using #+names: rather than org-ref's labels, gave
similar failures. If needed, I can reproduce these trials.

So I have a couple questions :

1) Is the confusion of source blocks and figures a bug, or do I miss a
subtle point ?

2) Is there some introductory material to the care and feeding of ox-
pandoc demonstrating the use of this exporter's options to enable the
addition of the needed features (figure inclusion, tables of tables /
figures / listings, etc...) ? The "manual" available as a README is way
too terse to be usable without diving in the source code and pandoc's
documentation.

Sincerely,

--
Emmanuel Charpentier

[-- Attachment #1.2: Type: text/html, Size: 8637 bytes --]

[-- Attachment #2: Min-Ref.org --]
[-- Type: application/octet-stream, Size: 1645 bytes --]


#+options: toc:nil
#+property: header-args:python :session
#+language: fr

#+title: What's up with references ?
#+author:
#+date: December 2018

#+toc: headlines
#+toc: figures
#+toc: tables
#+toc: listings

* Some reference samples

This is created using =org-ref= 's =label= 's and =ref= 's.

** A reference...

... to cite:gelmanBayesianDataAnalysis2013 ,a /good/ textbook.

** A table

A Python block producing a (silly) table.

#+caption: A (silly) Python block. label:lst:Python1
#+BEGIN_SRC python :results table :exports both
[[u+str(v) for v in range(1,4)] for u in ["a", "b"]]
#+END_SRC

#+caption: A (silly) Python table. label:tab:Python1
#+RESULTS:
| a1 | a2 | a3 |
| b1 | b2 | b3 |

The table ref:tab:Python1 is produced by the code ref:lst:Python1.

** A figure

A Python block producing a figure.

#+caption: A Python block producing a figure. label:lst:Python2
#+BEGIN_SRC python :results file :exports both
import matplotlib.pyplot as plt, numpy as np
from sympy import *
x=symbols("x")
f=lambda x:sin(x)/x
t=np.arange(-6*np.pi,6*np.pi, 0.1)
ft=[f(u) for u in t]
fig=plt.figure(figsize=(3,2))
plt.plot(t, ft, "b-")
fig.tight_layout()
plt.savefig("tstfig.pdf")
"tstfig.pdf"
#+END_SRC

#+caption: A (not so silly) figure produced by Python. label:fig:Python2
#+RESULTS:
[[file:tstfig.pdf]]

The figure ref:fig:Python2 is produced by the code ref:lst:Python2.

[[bibliographystyle:vancouver]]
[[bibliography:Minimal.bib]]

# Local Variables:
# org-latex-packages-alist: (("AUTO" "babel" t ("pdflatex")) ("AUTO" "polyglossia" t ("xelatex" "lualatex")))
# org-latex-pdf-process: ("latexmk -shell-escape -bibtex -f -pdf %f")
# End:

[-- Attachment #3: Min-Ref.docx --]
[-- Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document, Size: 10789 bytes --]

[-- Attachment #4: Min-Ref.tex --]
[-- Type: text/x-tex, Size: 2236 bytes --]

% Created 2018-12-17 lun. 15:49
% Intended LaTeX compiler: pdflatex
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\usepackage[frenchb]{babel}
\date{December 2018}
\title{What's up with references ?}
\hypersetup{
 pdfauthor={},
 pdftitle={What's up with references ?},
 pdfkeywords={},
 pdfsubject={},
 pdfcreator={Emacs 27.0.50 (Org mode 9.1.14)}, 
 pdflang={Frenchb}}
\begin{document}

\maketitle
\tableofcontents
\listoftables
\listoffigures

\section{Some reference samples}
\label{sec:orgfe4b8ad}

This is created using \texttt{org-ref} 's \texttt{label} 's and \texttt{ref} 's.

\subsection{A reference\ldots{}}
\label{sec:org22891f6}

\ldots{} to \cite{gelmanBayesianDataAnalysis2013} ,a \emph{good} textbook.

\subsection{A table}
\label{sec:org844d514}

A Python block producing a (silly) table.

\begin{verbatim}
[[u+str(v) for v in range(1,4)] for u in ["a", "b"]]
\end{verbatim}
\captionof{figure}{A (silly) Python block. \label{lst:Python1}}

\begin{table}[htbp]
\caption{A (silly) Python table. \label{tab:Python1}}
\centering
\begin{tabular}{lll}
a1 & a2 & a3\\
b1 & b2 & b3\\
\end{tabular}
\end{table}

The table \ref{tab:Python1} is produced by the code \ref{lst:Python1}.

\subsection{A figure}
\label{sec:orgf75a27d}

A Python block producing a figure.

\begin{verbatim}
import matplotlib.pyplot as plt, numpy as np
from sympy import *
x=symbols("x")
f=lambda x:sin(x)/x
t=np.arange(-6*np.pi,6*np.pi, 0.1)
ft=[f(u) for u in t]
fig=plt.figure(figsize=(3,2))
plt.plot(t, ft, "b-")
fig.tight_layout()
plt.savefig("tstfig.pdf")
"tstfig.pdf"
\end{verbatim}
\captionof{figure}{A Python block producing a figure. \label{lst:Python2}}

\begin{figure}[htbp]
\centering
\includegraphics[width=.9\linewidth]{tstfig.pdf}
\caption{A (not so silly) figure produced by Python. \label{fig:Python2}}
\end{figure}

The figure \ref{fig:Python2} is produced by the code \ref{lst:Python2}.

\bibliographystyle{vancouver}
\bibliography{Minimal}
\end{document}

[-- Attachment #5: Min-Ref exported by org-pandoc-export-to-odt.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 17044 bytes --]

[-- Attachment #6: Min-Ref exported by org-latex-export-to-pdf.pdf --]
[-- Type: application/pdf, Size: 143423 bytes --]

[-- Attachment #7: Min-Ref exported by org-odt-export-to-odt.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 18946 bytes --]

[-- Attachment #8: Min-Ref exported by org-pandoc-export-to-latex-pdf.pdf --]
[-- Type: application/pdf, Size: 202284 bytes --]

Problem with references to babel source blocks (possible bug).

[Emmanuel Charpentier]

I wish to be able to reference (i. e cross-references, lists) both some
tables or figures AND the code producing the objects.

To this effect, I added (distinct) #+caption:s to the source blocks AND
to the results, adorned with (distinct) org-ref's labels. An example ( 
Min-Ref.org) is included in this Google Drive directory*: 
https://drive.google.com/drive/folders/1T6N_-WwphlnL2mB4f6BgX0u1K5mLnz4i?usp=sharing
.

The comparison of this source, the LaTeX code obtained by org-latex
export-to latex (Min-Ref.tex) and the resultant PDF (Min-Ref exported
by org-latex-export-to-pdf.pdf) show that the labels attributed to
source blocks are mislabeled as figures. Furthermore, while the org
source requests a list of figure, a list of table and a list of
listings (in that order), the list of figures appears *after* the list
of tables.

I am tempted to conclude that there is some confusion between figures
and listings. Further attempts tend to show that the problem may live n
the core org's code, rather than any specific exporter :

The ODT "native" exporter (org-odt-export-to-odt) is much less capable,
as shown in Min-Ref exported by org-odt-export-to-odt.odt.

Attempts to export via Pandoc to PDF (Min-Ref exported by org-pandoc-
export-to-latex-pdf.pdf), ODT (Min-Ref exported by org-pandoc-export-
to-odt.odt) and DOCX (Min-Ref.docx) show that these exporters may need
some specific configurations in order to be even vaguely usable.

Previous trials, using #+names: rather than org-ref's labels, gave
similar failures. If needed, I can reproduce these trials.

So I have a couple questions :

1) Is the confusion of source blocks and figures a bug, or do I miss a
subtle point ?

2) Is there some introductory material to the care and feeding of ox-
pandoc demonstrating the use of this exporter's options to enable the
addition of the needed features (figure inclusion, tables of tables /
figures / listings, etc...) ? The "manual" available as a README is way
too terse to be usable without diving in the source code and pandoc's
documentation.

Sincerely,

--
Emmanuel Charpentier

* Six attempts at posting those files attached to the present mail have
convinced me that the list manager rejects at least the messages
containing some attachments (docx ? dot ?) ; I'm a little bit fed up
with this...

Re: Problem with references to babel source blocks (possible bug).

[John Kitchin]

I guess there is some subtle point missing. For the source blocks I
usually use the minted package, which I think makes code blocks as a
listing float. In your tex file, they are verbatim environments, and you
have \captionof{figure} under them which is presumably why they are
labeled as figures.

Try adding ("" "minted" nil) to # org-latex-packages-alist:

and add this to an init file: (setq org-latex-listings 'minted).

Best wishes,

Emmanuel Charpentier <emanuel.charpentier@gmail.com> writes:

> I wish to be able to reference (i. e cross-references, lists) both some
> tables or figures AND the code producing the objects.
>
> To this effect, I added (distinct) #+caption:s to the source blocks AND
> to the results, adorned with (distinct) org-ref's labels. An example (
> Min-Ref.org) is included in this Google Drive directory*:
> https://drive.google.com/drive/folders/1T6N_-WwphlnL2mB4f6BgX0u1K5mLnz4i?usp=sharing
> .
>
> The comparison of this source, the LaTeX code obtained by org-latex
> export-to latex (Min-Ref.tex) and the resultant PDF (Min-Ref exported
> by org-latex-export-to-pdf.pdf) show that the labels attributed to
> source blocks are mislabeled as figures. Furthermore, while the org
> source requests a list of figure, a list of table and a list of
> listings (in that order), the list of figures appears *after* the list
> of tables.
>
> I am tempted to conclude that there is some confusion between figures
> and listings. Further attempts tend to show that the problem may live n
> the core org's code, rather than any specific exporter :
>
> The ODT "native" exporter (org-odt-export-to-odt) is much less capable,
> as shown in Min-Ref exported by org-odt-export-to-odt.odt.
>
> Attempts to export via Pandoc to PDF (Min-Ref exported by org-pandoc-
> export-to-latex-pdf.pdf), ODT (Min-Ref exported by org-pandoc-export-
> to-odt.odt) and DOCX (Min-Ref.docx) show that these exporters may need
> some specific configurations in order to be even vaguely usable.
>
> Previous trials, using #+names: rather than org-ref's labels, gave
> similar failures. If needed, I can reproduce these trials.
>
> So I have a couple questions :
>
> 1) Is the confusion of source blocks and figures a bug, or do I miss a
> subtle point ?
>
> 2) Is there some introductory material to the care and feeding of ox-
> pandoc demonstrating the use of this exporter's options to enable the
> addition of the needed features (figure inclusion, tables of tables /
> figures / listings, etc...) ? The "manual" available as a README is way
> too terse to be usable without diving in the source code and pandoc's
> documentation.
>
> Sincerely,


--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

Re: Problem with references to babel source blocks (possible bug).

[Emmanuel Charpentier]

Dear John, dear list,

Indeed using minted works (at least when using labels. I have not yet
tried to use #+NAME:s). See a few remarks below.

Le jeu. 20 déc. 2018 à 21:47, John Kitchin <jkitchin@andrew.cmu.edu> a écrit :
>
> I guess there is some subtle point missing. For the source blocks I
> usually use the minted package, which I think makes code blocks as a
> listing float. In your tex file, they are verbatim environments, and you
> have \captionof{figure} under them which is presumably why they are
> labeled as figures.
>
> Try adding ("" "minted" nil) to # org-latex-packages-alist:
>
> and add this to an init file: (setq org-latex-listings 'minted).

The mistery starts with the "Src blocks" part of ox-latex (starting
line 895 in today's version of this file). In the default case (i. e.
when org-latex-listing is not set), this modules exports a verbatim
environment ... and a \labelof{figure} label !!!

Another part of the mystery is explained in the function
org-latex-keyword (starting at line 2218 of today's version of
org-latex.el). This function is, among others, in charge of
determining the environment of a table of contents for code snippets.
This tests org-latex-listings and switches :
nil --> listoffigures
minted --> listoflistings
otherwise --> lstlistoflitings

BTW, reading this code also allows to understand why org-mode complies
to #+TOC: headings, #+TOC: tables, #+TOC: listings, but NOT #+TOC:
figures.

I wonder why this choice has been made. Probably because this avoids
the need for a latex package for source code listings. hich is indeed
a bit of a quandary :

* listings is obsolete, unmaintained and has serious issues with
anything not strict ASCII (plays fast and loose with TeX catcodes...).

* minted needs to write and read intermediate file, which is a bt of a
security risk, hence not enabled by default.

The choice of figures as a default environment for code snippets has a
couple consequences :

* Problems at exporting anywhere but latex

* No way to have simultaneously a list of figures and list of listings

* No list of figures bt by direct use of "\listoffigures" in LaTeX.

Shouldn't we consider this a bit of a misdesign ? I dont (yet) seem a
way to en hance this.

Suggestions ?

--
Emmanuel Charpentier

> Best wishes,
>
> Emmanuel Charpentier <emanuel.charpentier@gmail.com> writes:
>
> > I wish to be able to reference (i. e cross-references, lists) both some
> > tables or figures AND the code producing the objects.
> >
> > To this effect, I added (distinct) #+caption:s to the source blocks AND
> > to the results, adorned with (distinct) org-ref's labels. An example (
> > Min-Ref.org) is included in this Google Drive directory*:
> > https://drive.google.com/drive/folders/1T6N_-WwphlnL2mB4f6BgX0u1K5mLnz4i?usp=sharing
> > .
> >
> > The comparison of this source, the LaTeX code obtained by org-latex
> > export-to latex (Min-Ref.tex) and the resultant PDF (Min-Ref exported
> > by org-latex-export-to-pdf.pdf) show that the labels attributed to
> > source blocks are mislabeled as figures. Furthermore, while the org
> > source requests a list of figure, a list of table and a list of
> > listings (in that order), the list of figures appears *after* the list
> > of tables.
> >
> > I am tempted to conclude that there is some confusion between figures
> > and listings. Further attempts tend to show that the problem may live n
> > the core org's code, rather than any specific exporter :
> >
> > The ODT "native" exporter (org-odt-export-to-odt) is much less capable,
> > as shown in Min-Ref exported by org-odt-export-to-odt.odt.
> >
> > Attempts to export via Pandoc to PDF (Min-Ref exported by org-pandoc-
> > export-to-latex-pdf.pdf), ODT (Min-Ref exported by org-pandoc-export-
> > to-odt.odt) and DOCX (Min-Ref.docx) show that these exporters may need
> > some specific configurations in order to be even vaguely usable.
> >
> > Previous trials, using #+names: rather than org-ref's labels, gave
> > similar failures. If needed, I can reproduce these trials.
> >
> > So I have a couple questions :
> >
> > 1) Is the confusion of source blocks and figures a bug, or do I miss a
> > subtle point ?
> >
> > 2) Is there some introductory material to the care and feeding of ox-
> > pandoc demonstrating the use of this exporter's options to enable the
> > addition of the needed features (figure inclusion, tables of tables /
> > figures / listings, etc...) ? The "manual" available as a README is way
> > too terse to be usable without diving in the source code and pandoc's
> > documentation.
> >
> > Sincerely,
>
>
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu