Commit a3c775a2 authored by Simon Spannagel's avatar Simon Spannagel
Browse files

Merge branch 'p/docs-pdf-fix-internal-refs' into 'master' 

docs: fix internal references in the PDF

See merge request allpix-squared/allpix-squared!789
parents 51239100 d996972f

doc/convert/convert_markdown.py

+51 −13
Original line number Diff line number Diff line
@@ -10,6 +10,7 @@ Convert GitLab Flavored Markdown to hugo or LaTeX using pandoc. 
import argparse

import functools

import os

import pathlib

import re

import subprocess

import sys
@@ -106,15 +107,15 @@ def latex_fix_images(string: str, file_path: str) -> str: 


    Args:

        string: String formatted in LaTeX.

        file_path: Path to the file where the string was extracted from.



    Returns:

        String formatted in LaTeX.

    """

    base_dir = os.path.dirname(file_path)

    string = re.sub(r'\\includegraphics{\./(.+?)}',

    return re.sub(r'\\includegraphics{\./(.+?)}',

                  rf'\\includegraphics[width=\\textwidth,height=0.6\\textheight,keepaspectratio]{{{base_dir}/\1}}',

                  string)

    return string





def latex_fix_duplicate_autocites(string: str) -> str:
@@ -144,9 +145,25 @@ def latex_convert_hugo_alert(string: str) -> str: 
        String formatted in LaTeX.

    """

    match = r'\\{\\{\\%\s+alert\s+title=``(.+?)\'\'\s+color=``(.+?)\'\'\s+\\%\\}\\}\s+(.+?)\s+\\{\\{\\%\s+/alert\s+\\%\\}\\}'

    return re.sub(match, r'\\begin{hugo\2}\n\\textbf{\1}:\n\3\n\\end{hugo\2}', string, flags=re.DOTALL)



    string = re.sub(match, r'\\begin{hugo\2}\n\\textbf{\1}:\n\3\n\\end{hugo\2}', string, flags=re.DOTALL)

    return string



def _get_path_relative_to_markdown_tree(file_path: str) -> str:

    """

    Return the path relative to the markdown tree (assuming at most one directory depth).



    For example, `/path/to/docs/01_introduction/_index.md` becomes `01_introduction/_index.md`.



    Args:

        file_path: Path to the file.



    Returns:

        String with the relative path.

    """

    file_path_pl = pathlib.Path(file_path).resolve()

    docs_dir_pl = file_path_pl.parents[1]

    file_path_rel_pl = file_path_pl.relative_to(docs_dir_pl)

    return file_path_rel_pl.as_posix()





def latex_convert_href_references(string: str, file_path: str) -> str:
@@ -157,11 +174,33 @@ def latex_convert_href_references(string: str, file_path: str) -> str: 


    Args:

        string: String formatted in LaTeX.

        file_path: Path to the file where the string was extracted from.



    Returns:

        String formatted in LaTeX.

    """

    return string  # TODO

    # Replace hypertargets with something that include part of the file path to prevent duplicate targets

    file_label_prefix = _get_path_relative_to_markdown_tree(file_path)

    # For the first target we don't want to include the section name as we don't have that in GLFM

    string = re.sub(r'^(\\hypertarget{)([^\n]+?)(}{%\n.+?\\label{)(.+?)(}})',

                    rf'\g<1>{file_label_prefix}\g<3>{file_label_prefix}\g<5>',

                    string, count=1, flags=re.DOTALL)

    # For the following targets we do want the section name to be included

    string = re.sub(r'(.+?\\hypertarget{)([^\n]+?)(}{%\n.+?\\label{)(.+?)(}})',

                    rf'\g<1>{file_label_prefix}-\g<2>\g<3>{file_label_prefix}-\g<4>\g<5>',

                    string, flags=re.DOTALL)

    # We need to adjust references in the same file as well though

    string = re.sub(r'(\\hyperlink{)(.+?)(}{)', rf'\g<1>{file_label_prefix}-\g<2>\g<3>', string)

    # Find references to other files

    refs = re.findall(r'(\\href{)(\.\.?/.+?)(})', string)

    for ref in refs:

        ref_rel_file_path = ref[1]

        ref_full_match = ref[0] + ref[1] + ref[2]

        ref_file_path = os.path.join(os.path.dirname(file_path), ref_rel_file_path)

        ref_replace = _get_path_relative_to_markdown_tree(ref_file_path).replace('\#', '-')

        string = re.sub(re.escape(ref_full_match), rf'\\protect\\hyperlink{{{ref_replace}}}', string)



    return string





def gitlab2hugo(string: str, isindexmd: bool) -> str:
@@ -170,15 +209,14 @@ def gitlab2hugo(string: str, isindexmd: bool) -> str: 


    Args:

        string: String formatted in GitLab Markdown.

        isindexmd: If true the file where string is extracted from is an index page for hugo.



    Returns:

        String formatted in hugo Markdown.

    """

    if not isindexmd:

        string = hugo_convert_relative_paths(string)

    string = hugo_reference_remove_md(string)



    return string

    return hugo_reference_remove_md(string)





def gitlab2pandoc(string: str) -> str:
@@ -191,9 +229,7 @@ def gitlab2pandoc(string: str) -> str: 
    Returns:

        String formatted in pandoc Markdown.

    """

    string = hugo_front_matter_convert_pandoc(string)



    return string

    return hugo_front_matter_convert_pandoc(string)





def pandoc2latex(string: str, file_path: str, extra_args: list[str] = None) -> str:
@@ -202,6 +238,7 @@ def pandoc2latex(string: str, file_path: str, extra_args: list[str] = None) -> s 


    Args:

        string: String formatted in pandoc Markdown.

        file_path: Path to the file where the string was extracted from.

        extra_args: List of additional arguments for pandoc.



    Returns:
@@ -242,6 +279,7 @@ def gitlab2latex(string: str, isindexmd: bool, file_path: str) -> str: 
    Args:

        string: String formatted in GitLab Markdown.

        isindexmd: If true, the top level division will be set to chapter.

        file_path: Path to the file where the string was extracted from.



    Returns:

        String formatted in LaTeX.

doc/usermanual/05_models/04_trapping.md

+1 −0
Original line number Diff line number Diff line
@@ -22,6 +22,7 @@ have been extracted under certain annealing conditions. A dependency on annealin 
Please refer to the corresponding reference publications for further details.



The following models for trapping of charge carriers can be selected:



## Ljubljana



In the Ljubljana (sometimes referred to as *Kramberger*) model \[[@kramberger]\], the trapping time follows the relation

doc/usermanual/11_testing/01_configurations.md

+2 −2
Original line number Diff line number Diff line
@@ -34,8 +34,8 @@ output has to be adapted after careful verification of the simulation result. 


Module tests are located within the individual module source folders and are only enabled if the respective module will be

built. For new modules, the directory in which the test files are located needs to be registered in the main CMake file of

the module as described in [Section 9.3](../09_development/03_new_module.md#cmakeliststxt). Module test files have to start

with a two-digit number and end with the file extension `.conf`, e.g. `01-mytest.conf`, to be detected.

the module as described in [Section 9.3](../09_development/03_new_module.md#files-of-a-module). Module test files have to

start with a two-digit number and end with the file extension `.conf`, e.g. `01-mytest.conf`, to be detected.



## Performance Tests