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https://github.com/jasedit/scriptorium

Repository creating a framework for providing a MultiMarkdown and LaTeX based system for easily writing academic papers.
https://github.com/jasedit/scriptorium

academic-publications latex markdown paper papers

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Repository creating a framework for providing a MultiMarkdown and LaTeX based system for easily writing academic papers.

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# Scriptorium



Framework for easily using MultiMarkdown and LaTeX based system to write academic papers, especially those with shared templates for organization. This system is designed with several important design guidelines and observations:



1. Many academic publications are collaborative, continuously evolving works.

2. Many academic publications provide LaTeX templates to meet the formatting guidelines for submission.

3. Research groups often use common templates for documents, such as submitting to a particular conference repeatedly over the years, or thesis/dissertation requirements at a particular university.

4. LaTeX can have a high learning curve for people unfamiliar with its syntax and style. Simpler markup langauges can sacrifice control for ease of use or readability. Ideally, a system would provide tools that cover the continuum between simplicity and control.

5. Academic publications can have a mix of visibility/availability between groups. Some papers may be private to an individual, a group, some mix of groups, or publicly available. The tools for building papers may not share this variability of privacy.



In light of these observations, this framework aims to provide:



1. Version control for documents, allowing concurrent collaboration, full history tracking, branching for edits, etc.

2. User friendly in syntax and operation, minimizing the requirement to learn gory internal details.

3. Provide the ability to selectively access lower level commands for power users to fine tune results.

4. A base for groups to use to distribute/share a common working base, with flexibility for individuals to choose documents which are present on their system.

5. Fine grained privacy controls for controlling access to documents and intellectual property.

6. Plain text as the basis for documents, ensuring that a wide variety of workflows and tools can be used to edit documents.



# Installation



## Linux Installation



1. Install external dependencies:

    1. [git](https://git-scm.com/)

    2. [LaTeX](http://www.latex-project.org/)

        1. Some distributions don't include [biber](http://biblatex-biber.sourceforge.net), which should be installed as well

    3. [Python](http://python.org/)

    4. [cmake](https://cmake.org/), which is required to build MultiMarkdown

2. Execute `pip install scriptorium`

3. Install the MultiMarkdown shared library by executing `sudo python -c "import pymmd; pymmd.build_mmd()"`



# Mac Installation



1. Install external dependencies:

    1. [git](https://git-scm.com/)

    2. [MacTeX](https://www.tug.org/mactex/)

    3. [pip](https://pip.pypa.io/en/latest/installing/#install-or-upgrade-pip)

2. Execute `pip install scriptorium`



## Windows Setup



These instructions provide a method to configure Scriptorium to work on Windows with a minimum of fuss. There are many other ways to configure this system, and cleaner instructions would be appreciated in a pull request



1. Install the [GitHub Desktop Client](https://desktop.github.com/), and follow the directions to configure it with your GitHub account.

2. Install [MikTex](http://miktex.org/)

3. Install [Python](https://www.python.org/downloads/)

4. Modify the Environment Variables to add Python to the `PATH` variable. Based on the helpful instructions [here](http://stackoverflow.com/questions/23400030/windows-7-add-path):

    1. Right click on "My Computer" and select Properties

    2. In the System Properties window, click on Advanced

    3. Click on the "Environment Variables" button

    4. Select the `PATH` variable, and add Python. The default values would be `C:\Python27` and `C:\Python27\Scripts` for Python 2.7, or `C:\Python35` and `C:\Python35\Scripts` for Python 3.5, although this would changed if the installation directories were changed in previous steps.

5. Open the "Git Shell" installed by GitHub, and verify that `python.exe` and `pip` are recognized commands.

7. Execute `pip install scriptorium`



# Tutorial



Scriptorium can be invoked directly from the command line using the name `scriptorium`.



Check that all external dependencies are installed and detected correctly, by veryifying the following command returns nothing:

```

scriptorium doctor

```



You can check where templates will be installed:

```

scriptorium config TEMPLATE_DIR

```



or change the directory:

```

scriptorium config TEMPLATE_DIR ~/.scriptorium/templates

```



Install some example [templates](https://github.com/jasedit/simple_templates):

```

scriptorium template -i https://github.com/jasedit/simple_templates.git

```



To list which templates are currently available in scriptorium:

```

scriptorium template -l

```



To create a new paper in the directory `example_report` using the report template previously installed:

```

scriptorium new example_report -t report -c author "John Doe" -c title "My Example Report"

```



Adding example content using the command:

```

echo "



# Introduction



This is an introductory section." >> example_report/paper.mmd

```



The PDF of the report can be built using:

```

scriptorium build example_report

```

or, if inside `example_report`:

```

scriptorium build

```



## Papers Organization



Since papers in development are generally not open-source, this framework pushes papers into standalone folders. Storing these folders in version control is **STRONGLY** encouraged, though not strictly required by the system. Generally, version control repositories don't handle binary files (e.g. images) particularly well, so it is recommended to break up papers into more repositories to require less overhead storing history, as well as providing finer granularity in sharing papers.



### Paper Metadata



In order to integrate the template system, the MultiMarkdown metadata header requires a few important statements. Consider an example header, as shown below.



```

Base Header Level: 3

latex author: Author

Title: Paper Title

myemail: [email protected]

latex input: template/setup.tex

latex footer: template/footer.ex

```



The Base Header Level is important for configuring MultiMarkdown to avoid section levels which may not be supported by the template being used. Level 1 is the `\chapter` command in LaTeX, which is often unused in conference papers. The `latex author` key bypasses input sanitization, allowing LaTeX specific commands in the authors title. `myemail` is the author's e-mail address. The input and footer are used to read the template preamble and footer. Some templates will also read a `metadata.tex` file, which provides a direct LaTeX file for specifying metadata when LaTeX specific commands are necessary.



## Template Organization



A template defines the latex setup defining how a paper is going to be laid out, which packages it will use, etc. For reference, consider templates in the [simple templates](https://github.com/jasedit/simple_templates) repository. A template is made in a few steps:



1. A folder inside the templates directory. The name of this folder is what is used to reference the template in a MultiMarkdown paper, by LaTeX's recursive subdirectory search.

2. A LaTeX file named `setup.tex` inside this folder, which contains the template preamble. The preamble should include everything at the start of the document before the content, through the `\begin{document}` statement. More may be included in this preamble, such as seen in the IEEEtran example in the simple templates.

3. A LaTeX file named `footer.tex` inside this folder, which contains any LaTeX which should be appended to the end of the file. This often includes the bibliography commands. The IEEEtran `footer.tex` file is a good example of such a footer.

4. An optional `frontmatter.mmd` and/or `metadata.tex` file, which contains a default values, minus the input and footer values. Any field can have a value starting with a dollar sign, and capital alphanumeric and `_`, `.`, or `-`, which are replaceable during the `new` command.