From 1392b08f7b92bbc87584c9cbcc084dc3dab7b79b Mon Sep 17 00:00:00 2001
From: tiyn <tiyn@mail-mk.eu>
Date: Wed, 24 Apr 2024 00:29:51 +0200
Subject: [PATCH] bibliographic software: added papis

---
 wiki/bibliographic_software.md |   9 +++
 wiki/linux/papis.md            | 133 +++++++++++++++++++++++++++++++++
 2 files changed, 142 insertions(+)
 create mode 100644 wiki/bibliographic_software.md
 create mode 100644 wiki/linux/papis.md

diff --git a/wiki/bibliographic_software.md b/wiki/bibliographic_software.md
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+# Bibliographic Software
+
+A bibliographic software is software that manages a database of citation or bibliographic records.
+It produces citations for the stored records that are used in scholarly research.
+
+## Software Solutions
+
+- [Papis](/wiki/linux/papis.md) is a [command-line based](/wiki/linux/shell.md) for
+  [Linux](/wiki/linux.md) bibliography manager that can be used for LaTeX using the BibTeX format.
diff --git a/wiki/linux/papis.md b/wiki/linux/papis.md
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+# Papis
+
+[Papis](/wiki/linux/papis.md) is a [command-line based](/wiki/linux/shell.md) for
+[Linux](/wiki/linux.md) [bibliography manager](/wiki/bibliographic_software.md) that can be used
+for LaTeX using the BibTeX format.
+
+## Setup
+
+Papis can be installed on most distributions by acquiring the `papis` package.
+Alternatively it can be downloaded from [the GitHub page](https://github.com/papis/papis).
+
+### Configuration
+
+To use Papis a config file needs to be created.
+The path of the global config file is `~/.config/papis/config`.
+A minimal config can look like the following.
+Make sure to change the path of the papers directory.
+
+```txt
+[papers]
+dir = ~/cloud/bibliography/papis
+
+[settings]
+default-library = papers
+```
+
+## Usage
+
+The following section describes various ways of usage of Papis.
+
+### Adding, Removing, Editing and Browsing Entries
+
+An entry can be added by running a command similar to the following.
+The values for the different keys needs to be changed, added or omitted accordingly.
+
+```sh
+papis add ~/Documents/interesting.pdf \
+    --folder-name interesting-paper-2021 \
+    --set author 'John Smith' \
+    --set title 'The interesting life of bees' \
+    --set year 1985 \
+    --set tags 'biology interesting bees'
+```
+
+Papis can also add sources directly via their DOI code.
+
+```sh
+papis add --from doi 10.10763/1.3237134
+```
+
+For the most well known journals are also recognized by Papis
+
+```sh
+papis add https://arxiv.org/abs/1712.03134
+```
+
+To remove an entry the following command can be run.
+Afterwards the entry that should be removed can be easily selected via the terminal user interface.
+
+```sh
+papis rm
+```
+
+Entries can be edited by using the following command.
+
+```sh
+papis edit
+```
+
+Entries can be browsed and viewed either in the terminal or via a local website.
+For the first run the following command.
+
+```sh
+papis browse
+```
+
+For the latter the following command can be run to start the server.
+The command-line output will show the address to reach the service.
+
+```sh
+papis serve
+```
+
+### Create a BibTeX file
+
+A BibTeX file containing all the entries of all the libraries can be created by running the
+following command.
+For this the command will create a file called `lib.bib`.
+
+```sh
+papis export --all --format bibtex --out lib.bib
+```
+
+### Clearing the Cache
+
+The cache of Papis can be cleared by running the following command.
+
+```sh
+papis --cc
+```
+
+### Import Entries from a BibTeX File
+
+This section will discuss the way to add the contents of a BibTeX file to the database.
+First the BibTeX file (in this case called `mylib.bib`) will be used to create a new database
+inside the folder `tmp-db`.
+
+```sh
+papis bibtex read mylib.bib import -a -o tmp-db
+```
+
+Afterwards the contents of the temporary database should be checked to be correctly imported.
+
+```sh
+papis -l tmp-db edit
+```
+
+Afterwards the contents of the temporary library should be moved to the actualy directory where
+papis stores its entries.
+The path for that can be found in the [config file](#configuration).
+
+```sh
+mv tmp-db/* /path/to/your/library/folder/
+```
+
+Finally the cache needs to be cleared for Papis to display the new entries correctly.
+
+```sh
+papis --cc
+```
+
+Finally the cache needs to be [cleared](#clearing-the-cache) for Papis to display the new entries
+correctly.