Features

New: Special papis_id key (#449)

In order to make plugin writing easier we have decided to introduce a papis_id key in the document's info files. This key essentially functions as a UUID for the document. Many commands have gained support for this, e.g.

papis list --id query
papis open papis_id:someid

For more information see the documentation.

Important: This change requires updating the database backend. This can be done by simply clearing the cache using papis --cc.

New: papis doctor command (#421)

A new papis doctor command was introduced that can be used to check that document information is correct, up to date, or is nicely linted. The command also supports fixing incorrect information for many cases!

It can be used as

papis doctor --checks files --explain query

There are several useful checks implemented already (non-exhaustive list):

• files: checks that the document files actually exist in the file system.
• keys-exist: checks that the provided keys exist in the document.
• bibtex-type: checks that the document type is a valid BibTeX type.
• refs: checks that the document ref exists and does not contain invalid characters.

For more information see the documentation.

New: papis citations command (#451)

A new papis citations command was added to handle retrieving citation information for a document. This includes both papers cited by the document and those which cite the document itself.

For more information see the documentation.

New: Add DBLP support (#489)

Add support for the DBLP database. The database can now be explored using

papis explore dblp -q query pick

and documents can be imported directly using the DBLP key or URL

papis add --from dblp 'conf/iccg/EncarnacaoAFFGM93'

Major improvements to the web application (#424)

The Papis web application, which can be accessed with papis serve, has seen major development since the last version. It now has support for

• editing of info.yaml file of a document (requires ace.js).
• viewing document PDF files directly in the browser (requires pdfjs).
• viewing LaTeX in titles, abstracts and others (requires KaTeX).
• exporting the document to BibTeX.
• showing citations for the document.
• showing errors from papis doctor.
• showing a timeline for queried documents.

And many other general interface and robustness improvements.

Other noteworthy features

• A major overhaul of the README (#415).
• Consistent use of ANSI colors (#462).
• Better notes handling in papis update (#404), papis edit (#391) and the papis picker (#319).
• Improvements to BiBTeX export ( #412 #444 #443 #468).
• Support NO_COLOR (#437).
• Major overhaul of the papis config command, which can now show defaults and select specific sections (#454).
• Fix shell completion on bash, zsh, and fish (#478).
• Update the logging format (#465).
• Updated multiple downloaders to support the latest version of the website and for better data extraction ( #441 #447).
• Avoid downloading files on papis add in certain scenarios (#505).
• Recognize DjVu files correctly (#522).
• Add USENIX downloader (#523).
• Support remote URLs in papis addto (#541).
• Add sort-reverse configuration option (#543).

Bug fixes

• Properly detach processes on papis open (#476).
• Fix link extraction in crossref (#480).
• Do not generate refs in downloaders (#483).
• Fix empty config file handling (#497).
• Fix database query for jinja2 (#499).
• Fix crash on trying to add a duplicate document (#510).
• Fix many typos (#540).

Many issues were resolved and new (and old) contributors made the following changes possible.

Add hook infrastructure

A basic hook infrastructure has been added to be able to use emacs-like hooks for some commands.

Add additional keyword for the formatter plugin system

papis bibtex

• Add import command to import bibtex files as papis documents into the library.
• Add filter-cited.

papis exec

• Add command exec to run python scripts in the environment of the papis executable.

papis picker

• You can now pick several elements with the key binding c-t
• Add support for fzf picker, check out the documentation.

papis merge

• Add the command papis merge to merge documents in pairs.

papis browse

• Add -n and --print to just print the url to be opened.

Downloaders

• Add an acm downloader
• Add an Project Euclid downloader

Notes

Now you can remove notes files with papis rm --notes or have templates for the notes. Check out the notes-template variable.

Web application papis serve

• The new, simple and experimental web application is available through the papis serve command. Feel free to make suggestions.

MacOS

• disable multiprocessing by default on mac due to lack of performance and source of strange behaviour.

Community

• usage of github discussions and #papis channel on libera.

papis explore

• Add add command to simply add documents retrieved.

papis.export

• Add the key _papis_local_folder so that third-party apps can get the documents' paths without having to go again through papis.

papis bibtex

• Add unique command to be able to merge different bib files and filter out repetitions.
• Add doctor to check for fields in a bibfile.
• Add iscited to check which bib items are cited in a text file.

Add Format plugin

• Sébastien Popoff has added a format plugin architecture, so now jinja2 is available again as a plugin.

Bibtex

• Improve the reference building routine.
• Change the default ref-format to

  "{doc[title]:.15} {doc[author]:.6} {doc[year]}",
  

• The default ref if no reference could be built will not be using the folder name as before, but using the values in the info.yaml limited to 30 characters.

papis add

• Create a reference at the time of adding if no reference exists.

papis browse

• Add more documentation.
• Add an ads handler to jump into the ads website of the paper using a doi.

VERSION v0.10

• Fix several bugs.
• Typecheck the whole codebase and drop support for python versions up to 3.4, the latter version included.
• Add --sort and --reverse flags to most command line commands, together with the sort-file configuration option. see doc.
• Add time-stamps in order to sort chronologically documents see doc.
• Add --doc-folder to most command line commands for better bash-scripting capabilities.
• Add --logfile flag in order to dump log messages to a file.
• Move papis.utils.format_doc to papis.document.format_doc in order to minimize circular dependencies.
• Add a --profile flag to profile the papis run.
• Define a new API for general pickers. (TBD)
• Add a citeseerx downloader.

papis add

• Add an experimental importer selector when smart matching inputs. See here.

papis bibtex

• Add papis bibtex browse.

Run and Git command

• Add --pick, --doc-folder, --all and --sort flags so that we can choose a document to run the shell or git command in that folder or in all folders matching a given query introduced by --pick.

VERSION v0.9

Plugin architecture

A new plugin architecture is in place. For more information please refer to the documentation

Git interface

Now some usual commands have a --git flag that lets the command work alongside git. For instance if the --git flag is passed to papis-edit, it will add and commit the info.yaml file automatically. The same applies to papis-add, papis-addto, papis-update and papis-rm.

You can activate by default the --git flag using the use-git configuration option. For devs: The main functions to implement this interface are found in the papis module papis.git.

papis add

• The configuration settings file-name and folder-name are now

  add-file-name
  add-folder-name
  

  so that they become more readable and understandable. Also the flag --name is now --folder-name.

• The flag --commit now has the name --git.

• The flag --dir now has the more descriptive name --subfolder.

• The flag --no-document has been finally removed.

• The most notable update is that papis is now able to guess a doi or arxiv id from a pdf that is being added, so the following could work

  papis add --confirm arxiv-paper.pdf
  

  or

  papis add --confirm some-random-paper.pdf
  

  with the --confirm flag it will ask if we want to use the doi or arxivid retrieved.

• We can query crossref with --from-crossref in order to get information and add a paper.

papis export

• The configuration settings export-text-format has been removed along with the export --text command. papis now support plugins so you should write your own instead.
• The flags --bibtex/--json/--yaml of the export command have been replaced by export --format=bibtex/json/yaml
• The flag --file has been removed, if you want to export the related files then just either export the folder or write a small script for it.

papis explore

• Change the flags for papis explore export to match the papis export command.

papis list

• Add -n, --notes flags to list notes.
• Remove the --pick flag and add the --all flag to be consistent with the behaviour of other commands.
• Remove the query argument in the run function for consistency with other commands.

papis browse

• Add --all flag, improve tests and log.

Databases

• The default papis database is now caching the document objects instead of only the paths, which means that no yaml parsing is necessary every time, which makes it around 10x faster than in version v0.8. For a library of 1200 documents, the speed of the papis database backend is comparable with the whoosh backend.
• The query language for the default papis database has changed, now the setter character is : instead of = to better conform with other common database engines like whoosh or xapian. For instance, before

  papis open 'author=einstein year=1905'
  

  and now it will be

  papis open 'author:einstein year:1905'
  

• Libraries can have multiple directories defined.

Configuration

• A ~/.config/papis/config.py python file has been added which is sourced after the ~/.config/papis/config file has been processed. This should enable some users to have more granularity in the customization.

Downloaders

• Some downloaders have been improved and a fallback downloader has been added. Now you will be able to retrieve information from many more websites by by virtue of the metadata of html websites.

One of the main developments for version 0.8 is to make papis less dependent on PyPi, for which some important dependencies have been added into the main source and is installed with it.

• Redesign of the picker and tui.

• Add text_area widget for duplication warnings and papis rm

• Add color to the logs and potentially throughout the project.

• Add rudimentary BASE parser and include it in papis explore and papis update.

• Update Hyperlink DOIs to preferred resolver (issue #136)

• Add click based shell completion for bash and zsh. Consult the docs.

• Add bibtex tests

• Update export format in bibtex

• Fix help string in commands

• papis export -o now appends and does not overwrite

• Fix existing paths in command addto

• Add @papis.cli.bypass decorator for scripts

• Remove xeditor config parameter

• Add external picker in api

• Erase all guis from papis main repository, they should be used in external scripts or projects, docs.

• Fix downloader testing framework.

• Add downloader for:

  • frontiersin.org
  • hal.fr

• Better support for prompt_toolkit
• Usage of click library for the command line interface.
• A new picker has been developed, which support multiline and colors.
• Bugs fixes.
• Guis have been deleted from the main papis, please install the guis on pypi using pip3.