Papis

=============

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](https://papis.readthedocs.io/en/latest/configuration.html#fzf-integration).

`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](https://papis.readthedocs.io/en/latest/configuration.html#config-settings-notes-template).

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.

=============

- 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](https://papis.readthedocs.io/en/latest/configuration.html#config-settings-sort-field).
- Add `time-stamps` in order to sort chronologically documents
see [doc](https://papis.readthedocs.io/en/latest/configuration.html#config-settings-time-stamp).
- 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](https://asciinema.org/a/i2kXyZMNaT8n7YRz7DcVIfqm5).

`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`.

============

Plugin architecture

A new plugin architecture is in place.
For more information please refer to
[the documentation](https://papis.readthedocs.io/en/latest/plugin.html)

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.

==============

- Change default colors for `header_formater`.
- Update `prompt_toolkit` version to `2.0.5`.

============

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](https://www.base-search.net/about/en/) 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](https://papis.readthedocs.io/en/latest/shell_completion.html).

- 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](https://papis.readthedocs.io/en/latest/gui.html).

- Fix downloader testing framework.
- Add downloader for:
- `frontiersin.org`
- `hal.fr`