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70
.woodpecker.yml
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@ -1,70 +0,0 @@
branches: main
pipeline:
code_lint:
image: python
commands:
- pip install poetry
- poetry install
- pip install black
- echo "----------------- running lint ------------------"
- python --version && poetry --version && black --version
- poetry run black .
build_dist:
image: python
commands:
- pip install poetry
- poetry install
- echo "----------------- running analysis ------------------"
- python --version && poetry --version
- poetry build
when:
event: tag
tag: v*
release_prep:
image: python
commands:
- echo "----------------- preparing release ------------------"
- python tools/extract-changelog.py
when:
event: tag
tag: v*
pypi_release:
image: python
commands:
- pip install poetry
- poetry install
- echo "----------------- publishing to pypi ------------------"
- poetry publish --username "$PYPI_USERNAME" --password "$PYPI_PASSWORD"
secrets: [ pypi_username, pypi_password ]
when:
event: tag
tag: v*
gitea_release:
image: plugins/gitea-release
settings:
api_key:
from_secret: gitea_release_token
base_url: https://git.martyoeh.me
files: dist/*
title: NEWEST_VERSION.md
note: NEWEST_CHANGES.md
when:
event: tag
tag: v*
github_release:
image: plugins/github-release
settings:
api_key:
from_secret: github_release_token
files: dist/*
title: NEWEST_VERSION.md
note: NEWEST_CHANGES.md
when:
event: tag
tag: v*

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CHANGELOG.md
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# Changelog
All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project tries to adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
<!--
## [Unreleased]
### Added
### Changed
### Fixed
-->
## [0.2.0] - 2023-01-13
### Added
* Added pypi release publication
* Try not to duplicate extracted annotations in existing notes
* Map annotation colors to custom tags in notes
* Add querying for publications to command (like list command)
### Fixed
* Grab annotations even if their content is empty or contains custom text
## [0.1.0] - 2022-12-25
* Extract highlights and annotations from a pubs doc file
* Optionally run automatically whenever file is added to pubs
* Optionally write annotations to pubs note file

165
LICENSE
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@ -1,165 +0,0 @@
GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
This version of the GNU Lesser General Public License incorporates
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License, supplemented by the additional permissions listed below.
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As used herein, "this License" refers to version 3 of the GNU Lesser
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A "Combined Work" is a work produced by combining or linking an
Application with the Library. The particular version of the Library
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The "Minimal Corresponding Source" for a Combined Work means the
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Corresponding Source.
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103
README.md
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@ -1,30 +1,14 @@
# pubs-extract
[![status-badge](https://ci.martyoeh.me/api/badges/Marty/pubs-extract/status.svg)](https://ci.martyoeh.me/Marty/pubs-extract)
![PyPI](https://img.shields.io/pypi/v/pubs-extract)
Quickly extract annotations from your pdf files with the help of the pubs bibliography manager.
Easily organize your highlights and thoughts next to your documents.
## Installation:
You can install from pypi with `pip install pubs-extract`.
Still a bit painful since I have not set up any package management:
Or you install manually by moving the `extract` directory into your pubs `plugs` directory,
so that the hierarchy is `pubs/plugs/extract/`
Put `extract` folder in your pubs `plugs` directory.
Then add `extract` to your plugin list in the pubs configuration file:
```ini
[plugins]
active = extract
```
To check if everything is working you can do `pubs --help` which should show you the new extract command.
You will be set up with the default options but if you want to change anything, read on in configuration below.
> **Note**
> This plugin is in fairly early development. It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation on your notes, or make use of the pubs-included git plugin.
Then add `extract` to your plugin list in the pubs configuration file.
## Configuration:
@ -126,20 +110,19 @@ the annotations. If a note already exists for any of the entries, it will instea
the annotations to the end of it, dropping all those that it already finds in the note
(essentially only adding new annotations to the end).
**PLEASE** Heed the note above and exercise caution with the `-w` option. It is
not intended to be destructive, but nevertheless create backups or version
control your files.
**PLEASE** Be aware that so far, I spent a single afternoon coding this plugin, it
contains no tests and operates on your notes. In my use nothing too bad happened but
only use it with adequate backup in place, or with your library being version controlled.
You can invoke the command with `-e` to instantly edit the notes in your editor:
You can invoke the command with `-e` to instantly edit the notes:
```bash
pubs extract -w -e Bayat2015 Peck2004
```
Will create/append annotations and drop you into the Bayat2015 note, when you
close it directly into the Peck2004 note. Take care that it will be fairly
annoying if you use this option with hundreds of entries being annotated as it
will open one entry after another for editing.
Will create/append annotations and drop you into the Bayat2015 note, when you close it
directly into the Peck2004 note. Take care that it will be fairly annoying if you use this
option with hundreds of entries being annotated.
To extract the annotations for all your existing entries in one go, you can use:
@ -158,7 +141,7 @@ Pull requests tackling one of these areas of course very welcome.
## Issues
A note on the extraction: Highlights in pdfs can be somewhat difficult to parse
A note on the extraction. Highlights in pdfs are somewhat difficult to parse
(as are most things in them). Sometimes they contain the selected text that is written on the
page, sometimes they contain the annotators thoughts as a note, sometimes they contain nothing.
This plugin makes an effort to find the right combination and extract the written words,
@ -166,18 +149,60 @@ as well as any additional notes made - but things *will* slip through or extract
and again.
The easiest extraction is provided if your program writes the selection itself into the highlight
content, because then we can just use that. It is harder to parse if it does not and will sometimes
get additional words in front or behind (especially if the highlight ends in the middle of a line)
or even cut a few off.
content, because then we can just use that. It is harder to parse if it does not.
I am not sure if there is much I can do about this.
## Roadmap:
---
- [x] extracts highlights and annotations from a doc file (e.g. using PyMuPDF)
- [x] puts those in the annotation file of a doc in a customizable format
- [x] option to have it automatically run after a file is added?
- option to have it run whenever a pdf in the library was updated?
- [ ] needs some way to delimit where it puts stuff and user stuff is in note
- [ ] one way is to have it look at `> [17] here be extracted annotation from page seventeen` annotations and put it in between
- [x] another, probably simpler first, is to just append missing annotations to the end of the note
- [ ] use similarity search instead of literal search for existing annotation (levenshtein)
- [x] some highlights (or annotations in general) do not contain text as content
- [x] pymupdf can extract the content of the underlying rectangle (mostly)
- [x] issue is that sometimes the highlight contents are in content, sometimes a user comment instead
- [x] we could have a comparison function which estimates how 'close' the two text snippets are and act accordingly -> using levenshtein distance
- [x] config option to map colors in annotations to meaning ('read', 'important', 'extra') in pubs
- [x] colors are given in very exact 0.6509979 RGB values, meaning we could once again estimate if a color is 'close enough' in distance to tag it accordingly -> using euclidian distance
- [ ] support custom colors by setting a float tuple in configuration
- [x] make invoking the command run a query if corresponding option provided (or whatever) in pubs syntax and use resulting papers
- [x] confirm for many papers?
- [ ] warning when the amount of annotations in file is different than the amount extracted?
- [ ] tests tests tests tests tests, lah-di-dah
If you spot a bug or have an idea feel free to open an issue.\
I might be slow to respond but will consider them all!
## Things that would also be nice in pubs in general and don't really belong in this repository
Pull requests are warmly welcomed.\
If they are big changes or additions let's talk about them in an issue first.
Thanks for using my software ❤️
- `show` command which simply displays given entry in a nice way
- could take multiple entries but present them all in the same larger way
- a metadata command which shows the metadata connected to an entry (e.g. `show --meta`)
- XDG compliance
- a way to insert env vars into the configuration paths
- looking in XDG_CONFIG_HOME and XDG_DATA_HOME by default
- accepting env vars for overriding the directories
- isbn import re-enabled with -> `api.paperpile.com/api/public/convert`
- example request: `curl -X POST -d '{"fromIds":true,"input":"9780816530441","targetFormat":"Bibtex"}' -H "Content-Type: application/json" https://api.paperpile.com/api/public/convert`
- example reponse: `{"output":"@BOOK{Igoe2017-cu,\n title = \"The nature of spectacle\",\n author = \"Igoe, James\",\n publisher = \"University of Arizona Press\",\n series = \"Critical Green Engagements: Investigating the Green Economy and\n its Alternatives\",\n month = jun,\n year = 2017,\n address = \"Tucson, AZ\",\n language = \"en\"\n}\n","token":"3ca6b666-2b9d-4962-8017-a0c8f1f86bfd","tags":[],"withErrors":false}`
- side-by-side command to open annotation file and document at the same time
- fzf-mode/bemenu mode to look through documents
- batch-edit? a way to quickly modify items matching a query, e.g. removing file entry for all those from year:2022 or whatever
- link related items
- a special tag?
- building relationships: two-way (related, e.g. same working paper), or single direction, e.g. a re-print, a compendium, etc
- should still always be traceable from both sides
- automatically keeping a main bibtex file up-to-date
- can be done through the `export` command, e.g. as a git hook when the repo is updated
- better git commit names for git plugin
- more direct linking to individual annotations
- e.g. you have an annotation on page 17, allow opening that page from there and vice versa
- can use e.g. existing markdown quote pattern:
> [17] To be or not to be blabla
which would then open page 17 in the document
- makes most sense as plugin probably (which also allows setting the pattern by which it finds citations in the notes)
- fuzzy matching
- either by default, as a config setting or with the ~prefix
- why are we doing tags in metadata not in the bibtex files?
- default replacement bibkey for files which are missing part of what makes it up
- e.g. if you use {authorname}{year} as bibkey, a file missing author would substitute with this

0
pubs/plugs/extract/__init__.py → extract/__init__.py
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3
pubs/plugs/extract/annotation.py → extract/annotation.py
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@ -87,8 +87,7 @@ class Annotation:
def colorname(self):
"""Return the stringified version of the annotation color.
Finds the closest named color to the annotation and returns it,
using euclidian distance between the two color vectors.
Finds the closest named color to the annotation and returns it.
"""
annot_colors = (
self.colors.get("stroke") or self.colors.get("fill") or (0.0, 0.0, 0.0)

13
pubs/plugs/extract/extract.py → extract/extract.py
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@ -225,8 +225,7 @@ class ExtractPlugin(PapersPlugin):
that is only the written words, sometimes that is only
annotation notes, sometimes it is both. Runs a similarity
comparison between strings to find out whether they
should both be included or are doubling up, using
Levenshtein distance.
should both be included or are doubling up.
"""
content = annotation.info["content"].replace("\n", " ")
written = page.get_textbox(annotation.rect).replace("\n", " ")
@ -251,7 +250,9 @@ class ExtractPlugin(PapersPlugin):
"""
output = ""
for paper in annotated_papers:
output += f"\n------ {paper.headline(self.short_header, self.max_authors)} ------\n\n"
output += (
f"\n------ {paper.headline(self.short_header, self.max_authors)} ------\n\n"
)
for annotation in paper.annotations:
output += f"{annotation.format(self.formatting)}\n"
output += "\n"
@ -270,11 +271,7 @@ class ExtractPlugin(PapersPlugin):
if check_file(notepath, fail=False):
self._append_to_note(notepath, paper)
else:
self._write_new_note(
notepath,
paper,
paper.headline(short=True, max_authors=self.max_authors),
)
self._write_new_note(notepath, paper, paper.headline(short=True, max_authors=self.max_authors))
self.ui.info(f"Wrote annotations to {paper.citekey} note {notepath}.")
if edit is True:

4
pyproject.toml
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@ -1,11 +1,11 @@
[tool.poetry]
name = "pubs-extract"
version = "0.2.0"
version = "0.1.0"
description = "A pdf annotation extraction plugin for pubs bibliography manager"
authors = ["Marty Oehme <marty.oehme@gmail.com>"]
license = "LGPL-3.0"
readme = "README.md"
packages = [{include = "pubs"}]
packages = [{include = "extract"}]
[tool.poetry.dependencies]
python = "^3.10"

56
tools/extract-changelog.py
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@ -1,56 +0,0 @@
import re
## Extracts the version and newest changes from a semantic changelog.
#
# Important, it only works with three-parted version numbers
# a-la 1.2.3 or 313.01.1888 -- needs \d.\d.\d to work.
#
# The version number and changeset will be put in `NEWEST_VERSION.md`
# and `NEWEST_CHANGES.md` respectively, for further use in releases.
OUTPUT_FILE_VERSION = "NEWEST_VERSION.md"
OUTPUT_FILE_CHANGES = "NEWEST_CHANGES.md"
def getVersion(file):
for line in file:
m = re.match(r"^## \[(\d+\.\d+\.\d+)\]", line)
if m and m.group(1):
return m.group(1)
def getSection(file):
inRecordingMode = False
for line in file:
if not inRecordingMode:
if re.match(r"^## \[\d+\.\d+\.\d+\]", line):
inRecordingMode = True
elif re.match(r"^## \[\d+\.\d+\.\d+\]", line):
inRecordingMode = False
break
elif re.match(r"^$", line):
pass
else:
yield line
def toFile(fname, content):
file = open(fname, "w")
file.write(content)
file.close()
with open("CHANGELOG.md") as file:
title = getVersion(file)
print(title)
toFile(OUTPUT_FILE_VERSION, title)
with open("CHANGELOG.md") as file:
newest_changes_gen = getSection(file)
newest_changes = ""
for line in newest_changes_gen:
newest_changes += line
print("[Extracted Changelog]")
print(newest_changes)
toFile(OUTPUT_FILE_CHANGES, newest_changes)
file.close()