Remove double backup note from README

Moved the plugin files to the directory structure they will have in the
python site-packages directory, being placed within the plugs directory
of the pubs application directory.

.woodpecker.yml

@@ -0,0 +1,70 @@
+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*

CHANGELOG.md

@@ -0,0 +1,35 @@
+# 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

LICENSE

@@ -0,0 +1,165 @@
+                   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
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

README.md

@@ -1,14 +1,30 @@
 # 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:
 
-Still a bit painful since I have not set up any package management:
+You can install from pypi with `pip install pubs-extract`.
 
-Put `extract` folder in your pubs `plugs` directory.
+Or you install manually by moving the `extract` directory into your pubs `plugs` directory,
+so that the hierarchy is `pubs/plugs/extract/`
 
-Then add `extract` to your plugin list in the pubs configuration file.
+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.
 
 ## Configuration:
 
@@ -110,19 +126,20 @@ 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** 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.
+**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.
 
-You can invoke the command with `-e` to instantly edit the notes:
+You can invoke the command with `-e` to instantly edit the notes in your editor:
 
 ```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.
+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.
 
 To extract the annotations for all your existing entries in one go, you can use:
 
@@ -141,7 +158,7 @@ Pull requests tackling one of these areas of course very welcome.
 
 ## Issues
 
-A note on the extraction. Highlights in pdfs are somewhat difficult to parse
+A note on the extraction: Highlights in pdfs can be 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,
@@ -149,60 +166,18 @@ 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.
+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.
 
-## Roadmap:
+I am not sure if there is much I can do about this.
 
-- [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
+---
 
-## Things that would also be nice in pubs in general and don't really belong in this repository
+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!
 
-- `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
+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 ❤️

pubs/plugs/extract/annotation.py

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

pubs/plugs/extract/extract.py

@@ -225,7 +225,8 @@ 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.
+        should both be included or are doubling up, using
+        Levenshtein distance.
         """
         content = annotation.info["content"].replace("\n", " ")
         written = page.get_textbox(annotation.rect).replace("\n", " ")
@@ -250,9 +251,7 @@ 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"
@@ -271,7 +270,11 @@ 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:

pyproject.toml

@@ -1,11 +1,11 @@
 [tool.poetry]
 name = "pubs-extract"
-version = "0.1.0"
+version = "0.2.0"
 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 = "extract"}]
+packages = [{include = "pubs"}]
 
 [tool.poetry.dependencies]
 python = "^3.10"

tools/extract-changelog.py

@@ -0,0 +1,56 @@
+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()