test: Ignore swig 4.3 deprecation warnings in pytest

Change minimum python version support from 3.11 to 3.10, which mirrors
the upcoming minimum version for papis itself, probably from the next
major papis version (0.15).

.papis.config

@@ -1,7 +1,12 @@
 [settings]
 default-library = main
 picktool = papis
-formater = python
+formatter = python
 
 [main]
+database-backend = whoosh
+use-cache = False
 dir = temp/lib
+
+[plugins.extract]
+tags = {"red": "important", "green": "extra", "blue": "toread"}

README.md

@@ -1,6 +1,7 @@
 # papis-extract
 
 [![status-badge](https://ci.martyoeh.me/api/badges/Marty/papis-extract/status.svg)](https://ci.martyoeh.me/Marty/papis-extract)
+
 <!-- TODO have to set up pypi badge
 ![PyPI](https://img.shields.io/pypi/v/papis-extract)
 -->
@@ -11,6 +12,7 @@ Easily organize all your highlights and thoughts next to your documents and refe
 ## Installation
 
 <!-- TODO set up pypi repository / explain git install path -->
+
 You can install through pip with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`.
 
 That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global),
@@ -26,7 +28,7 @@ You will be set up with the default options but if you want to change anything,
 
 > **Note**
 > This plugin is still 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 which could affect your notes, or make use of the papis-included git options.
+> It does what I need it to do, but if you have a meticulously organized library _please_ make backups before doing any operation which could affect your notes, or make use of the papis-included git options.
 > Take care to read the Issues section of this README if you intend to run it over a large collection.
 
 ## Usage
@@ -66,7 +68,7 @@ use `--all` as usual with papis:
 papis extract --all "author:Einstein"
 ```
 
-The above command will print out your annotations made on *all* papers by Einstein.
+The above command will print out your annotations made on _all_ papers by Einstein.
 
 You can invoke the command with `--manual` to instantly edit the notes in your editor:
 
@@ -85,7 +87,7 @@ papis extract --write --all
 ```
 
 However, the warning for your notes' safety goes doubly for this command since it will touch
-*most* or *all* of your notes, depending on how many entries in your library have pdfs with annotations attached.
+_most_ or _all_ of your notes, depending on how many entries in your library have pdfs with annotations attached.
 
 While I have not done extensive optimizations the process should be relatively quick even for larger libraries:
 On my current laptop, extracting ~4000 annotations from ~1000 library documents takes around 90 seconds,
@@ -116,7 +118,7 @@ papis extract --output count
 
 For now, these are the only formatters the plugin knows about.
 
-Be aware that if you re-write to your notes using a completely different output format than the original the plugin will *not* detect old annotations and drop them,
+Be aware that if you re-write to your notes using a completely different output format than the original the plugin will _not_ detect old annotations and drop them,
 so you will be doubling up your annotations.
 See the `minimum_similarity` configuration option for more details.
 
@@ -150,7 +152,7 @@ If you set `on_import` to `True`,
 extraction into notes is automatically run whenever a new document is added to the library,
 if `False` extraction only happens when you explicitly invoke it.
 
-Extraction will *not* happen automatically when you add new annotations to an existing document,
+Extraction will _not_ happen automatically when you add new annotations to an existing document,
 regardless of this setting.
 
 > **Note**
@@ -190,11 +192,11 @@ Generally, this should be fine as it is but you should change this value if you
 
 ---
 
-`minimum_similarity_content` sets the required similarity of an annotation's note and in-pdf written words to be viewed as one. Any annotation that has both and is *under* the minimum similarity will be added in the following form:
+`minimum_similarity_content` sets the required similarity of an annotation's note and in-pdf written words to be viewed as one. Any annotation that has both and is _under_ the minimum similarity will be added in the following form:
 
 ```markdown
 > my annotation
-Note: my additional thoughts
+> Note: my additional thoughts
 ```
 
 That is, the extractor detects additional written words by whoever annotated and adds them to the extraction.
@@ -220,55 +222,6 @@ Then import the resulting `.html` file into the library like any other document
 (or `papis addto` to add it to existing document references).
 You are then ready to use extract to get those annotations from the exported list into your notes.
 
-## TODO: Roadmap to first release
-
-Known issues to be fixed:
-
-- [x] if both content and text are empty, do not extract an annotation
-- [x] Speed?
-    - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations
-- [x] ensure all cmdline options do what they should
-- [x] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals
-- [x] docstrings, docstrings!
-- [ ] testing testing testing!!
-    - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation)
-- [ ] dependency injection for extractor/exporter/formatter/annotation modules
-    - [ ] any call to papis.config should start from init and be injected?
-
-features to be implemented:
-
-- [ ] CICD
-    - [x] static analysis (lint, typecheck etc) on pushes
-    - [x] test pipeline on master pushes
-    - [ ] release pipeline to pypi on tags
-- [x] add page number if available
-    - exists in Annotation, just need to place in output
-- [ ] show overall amount of extractions at the end
-    - implemented for writing to notes (notes exporter)
-    - KNOWN ISSUE: currently returns number of annotation rows (may be multiple per annot)
-- [ ] custom formatting decided by user
-    - in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"}
-- [ ] improved default exporters
-    - [x] markdown into notes
-    - [ ] pretty display on stdout (rich?)
-    - [x] csv/tsv to stdout
-    - [ ] table fmt stdout?
-- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)})
-- [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note
-- [x] `--force` mode where we simply do not drop anything
-- [x] `--format` option to choose from default or set up a custom formatter
-    - called `--output` in current implementation
-- [ ] on_add hook to extract annotations as files are added
-    - needs upstream help, 'on_add' hook, and pass-through of affected documents
-- [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.13)
-- [ ] change detection:
-    - how does it handle updated citations? updated colors? should it be configurable?
-
-upstream changes:
-
-- [ ] need a hook for adding a document/file
-- [ ] need hooks to actually pass through information on the thing they worked on (i.e. their document)
-
 ## Issues
 
 First, a note in general: There is the functionality to run this plugin over your whole library in a single command and also in a way that makes permanent changes to that library.
@@ -281,12 +234,12 @@ 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,
-as well as any additional notes made - but things *will* slip through or extract weirdly every now
+as well as any additional notes made - but things _will_ slip through or extract weirdly every now
 and again.
 
 Secondly, a note on the pages: I use the page number that the mupdf library gives me when it
 extracts anything from the pdf file. Sometimes that number will be correct for the document,
-sometimes it will however be the number of the *pdf document* internally. This can happen if
+sometimes it will however be the number of the _pdf document_ internally. This can happen if
 e.g. an article or a book has frontmatter without numbering scheme or with a different one.
 Sometimes the correct pages will still be embedded in the pdf and everything will work,
 others it won't. So always double check your page numbers!
@@ -298,19 +251,19 @@ I am not sure if there is much I can do about these issues for now.
 and for myself whenever I forget. The basic building blocks currently in here are three:
 
 - extractors (= input format)
-: Extract data from a source file attached to a papis document.
+  : Extract data from a source file attached to a papis document.
   Crawls the actual files attached to documents to put them into annotation-friendly formats.
 
 - formatters (= output format)
-: Make sure the exporter saves the annotation data according to your preferred layout,
+  : Make sure the exporter saves the annotation data according to your preferred layout,
   such as a markdown syntax or csv-structure.
 
 - annotations
-: The actual extracted blocks of text, containing some metadata
+  : The actual extracted blocks of text, containing some metadata
   info as well, such as their color, type, page.
 
 - exporters
-: Put the extracted data somewhere. For now stdout or into your notes.
+  : Put the extracted data somewhere. For now stdout or into your notes.
 
 Splitting it into those building blocks makes it easier to recombine them in any way,
 should someone want to save highlights as csv data in their notes,
@@ -329,7 +282,7 @@ However, what I do on my system instead to enable quick testing is inject it int
 system-wide (but isolated with `pipx`) papis setup:
 
 ```bash
-pipx install papis # create an isolated papis installation reachable form anywhere
+pipx install papis             # create an isolated papis installation reachable form anywhere
 pipx inject --editable papis . # inject this folder into the environment and keep up with any changes
 ```
 

ROADMAP

@@ -0,0 +1,49 @@
+# ROADMAP to first release
+
+Known issues to be fixed:
+
+- [x] if both content and text are empty, do not extract an annotation
+- [x] Speed?
+    - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations
+- [x] ensure all cmdline options do what they should
+- [x] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals
+- [x] docstrings, docstrings!
+- [ ] testing testing testing!!
+    - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation)
+- [ ] dependency injection for extractor/exporter/formatter/annotation modules
+    - [ ] any call to papis.config should start from init and be injected?
+
+features to be implemented:
+
+- [ ] CICD
+    - [x] static analysis (lint, typecheck etc) on pushes
+    - [x] test pipeline on master pushes
+    - [ ] release pipeline to pypi on tags
+- [x] add page number if available
+    - exists in Annotation, just need to place in output
+- [ ] show overall amount of extractions at the end
+    - implemented for writing to notes (notes exporter)
+    - KNOWN ISSUE: currently returns number of annotation rows (may be multiple per annot)
+- [ ] custom formatting decided by user
+    - in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"}
+- [ ] improved default exporters
+    - [x] markdown into notes
+    - [ ] pretty display on stdout (rich?)
+    - [x] csv/tsv to stdout
+    - [ ] table fmt stdout?
+- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)})
+- [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note
+- [x] `--force` mode where we simply do not drop anything
+    - called `--duplicates` in current implementation
+- [x] `--format` option to choose from default or set up a custom formatter
+    - called `--output` in current implementation
+- [ ] on_add hook to extract annotations as files are added
+    - needs upstream help, 'on_add' hook, and pass-through of affected documents
+- [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.14, 3.10 for upcoming papis ~0.15)
+- [ ] change detection:
+    - how does it handle updated citations? updated colors? should it be configurable?
+
+upstream changes:
+
+- [ ] need a hook for adding a document/file
+- [ ] need hooks to actually pass through information on the thing they worked on (i.e. their document)

papis_extract/annotation.py

@@ -1,4 +1,5 @@
 import math
+from functools import total_ordering
 from types import NotImplementedType
 from typing import Any, cast
 
@@ -21,6 +22,7 @@ COLORS: dict[str, tuple[float, float, float]] = {
 }
 
 
+@total_ordering
 class Annotation:
     """A PDF annotation object.
 

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 authors = [{ name = "Marty Oehme", email = "contact@martyoeh.me" }]
 license = { text = "GPL-3.0-or-later" }
-requires-python = "<4.0,>=3.11"
+requires-python = "<4.0,>=3.10"
 dependencies = [
     "pymupdf<2.0.0,>=1.24.2",
     "levenshtein<1.0.0,>=0.25.1",
@@ -62,3 +62,11 @@ build-backend = "hatchling.build"
 
 [tool.pyright]
 typeCheckingMode = "strict"
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    # see https://github.com/swig/swig/issues/2881#issuecomment-2877988848
+    # should hopefully be redundant with swig-4.4
+    "ignore:.*builtin type SwigPy\\w* has no __module__ attribute.*:DeprecationWarning",
+    "ignore:.*builtin type swigvarlink has no __module__ attribute.*:DeprecationWarning"
+]

tests/test_annotation.py

@@ -4,7 +4,7 @@ from papis.document import Document
 from papis_extract.annotation import Annotation
 
 
-def test_value_comparison_works():
+def test_value_inequality_comparison():
     sut = Annotation("myfile", content="Here be content!", note="and a note")
     other = Annotation(
         "myfile", content="Here be different content!", note="but still a note"
@@ -12,6 +12,34 @@ def test_value_comparison_works():
     assert sut != other
 
 
+def test_oder_lt_comparison():
+    sut = Annotation("myfile", content="Here be content!", note="and a note", page=2)
+    other = Annotation(
+        "myfile", content="Here be different content!", note="but still a note", page=10
+    )
+    assert sut < other
+
+
+def test_oder_ge_comparison():
+    big = Annotation("mf", content="ct", note="nt", page=10)
+    small = Annotation("mf", content="ct", note="nt", page=2)
+    alsosmall = Annotation("mf", content="ct", note="nt", page=2)
+    assert big >= small
+    assert small >= alsosmall
+
+
+def test_oder_gt_comparison_single_nopage():
+    zeropage = Annotation("mf", content="ct", note="nt", page=0)
+    small = Annotation("mf", content="ct", note="nt", page=2)
+    assert zeropage > small
+
+
+def test_oder_le_comparison_all_nopage():
+    zeropage = Annotation("mf", content="ct", note="nt", page=0)
+    small = Annotation("mf", content="ct", note="nt", page=0)
+    assert zeropage <= small
+
+
 @pytest.mark.parametrize(
     "fmt_string,expected",
     [

uv.lock

@@ -1,12 +1,13 @@
 version = 1
 revision = 3
-requires-python = ">=3.11, <4.0"
+requires-python = ">=3.10, <4.0"
 
 [[package]]
 name = "anyio"
 version = "4.10.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
+    { name = "exceptiongroup", marker = "python_full_version < '3.11'" },
     { name = "idna" },
     { name = "sniffio" },
     { name = "typing-extensions", marker = "python_full_version < '3.13'" },
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