.markdownlint.yaml

@@ -1,6 +0,0 @@
-MD013: false
-
-MD025: false
-
-MD007:
-  indent: 4

.papis.config

@@ -1,7 +0,0 @@
-[settings]
-default-library = main
-picktool = papis
-formater = python
-
-[main]
-dir = temp/lib

README.md

@@ -8,10 +8,10 @@
 Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\
 Easily organize all your highlights and thoughts next to your documents and references.\
 
-## Installation
+## 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`.
+You can install from pypi 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),
 everything should now be set up.
@@ -24,8 +24,7 @@ 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.
-
+## Usage:
-## Usage
 
 `papis extract [OPTIONS] [QUERY]`
 
@@ -88,44 +87,16 @@ On my current laptop, extracting ~4000 annotations from ~1000 library documents
 though this will vary with the length and size of the PDFs you have.
 For smaller workloads the process should be almost instant.
 
-You can change the format that you want your annotations in with the `--template` option.
-To output annotations in a markdown-compatible syntax (the default), do:
-
-```bash
-papis extract --template markdown
-```
-
-There are sub-variants of the formatter for atx-style headers, with `--template markdown-atx` (`# Headings`),
-or setext-style with `--template markdown-setext` (the default style).
-
-To instead see them in a csv syntax simply invoke:
-
-```bash
-papis extract --template csv
-```
-
-And if you only want to know how many annotations exist in the documents, you can invoke:
-
-```bash
-papis extract --template count
-```
-
-For now, these are the only formatters the plugin knows about.
-
-Be aware that if you write to your notes using a different template the plugin will *not* detect old annotations and drop them,
-so you will be doubling up your annotations.
-
 ## Configuration
 
 ### Basic configuration
-
 Add `extract` plugin settings to your papis `config` file (usually `~/.config/papis/config`):
 You will rarely have to set everything explained in the next few paragraphs -
 in fact you can use the plugin without having to set up any of it if you are happy with the defaults.
 
 The full default settings look as follows:
 
-```conf
+```yaml
 [plugins.extract]
 on_import: False
 tags = {"important": "red", "toread": "blue"}
@@ -136,7 +107,7 @@ minimum_similarity_color = 0.833  # for matching tag to color
 
 ### Automatic extraction
 
-```conf
+```yaml
 [plugins.extract]
 on_import: True
 ```
@@ -148,7 +119,7 @@ if `False` extraction only happens when you explicitly invoke it.
 Extraction will *not* happen automatically when you add new annotations to an existing document,
 regardless of this setting.
 
-### Automatic tagging
+#### Automatic tagging
 
 By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`, 
 you can enable automatic tagging for your annotations.
@@ -157,7 +128,7 @@ You thus ascribe specific meanings to the colors you use in highlighting.
 
 For example, if you always highlight the most essential arguments and findings in red and always highlight things you have to follow up on in blue, you can assign the meanings 'important' and 'todo' to them respectively as follows:
 
-```conf
+```yaml
 [plugins.extract]
 tags = {"red": "important", "blue": "toread"}
 ```
@@ -169,7 +140,7 @@ no defaults are set here.
 
 ### Advanced configuration
 
-```conf
+```yaml
 [plugins.extract]
 minimum_similarity: 0.75,  # for checking against existing annotations
 minimum_similarity_content: 0.9,  # for checking if highlight or note
@@ -206,12 +177,10 @@ Known issues to be fixed:
 - [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
+- [ ] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals
-- [x] docstrings, docstrings!
+- [ ] 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:
 
@@ -219,7 +188,7 @@ features to be implemented:
     - [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
+- [ ] add page number if available
     - exists in Annotation, just need to place in output
 - [ ] show overall amount of extractions at the end
 - [ ] custom formatting decided by user
@@ -232,8 +201,7 @@ features to be implemented:
 - [ ] 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
 - [ ] `--force` mode where we simply do not drop anything
-- [x] `--format` option to choose from default or set up a custom formatter
+- [ ] `--format` option to choose from default or set up a custom formatter
-    - called `--template` 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
 
@@ -251,36 +219,12 @@ This plugin makes an effort to find the right combination and extract the writte
 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
+The easiest extraction is provided if your program writes the selection itself into the highlight
-extracts anything from the pdf file. Sometimes that number will be correct for the document,
+content, because then we can just use that. It is harder to parse if it does not and will sometimes
-sometimes it will however be the number of the *pdf document* internally. This can happen if
+get additional words in front or behind (especially if the highlight ends in the middle of a line)
-e.g. an article or a book has frontmatter without numbering scheme or with a different one.
+or even cut a few off.
-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!
 
-I am not sure if there is much I can do about these issues for now.
+I am not sure if there is much I can do about this.
-
-## For developers
-
-and for myself whenever I forget. The basic building blocks currently in here are three:
-
-- extractors
-: Extract data from a source file attached to a papis document.
-
-- annotations
-: 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.
-
-- formatters
-: Make sure the exporter saves the data according to your preferred layout,
-  such as a markdown syntax or csv-structure.
-
-Splitting it into those three building blocks makes it easier to recombine them in any way,
-should someone want to save highlights as csv data in their notes,
-or should we ever include more extractors than the one for PDFs.
 
 ---
 

papis_extract/__init__.py

@@ -8,10 +8,7 @@ import papis.strings
 from papis.document import Document
 
 from papis_extract import extractor, exporter
-from papis_extract.formatter import (
+from papis_extract.annotation_data import AnnotatedDocument
-    Formatter,
-    formatters
-)
 
 logger = papis.logging.get_logger(__name__)
 
@@ -31,54 +28,41 @@ papis.config.register_default_settings(DEFAULT_OPTIONS)
 @click.help_option("-h", "--help")
 @papis.cli.query_argument()
 @papis.cli.doc_folder_option()
-@papis.cli.git_option(help="Commit changes made to the notes files.")
+@papis.cli.git_option(help="Add changes made to the notes files")
 @papis.cli.all_option()
-@click.option(
-    "--write/--no-write",
-    "-w",
-    help="Do not write annotations to notes only print results to stdout.",
-)
 @click.option(
     "--manual/--no-manual",
     "-m",
-    help="Open note in editor for manual editing after annotation extraction.",
+    help="Open each note in editor for manual editing after extracting its annotations",
 )
 @click.option(
-    "--template",
+    "--write/--no-write",
-    "-t",
+    "-w",
-    type=click.Choice(
+    help="Do not write annotations to notes only print results to stdout",
-        ["markdown", "markdown-setext", "markdown-atx", "count", "csv"],
-        case_sensitive=False,
-    ),
-    help="Choose an output template to format annotations with.",
-)
-@click.option(
-    "--force/--no-force",
-    "-f",
-    help="Do not drop any annotations because they already exist.",
 )
 def main(
     query: str,
+    # info: bool,
     # _papis_id: bool,
     # _file: bool,
+    # notes: bool,
     # _dir: bool,
+    # _format: str,
     _all: bool,
     doc_folder: str,
     manual: bool,
     write: bool,
-    template: str,
     git: bool,
 ) -> None:
-    """Extract annotations from any pdf document.
+    """Extract annotations from any pdf document
 
     The extract plugin allows manual or automatic extraction of all annotations
-    contained in the pdf documents belonging to entries of the papis library.
+    contained in the pdf documents belonging to entries of the pubs library.
     It can write those changes to stdout or directly create and update notes
     for papis documents.
 
     It adds a `papis extract` subcommand through which it is invoked, but can
-    optionally run whenever a new document is imported for a papis entry,
+    optionally run whenever a new document is imported for a pubs entry.
-    if set in the plugin configuration.
     """
     documents = papis.cli.handle_doc_folder_query_all_sort(
         query, doc_folder, sort_field=None, sort_reverse=False, _all=_all
@@ -87,22 +71,19 @@ def main(
         logger.warning(papis.strings.no_documents_retrieved_message)
         return
 
-    formatter = formatters[template]
+    run(documents, edit=manual, write=write, git=git)
-
-    run(documents, edit=manual, write=write, git=git, formatter=formatter)
 
 
 def run(
     documents: list[Document],
-    formatter: Formatter,
     edit: bool = False,
     write: bool = False,
     git: bool = False,
 ) -> None:
-    annotated_docs = extractor.start(documents)
+
+    doc_annotations: list[AnnotatedDocument] = extractor.start(documents)
+
     if write:
-        exporter.to_notes(
+        exporter.to_notes(doc_annotations, edit=edit, git=git)
-            formatter=formatter, annotated_docs=annotated_docs, edit=edit, git=git
-        )
     else:
-        exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs)
+        exporter.to_stdout(doc_annotations)

papis_extract/annotation_data.py

@@ -20,10 +20,7 @@ COLORS = {
 
 @dataclass
 class Annotation:
-    """A PDF annotation object.
+    """A PDF annotation object"""
-
-    Contains all information necessary for the annotation itself, content and metadata.
-    """
 
     file: str
     colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0))
@@ -34,7 +31,7 @@ class Annotation:
     type: str = "Highlight"
     minimum_similarity_color: float = 1.0
 
-    def format(self, formatting: str, doc: Document = Document()):
+    def format(self, formatting):
         """Return a formatted string of the annotation.
 
         Given a provided formatting pattern, this method returns the annotation
@@ -48,7 +45,6 @@ class Annotation:
             "page": self.page,
             "tag": self.tag,
             "type": self.type,
-            "doc": doc,
         }
         return chevron.render(formatting, data)
 
@@ -59,7 +55,9 @@ class Annotation:
         Finds the closest named color to the annotation and returns it,
         using euclidian distance between the two color vectors.
         """
-        annot_colors = self.colors or (0.0, 0.0, 0.0)
+        annot_colors = (
+            self.colors or (0.0, 0.0, 0.0)
+        )
         nearest = None
         minimum_similarity = (
             papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0
@@ -85,11 +83,5 @@ class Annotation:
 
 @dataclass
 class AnnotatedDocument:
-    """Contains all annotations belonging to a single papis document.
-
-    Combines a document with a list of annotations which belong to it."""
-
     document: Document
     annotations: list[Annotation]
-
-    # TODO could implement a from_doc() static method to generate annotation list?

papis_extract/exporter.py

@@ -6,41 +6,64 @@ import papis.api
 import papis.git
 import papis.config
 import Levenshtein
-from papis_extract.annotation import AnnotatedDocument
 
-from papis_extract.formatter import Formatter
+from papis_extract.annotation_data import AnnotatedDocument, Annotation
 
 logger = papis.logging.get_logger(__name__)
 
 
-def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> None:
+def _format_annotation(annotation: Annotation) -> str:
+    note = f"NOTE: {annotation.content}" if annotation.content else ""
+    return f"> {annotation.text}\n  {note}"
+
+
+def to_stdout(annots: list[AnnotatedDocument]) -> None:
     """Pretty print annotations to stdout.
 
     Gives a nice human-readable representations of
     the annotations in somewhat of a list form.
     Not intended for machine-readability.
     """
-    output: str = formatter(annotated_docs)
+    if not annots:
-    print(output.rstrip("\n"))
+        return
+
+    for entry in annots:
+        if not entry.annotations:
+            continue
+
+        title_decoration = (
+            f"{'=' * len(entry.document.get('title', ''))}   "
+            f"{'-' * len(entry.document.get('author', ''))}"
+        )
+        print(
+            f"{title_decoration}\n{papis.document.describe(entry.document)}\n{title_decoration}\n"
+        )
+        for a in entry.annotations:
+            print(_format_annotation(a))
+
+        if entry != annots[-1]:
+            print("\n")
 
 
-def to_notes(
+def to_notes(annots: list[AnnotatedDocument], edit: bool, git: bool) -> None:
-    formatter: Formatter,
-    annotated_docs: list[AnnotatedDocument],
-    edit: bool,
-    git: bool,
-    force: bool,
-) -> None:
     """Write annotations into document notes.
 
     Permanently writes the given annotations into notes
     belonging to papis documents. Creates new notes for
     documents missing a note field or appends to existing.
     """
-    for entry in annotated_docs:
+    if not annots:
-        formatted_annotations = formatter([entry]).split("\n")
+        return
-        if formatted_annotations:
+
-            _add_annots_to_note(entry.document, formatted_annotations, force=force)
+    for entry in annots:
+        if not entry.annotations:
+            continue
+
+        formatted_annotations: list[str] = []
+        for a in entry.annotations:
+            formatted_annotations.append(_format_annotation(a))
+
+        _add_annots_to_note(entry.document, formatted_annotations)
 
         if edit:
             papis.commands.edit.edit_notes(entry.document, git=git)
@@ -50,26 +73,11 @@ def _add_annots_to_note(
     document: papis.document.Document,
     formatted_annotations: list[str],
     git: bool = False,
-    force: bool = False,
 ) -> None:
-    """
+    """Append new annotations to the end of a note.
-    Append new annotations to the end of a note.
 
-    This function appends new annotations to the end of a note file. It takes in a
+    Looks through note to determine any new annotations which should be
-    document object containing the note, a list of formatted annotations to be
+    added and adds them to the end of the note file.
-    added, and optional flags git and force. If git is True, the changes will be
-    committed to git. If force is True, the annotations will be added even if they
-    already exist in the note.
-
-    :param document: The document object representing the note
-    :type document: class:`papis.document.Document`
-    :param formatted_annotations: A list of already formatted annotations to be added
-    :type formatted_annotations: list[str]
-    :param git: Flag indicating whether to commit changes to git, defaults to False.
-    :type git: bool, optional
-    :param force:  Flag indicating whether to force adding annotations even if they 
-        already exist, defaults to False.
-    :type force: bool, optional
     """
     logger.debug("Adding annotations to note.")
     notes_path = papis.notes.notes_path_ensured(document)
@@ -78,9 +86,9 @@ def _add_annots_to_note(
     with open(notes_path, "r") as file_read:
         existing = file_read.readlines()
 
-    new_annotations: list[str] = []
+    new_annotations: list[str] = _drop_existing_annotations(
-    if not force:
+        formatted_annotations, existing
-        new_annotations = _drop_existing_annotations(formatted_annotations, existing)
+    )
     if not new_annotations:
         return
 
@@ -88,8 +96,7 @@ def _add_annots_to_note(
         # add newline if theres no empty space at file end
         if len(existing) > 0 and existing[-1].strip() != "":
             f.write("\n")
-        print(new_annotations)
+        f.write("\n".join(new_annotations))
-        f.write("\n\n".join(new_annotations))
         f.write("\n")
         logger.info(
             f"Wrote {len(new_annotations)} "
@@ -109,14 +116,6 @@ def _add_annots_to_note(
 def _drop_existing_annotations(
     formatted_annotations: list[str], file_lines: list[str]
 ) -> list[str]:
-    """Returns the input annotations dropping any existing.
-
-    Takes a list of formatted annotations and a list of strings
-    (most probably existing lines in a file). If anny annotations
-    match an existing line closely enough, they will be dropped.
-
-    Returns list of annotations without duplicates.
-    """
     minimum_similarity = (
         papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0
     )
@@ -124,9 +123,7 @@ def _drop_existing_annotations(
     remaining: list[str] = []
     for an in formatted_annotations:
         an_split = an.splitlines()
-        if an_split and not _test_similarity(
+        if not _test_similarity(an_split[0], file_lines, minimum_similarity):
-            an_split[0], file_lines, minimum_similarity
-        ):
             remaining.append(an)
 
     return remaining

papis_extract/extractor.py

@@ -10,7 +10,7 @@ import papis.config
 import papis.document
 from papis.document import Document
 
-from papis_extract.annotation import Annotation, AnnotatedDocument
+from papis_extract.annotation_data import Annotation, AnnotatedDocument
 
 logger = papis.logging.get_logger(__name__)
 
@@ -83,7 +83,6 @@ def extract(filename: Path) -> list[Annotation]:
 
 
 def is_pdf(fname: Path) -> bool:
-    """Check if file is a pdf, using mime type."""
     return magic.from_file(fname, mime=True) == "application/pdf"
 
 

papis_extract/formatter.py

@@ -1,94 +0,0 @@
-from collections.abc import Callable
-
-from papis_extract.annotation import AnnotatedDocument
-
-Formatter = Callable[[list[AnnotatedDocument]], str]
-
-
-def format_markdown(
-    docs: list[AnnotatedDocument] = [], atx_headings: bool = False
-) -> str:
-    template = (
-        "{{#tag}}#{{tag}}\n{{/tag}}"
-        "{{#quote}}> {{quote}}{{/quote}}{{#page}} [p. {{page}}]{{/page}}"
-        "{{#note}}\n  NOTE: {{note}}{{/note}}"
-    )
-    output = ""
-    for entry in docs:
-        if not entry.annotations:
-            continue
-
-        heading = f"{entry.document['title']} - {entry.document['author']}\n"
-        if atx_headings:
-            output += f"# {heading}\n"
-        else:
-            title_decoration = (
-                f"{'=' * len(entry.document.get('title', ''))}   "
-                f"{'-' * len(entry.document.get('author', ''))}"
-            )
-            output += f"{title_decoration}\n" f"{heading}" f"{title_decoration}\n\n"
-
-        for a in entry.annotations:
-            output += a.format(template)
-            output += "\n\n"
-
-        output += "\n\n\n"
-
-    return output.rstrip()
-
-
-def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str:
-    return format_markdown(docs, atx_headings=True)
-
-
-def format_markdown_setext(docs: list[AnnotatedDocument] = []) -> str:
-    return format_markdown(docs, atx_headings=False)
-
-
-def format_count(docs: list[AnnotatedDocument] = []) -> str:
-    output = ""
-    for entry in docs:
-        if not entry.annotations:
-            continue
-
-        count = 0
-        for _ in entry.annotations:
-            count += 1
-
-        d = entry.document
-        output += (
-            f"{d['author'] if 'author' in d else ''}"
-            f"{' - ' if 'author' in d else ''}"  # only put separator if author
-            f"{entry.document['title'] if 'title' in d else ''}: "
-            f"{count}\n"
-        )
-
-    return output.rstrip()
-
-
-def format_csv(docs: list[AnnotatedDocument] = []) -> str:
-    header: str = "type,tag,page,quote,note,author,title,ref,file"
-    template: str = (
-        '{{type}},{{tag}},{{page}},"{{quote}}","{{note}}",'
-        '"{{doc.author}}","{{doc.title}}","{{doc.ref}}","{{file}}"'
-    )
-    output = f"{header}\n"
-    for entry in docs:
-        if not entry.annotations:
-            continue
-
-        d = entry.document
-        for a in entry.annotations:
-            output += a.format(template, doc=d)
-            output += "\n"
-
-    return output.rstrip()
-
-
-formatters: dict[str, Formatter] = {
-    "count": format_count,
-    "csv": format_csv,
-    "markdown": format_markdown,
-    "markdown_atx": format_markdown_atx,
-    "markdown_setext": format_markdown_setext,
-}

poetry.lock

@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
 [[package]]
 name = "arxiv2bib"
@@ -183,70 +183,6 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
-[[package]]
-name = "coverage"
-version = "7.3.1"
-description = "Code coverage measurement for Python"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "coverage-7.3.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:cd0f7429ecfd1ff597389907045ff209c8fdb5b013d38cfa7c60728cb484b6e3"},
-    {file = "coverage-7.3.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:966f10df9b2b2115da87f50f6a248e313c72a668248be1b9060ce935c871f276"},
-    {file = "coverage-7.3.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0575c37e207bb9b98b6cf72fdaaa18ac909fb3d153083400c2d48e2e6d28bd8e"},
-    {file = "coverage-7.3.1-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:245c5a99254e83875c7fed8b8b2536f040997a9b76ac4c1da5bff398c06e860f"},
-    {file = "coverage-7.3.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4c96dd7798d83b960afc6c1feb9e5af537fc4908852ef025600374ff1a017392"},
-    {file = "coverage-7.3.1-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:de30c1aa80f30af0f6b2058a91505ea6e36d6535d437520067f525f7df123887"},
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 ]
 
 [[package]]
@@ -712,13 +648,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.0"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -730,24 +666,6 @@ pluggy = ">=0.12,<2.0"
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
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-pytest = ">=4.6"
-
-[package.extras]
-testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
-
 [[package]]
 name = "python-doi"
 version = "0.2.0"
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-    {file = "rapidfuzz-3.3.0.tar.gz", hash = "sha256:5e71bc5829f41e78b2d009431aedeb308ee3699d2bbbc68b7739db9b40bd1465"},
 ]
 
 [package.extras]
@@ -981,13 +883,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "soupsieve"
-version = "2.5"
+version = "2.4.1"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
-    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
+    {file = "soupsieve-2.4.1-py3-none-any.whl", hash = "sha256:1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8"},
-    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
+    {file = "soupsieve-2.4.1.tar.gz", hash = "sha256:89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea"},
 ]
 
 [[package]]
@@ -1037,13 +939,13 @@ telegram = ["requests"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.8.0"
+version = "4.7.1"
-description = "Backported and Experimental Type Hints for Python 3.8+"
+description = "Backported and Experimental Type Hints for Python 3.7+"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
-    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
-    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
 [[package]]
@@ -1078,7 +980,7 @@ files = [
 name = "whoosh"
 version = "2.7.4"
 description = "Fast, pure-Python full text indexing, search, and spell checking library."
-optional = true
+optional = false
 python-versions = "*"
 files = [
     {file = "Whoosh-2.7.4-py2.py3-none-any.whl", hash = "sha256:aa39c3c3426e3fd107dcb4bde64ca1e276a65a889d9085a6e4b54ba82420a852"},
@@ -1086,10 +988,7 @@ files = [
     {file = "Whoosh-2.7.4.zip", hash = "sha256:e0857375f63e9041e03fedd5b7541f97cf78917ac1b6b06c1fcc9b45375dda69"},
 ]
 
-[extras]
-whoosh = ["whoosh"]
-
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "02d5ac314a19f14103372c7ceccdaec080df3fdc2fdb1381f2f6343cd6d17db4"
+content-hash = "a3af36ed2941235df158c20ba9b66bdf5a0af0554235fd004ec77c3e88def3c3"

pyproject.toml

@@ -12,21 +12,17 @@ pymupdf = "^1.23.1"
 levenshtein = "^0.21.1"
 papis = "^0.13"
 click = "^8.1.7"
-whoosh = { version = "^2.7.4", optional = true }
+whoosh = "^2.7.4"
 python-magic = "^0.4.27"
 chevron = "^0.14.0"
 
-[tool.poetry.extras]
-whoosh = ["whoosh"]
-
-[tool.poetry.group.dev.dependencies]
-pytest = "^7.4.0"
-coverage = "^7.3.1"
-pytest-cov = "^4.1.0"
-
 [tool.poetry.plugins."papis.command"]
 extract = "papis_extract:main"
 
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.4.0"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

tests/test_annotation.py

@@ -1,6 +1,5 @@
-from papis.document import Document
 import pytest
-from papis_extract.annotation import Annotation
+from papis_extract.annotation_data import Annotation
 
 
 @pytest.mark.parametrize(
@@ -17,7 +16,7 @@ from papis_extract.annotation import Annotation
         ),
     ],
 )
-def test_formatting_replacements(fmt_string, expected):
+def test_formatting(fmt_string, expected):
     sut = Annotation(
         "myfile",
         text="I am the text value",
@@ -26,30 +25,13 @@ def test_formatting_replacements(fmt_string, expected):
 
     assert sut.format(fmt_string) == expected
 
-@pytest.mark.parametrize(
-    "fmt_string,expected",
-    [
-        ("{{doc.title}}", "document-title"),
-        ("{{doc.title}}-{{doc.author}}", "document-title-document-author"),
-        ("{{quote}} ({{doc.author}})", "I am the text value (document-author)"),
-    ]
-)
-def test_formatting_document_access(fmt_string, expected):
-    sut = Annotation(
-        "myfile",
-        text="I am the text value",
-        content="Whereas I represent the note",
-    )
-    doc = Document(data= {"title": "document-title", "author": "document-author"})
-
-    assert sut.format(fmt_string, doc=doc) == expected
-
 def test_colorname_matches_exact():
-    sut = Annotation("testfile", colors=(1.0, 0.0, 0.0), minimum_similarity_color=1.0)
+    sut = Annotation(
+        "testfile", colors=(1.0,0.0,0.0), minimum_similarity_color=1.0
+    )
     c_name = sut.colorname
     assert c_name == "red"
 
-
 # TODO inject closeness value instead of relying on default
 @pytest.mark.parametrize(
     "color_value",
@@ -62,6 +44,8 @@ def test_colorname_matches_exact():
     ],
 )
 def test_matches_inexact_colorname(color_value):
-    sut = Annotation("testfile", colors=color_value, minimum_similarity_color=0.833)
+    sut = Annotation(
+        "testfile", colors=color_value, minimum_similarity_color=0.833
+    )
     c_name = sut.colorname
     assert c_name == "red"

tests/test_formatting.py

@@ -1,80 +0,0 @@
-from papis.document import Document
-from papis_extract.annotation import AnnotatedDocument, Annotation
-
-from papis_extract.formatter import (
-    format_count,
-    format_csv,
-    format_markdown,
-    format_markdown_atx,
-    format_markdown_setext,
-)
-
-an_doc: AnnotatedDocument = AnnotatedDocument(
-    Document(data={"author": "document-author", "title": "document-title"}),
-    [
-        Annotation("myfile.pdf", text="my lovely text"),
-        Annotation("myfile.pdf", text="my second text", content="with note"),
-    ],
-)
-md_default_output = """==============   ---------------
-document-title - document-author
-==============   ---------------
-
-> my lovely text
-
-> my second text
-  NOTE: with note"""
-
-
-def test_markdown_default():
-    fmt = format_markdown
-    assert fmt([an_doc]) == md_default_output
-
-
-def test_markdown_atx():
-    fmt = format_markdown_atx
-    assert fmt([an_doc]) == (
-        """# document-title - document-author
-
-> my lovely text
-
-> my second text
-  NOTE: with note"""
-    )
-
-
-def test_markdown_setext():
-    fmt = format_markdown_setext
-    assert fmt([an_doc]) == md_default_output
-
-
-def test_count_default():
-    fmt = format_count
-    assert fmt([an_doc]) == ("""document-author - document-title: 2""")
-
-
-def test_csv_default():
-    fmt = format_csv
-    assert fmt([an_doc]) == (
-        "type,tag,page,quote,note,author,title,ref,file\n"
-        'Highlight,,0,"my lovely text","","document-author",'
-        '"document-title","","myfile.pdf"\n'
-        'Highlight,,0,"my second text","with note","document-author",'
-        '"document-title","","myfile.pdf"'
-    )
-
-
-# sadpath - no annotations contained for each format
-def test_markdown_no_annotations():
-    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
-    assert format_markdown([d]) == ""
-
-
-def test_count_no_annotations():
-    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
-    assert format_count([d]) == ""
-
-
-def test_csv_no_annotations():
-    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
-    assert format_csv([d]) == "type,tag,page,quote,note,author,title,ref,file"