fix: Only inform if no extractor finds valid files

Until now whenever an extractor could not find any valid files for a
document it would inform the user of this case. However, this is not
very useful: if you have a pdf and an epub extractor running, it would
inform you for each document which only had one of the two formats as
well as those which actually did not have any valid files for *any* of
the extractors running.

This commit changes the behavior to only inform the user when none of
the running extractors find a valid file, since that is the actual case
a user might want to be informed about.

papis_extract/__init__.py

@@ -1,3 +1,4 @@
+import re
 import click
 import papis.cli
 import papis.config
@@ -7,16 +8,16 @@ import papis.notes
 import papis.strings
 from papis.document import Document
 
-from papis_extract.annotation import Annotation
 from papis_extract import extraction
+from papis_extract.annotation import Annotation
 from papis_extract.exporter import Exporter
-from papis_extract.extractors import all_extractors
 from papis_extract.exporters import all_exporters
+from papis_extract.extractors import all_extractors
 from papis_extract.formatter import Formatter, formatters
 
 logger = papis.logging.get_logger(__name__)
 
-DEFAULT_OPTIONS = {
+DEFAULT_OPTIONS: dict[str, dict[str, bool | float | dict[str, str]]] = {
     "plugins.extract": {
         "tags": {},
         "on_import": False,
@@ -88,10 +89,11 @@ def main(
     git: bool,
     force: bool,
 ) -> None:
-    """Extract annotations from any pdf document.
+    """Extract annotations from any documents.
 
     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 documents belonging to entries of the papis library,
+    primarily targeting PDF documents currently.
     It can write those changes to stdout or directly create and update notes
     for papis documents.
 
@@ -128,25 +130,34 @@ def run(
     git: bool = False,
     force: bool = False,
 ) -> None:
+    exporter: Exporter
     if write:
-        exporter: Exporter = all_exporters["notes"](
+        exporter = all_exporters["notes"](
             formatter=formatter or formatters["markdown-atx"],
             edit=edit,
             git=git,
             force=force,
         )
     else:
-        exporter: Exporter = all_exporters["stdout"](
+        exporter = all_exporters["stdout"](
             formatter=formatter or formatters["markdown"]
         )
 
     doc_annots: list[tuple[Document, list[Annotation]]] = []
     for doc in documents:
         annotations: list[Annotation] = []
+        valid_files: int = 0
         for ext in extractors:
             if not ext:
                 continue
-            annotations.extend(extraction.start(ext, doc))
+            added = extraction.start(ext, doc)
+            if added is not None:
+                valid_files += 1
+                annotations.extend(added)
         doc_annots.append((doc, annotations))
 
+        if valid_files == 0:
+            # have to remove curlys or papis logger gets upset
+            desc = re.sub("[{}]", "", papis.document.describe(doc))
+            logger.info(f"Document {desc} has no valid extractors for any of its files.")
     exporter.run(doc_annots)

papis_extract/annotation.py

@@ -1,6 +1,6 @@
 import math
 from dataclasses import dataclass
-from typing import Any, Optional
+from typing import Any, Optional, cast
 
 import chevron
 import papis.config
@@ -127,7 +127,7 @@ class Annotation:
         """
         rawvalue: Any = papis.config.general_get(key, section=section)
         if isinstance(rawvalue, dict):
-            return rawvalue
+            return cast(dict[str, str], rawvalue)
         try:
             rawvalue = eval(rawvalue)
         except Exception:
@@ -142,4 +142,4 @@ class Annotation:
                     )
                 )
 
-            return rawvalue
+            return cast(dict[str, str], rawvalue)

papis_extract/exceptions.py

@@ -0,0 +1,8 @@
+class ExtractionError(Exception):
+    """Raised for exceptions during extraction.
+
+    Something went wrong during the extraction process in the extractor
+    run routine itself.
+    """
+
+    pass

papis_extract/exporter.py

@@ -24,5 +24,4 @@ class Exporter(Protocol):
 
     def run(
         self, annot_docs: list[tuple[papis.document.Document, list[Annotation]]]
-    ) -> None:
+    ) -> None: ...
-        ...

papis_extract/exporters/__init__.py

@@ -1,4 +1,3 @@
-
 import papis.logging
 
 from papis_extract.exporter import Exporter

papis_extract/exporters/notes.py

@@ -28,7 +28,10 @@ class NotesExporter:
         documents missing a note field or appends to existing.
         """
         for doc, annots in annot_docs:
-            formatted_annotations = self.formatter(doc, annots).split("\n")
+            # first always true since we write single doc per note
+            formatted_annotations: list[str] = self.formatter(
+                doc, annots, first=True
+            ).split("\n")
             if formatted_annotations:
                 self._add_annots_to_note(doc, formatted_annotations, force=self.force)
 
@@ -80,7 +83,9 @@ class NotesExporter:
             # add newline if theres no empty space at file end
             if len(existing) > 0 and existing[-1].strip() != "":
                 f.write("\n")
-            f.write("\n\n".join(new_annotations))
+            # FIXME this either joins them too close or moves them too far apart
+            # We need a better algorithm which knows what a full 'annotation' is.
+            f.write("\n".join(new_annotations))
             f.write("\n")
             logger.info(
                 f"Wrote {len(new_annotations)} "

papis_extract/exporters/stdout.py

@@ -20,7 +20,9 @@ class StdoutExporter:
         the annotations in somewhat of a list form.
         Not intended for machine-readability.
         """
+        first_entry = True
         for doc, annots in annot_docs:
-            output: str = self.formatter(doc, annots)
+            output: str = self.formatter(doc, annots, first=first_entry)
             if output:
                 print("{output}\n".format(output=output.rstrip("\n")))
+                first_entry = False

papis_extract/extraction.py

@@ -2,33 +2,33 @@ import re
 from pathlib import Path
 from typing import Protocol
 
-import fitz
 import papis.config
 import papis.document
 import papis.logging
 from papis.document import Document
 
 from papis_extract.annotation import Annotation
+from papis_extract.exceptions import ExtractionError
 
 logger = papis.logging.get_logger(__name__)
 
 
 class Extractor(Protocol):
-    def can_process(self, filename: Path) -> bool:
+    def can_process(self, filename: Path) -> bool: ...
-        ...
 
-    def run(self, filename: Path) -> list[Annotation]:
+    def run(self, filename: Path) -> list[Annotation]: ...
-        ...
 
 
 def start(
     extractor: Extractor,
     document: Document,
-) -> list[Annotation]:
+) -> list[Annotation] | None:
     """Extract all annotations from passed documents.
 
     Returns all annotations contained in the papis
-    documents passed in.
+    documents passed in (empty list if no annotations).
+    If there are no files that the extractor can process,
+    returns None instead.
     """
     annotations: list[Annotation] = []
     file_available: bool = False
@@ -41,12 +41,10 @@ def start(
 
         try:
             annotations.extend(extractor.run(fname))
-        except fitz.FileDataError as e:
+        except ExtractionError as e:
-            print(f"File structure errors for {file}.\n{e}")
+            logger.error(f"File extraction errors for {file}. File may be damaged.\n{e}")
 
     if not file_available:
-        # have to remove curlys or papis logger gets upset
+        return None
-        desc = re.sub("[{}]", "", papis.document.describe(document))
-        logger.info(f"No {type(extractor)} file for document: {desc}")
 
     return annotations

papis_extract/extractors/pdf.py

@@ -1,12 +1,15 @@
+# pyright: strict, reportMissingTypeStubs=false, reportUnknownMemberType=false
 from pathlib import Path
+from typing import cast
 
-import fitz
 import Levenshtein
 import magic
 import papis.config
 import papis.logging
+import pymupdf as mu
 
 from papis_extract.annotation import Annotation
+from papis_extract.exceptions import ExtractionError
 
 logger = papis.logging.get_logger(__name__)
 
@@ -26,31 +29,45 @@ class PdfExtractor:
         Returns all readable annotations contained in the file
         passed in. Only returns Highlight or Text annotations.
         """
-        annotations = []
+        annotations: list[Annotation] = []
-        with fitz.Document(filename) as doc:
+        try:
-            for page in doc:
+            with mu.Document(filename) as doc:
-                for annot in page.annots():
+                for (
-                    quote, note = self._retrieve_annotation_content(page, annot)
+                    page
-                    if not quote and not note:
+                ) in doc:  # pyright: ignore [reportUnknownVariableType] - missing stub
-                        continue
+                    page = cast(mu.Page, page)
-                    col = (
+                    annot: mu.Annot
-                        annot.colors.get("fill")
+                    for annot in page.annots():
-                        or annot.colors.get("stroke")
+                        quote, note = self._retrieve_annotation_content(page, annot)
-                        or (0.0, 0.0, 0.0)
+                        if not quote and not note:
-                    )
+                            continue
-                    a = Annotation(
+                        color: tuple[float, float, float] = cast(
-                        file=str(filename),
+                            tuple[float, float, float],
-                        content=quote or "",
+                            (
-                        note=note or "",
+                                annot.colors.get("fill")
-                        color=col,
+                                or annot.colors.get("stroke")
-                        type=annot.type[1],
+                                or (0.0, 0.0, 0.0)
-                        page=(page.number or 0) + 1,
+                            ),
-                    )
+                        )
-                    annotations.append(a)
+                        page_nr: int = cast(int, page.number or 0)
-        logger.debug(
+                        highlight_type: str = cast(str, annot.type[1] or "")
-            f"Found {len(annotations)} "
+                        a = Annotation(
-            f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
+                            file=str(filename),
-        )
+                            content=quote or "",
+                            note=note or "",
+                            color=color,
+                            type=highlight_type,
+                            page=page_nr,
+                        )
+                        annotations.append(a)
+            logger.debug(
+                f"Found {len(annotations)} "
+                f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
+            )
+
+        except mu.FileDataError:
+            raise ExtractionError
+
         return annotations
 
     def _is_pdf(self, fname: Path) -> bool:
@@ -58,7 +75,7 @@ class PdfExtractor:
         return magic.from_file(fname, mime=True) == "application/pdf"
 
     def _retrieve_annotation_content(
-        self, page: fitz.Page, annotation: fitz.Annot
+        self, page: mu.Page, annotation: mu.Annot
     ) -> tuple[str | None, str | None]:
         """Gets the text content of an annotation.
 
@@ -69,7 +86,7 @@ class PdfExtractor:
         should both be included or are the same, using
         Levenshtein distance.
         """
-        content = annotation.info["content"].replace("\n", " ")
+        content = cast(str, annotation.info["content"].replace("\n", " "))
         written = page.get_textbox(annotation.rect).replace("\n", " ")
 
         # highlight with selection in note

papis_extract/extractors/pocketbook.py

@@ -1,3 +1,4 @@
+# pyright: strict, reportUnknownMemberType=false
 from pathlib import Path
 
 import magic
@@ -42,9 +43,18 @@ class PocketBookExtractor:
 
         annotations: list[Annotation] = []
         for bm in html.select("div.bookmark"):
-            content = (bm.select_one("div.bm-text>p") or html.new_string("")).text
+            content = str(
-            note = (bm.select_one("div.bm-note>p") or html.new_string("")).text
+                (bm.select_one("div.bm-text>p") or html.new_string("")).text
-            page = (bm.select_one("p.bm-page") or html.new_string("")).text
+                or ""  # pyright: ignore [reportUnknownArgumentType]
+            )
+            note = str(
+                (bm.select_one("div.bm-note>p") or html.new_string("")).text
+                or ""  # pyright: ignore [reportUnknownArgumentType]
+            )
+            page = int(
+                (bm.select_one("p.bm-page") or html.new_string("")).text
+                or 0  # pyright: ignore [reportUnknownArgumentType]
+            )
 
             el_classes = bm.attrs.get("class", "").split(" ")
             color = (0, 0, 0)
@@ -55,11 +65,11 @@ class PocketBookExtractor:
 
             a = Annotation(
                 file=str(filename),
-                content=content or "",
+                content=content,
-                note=note or "",
+                note=note,
                 color=color,
                 type="Highlight",
-                page=int(page),
+                page=page,
             )
             annotations.append(a)
 

papis_extract/formatter.py

@@ -1,15 +1,32 @@
-from collections.abc import Callable
+from typing import Protocol
-
 from papis.document import Document
 
 from papis_extract.annotation import Annotation
 
-Formatter = Callable[[Document, list[Annotation]], str]
+
+class Formatter(Protocol):
+    """Basic formatter protocol.
+
+    Every valid formatter must implement at least this protocol.
+    A formatter is a function which receives a document and a list
+    of annotations and spits them out in some formatted way.
+
+    Formatters additionally must take the (often optional) passed
+    parameter 'first' which signals to the formatter that the current
+    document entry is the very first one to be printed in whatever
+    exporter is used, if multiple entries are printed.
+    This can be useful for adding a header if necessary for the format.
+    """
+
+    def __call__(
+        self, document: Document, annotations: list[Annotation], first: bool
+    ) -> str: ...
 
 
 def format_markdown(
     document: Document = Document(),
     annotations: list[Annotation] = [],
+    first: bool = False,
     headings: str = "setext",  # setext | atx | None
 ) -> str:
     if not annotations:
@@ -23,15 +40,13 @@ def format_markdown(
 
     heading = f"{document.get('title', '')} - {document.get('author', '')}"
     if headings == "atx":
-        output = f"# {heading}\n\n"
+        output += f"# {heading}\n\n"
     elif headings == "setext":
         title_decoration = (
             f"{'=' * len(document.get('title', ''))}   "
             f"{'-' * len(document.get('author', ''))}"
         )
-        output = f"{title_decoration}\n{heading}\n{title_decoration}\n\n"
+        output += f"{title_decoration}\n{heading}\n{title_decoration}\n\n"
-    else:
-        output = ""
 
     for a in annotations:
         output += a.format(template)
@@ -45,6 +60,7 @@ def format_markdown(
 def format_markdown_atx(
     document: Document = Document(),
     annotations: list[Annotation] = [],
+    first: bool = False,
 ) -> str:
     return format_markdown(document, annotations, headings="atx")
 
@@ -52,6 +68,7 @@ def format_markdown_atx(
 def format_markdown_setext(
     document: Document = Document(),
     annotations: list[Annotation] = [],
+    first: bool = False,
 ) -> str:
     return format_markdown(document, annotations, headings="setext")
 
@@ -59,6 +76,7 @@ def format_markdown_setext(
 def format_count(
     document: Document = Document(),
     annotations: list[Annotation] = [],
+    first: bool = False,
 ) -> str:
     if not annotations:
         return ""
@@ -68,23 +86,24 @@ def format_count(
         count += 1
 
     return (
+        f"{count} "
         f"{document.get('author', '')}"
-        f"{' - ' if 'author' in document else ''}"  # only put separator if author
+        f"{': ' if 'author' in document else ''}"  # only put separator if author
-        f"{document.get('title', '')}: "
+        f"{document.get('title', '')}"
-        f"{count}\n"
     ).rstrip()
 
 
 def format_csv(
     document: Document = Document(),
     annotations: list[Annotation] = [],
+    first: bool = False,
 ) -> 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"
+    output = f"{header}\n" if first else ""
     if not annotations:
         return ""
 

poetry.lock

@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "arxiv2bib"
@@ -46,13 +46,13 @@ pyparsing = ">=2.0.3"
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2024.6.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
+    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
-    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
 ]
 
 [[package]]
@@ -203,63 +203,63 @@ files = [
 
 [[package]]
 name = "coverage"
-version = "7.4.0"
+version = "7.5.3"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "coverage-7.5.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a6519d917abb15e12380406d721e37613e2a67d166f9fb7e5a8ce0375744cd45"},
-    {file = "coverage-7.4.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0676cd0ba581e514b7f726495ea75aba3eb20899d824636c6f59b0ed2f88c471"},
+    {file = "coverage-7.5.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:aea7da970f1feccf48be7335f8b2ca64baf9b589d79e05b9397a06696ce1a1ec"},
-    {file = "coverage-7.4.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d0ca5c71a5a1765a0f8f88022c52b6b8be740e512980362f7fdbb03725a0d6b9"},
+    {file = "coverage-7.5.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:923b7b1c717bd0f0f92d862d1ff51d9b2b55dbbd133e05680204465f454bb286"},
-    {file = "coverage-7.4.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a7c97726520f784239f6c62506bc70e48d01ae71e9da128259d61ca5e9788516"},
+    {file = "coverage-7.5.3-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:62bda40da1e68898186f274f832ef3e759ce929da9a9fd9fcf265956de269dbc"},
-    {file = "coverage-7.4.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:815ac2d0f3398a14286dc2cea223a6f338109f9ecf39a71160cd1628786bc6f5"},
+    {file = "coverage-7.5.3-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d8b7339180d00de83e930358223c617cc343dd08e1aa5ec7b06c3a121aec4e1d"},
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+    {file = "coverage-7.5.3-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:25a5caf742c6195e08002d3b6c2dd6947e50efc5fc2c2205f61ecb47592d2d83"},
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+    {file = "coverage-7.5.3-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:05ac5f60faa0c704c0f7e6a5cbfd6f02101ed05e0aee4d2822637a9e672c998d"},
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+    {file = "coverage-7.5.3-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:239a4e75e09c2b12ea478d28815acf83334d32e722e7433471fbf641c606344c"},
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+    {file = "coverage-7.5.3-cp310-cp310-win32.whl", hash = "sha256:a5812840d1d00eafae6585aba38021f90a705a25b8216ec7f66aebe5b619fb84"},
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+    {file = "coverage-7.5.3-cp310-cp310-win_amd64.whl", hash = "sha256:33ca90a0eb29225f195e30684ba4a6db05dbef03c2ccd50b9077714c48153cac"},
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 [package.extras]
@@ -289,13 +289,13 @@ files = [
 
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+version = "1.2.6"
 description = "Low Level Client for Crossref Search API"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -304,17 +304,18 @@ tqdm = "*"
 
 [package.extras]
 all = ["pytest"]
+bibtex = ["bibtexparser (>=2.0.0)"]
 test = ["pytest"]
 
 [[package]]
 name = "idna"
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 description = "Internationalized Domain Names in Applications (IDNA)"
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 python-versions = ">=3.5"
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 ]
 
 [[package]]
@@ -443,106 +444,171 @@ rapidfuzz = ">=3.8.0,<4.0.0"
 
 [[package]]
 name = "lxml"
-version = "5.1.0"
+version = "5.2.2"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
 optional = false
 python-versions = ">=3.6"
 files = [
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 html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=3.0.7)"]
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 description = "Core utilities for Python packages"
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 [[package]]
@@ -595,13 +661,13 @@ files = [
 
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 name = "pluggy"
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 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
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 [package.extras]
@@ -610,13 +676,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
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 [package.dependencies]
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+    {file = "rapidfuzz-3.9.3.tar.gz", hash = "sha256:b398ea66e8ed50451bce5997c430197d5e4b06ac4aa74602717f792d8d8d06e2"},
 ]
 
 [package.extras]
@@ -941,13 +1010,13 @@ full = ["numpy"]
 
 [[package]]
 name = "requests"
-version = "2.31.0"
+version = "2.32.3"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
+    {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"},
-    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
+    {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"},
 ]
 
 [package.dependencies]
@@ -973,13 +1042,13 @@ files = [
 
 [[package]]
 name = "stevedore"
-version = "5.1.0"
+version = "5.2.0"
 description = "Manage dynamic plugins for Python applications"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "stevedore-5.1.0-py3-none-any.whl", hash = "sha256:8cc040628f3cea5d7128f2e76cf486b2251a4e543c7b938f58d9a377f6694a2d"},
+    {file = "stevedore-5.2.0-py3-none-any.whl", hash = "sha256:1c15d95766ca0569cad14cb6272d4d31dae66b011a929d7c18219c176ea1b5c9"},
-    {file = "stevedore-5.1.0.tar.gz", hash = "sha256:a54534acf9b89bc7ed264807013b505bf07f74dbe4bcfa37d32bd063870b087c"},
+    {file = "stevedore-5.2.0.tar.gz", hash = "sha256:46b93ca40e1114cea93d738a6c1e365396981bb6bb78c27045b7587c9473544d"},
 ]
 
 [package.dependencies]
@@ -998,13 +1067,13 @@ files = [
 
 [[package]]
 name = "tqdm"
-version = "4.66.1"
+version = "4.66.4"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"},
+    {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"},
-    {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"},
+    {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"},
 ]
 
 [package.dependencies]
@@ -1018,28 +1087,29 @@ telegram = ["requests"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.9.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
-    {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "2.1.0"
+version = "2.2.1"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.1.0-py3-none-any.whl", hash = "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3"},
+    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.1.0.tar.gz", hash = "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"},
+    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
 ]
 
 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 

pyproject.toml

@@ -45,3 +45,6 @@ extract = "papis_extract:main"
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.pyright]
+typeCheckingMode = "strict"

tests/test_annotation.py

@@ -18,7 +18,7 @@ from papis_extract.annotation import Annotation
         ),
     ],
 )
-def test_formatting_replacements(fmt_string, expected):
+def test_formatting_replacements(fmt_string: str, expected: str):
     sut = Annotation(
         "myfile",
         content="I am the text value",
@@ -36,7 +36,7 @@ def test_formatting_replacements(fmt_string, expected):
         ("{{quote}} ({{doc.author}})", "I am the text value (document-author)"),
     ],
 )
-def test_formatting_document_access(fmt_string, expected):
+def test_formatting_document_access(fmt_string: str, expected: str):
     sut = Annotation(
         "myfile",
         content="I am the text value",
@@ -64,7 +64,7 @@ def test_colorname_matches_exact():
         (0.51, 0.0, 0.0),
     ],
 )
-def test_matches_inexact_colorname(color_value):
+def test_matches_inexact_colorname(color_value: tuple[float, float, float]):
     sut = Annotation("testfile", color=color_value, minimum_similarity_color=0.833)
     c_name = sut.colorname
     assert c_name == "red"

tests/test_formatting.py

@@ -48,12 +48,22 @@ def test_markdown_setext():
 
 def test_count_default():
     fmt = format_count
-    assert fmt(document, annotations) == ("""document-author - document-title: 2""")
+    assert fmt(document, annotations) == ("""2 document-author: document-title""")
 
 
 def test_csv_default():
     fmt = format_csv
     assert fmt(document, annotations) == (
+        '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"'
+    )
+
+
+def test_csv_with_header():
+    fmt = format_csv
+    assert fmt(document, annotations, first=True) == (
         "type,tag,page,quote,note,author,title,ref,file\n"
         'Highlight,,0,"my lovely text","","document-author",'
         '"document-title","","myfile.pdf"\n'