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4 changed files with 280 additions and 4 deletions
40
README.md
40
README.md
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@ -10,6 +10,33 @@ Put `extract` folder in your pubs `plugs` directory.
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Then add `extract` to your plugin list in the pubs configuration file.
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## Configuration:
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In your pubs configuration file:
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```ini
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[plugins]
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active = extract
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[[extract]]
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on_import = False
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minimum_similarity = 0.75
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```
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If `on_import` is `True` extraction is automatically run whenever a new document is added to the library,
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if false extraction has to be handled manually.
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`minimum_similarity` sets the required similarity of an annotation's note and written words to be viewed
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as one. Any annotation that has both and is *under* the minimum similarity will be added in the following form:
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```markdown
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> [13] my annotation
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Note: my additional thoughts
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```
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That is, the extractor detects additional written words by whoever annotated and adds them to the extraction.
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The option generally should not take too much tuning, but it is there if you need it.
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## Usage:
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`pubs extract [-h|-w|-e] <citekeys>`
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@ -62,6 +89,18 @@ What follows is a not-very-sorted train of though on where the plugin is at and
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could see myself taking it one day, provided I find the time.
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Pull requests tackling one of these areas of course very welcome.
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## Issues
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A note on the extraction. Highlights in pdfs are somewhat difficult to parse
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(as are most things in them). Sometimes they contain the selected text that is written on the
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page, sometimes they contain the annotators thoughts as a note, sometimes they contain nothing.
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This plugin makes an effort to find the right combination and extract the written words,
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as well as any additional notes made - but things *will* slip through or extract weirdly every now
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and again.
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The easiest extraction is provided if your program writes the selection itself into the highlight
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content, because then we can just use that. It is harder to parse if it does not.
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## Roadmap:
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- [x] extracts highlights and annotations from a doc file (e.g. using PyMuPDF)
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@ -79,6 +118,7 @@ Pull requests tackling one of these areas of course very welcome.
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- [ ] 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
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- [ ] make invoking the command run a query if corresponding option provided (or whatever) in pubs syntax and use resulting papers
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- [ ] confirm for many papers?
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- [ ] warning when the amount of annotations in file is different than the amount extracted?
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## Things that would also be nice in pubs in general and don't really belong in this repository
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@ -2,6 +2,7 @@ import os
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import argparse
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import fitz
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import Levenshtein
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from pubs.plugins import PapersPlugin
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from pubs.events import DocAddEvent, NoteEvent
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@ -39,6 +40,7 @@ class ExtractPlugin(PapersPlugin):
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# or `:: {annotation} :: {page} ::`
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# and so on
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self.onimport = conf["plugins"].get("extract", {}).get("onimport", False)
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self.minimum_similarity = float(conf["plugins"].get("extract", {}).get("minimum_similarity", 0.75))
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def update_parser(self, subparsers, conf):
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"""Allow the usage of the pubs extract subcommand"""
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@ -129,13 +131,29 @@ class ExtractPlugin(PapersPlugin):
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with fitz.Document(filename) as doc:
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for page in doc:
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for annot in page.annots():
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content = annot.get_text() or annot.info["content"].replace(
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"\n", ""
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)
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content = self._retrieve_annotation_content(page, annot)
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if content:
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annotations.append(f"[{(page.number or 0) + 1}] {content}")
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return annotations
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def _retrieve_annotation_content(self, page, annotation, connector = "\nNote: "):
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"""Gets the text content of an annotation.
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Returns the actual content of an annotation. Sometimes
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that is only the written words, sometimes that is only
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annotation notes, sometimes it is both. Runs a similarity
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comparison between strings to find out whether they
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should both be included or are doubling up.
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"""
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content = annotation.info["content"].replace("\n", " ")
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written = page.get_textbox(annotation.rect).replace("\n", " ")
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if Levenshtein.ratio(content,written) > self.minimum_similarity:
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return content
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elif content:
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return f"{written}{connector}{content}"
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return written
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def _to_stdout(self, annotated_papers):
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"""Write annotations to stdout.
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219
poetry.lock
generated
219
poetry.lock
generated
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@ -101,6 +101,121 @@ files = [
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{file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
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]
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[[package]]
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name = "levenshtein"
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version = "0.20.8"
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description = "Python extension for computing string edit distances and similarities."
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category = "main"
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optional = false
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python-versions = ">=3.6"
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files = [
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[[package]]
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{file = "rapidfuzz-2.13.7-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:fa4c598ed77f74ec973247ca776341200b0f93ec3883e34c222907ce72cb92a4"},
|
||||
{file = "rapidfuzz-2.13.7-cp37-cp37m-win32.whl", hash = "sha256:c2523f8180ebd9796c18d809e9a19075a1060b1a170fde3799e83db940c1b6d5"},
|
||||
{file = "rapidfuzz-2.13.7-cp37-cp37m-win_amd64.whl", hash = "sha256:5ada0a14c67452358c1ee52ad14b80517a87b944897aaec3e875279371a9cb96"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:ca8a23097c1f50e0fdb4de9e427537ca122a18df2eead06ed39c3a0bef6d9d3a"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:9be02162af0376d64b840f2fc8ee3366794fc149f1e06d095a6a1d42447d97c5"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:af4f7c3c904ca709493eb66ca9080b44190c38e9ecb3b48b96d38825d5672559"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1f50d1227e6e2a0e3ae1fb1c9a2e1c59577d3051af72c7cab2bcc430cb5e18da"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c71d9d512b76f05fa00282227c2ae884abb60e09f08b5ca3132b7e7431ac7f0d"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:b52ac2626945cd21a2487aeefed794c14ee31514c8ae69b7599170418211e6f6"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:ca00fafd2756bc9649bf80f1cf72c647dce38635f0695d7ce804bc0f759aa756"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d248a109699ce9992304e79c1f8735c82cc4c1386cd8e27027329c0549f248a2"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:c88adbcb933f6b8612f6c593384bf824e562bb35fc8a0f55fac690ab5b3486e5"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:c8601a66fbfc0052bb7860d2eacd303fcde3c14e87fdde409eceff516d659e77"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-musllinux_1_1_ppc64le.whl", hash = "sha256:27be9c63215d302ede7d654142a2e21f0d34ea6acba512a4ae4cfd52bbaa5b59"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-musllinux_1_1_s390x.whl", hash = "sha256:3dcffe1f3cbda0dc32133a2ae2255526561ca594f15f9644384549037b355245"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:8450d15f7765482e86ef9be2ad1a05683cd826f59ad236ef7b9fb606464a56aa"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-win32.whl", hash = "sha256:460853983ab88f873173e27cc601c5276d469388e6ad6e08c4fd57b2a86f1064"},
|
||||
{file = "rapidfuzz-2.13.7-cp38-cp38-win_amd64.whl", hash = "sha256:424f82c35dbe4f83bdc3b490d7d696a1dc6423b3d911460f5493b7ffae999fd2"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:c3fbe449d869ea4d0909fc9d862007fb39a584fb0b73349a6aab336f0d90eaed"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:16080c05a63d6042643ae9b6cfec1aefd3e61cef53d0abe0df3069b9d4b72077"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:dbcf5371ea704759fcce772c66a07647751d1f5dbdec7818331c9b31ae996c77"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:114810491efb25464016fd554fdf1e20d390309cecef62587494fc474d4b926f"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:99a84ab9ac9a823e7e93b4414f86344052a5f3e23b23aa365cda01393ad895bd"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:81642a24798851b118f82884205fc1bd9ff70b655c04018c467824b6ecc1fabc"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:c3741cb0bf9794783028e8b0cf23dab917fa5e37a6093b94c4c2f805f8e36b9f"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:759a3361711586a29bc753d3d1bdb862983bd9b9f37fbd7f6216c24f7c972554"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:1333fb3d603d6b1040e365dca4892ba72c7e896df77a54eae27dc07db90906e3"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:916bc2e6cf492c77ad6deb7bcd088f0ce9c607aaeabc543edeb703e1fbc43e31"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-musllinux_1_1_ppc64le.whl", hash = "sha256:23524635840500ce6f4d25005c9529a97621689c85d2f727c52eed1782839a6a"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-musllinux_1_1_s390x.whl", hash = "sha256:ebe303cd9839af69dd1f7942acaa80b1ba90bacef2e7ded9347fbed4f1654672"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:fe56659ccadbee97908132135de4b875543353351e0c92e736b7c57aee298b5a"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-win32.whl", hash = "sha256:3f11a7eff7bc6301cd6a5d43f309e22a815af07e1f08eeb2182892fca04c86cb"},
|
||||
{file = "rapidfuzz-2.13.7-cp39-cp39-win_amd64.whl", hash = "sha256:e8914dad106dacb0775718e54bf15e528055c4e92fb2677842996f2d52da5069"},
|
||||
{file = "rapidfuzz-2.13.7-pp37-pypy37_pp73-macosx_10_9_x86_64.whl", hash = "sha256:7f7930adf84301797c3f09c94b9c5a9ed90a9e8b8ed19b41d2384937e0f9f5bd"},
|
||||
{file = "rapidfuzz-2.13.7-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c31022d9970177f6affc6d5dd757ed22e44a10890212032fabab903fdee3bfe7"},
|
||||
{file = "rapidfuzz-2.13.7-pp37-pypy37_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:f42b82f268689f429def9ecfb86fa65ceea0eaf3fed408b570fe113311bf5ce7"},
|
||||
{file = "rapidfuzz-2.13.7-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8b477b43ced896301665183a5e0faec0f5aea2373005648da8bdcb3c4b73f280"},
|
||||
{file = "rapidfuzz-2.13.7-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:d63def9bbc6b35aef4d76dc740301a4185867e8870cbb8719ec9de672212fca8"},
|
||||
{file = "rapidfuzz-2.13.7-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:c66546e30addb04a16cd864f10f5821272a1bfe6462ee5605613b4f1cb6f7b48"},
|
||||
{file = "rapidfuzz-2.13.7-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f799d1d6c33d81e983d3682571cc7d993ae7ff772c19b3aabb767039c33f6d1e"},
|
||||
{file = "rapidfuzz-2.13.7-pp38-pypy38_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:d82f20c0060ffdaadaf642b88ab0aa52365b56dffae812e188e5bdb998043588"},
|
||||
{file = "rapidfuzz-2.13.7-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:042644133244bfa7b20de635d500eb9f46af7097f3d90b1724f94866f17cb55e"},
|
||||
{file = "rapidfuzz-2.13.7-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:75c45dcd595f8178412367e302fd022860ea025dc4a78b197b35428081ed33d5"},
|
||||
{file = "rapidfuzz-2.13.7-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:3d8b081988d0a49c486e4e845a547565fee7c6e7ad8be57ff29c3d7c14c6894c"},
|
||||
{file = "rapidfuzz-2.13.7-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:16ffad751f43ab61001187b3fb4a9447ec2d1aedeff7c5bac86d3b95f9980cc3"},
|
||||
{file = "rapidfuzz-2.13.7-pp39-pypy39_pp73-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:020858dd89b60ce38811cd6e37875c4c3c8d7fcd8bc20a0ad2ed1f464b34dc4e"},
|
||||
{file = "rapidfuzz-2.13.7-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:cda1e2f66bb4ba7261a0f4c2d052d5d909798fca557cbff68f8a79a87d66a18f"},
|
||||
{file = "rapidfuzz-2.13.7-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:b6389c50d8d214c9cd11a77f6d501529cb23279a9c9cafe519a3a4b503b5f72a"},
|
||||
{file = "rapidfuzz-2.13.7.tar.gz", hash = "sha256:8d3e252d4127c79b4d7c2ae47271636cbaca905c8bb46d80c7930ab906cf4b5c"},
|
||||
]
|
||||
|
||||
[package.extras]
|
||||
full = ["numpy"]
|
||||
|
||||
[[package]]
|
||||
name = "requests"
|
||||
version = "2.28.1"
|
||||
|
|
@ -322,4 +539,4 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
|
|||
[metadata]
|
||||
lock-version = "2.0"
|
||||
python-versions = "^3.10"
|
||||
content-hash = "fef247962b563c632703d99f7f7315f66e49cc1625ef026d120ccc84339c05db"
|
||||
content-hash = "becf02a3ad8360833ab2a43a36fe0dc224cd028d5713e7de3daf61b6b99959fe"
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ packages = [{include = "extract"}]
|
|||
[tool.poetry.dependencies]
|
||||
python = "^3.10"
|
||||
pymupdf = "^1.21.1"
|
||||
levenshtein = "^0.20.8"
|
||||
|
||||
[tool.poetry.group.dev.dependencies]
|
||||
pubs = "^0.9.0"
|
||||
|
|
|
|||
Loading…
Reference in a new issue