Add continuous integration pipeline
Added static analysis (lint, type checking) to be done on each push, and testing to be done on each master branch commit.
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8 changed files with 168 additions and 41 deletions
16
.woodpecker/lint.yml
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16
.woodpecker/lint.yml
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@ -0,0 +1,16 @@
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pipeline:
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lint_ruff:
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image: python
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commands:
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- pip install ruff
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- python --version && poetry --version && ruff --version
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- echo "----------------- running ruff lint ------------------"
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- ruff check .
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lint_black:
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image: python
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commands:
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- pip install black
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- python --version && poetry --version && black --version
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- echo "----------------- running black lint ----------------"
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- black --check .
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9
.woodpecker/static_analysis.yml
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9
.woodpecker/static_analysis.yml
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@ -0,0 +1,9 @@
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pipeline:
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pyright:
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image: nikolaik/python-nodejs
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commands:
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- npm install --global pyright
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- poetry install
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- python --version && poetry --version && pyright --version
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- echo "------------- running pyright typecheck -------------"
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- poetry run pyright
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10
.woodpecker/test.yml
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10
.woodpecker/test.yml
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@ -0,0 +1,10 @@
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branches: master
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pipeline:
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pytest:
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image: ghcr.io/withlogicco/poetry:1.5.1
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commands:
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- poetry install
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- python --version && poetry --version
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- echo "------------- running pytest -------------"
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- poetry run pytest
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38
README.md
38
README.md
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@ -1,8 +1,8 @@
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# papis-extract
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<!-- TODO have to set up status and badge
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[](https://ci.martyoeh.me/Marty/pubs-extract)
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[](https://ci.martyoeh.me/Marty/papis-extract)
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<!-- TODO have to set up pypi badge
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-->
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Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\
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@ -11,11 +11,14 @@ Easily organize all your highlights and thoughts next to your documents and refe
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## Installation:
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<!-- TODO set up pypi repository / explain git install path -->
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You can install from pypi with `pip install git+`.
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You can install from pypi with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`.
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That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global),
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everything should now be set up.
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I am currently working towards the first release for pypi, see the below roadmap;
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when that is done you will also be able to install in the usual pypi way.
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To check if everything is working you should now see the `extract` command listed when running `papis --help`.
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You will be set up with the default options but if you want to change anything, read on in configuration below.
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@ -166,27 +169,46 @@ The option should generally not take too much tuning, but it is there if you nee
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This should generally be an alright default but is here to be changed for example if you work with a lot of different annotation colors (where dark purple and light purple may different meanings) and get false positives in automatic tag recognition, or no tags are recognized at all.
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## Roadmap
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## Roadmap to first release
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Known issues to be fixed:
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- [x] if both content and text are empty, do not extract an annotation
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- [x] Speed?
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- should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations
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- [ ] ensure all cmdline options do what they should
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- [x] ensure all cmdline options do what they should
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- [ ] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals
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- [ ] docstrings, docstrings!
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- [ ] testing testing testing!!
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- [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation)
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features to be implemented:
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- [ ] on_add hook to extract annotations as files are added
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- [ ] CICD
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- [x] static analysis (lint, typecheck etc) on pushes
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- [x] test pipeline on master pushes
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- [ ] release pipeline to pypi on tags
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- [ ] add page number if available
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- exists in Annotation, just need to place in output
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- [ ] show overall amount of extractions at the end
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- [ ] custom formatting decided by user
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- in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"}
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- [ ] improved default exporters
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- markdown into notes
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- pretty display on stdout (rich?)
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- csv/tsv to stdout
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- table fmt stdout?
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- [ ] arbitrary color -> name settings not dependent on color name existing
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- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)})
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- [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note
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- [ ] `--force` mode where we simply do not drop anything
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- [ ] `--format` option to choose from default or set up a custom formatter
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- [ ] on_add hook to extract annotations as files are added
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- needs upstream help, 'on_add' hook, and pass-through of affected documents
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upstream changes:
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- [ ] need a hook for adding a document/file
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- [ ] need hooks to actually pass through information on the thing they worked on (i.e. their document)
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## Issues
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@ -82,6 +82,7 @@ def _retrieve_annotation_content(
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# just a highlight without any text
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return (None, None)
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# mimics the functions in papis.config.{getlist,getint,getfloat} etc.
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def getdict(key: str, section: Optional[str] = None) -> dict[str, str]:
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"""Dict getter
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@ -97,13 +98,14 @@ def getdict(key: str, section: Optional[str] = None) -> dict[str, str]:
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rawvalue = eval(rawvalue)
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except Exception:
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raise SyntaxError(
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"The key '{}' must be a valid Python object: {}"
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.format(key, rawvalue))
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"The key '{}' must be a valid Python object: {}".format(key, rawvalue)
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)
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else:
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if not isinstance(rawvalue, dict):
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raise SyntaxError(
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"The key '{}' must be a valid Python dict. Got: {} (type {!r})"
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.format(key, rawvalue, type(rawvalue).__name__))
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"The key '{}' must be a valid Python dict. Got: {} (type {!r})".format(
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key, rawvalue, type(rawvalue).__name__
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)
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)
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return rawvalue
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111
poetry.lock
generated
111
poetry.lock
generated
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@ -224,6 +224,17 @@ 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 = "iniconfig"
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version = "2.0.0"
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description = "brain-dead simple config-ini parsing"
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optional = false
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python-versions = ">=3.7"
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files = [
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{file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
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{file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
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]
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[[package]]
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name = "isbnlib"
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version = "3.10.14"
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@ -456,6 +467,17 @@ html5 = ["html5lib"]
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htmlsoup = ["BeautifulSoup4"]
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source = ["Cython (>=0.29.35)"]
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[[package]]
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name = "packaging"
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version = "23.1"
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description = "Core utilities for Python packages"
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optional = false
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python-versions = ">=3.7"
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files = [
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{file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"},
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{file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
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]
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[[package]]
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name = "papis"
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version = "0.13"
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@ -504,6 +526,21 @@ files = [
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{file = "pbr-5.11.1.tar.gz", hash = "sha256:aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3"},
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]
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[[package]]
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name = "pluggy"
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version = "1.3.0"
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description = "plugin and hook calling mechanisms for python"
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optional = false
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python-versions = ">=3.8"
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files = [
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{file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
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{file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
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]
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[package.extras]
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dev = ["pre-commit", "tox"]
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testing = ["pytest", "pytest-benchmark"]
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[[package]]
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name = "prompt-toolkit"
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version = "3.0.39"
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@ -534,36 +571,36 @@ plugins = ["importlib-metadata"]
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[[package]]
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name = "pymupdf"
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version = "1.23.1"
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version = "1.23.2"
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description = "A high performance Python library for data extraction, analysis, conversion & manipulation of PDF (and other) documents."
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optional = false
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python-versions = ">=3.8"
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files = [
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{file = "PyMuPDF-1.23.1-cp310-none-macosx_10_9_x86_64.whl", hash = "sha256:eb85e8c8d5ceebe078206f779e5cd918919616e865e081fad3993f90159e61c1"},
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{file = "PyMuPDF-1.23.1-cp310-none-macosx_11_0_arm64.whl", hash = "sha256:a3a23857d655180f6147dbc9886f109e627b6654e37ba5088d1b038f6d7861c0"},
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{file = "PyMuPDF-1.23.1-cp310-none-manylinux2014_aarch64.whl", hash = "sha256:9216ca0805892b481be9544f3d3f9efbc06258fd26ba95295d540c2fa0ae0fea"},
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{file = "PyMuPDF-1.23.1-cp310-none-manylinux2014_x86_64.whl", hash = "sha256:c8173a1b8c8539ee466f74263a7c6bdf1427b8f5dc32c66ccaca22222a89e339"},
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{file = "PyMuPDF-1.23.1-cp310-none-win32.whl", hash = "sha256:0d709d3d7c9b894ad5400fa5037bf34e82133b3386b5f3f7bb60b16e9666a1bb"},
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{file = "PyMuPDF-1.23.1-cp310-none-win_amd64.whl", hash = "sha256:11af6e9e86e2a4ad1ecf8085bb64a48323614769188fbf5eaa5a198acef5de39"},
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{file = "PyMuPDF-1.23.1-cp311-none-macosx_10_9_x86_64.whl", hash = "sha256:08b93208eaccac85a78b7aa2b3020645824fb97dda2ab4f6d3a07290ac99b078"},
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|
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|
||||
{file = "PyMuPDF-1.23.2-cp39-none-macosx_10_9_x86_64.whl", hash = "sha256:ac236156688627bca0a8062bb4153f77108f072dd4a06a80626fd089c2879e04"},
|
||||
{file = "PyMuPDF-1.23.2-cp39-none-macosx_11_0_arm64.whl", hash = "sha256:c1a08531194d038e068641be92fdc31276efbee2b718a8dc4281dc593f1a99e7"},
|
||||
{file = "PyMuPDF-1.23.2-cp39-none-manylinux2014_aarch64.whl", hash = "sha256:78b6c87fd375d1b017c63a426432be7ee4859f2142108b9c5dc8283599c112eb"},
|
||||
{file = "PyMuPDF-1.23.2-cp39-none-manylinux2014_x86_64.whl", hash = "sha256:41d9cd45bb61cda890d446baeeded454fb4404086cf7f7e385e440123e9ecb56"},
|
||||
{file = "PyMuPDF-1.23.2-cp39-none-win32.whl", hash = "sha256:d34da29cd4305c4b85ea57528c1a31cfc6abfac7921d27153e633470e9dac104"},
|
||||
{file = "PyMuPDF-1.23.2-cp39-none-win_amd64.whl", hash = "sha256:86127075227f868a6b115eb96a74405539dde90168cd1a98781b0f1f6d4f9d7c"},
|
||||
{file = "PyMuPDF-1.23.2.tar.gz", hash = "sha256:32302d0eb0e28d60ba305f5d74702fb0fab2ed9d9f6b3a9d853429e5023bc6bb"},
|
||||
]
|
||||
|
||||
[package.dependencies]
|
||||
|
|
@ -598,6 +635,26 @@ files = [
|
|||
[package.extras]
|
||||
diagrams = ["jinja2", "railroad-diagrams"]
|
||||
|
||||
[[package]]
|
||||
name = "pytest"
|
||||
version = "7.4.0"
|
||||
description = "pytest: simple powerful testing with Python"
|
||||
optional = false
|
||||
python-versions = ">=3.7"
|
||||
files = [
|
||||
{file = "pytest-7.4.0-py3-none-any.whl", hash = "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32"},
|
||||
{file = "pytest-7.4.0.tar.gz", hash = "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"},
|
||||
]
|
||||
|
||||
[package.dependencies]
|
||||
colorama = {version = "*", markers = "sys_platform == \"win32\""}
|
||||
iniconfig = "*"
|
||||
packaging = "*"
|
||||
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"]
|
||||
|
||||
[[package]]
|
||||
name = "python-doi"
|
||||
version = "0.2.0"
|
||||
|
|
@ -923,4 +980,4 @@ files = [
|
|||
[metadata]
|
||||
lock-version = "2.0"
|
||||
python-versions = "^3.11"
|
||||
content-hash = "2e158747df6100e105c98494d8b5f4b23b7076ae76295ce7a28facf02488ebd5"
|
||||
content-hash = "d519605837788792d06ffc7bca7a92b315612ca6052227c53c558ec49dffec9f"
|
||||
|
|
|
|||
|
|
@ -18,6 +18,10 @@ python-magic = "^0.4.27"
|
|||
[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"
|
||||
|
|
|
|||
7
tests/test_annotation.py
Normal file
7
tests/test_annotation.py
Normal file
|
|
@ -0,0 +1,7 @@
|
|||
from papis_extract.annotation_data import Annotation
|
||||
|
||||
|
||||
def test_matches_colorname_exact():
|
||||
sut = Annotation("testfile", colors={"stroke": (1.0, 0.0, 0.0)})
|
||||
c_name = sut.colorname
|
||||
assert c_name == "red"
|
||||
Loading…
Reference in a new issue