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Added static analysis (lint, type checking) to be done on each push, and
testing to be done on each master branch commit.
This commit is contained in:
Marty Oehme 2023-08-29 12:15:10 +02:00
parent c6b95a4742
commit b564ab4792
Signed by: Marty
GPG key ID: EDBF2ED917B2EF6A
8 changed files with 168 additions and 41 deletions
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16
.woodpecker/lint.yml Normal file
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@ -0,0 +1,16 @@
pipeline:
lint_ruff:
image: python
commands:
- pip install ruff
- python --version && poetry --version && ruff --version
- echo "----------------- running ruff lint ------------------"
- ruff check .
lint_black:
image: python
commands:
- pip install black
- python --version && poetry --version && black --version
- echo "----------------- running black lint ----------------"
- black --check .

9
.woodpecker/static_analysis.yml Normal file
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@ -0,0 +1,9 @@
pipeline:
pyright:
image: nikolaik/python-nodejs
commands:
- npm install --global pyright
- poetry install
- python --version && poetry --version && pyright --version
- echo "------------- running pyright typecheck -------------"
- poetry run pyright

10
.woodpecker/test.yml Normal file
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@ -0,0 +1,10 @@
branches: master
pipeline:
pytest:
image: ghcr.io/withlogicco/poetry:1.5.1
commands:
- poetry install
- python --version && poetry --version
- echo "------------- running pytest -------------"
- poetry run pytest

38
README.md
View file

@ -1,8 +1,8 @@
# papis-extract # papis-extract
<!-- TODO have to set up status and badge [![status-badge](https://ci.martyoeh.me/api/badges/Marty/papis-extract/status.svg)](https://ci.martyoeh.me/Marty/papis-extract)
[![status-badge](https://ci.martyoeh.me/api/badges/Marty/pubs-extract/status.svg)](https://ci.martyoeh.me/Marty/pubs-extract) <!-- TODO have to set up pypi badge
![PyPI](https://img.shields.io/pypi/v/pubs-extract) ![PyPI](https://img.shields.io/pypi/v/papis-extract)
--> -->
Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\ Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\
@ -11,11 +11,14 @@ Easily organize all your highlights and thoughts next to your documents and refe
## Installation: ## Installation:
<!-- TODO set up pypi repository / explain git install path --> <!-- TODO set up pypi repository / explain git install path -->
You can install from pypi with `pip install 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), 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. everything should now be set up.
I am currently working towards the first release for pypi, see the below roadmap;
when that is done you will also be able to install in the usual pypi way.
To check if everything is working you should now see the `extract` command listed when running `papis --help`. To check if everything is working you should now see the `extract` command listed when running `papis --help`.
You will be set up with the default options but if you want to change anything, read on in configuration below. You will be set up with the default options but if you want to change anything, read on in configuration below.
@ -166,27 +169,46 @@ The option should generally not take too much tuning, but it is there if you nee
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. 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.
## Roadmap ## Roadmap to first release
Known issues to be fixed: Known issues to be fixed:
- [x] if both content and text are empty, do not extract an annotation - [x] if both content and text are empty, do not extract an annotation
- [x] Speed? - [x] Speed?
- should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations
- [ ] ensure all cmdline options do what they should - [x] ensure all cmdline options do what they should
- [ ] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals
- [ ] docstrings, docstrings!
- [ ] testing testing testing!!
- [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation)
features to be implemented: features to be implemented:
- [ ] on_add hook to extract annotations as files are added - [ ] CICD
- [x] static analysis (lint, typecheck etc) on pushes
- [x] test pipeline on master pushes
- [ ] release pipeline to pypi on tags
- [ ] 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 - [ ] show overall amount of extractions at the end
- [ ] custom formatting decided by user - [ ] custom formatting decided by user
- in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"}
- [ ] improved default exporters - [ ] improved default exporters
- markdown into notes - markdown into notes
- pretty display on stdout (rich?) - pretty display on stdout (rich?)
- csv/tsv to stdout - csv/tsv to stdout
- table fmt stdout? - table fmt stdout?
- [ ] arbitrary color -> name settings not dependent on color name existing - [ ] 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
- [ ] `--format` option to choose from default or set up a custom formatter
- [ ] on_add hook to extract annotations as files are added
- needs upstream help, 'on_add' hook, and pass-through of affected documents
upstream changes:
- [ ] need a hook for adding a document/file
- [ ] need hooks to actually pass through information on the thing they worked on (i.e. their document)
## Issues ## Issues

14
papis_extract/extractor.py
View file

@ -42,7 +42,7 @@ def start(filename: Path) -> list[Annotation]:
def _tag_from_colorname(colorname: str) -> str: def _tag_from_colorname(colorname: str) -> str:
color_mapping: dict[str,str] = getdict("tags", "plugins.extract") color_mapping: dict[str, str] = getdict("tags", "plugins.extract")
if not color_mapping: if not color_mapping:
return "" return ""
@ -82,6 +82,7 @@ def _retrieve_annotation_content(
# just a highlight without any text # just a highlight without any text
return (None, None) return (None, None)
# mimics the functions in papis.config.{getlist,getint,getfloat} etc. # mimics the functions in papis.config.{getlist,getint,getfloat} etc.
def getdict(key: str, section: Optional[str] = None) -> dict[str, str]: def getdict(key: str, section: Optional[str] = None) -> dict[str, str]:
"""Dict getter """Dict getter
@ -97,13 +98,14 @@ def getdict(key: str, section: Optional[str] = None) -> dict[str, str]:
rawvalue = eval(rawvalue) rawvalue = eval(rawvalue)
except Exception: except Exception:
raise SyntaxError( raise SyntaxError(
"The key '{}' must be a valid Python object: {}" "The key '{}' must be a valid Python object: {}".format(key, rawvalue)
.format(key, rawvalue)) )
else: else:
if not isinstance(rawvalue, dict): if not isinstance(rawvalue, dict):
raise SyntaxError( raise SyntaxError(
"The key '{}' must be a valid Python dict. Got: {} (type {!r})" "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format(
.format(key, rawvalue, type(rawvalue).__name__)) key, rawvalue, type(rawvalue).__name__
)
)
return rawvalue return rawvalue

111
poetry.lock generated
View file

@ -224,6 +224,17 @@ files = [
{file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"}, {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
] ]
[[package]]
name = "iniconfig"
version = "2.0.0"
description = "brain-dead simple config-ini parsing"
optional = false
python-versions = ">=3.7"
files = [
{file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
{file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
]
[[package]] [[package]]
name = "isbnlib" name = "isbnlib"
version = "3.10.14" version = "3.10.14"
@ -456,6 +467,17 @@ html5 = ["html5lib"]
htmlsoup = ["BeautifulSoup4"] htmlsoup = ["BeautifulSoup4"]
source = ["Cython (>=0.29.35)"] source = ["Cython (>=0.29.35)"]
[[package]]
name = "packaging"
version = "23.1"
description = "Core utilities for Python packages"
optional = false
python-versions = ">=3.7"
files = [
{file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"},
{file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
]
[[package]] [[package]]
name = "papis" name = "papis"
version = "0.13" version = "0.13"
@ -504,6 +526,21 @@ files = [
{file = "pbr-5.11.1.tar.gz", hash = "sha256:aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3"}, {file = "pbr-5.11.1.tar.gz", hash = "sha256:aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3"},
] ]
[[package]]
name = "pluggy"
version = "1.3.0"
description = "plugin and hook calling mechanisms for python"
optional = false
python-versions = ">=3.8"
files = [
{file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
{file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
]
[package.extras]
dev = ["pre-commit", "tox"]
testing = ["pytest", "pytest-benchmark"]
[[package]] [[package]]
name = "prompt-toolkit" name = "prompt-toolkit"
version = "3.0.39" version = "3.0.39"
@ -534,36 +571,36 @@ plugins = ["importlib-metadata"]
[[package]] [[package]]
name = "pymupdf" name = "pymupdf"
version = "1.23.1" version = "1.23.2"
description = "A high performance Python library for data extraction, analysis, conversion & manipulation of PDF (and other) documents." description = "A high performance Python library for data extraction, analysis, conversion & manipulation of PDF (and other) documents."
optional = false optional = false
python-versions = ">=3.8" python-versions = ">=3.8"
files = [ files = [
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{file = "PyMuPDF-1.23.1.tar.gz", hash = "sha256:34cac956024f1a30f5204a1a987d7b2c8d4b2b5df57806b82c2842e3e108786b"}, {file = "PyMuPDF-1.23.2.tar.gz", hash = "sha256:32302d0eb0e28d60ba305f5d74702fb0fab2ed9d9f6b3a9d853429e5023bc6bb"},
] ]
[package.dependencies] [package.dependencies]
@ -598,6 +635,26 @@ files = [
[package.extras] [package.extras]
diagrams = ["jinja2", "railroad-diagrams"] 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]] [[package]]
name = "python-doi" name = "python-doi"
version = "0.2.0" version = "0.2.0"
@ -923,4 +980,4 @@ files = [
[metadata] [metadata]
lock-version = "2.0" lock-version = "2.0"
python-versions = "^3.11" python-versions = "^3.11"
content-hash = "2e158747df6100e105c98494d8b5f4b23b7076ae76295ce7a28facf02488ebd5" content-hash = "d519605837788792d06ffc7bca7a92b315612ca6052227c53c558ec49dffec9f"

4
pyproject.toml
View file

@ -18,6 +18,10 @@ python-magic = "^0.4.27"
[tool.poetry.plugins."papis.command"] [tool.poetry.plugins."papis.command"]
extract = "papis_extract:main" extract = "papis_extract:main"
[tool.poetry.group.dev.dependencies]
pytest = "^7.4.0"
[build-system] [build-system]
requires = ["poetry-core"] requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api" build-backend = "poetry.core.masonry.api"

7
tests/test_annotation.py Normal file
View 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"