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* Merge branch 'martin-datacite-import'Martin Czygan2020-01-081-0/+3
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Pipfile.lock is broken. * martin-datacite-import: (68 commits) datacite: pass in doi into factored out method datacite: reformat test cases and use jq . --sort-keys datacite: factor out contributor handling datacite: catch type mismatch in language detection datacite: adjust tests for release_month datacite: name extra.month, extra.release_month datacite: mark additional files as stub datacite: CCDC are entries, mostly datacite: use more specific release_type, if possible datacite: ignore certain names datacite: over 3% records have the same title: stub datacite: fill a few more release_type gaps datacite: adding datacite-specific extra metadata datacite: apply pylint suggestions datacite: fix typos datacite: set release_stage to published by default datacite: month field should be top-level datacite: include month in extra datacite: indicate mismatched file in test datacite: clean abstracts, use unknown value tokens ...
| * add pycountry dependencyMartin Czygan2020-01-031-0/+1
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| * add missing pathlib2 dependencyMartin Czygan2020-01-031-0/+1
| | | | | | | | | | first seen in CI (jobs/230137), slightly related: https://github.com/pytest-dev/pytest/issues/3953
| * remove langcodes dependencyMartin Czygan2019-12-281-1/+0
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| * address first round of MR14 commentsMartin Czygan2019-12-281-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | * add missing langdetect * use entity_to_dict for json debug output * factor out code for fields in function and add table driven tests * update citeproc types * add author as default role * add raw_affiliation * include relations from datacite * remove url (covered by doi already) Using yapf for python formatting.
* | pipenv: update pytest to 5.x; remove langcodesBryan Newbold2020-01-031-2/+1
|/ | | | | | | | | | pytest has been pinned to the 4.x series to work around a test import package mangling problem with citeproc_styles. Now that pytest.ini explicitly lists test files, this seems to no longer be a problem and pytest can be updated to the most recent version. Also re-locked Pipfile.lock with updated dependencies (only minor changes).
* pipenv: update depsBryan Newbold2019-12-171-2/+2
| | | | | | | | loginpass patches got accepted upstream a while back, so don't need to pin to a git version ipython 7.10 seems to have problems installing, so restricting to earlier 6.x versions
* pipenv: restrict pytest<5.0.0Bryan Newbold2019-12-171-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | This prevents a test exception that presents like: tests/transform_csl.py:46: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ fatcat_tools/transforms/csl.py:204: in citeproc_csl style_path = get_style_filepath(style) .venv/lib/python3.5/site-packages/citeproc_styles/__init__.py:74: in get_style_filepath if resource_exists(__name__, independent_style): .venv/lib/python3.5/site-packages/pkg_resources/__init__.py:1134: in resource_exists return get_provider(package_or_requirement).has_resource(resource_name) .venv/lib/python3.5/site-packages/pkg_resources/__init__.py:1404: in has_resource return self._has(self._fn(self.module_path, resource_name)) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pkg_resources.NullProvider object at 0x7f4f38c0bb00> path = '/home/bnewbold/code/fatcat/python/.venv/lib/python3.5/site-packages/citeproc_styles/styles/bibtex.csl' def _has(self, path): raise NotImplementedError( > "Can't perform this operation for unregistered loader type" ) E NotImplementedError: Can't perform this operation for unregistered loader type
* pipenv: update Pipfile and Pipfile.lockBryan Newbold2019-12-171-2/+2
| | | | | | This is still manually tweaked. I believe i've bifurcated the source of the CSL/citeproc_style import error to upgrade of the 'pytest' module. This commit upgrades all packages except pytest.
* pipfile: add langcodes and dateparser dependenciesBryan Newbold2019-12-171-0/+2
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* pipenv: add elasticsearch and elasticsearch-dsl librariesBryan Newbold2019-12-101-0/+2
| | | | | These are low-level and high-level (respectively) client wrappers for elasticsearch
* add pytest-mock helper library to dev depsBryan Newbold2019-12-061-0/+1
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* add confluent-kafka library (to replace pykafka)Bryan Newbold2019-09-201-0/+1
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* update all other mentions of python client libBryan Newbold2019-09-051-2/+2
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* import pygalBryan Newbold2019-09-041-4/+4
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* make fatcat_client not relocatableBryan Newbold2019-06-201-1/+1
| | | | This is necessary to for build artifacts.
* pipenv: beautiful soup and pylatexencBryan Newbold2019-05-211-1/+2
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* point loginpass to upstream (patch accepted)Bryan Newbold2019-04-101-1/+1
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* use patched loginpass (temporarily)Bryan Newbold2019-04-101-1/+1
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* flask-mwoauth for Wikipedia OAuth loginsBryan Newbold2019-04-091-0/+1
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* pytest improvements: squelch raven deprecation; run pylintBryan Newbold2019-04-041-0/+1
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* markdown rendering of comments/annotationsBryan Newbold2019-04-031-0/+1
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* add wtforms depsBryan Newbold2019-03-201-0/+2
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* dep: python-magicBryan Newbold2019-03-191-0/+1
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* add missing beautifulsoup python depBryan Newbold2019-03-191-0/+1
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* citeproc-py depBryan Newbold2019-03-111-0/+2
| | | | | The style package has 40+ MByte of style info (thousands of files), which is unforunately large.
* ftfy all over (needs Pipfile.lock)Bryan Newbold2019-01-231-0/+1
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* continue breaking out python clientBryan Newbold2019-01-091-0/+1
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* update python dependenciesBryan Newbold2019-01-081-6/+5
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* require pymacaroonsBryan Newbold2019-01-031-0/+1
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* start on webface oauth2/oidc web authBryan Newbold2019-01-021-2/+6
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* add python-snappy (for pykafka)Bryan Newbold2018-12-101-0/+1
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* enable sentry exceptions for fatcat-webBryan Newbold2018-11-211-1/+1
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* remove Pipfile cruftBryan Newbold2018-11-211-6/+0
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* initial OAI-PMH harvestersBryan Newbold2018-11-191-0/+1
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* large refactor of python names/pathsBryan Newbold2018-11-151-0/+9
| | | | | | | - Add __init__.py files for fatcat_tools submodules, and use them in imports - Add a bunch of comments to files. - rename a number of classes and functions to be less verbose
* pipfile: pykafkaBryan Newbold2018-11-041-0/+2
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* need debugbar for deploymentBryan Newbold2018-05-311-1/+1
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* uuids in flask routesBryan Newbold2018-05-281-0/+1
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* move python code to subdirectoryBryan Newbold2018-05-161-0/+28
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