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We had some pre-3.6 work arounds. Also seems like a reasonable time to
update all depdencies to most recent versions.
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Also updates dependencies.
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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
...
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first seen in CI (jobs/230137), slightly related:
https://github.com/pytest-dev/pytest/issues/3953
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via: $ pipenv lock
CI complained with a slightly cryptic:
> TypeError: __init__() missing 1 required positional argument: 'self'
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* 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.
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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).
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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
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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
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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.
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These are low-level and high-level (respectively)
client wrappers for elasticsearch
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When pipenv upgraded all dependencies after installing pygal, tests
failed due to errors like:
NotImplementedError: Can't perform this operation for unregistered loader type
coming from citeproc style code, via `pkg_resource`. Still not sure what
the root cause is, as that package itself wasn't upgraded. I tried a bit
of bisecting dependency upgrades but nothing obvious was the cause, and
a full bisection would take forever.
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This is necessary to for build artifacts.
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The style package has 40+ MByte of style info (thousands of files),
which is unforunately large.
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