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  • xarray · 24 ✖

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  • aurghs · 24 ✖
sha message author_date ▲ committer_date raw_author raw_committer repo author committer
eea76733770be03e78a0834803291659136bca31 Improve error message for guess engine (#5455) * fix normalize_path in pynio_.py * draft: refactor to improve not found engine error * fix backend registration and tests * fix not workng jet * fix error call guess_can_open * fix * fix * add tests * update message error engine not fuond * update tests * fix if else * fix message error and tests * revert changes in error messages * revert changes in error messages 2021-06-23T08:18:07Z 2021-06-23T08:18:07Z Aureliana Barghini ea8aa69e44361b315c67c897b0d24b4b846f772a GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
18ed29e4086145c29fde31c9d728a939536911c9 Fix open_dataset regression (#5135) * add in os.path.expanduser backends where needed to allow ~ in filename_or_obj * Update xarray/backends/pseudonetcdf_.py Co-authored-by: Alessandro Amici <a.amici@bopen.eu> * use: normalize_path * fix circular import * pre-commit * use _normalized_path in netCDF4 pseudonetcdf zarr * pre-commit Co-authored-by: Alessandro Amici <a.amici@bopen.eu> 2021-04-15T12:11:34Z 2021-04-15T12:11:34Z Aureliana Barghini ea8aa69e44361b315c67c897b0d24b4b846f772a GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
32ccc93e899ac083834127ca382204b467ed89a3 Fix broken engine breakes xarray.open_dataset (#5136) * Add try except in load engines to avoid that a broken engines brakes xarray test added * replaced loggig with warning * black * Update xarray/backends/plugins.py Co-authored-by: Alessandro Amici <a.amici@bopen.eu> * align test to new error message Co-authored-by: Alessandro Amici <a.amici@bopen.eu> 2021-04-10T23:55:01Z 2021-04-10T23:55:01Z Aureliana Barghini ea8aa69e44361b315c67c897b0d24b4b846f772a GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
d2582c2f8811a3bd527d47c945b1cccd4983a1d3 WIP: add new backend api documentation (#4810) * documentation first draft * documentation update * documentation update * update documentation * update backend documentation * incompletre draft: update Backend Documentation * fix * fix syle * Update doc/internals.rst Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Mathias Hauser <mathause@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: keewis <keewis@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Mathias Hauser <mathause@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Mathias Hauser <mathause@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Mathias Hauser <mathause@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Mathias Hauser <mathause@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Mathias Hauser <mathause@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: keewis <keewis@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: keewis <keewis@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Mathias Hauser <mathause@users.noreply.github.com> * update section lazy laoding * Update doc/internals.rst Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * Update doc/internals.rst Co-authored-by: Deepak Cherian <dcherian@users.n… 2021-03-08T19:16:57Z 2021-03-08T19:16:57Z Aureliana Barghini ea8aa69e44361b315c67c897b0d24b4b846f772a GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
6e4d66734f63fb60b13ba25d2a7da33fbfab2b4b Sort backends (#4886) * style * order the plugins and tests * style * fix post merge * fix plugin_test * capitalize global variable 2021-02-12T17:48:24Z 2021-02-12T17:48:24Z Aureliana Barghini ea8aa69e44361b315c67c897b0d24b4b846f772a GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
8cc34cb412ba89ebca12fc84f76a9e452628f1bc WIP: backend interface, now it uses subclassing (#4836) * draft * working version * fix: instantiate BackendEtrypoints * rename AbstractBackendEntrypoint in BackendEntrypoint * fix plugins tests * style * style * raise NotImplemetedError if BackendEntrypoint.open_dataset is not implemented 2021-01-28T15:20:59Z 2021-01-28T15:20:59Z Aureliana Barghini ea8aa69e44361b315c67c897b0d24b4b846f772a GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
7dbbdcafed7f796ab77039ff797bcd31d9185903 Bugfix in list_engine (#4811) * fix list_engine * fix store engine and netcdf4 * reve * revert changes in guess_engine * add resister of backend if dependencies aere instralled * style mypy * fix import * use import instead of importlib * black * replace ImportError with ModuleNotFoundError * fix typo * fix typos * remove else * Revert remove imports inside backends functions * Revert remove imports inside cfgrib * modify check on imports inside the backends * remove not used import 2021-01-19T10:10:25Z 2021-01-19T10:10:25Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
ac234619d5471e789b0670a673084dbb01df4f9e Remove entrypoints in setup for internal backends (#4724) * add a dictionary for internal backends * remove entrypoints in setup.cfg * create global variable BACKEND_ENTRYPOINT move BackendEtrypoints in common to solve circular dependecy * fix and update tests * fix in tests_plugins to remove a warning 2020-12-24T16:29:44Z 2020-12-24T16:29:44Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
1525fb0b23b8e92420ab428dc3d918a658e92dd4 remove autoclose in open_dataset and related warning test (#4725) * remove autoclose in open_dataset and related warning test * black * remove autoclose from open_mfdataset * update what's new 2020-12-24T16:25:26Z 2020-12-24T16:25:26Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
03d8d56c9b6d090f0de2475202368b08435eaeb5 Remove unexpected warnings in tests (#4728) * fix test on chunking (warnings for not close files) * add filterwarnings in test_chunking_consistency * add filterwarnings in test_remove_duplicates 2020-12-24T13:12:40Z 2020-12-24T13:12:40Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
ed0dadc273fc05766ec7e73a6980e02a8a360069 Fix warning on chunks compatibility (#4726) * fix warning on last chunk and modify test * black * update tests * style: rename variable 2020-12-24T11:32:42Z 2020-12-24T11:32:42Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
5179cd92fd0d5438e2b7366619e21a242d0d55c3 Remove close_on_error store.py (#4719) * remove close on error for external store * remove not used import 2020-12-22T14:31:04Z 2020-12-22T14:31:04Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
138679748558f41cd28f82a25046bc96b1c4d1ef Port all the engines to apiv2 (#4673) * first draft: not working * fix and black * remove test_autoclose_future_warning * remove blanc lines * fix * reverted delete autoclose test. Added warning in apiv2 * isort * revert delete test_autoclose_future_warning * for backward compatibility: add store-backend used in open_dataset if a store is passed instead a file_name and an engine * fix default in store.py * remove not open_dataset_paramenters definition in store.py * remove "**kwrargs" in pseudonetcdf_backend.open_dataset_parameter definition * add a comment to explain why the open_dataset_parameters are explicity defined in peseudonetcdf_.py * use store.open_backend_dataset_store to reduce duplicated code inside backends * style Co-authored-by: Alessandro Amici <a.amici@bopen.eu> 2020-12-17T16:21:57Z 2020-12-17T16:21:57Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
91318d2ee63149669404489be9198f230d877642 add encodings["preferred_chunks"], used in open_dataset instead of en… (#4669) * add encodings["preferred_chunks"], used in open_dataset instead of encodings["chunks"] * modify preferred_chunks: now it's a dictionary not a list * fix if preferred_chunks is not defined 2020-12-17T16:05:56Z 2020-12-17T16:05:56Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
76d5c0c075628475b555997b82c55dd18a34936e change default in ds.chunk and datarray.chunk variable.chunk (#4633) * change default in ds.chunk and datarray.chunk variable.chunk and add warning * add comment for chunks={} in dataset.chunk and dataarray.chunk * fix: revert delete line 2020-12-10T10:38:05Z 2020-12-10T10:38:05Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
6d4a292f65cca30647fd222109325b6d5c3154ea unify zarr chunking with other chunking in apiv2.open_dataset (#4667) 2020-12-10T10:18:46Z 2020-12-10T10:18:46Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
74dffffbfea2ba9aea18ce194fe868f2cb00907d Backends entrypoints (#4577) * Define _get_backends_cls function inside apiv2.py to read engines from plugins.py * Read open_backends_dataset_* from entrypoints. * Add backend entrypoints in setup.cfg * Pass apiv2.py isort and black formatting tests. * add dependencies * add backend entrypoints and check on conflicts * black * removed global variable EMGINES add class for entrypointys * black isort * add detect_engines in __all__ init.py * removed entrypoints in py36-bare-minimum.yml and py36-min-all-deps.yml * add entrypoints in IGNORE_DEPS * Plugins test (#20) - replace entrypoints with pkg_resources - add tests * fix typo Co-authored-by: keewis <keewis@users.noreply.github.com> * style Co-authored-by: keewis <keewis@users.noreply.github.com> * style * Code style * Code style * fix: updated plugins.ENGINES with plugins.list_engines() * fix * One more correctness fix of the latest merge from master Co-authored-by: TheRed86 <m.rossetti@bopen.eu> Co-authored-by: keewis <keewis@users.noreply.github.com> Co-authored-by: Alessandro Amici <a.amici@bopen.eu> 2020-12-10T09:56:12Z 2020-12-10T09:56:12Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
9802411b35291a6149d850e8e573cde71a93bfbf Modify zarr chunking as suggested in #4496 (#4646) * modify get_chunks to align zarr chunking as described in issue #4496 * fix: maintain old open_zarr chunking interface * add and fix tests * black * bugfix * add few documentation on open_dataset chunking * in test: re-add xafils for negative steps without dask * Specify in reason that only zarr is expected to fail * unify backend test negative_step with dask and without dask * Add comment on has_dask usage Co-authored-by: Alessandro Amici <a.amici@bopen.eu> 2020-12-09T12:26:44Z 2020-12-09T12:26:44Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
8ac3d862197204e6212a9882051808eb4b1cf3ff Refactor apiv2.open_dataset (#4642) * in apiv2: rename ds in backend_ds and ds2 in ds * add function _chunks_ds to simplify dataset_from_backend_dataset * add small function _get_mtime to simplify _chunks_ds * make resolve_decoders_kwargs and dataset_from_backend_dataset private 2020-12-02T13:17:26Z 2020-12-02T13:17:26Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
65308954787d313d81ced5fe33e6a4a49bcc2167 Move get_chunks from zarr.py to dataset.py (#4632) * move get_chunks from zarr to dateset and removed maybe_chunks in zarr * move get_chunks from zarr to dateset and removed maybe_chunks in zarr * black * removed not used import * update warning message in get_chunks * Reformat warning text to use f-strings Co-authored-by: Alessandro Amici <a.amici@bopen.eu> 2020-12-02T09:25:00Z 2020-12-02T09:25:00Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
ba989f65e800c1dd5a308c7f14bda89963ee2bd5 Update signature open_dataset for API v2 (#4547) * add in api.open_dataset dispatching to stub apiv2 * remove in apiv2 check for input AbstractDataStore * bugfix typo * add kwarg engines in _get_backend_cls needed by apiv2 * add alpha support for h5netcdf * style: clean not used code, modify some variable/function name * Add ENGINES entry for cfgrib. * Define function open_backend_dataset_cfgrib() to be used in apiv2.py. Add necessary imports for this function. * Apply black to check formatting. * Apply black to check formatting. * add dummy zarr apiv2 backend * align apiv2.open_dataset to api.open_dataset * remove unused extra_coords in open_backend_dataset_* * remove extra_coords in open_backend_dataset_cfgrib * transform zarr maybe_chunk and get_chunks in classmethod - to be used in apiv2 without instantiate the object * make alpha zarr apiv2 working * refactor apiv2.open_dataset: - modify signature - move default setting inside backends * move dataset_from_backend_dataset out of apiv2.open_dataset * remove blank lines * remove blank lines * style * Re-write error messages * Fix code style * Fix code style * remove unused import * replace warning with ValueError for not supported kwargs in backends * change zarr.ZarStore.get_chunks into a static method * group `backend_kwargs` and `kwargs` in `extra_tokes` argument in apiv2.dataset_from_backend_dataset` * remove in open_backend_dayaset_${engine} signature kwarags and the related error message * black * Change signature of open_dataset function in apiv2 to include explicit decodings. * Set an alias for chunks='auto'. * Allign empty rows with previous version. * reverse changes in chunks management * move check on decoders from backends to open_dataset (apiv2) * update documentation * Change signature of open_dataset function in apiv2 to include explicit decodings. * Set an alias for chunks='auto'. * Allign empty rows with previous version. *… 2020-11-06T14:43:09Z 2020-11-06T14:43:09Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
cc271e61077c543e0f3b1a06ad5e905ea2c91617 WIP: Proposed refactor of read API for backends (#4477) * add in api.open_dataset dispatching to stub apiv2 * remove in apiv2 check for input AbstractDataStore * bugfix typo * add kwarg engines in _get_backend_cls needed by apiv2 * add alpha support for h5netcdf * style: clean not used code, modify some variable/function name * Add ENGINES entry for cfgrib. * Define function open_backend_dataset_cfgrib() to be used in apiv2.py. Add necessary imports for this function. * Apply black to check formatting. * Apply black to check formatting. * add dummy zarr apiv2 backend * align apiv2.open_dataset to api.open_dataset * remove unused extra_coords in open_backend_dataset_* * remove extra_coords in open_backend_dataset_cfgrib * transform zarr maybe_chunk and get_chunks in classmethod - to be used in apiv2 without instantiate the object * make alpha zarr apiv2 working * refactor apiv2.open_dataset: - modify signature - move default setting inside backends * move dataset_from_backend_dataset out of apiv2.open_dataset * remove blank lines * remove blank lines * style * Re-write error messages * Fix code style * Fix code style * remove unused import * replace warning with ValueError for not supported kwargs in backends * change zarr.ZarStore.get_chunks into a static method * group `backend_kwargs` and `kwargs` in `extra_tokes` argument in apiv2.dataset_from_backend_dataset` * remove in open_backend_dayaset_${engine} signature kwarags and the related error message * black * Try add a strategy with an environment variable * Try add a strategy with an environment variable * black Co-authored-by: TheRed86 <m.rossetti@bopen.eu> Co-authored-by: Alessandro Amici <a.amici@bopen.eu> 2020-10-22T15:06:38Z 2020-10-22T15:06:38Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
49e3032ddfa3fe86361300fd08db4764ee718bf1 Remove maybe chunck duplicated function (#4494) * move functions selkeys and maybechunk outside dataset.chunk add in maybechunk the key overwrite_encoded_chunks for zarr * replace ZarrStore.maybe_chunk with dataset._maybe_chunck + ZarrStore.get_chunks * remove no more used ZarrStore.maybe_chunk * style * style * style * fix typo * move `dataset._selkeys` logic inside _maybe_chunk 2020-10-08T15:10:45Z 2020-10-08T15:10:45Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447
742d00076c8e79cb753b4b4856dbbef5f52878c6 #1621 optional decode timedelta (#4071) * add decode_timedelta kwarg in decode_cf and open_* functions and test. * Fix style issue * Add chang author reference * removed check decode_timedelta in open_dataset * fix docstring indentation * fix: force dtype in test decode_timedelta 2020-05-19T15:43:53Z 2020-05-19T15:43:53Z aurghs 1c23ee020f875c83a25f902c0d72d85cbd48eee3 GitHub cd792325681cbad9f663f2879d8b69f1edbb678f xarray 13221727 aurghs 35919497 web-flow 19864447

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