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  • Fix missing dependecy definition of 'packaging' · 19 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1026327684 https://github.com/pydata/xarray/pull/6207#issuecomment-1026327684 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849LISE max-sixty 5635139 2022-01-31T23:51:54Z 2022-01-31T23:51:54Z MEMBER

I'll merge now though do the release this eve

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1026306642 https://github.com/pydata/xarray/pull/6207#issuecomment-1026306642 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849LDJS jhamman 2443309 2022-01-31T23:16:11Z 2022-01-31T23:16:11Z MEMBER

This is ready to merge. @max-sixty - whenever you are ready, go ahead and merge and make the release.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1025992494 https://github.com/pydata/xarray/pull/6207#issuecomment-1025992494 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849J2cu jhamman 2443309 2022-01-31T16:54:46Z 2022-01-31T16:58:13Z MEMBER

@pydata/xarray - we should try to get this merged and a new release up ASAP as bug reports are starting to pile up. I've pushed changes to the CI configs, documentation, and elsewhere. I've also pulled in the recent changes on main which should hopefully fix the failing CI in the first commit.

Also, thanks @s-weigand for opening this PR and raising the issue.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1025994647 https://github.com/pydata/xarray/pull/6207#issuecomment-1025994647 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849J2-X max-sixty 5635139 2022-01-31T16:57:00Z 2022-01-31T16:57:00Z MEMBER

I can do the release later today if no one gets there first

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1025230165 https://github.com/pydata/xarray/pull/6207#issuecomment-1025230165 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849G8VV keewis 14808389 2022-01-30T21:01:12Z 2022-01-30T21:05:48Z MEMBER

other than the environment files and the asv config we also need to update doc/getting-started/installing.rst: the Required dependencies section, and maybe also the Minimum dependency versions. For the latter, we need to figure out a rule, though. For setuptools we had "42 months, but no older than 40.4", where 40.4 was the oldest version of setuptools installable from conda-forge.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1025228982 https://github.com/pydata/xarray/pull/6207#issuecomment-1025228982 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849G8C2 keewis 14808389 2022-01-30T20:54:39Z 2022-01-30T20:54:39Z MEMBER

just for the record, we decided that packaging related tools (i.e. setuptools, not sure if that also applies to packaging) should be released just before the earliest supported python version, so we would have to decide between 19.2 and 20. However, since the release notes of packaging state that 20 is the first version to officially support py38 I'd say using packaging>=20 should be uncontroversial.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1025200701 https://github.com/pydata/xarray/pull/6207#issuecomment-1025200701 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849G1I9 Illviljan 14371165 2022-01-30T18:23:53Z 2022-01-30T18:23:53Z MEMBER

Following dask seems like a good idea! We probably should add packaging in our ci installs as well: https://github.com/pydata/xarray/tree/main/ci/requirements and the asv config: https://github.com/pydata/xarray/blob/main/asv_bench/asv.conf.json

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1025001036 https://github.com/pydata/xarray/pull/6207#issuecomment-1025001036 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849GEZM s-weigand 9513634 2022-01-29T22:47:26Z 2022-01-29T23:42:06Z CONTRIBUTOR

Dask has packaging>=20 which was released over 2y ago guess this is kinda reasonable. I also ran the tests with packaging=17.1 (first py_0 version compatible with py38 on conda) released about 3y ago and all passed (windows but all imports should have been hit). For older versions, conda couldn't resolve the version.

❤️ 17.1 👍 20

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024993880 https://github.com/pydata/xarray/pull/6207#issuecomment-1024993880 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849GCpY keewis 14808389 2022-01-29T21:55:50Z 2022-01-29T21:55:50Z MEMBER

no, I think we should still add packaging to the dependencies, even if it doesn't cause any failures: we unconditionally import it in at least xarray.core.pycompat. We need to add a reasonable minimum version, though.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024956677 https://github.com/pydata/xarray/pull/6207#issuecomment-1024956677 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849F5kF max-sixty 5635139 2022-01-29T17:50:02Z 2022-01-29T17:50:02Z MEMBER

Thanks everyone! Are we ok to close this then?

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024896245 https://github.com/pydata/xarray/pull/6207#issuecomment-1024896245 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849Fqz1 s-weigand 9513634 2022-01-29T11:48:47Z 2022-01-29T11:48:47Z CONTRIBUTOR

Yes, I think I just expressed it wrong. What I wanted to say: zhe failure you see here is not caused by #6200 but by a new release of dask. And this is independent of your issue with packaging.

Ahhh now I get it 😅

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024896079 https://github.com/pydata/xarray/pull/6207#issuecomment-1024896079 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849FqxP mathause 10194086 2022-01-29T11:47:42Z 2022-01-29T11:47:42Z MEMBER

Yes, I think I just expressed it wrong. What I wanted to say: zhe failure you see here is not caused by #6200 but by a new release of dask. And this is independent of your issue with packaging.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024896045 https://github.com/pydata/xarray/pull/6207#issuecomment-1024896045 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849Fqwt Illviljan 14371165 2022-01-29T11:47:29Z 2022-01-29T11:47:29Z MEMBER

https://docs.python.org/3/whatsnew/3.10.html#distutils-deprecated recommends importing packaging instead, so if we want to do version checking maybe we should just add it as a dependency?

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024892207 https://github.com/pydata/xarray/pull/6207#issuecomment-1024892207 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849Fp0v s-weigand 9513634 2022-01-29T11:20:49Z 2022-01-29T11:46:40Z CONTRIBUTOR

packaging is imported in 16 other python files e.g. xarray.core.indexing, I think there is no way around adding it as a dependency. Hiding all the imports in closures will be quite error prawn especially since tests won't catch it since pytest bring packaging along with it.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024890863 https://github.com/pydata/xarray/pull/6207#issuecomment-1024890863 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849Fpfv s-weigand 9513634 2022-01-29T11:11:22Z 2022-01-29T11:11:51Z CONTRIBUTOR

On second thought I think the problem is the release of dask 2022.01.1.

We don't have dask as a dependency ```console $ johnnydep pyglotaran 2022-01-29 10:55:08 [info ] init johnnydist [johnnydep.lib] dist=pyglotaran parent=None 2022-01-29 10:55:11 [info ] init johnnydist [johnnydep.lib] dist=asteval>=0.9.21 parent=pyglotaran 2022-01-29 10:55:24 [info ] init johnnydist [johnnydep.lib] dist=click>=7.0 parent=pyglotaran 2022-01-29 10:55:26 [info ] init johnnydist [johnnydep.lib] dist=netCDF4>=1.5.3 parent=pyglotaran 2022-01-29 10:55:29 [info ] init johnnydist [johnnydep.lib] dist=numba>=0.52 parent=pyglotaran 2022-01-29 10:55:32 [info ] init johnnydist [johnnydep.lib] dist=numpy<1.21,>=1.20.0 parent=pyglotaran 2022-01-29 10:55:36 [info ] init johnnydist [johnnydep.lib] dist=pandas>=0.25.2 parent=pyglotaran 2022-01-29 10:55:39 [info ] init johnnydist [johnnydep.lib] dist=rich>=10.9.0 parent=pyglotaran 2022-01-29 10:55:42 [info ] init johnnydist [johnnydep.lib] dist=ruamel.yaml>=0.17.17 parent=pyglotaran 2022-01-29 10:55:45 [info ] init johnnydist [johnnydep.lib] dist=scipy>=1.3.2 parent=pyglotaran 2022-01-29 10:55:49 [info ] init johnnydist [johnnydep.lib] dist=sdtfile>=2020.8.3 parent=pyglotaran 2022-01-29 10:55:51 [info ] init johnnydist [johnnydep.lib] dist=setuptools>=41.2 parent=pyglotaran 2022-01-29 10:55:54 [info ] init johnnydist [johnnydep.lib] dist=tabulate>=0.8.8 parent=pyglotaran 2022-01-29 10:55:56 [info ] init johnnydist [johnnydep.lib] dist=xarray!=0.20.0,!=0.20.1,>=0.16.2 parent=pyglotaran 2022-01-29 10:55:58 [info ] init johnnydist [johnnydep.lib] dist=colorama parent=click>=7.0 2022-01-29 10:56:00 [info ] init johnnydist [johnnydep.lib] dist=cftime parent=netCDF4>=1.5.3 2022-01-29 10:56:03 [info ] init johnnydist [johnnydep.lib] dist=numpy>=1.9 parent=netCDF4>=1.5.3 2022-01-29 10:56:07 [info ] init johnnydist [johnnydep.lib] dist=numpy>1.13.3 parent=cftime 2022-01-29 10:56:11 [info ] init johnnydist [johnnydep.lib] dist=llvmlite<0.39,>=0.38.0rc1 parent=numba>=0.52 2022-01-29 10:56:15 [info ] init johnnydist [johnnydep.lib] dist=numpy<1.22,>=1.18 parent=numba>=0.52 2022-01-29 10:56:18 [info ] init johnnydist [johnnydep.lib] dist=setuptools parent=numba>=0.52 2022-01-29 10:56:21 [info ] init johnnydist [johnnydep.lib] dist=numpy>=1.18.5 parent=pandas>=0.25.2 2022-01-29 10:56:25 [info ] init johnnydist [johnnydep.lib] dist=python-dateutil>=2.8.1 parent=pandas>=0.25.2 2022-01-29 10:56:27 [info ] init johnnydist [johnnydep.lib] dist=pytz>=2020.1 parent=pandas>=0.25.2 2022-01-29 10:56:29 [info ] init johnnydist [johnnydep.lib] dist=six>=1.5 parent=python-dateutil>=2.8.1 2022-01-29 10:56:31 [info ] init johnnydist [johnnydep.lib] dist=colorama<0.5.0,>=0.4.0 parent=rich>=10.9.0 2022-01-29 10:56:34 [info ] init johnnydist [johnnydep.lib] dist=commonmark<0.10.0,>=0.9.0 parent=rich>=10.9.0 2022-01-29 10:56:36 [info ] init johnnydist [johnnydep.lib] dist=pygments<3.0.0,>=2.6.0 parent=rich>=10.9.0 2022-01-29 10:56:38 [info ] init johnnydist [johnnydep.lib] dist=ruamel.yaml.clib>=0.2.6 parent=ruamel.yaml>=0.17.17 2022-01-29 10:56:40 [info ] init johnnydist [johnnydep.lib] dist=numpy<1.23.0,>=1.16.5 parent=scipy>=1.3.2 2022-01-29 10:56:44 [info ] init johnnydist [johnnydep.lib] dist=numpy>=1.15.1 parent=sdtfile>=2020.8.3 2022-01-29 10:56:48 [info ] init johnnydist [johnnydep.lib] dist=numpy>=1.18 parent=xarray!=0.20.0,!=0.20.1,>=0.16.2 2022-01-29 10:56:51 [info ] init johnnydist [johnnydep.lib] dist=pandas>=1.1 parent=xarray!=0.20.0,!=0.20.1,>=0.16.2 2022-01-29 10:56:55 [info ] init johnnydist [johnnydep.lib] dist=numpy>=1.18.5 parent=pandas>=1.1 2022-01-29 10:56:55 [info ] init johnnydist [johnnydep.lib] dist=python-dateutil>=2.8.1 parent=pandas>=1.1 2022-01-29 10:56:55 [info ] init johnnydist [johnnydep.lib] dist=pytz>=2020.1 parent=pandas>=1.1 2022-01-29 10:56:55 [info ] init johnnydist [johnnydep.lib] dist=six>=1.5 parent=python-dateutil>=2.8.1 name summary ------------------------------------ ---------------------------------------------------------------------------------------------------------------- ------------ pyglotaran The Glotaran fitting engine. ├── asteval>=0.9.21 Safe, minimalistic evaluator of python expression using ast module ├── click>=7.0 Composable command line interface toolkit │ └── colorama Cross-platform colored terminal text. ├── netCDF4>=1.5.3 Provides an object-oriented python interface to the netCDF version 4 library. │ ├── cftime Time-handling functionality from netcdf4-python │ │ └── numpy>1.13.3 NumPy is the fundamental package for array computing with Python. │ └── numpy>=1.9 NumPy is the fundamental package for array computing with Python. ├── numba>=0.52 compiling Python code using LLVM │ ├── llvmlite<0.39,>=0.38.0rc1 lightweight wrapper around basic LLVM functionality │ ├── numpy<1.22,>=1.18 NumPy is the fundamental package for array computing with Python. │ └── setuptools Easily download, build, install, upgrade, and uninstall Python packages ├── numpy<1.21,>=1.20.0 NumPy is the fundamental package for array computing with Python. ├── pandas>=0.25.2 Powerful data structures for data analysis, time series, and statistics │ ├── numpy>=1.18.5 NumPy is the fundamental package for array computing with Python. │ ├── python-dateutil>=2.8.1 Extensions to the standard Python datetime module │ │ └── six>=1.5 Python 2 and 3 compatibility utilities │ └── pytz>=2020.1 World timezone definitions, modern and historical ├── rich>=10.9.0 Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal │ ├── colorama<0.5.0,>=0.4.0 Cross-platform colored terminal text. │ ├── commonmark<0.10.0,>=0.9.0 Python parser for the CommonMark Markdown spec │ └── pygments<3.0.0,>=2.6.0 Pygments is a syntax highlighting package written in Python. ├── ruamel.yaml>=0.17.17 ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and m ap key order │ └── ruamel.yaml.clib>=0.2.6 C version of reader, parser and emitter for ruamel.yaml derived from libyaml ├── scipy>=1.3.2 SciPy: Scientific Library for Python │ └── numpy<1.23.0,>=1.16.5 NumPy is the fundamental package for array computing with Python. ├── sdtfile>=2020.8.3 Read Becker & Hickl SDT files │ └── numpy>=1.15.1 NumPy is the fundamental package for array computing with Python. ├── setuptools>=41.2 Easily download, build, install, upgrade, and uninstall Python packages ├── tabulate>=0.8.8 Pretty-print tabular data └── xarray!=0.20.0,!=0.20.1,>=0.16.2 N-D labeled arrays and datasets in Python ├── numpy>=1.18 NumPy is the fundamental package for array computing with Python. └── pandas>=1.1 Powerful data structures for data analysis, time series, and statistics ├── numpy>=1.18.5 NumPy is the fundamental package for array computing with Python. ├── python-dateutil>=2.8.1 Extensions to the standard Python datetime module │ └── six>=1.5 Python 2 and 3 compatibility utilities └── pytz>=2020.1 World timezone definitions, modern and historical ```

As far as I can see xarray/__init__.py triggers the following import chain : xarray.testing->xarray.core.duck_array_ops->xarray.core.dask_array_compat which triggers the import of packaging

Traceback starting from our package ```python File "/home/runner/work/pyglotaran/pyglotaran/benchmark/.asv/env/76391772e92136ec87b9940d70226329/lib/python3.8/site-packages/glotaran/io/prepare_dataset.py", line 6, in <module> import xarray as xr File "/home/runner/work/pyglotaran/pyglotaran/benchmark/.asv/env/76391772e92136ec87b9940d70226329/lib/python3.8/site-packages/xarray/__init__.py", line 1, in <module> from . import testing, tutorial, ufuncs File "/home/runner/work/pyglotaran/pyglotaran/benchmark/.asv/env/76391772e92136ec87b9940d70226329/lib/python3.8/site-packages/xarray/testing.py", line 8, in <module> from xarray.core import duck_array_ops, formatting, utils File "/home/runner/work/pyglotaran/pyglotaran/benchmark/.asv/env/76391772e92136ec87b9940d70226329/lib/python3.8/site-packages/xarray/core/duck_array_ops.py", line 24, in <module> from . import dask_array_compat, dask_array_ops, dtypes, npcompat, nputils File "/home/runner/work/pyglotaran/pyglotaran/benchmark/.asv/env/76391772e92136ec87b9940d70226329/lib/python3.8/site-packages/xarray/core/dask_array_compat.py", line 4, in <module> from packaging.version import Version ModuleNotFoundError: No module named 'packaging' ``` 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024884846 https://github.com/pydata/xarray/pull/6207#issuecomment-1024884846 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849FoBu mathause 10194086 2022-01-29T10:30:23Z 2022-01-29T10:55:14Z MEMBER

Thanks. I think it makes sense to revert #6200 then, it's not critical. I opened #6208 for this.

Thanks for the report and the PR.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024887103 https://github.com/pydata/xarray/pull/6207#issuecomment-1024887103 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849Fok_ mathause 10194086 2022-01-29T10:46:12Z 2022-01-29T10:46:12Z MEMBER

On second thought I think the problem is the release of dask 2022.01.1.

 
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   Fix missing dependecy definition of 'packaging' 1118113789
1024884870 https://github.com/pydata/xarray/pull/6207#issuecomment-1024884870 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849FoCG mathause 10194086 2022-01-29T10:30:38Z 2022-01-29T10:30:38Z MEMBER

cc @pydata/xarray 

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   Fix missing dependecy definition of 'packaging' 1118113789
1024868369 https://github.com/pydata/xarray/pull/6207#issuecomment-1024868369 https://api.github.com/repos/pydata/xarray/issues/6207 IC_kwDOAMm_X849FkAR s-weigand 9513634 2022-01-29T08:44:10Z 2022-01-29T08:44:10Z CONTRIBUTOR

The failing tests are unrelated to this change and originate from this commit.

 
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   Fix missing dependecy definition of 'packaging' 1118113789

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   [issue] INTEGER REFERENCES [issues]([id])
);
CREATE INDEX [idx_issue_comments_issue]
    ON [issue_comments] ([issue]);
CREATE INDEX [idx_issue_comments_user]
    ON [issue_comments] ([user]);