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  • s-weigand · 5 ✖

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  • Fix missing dependecy definition of 'packaging' · 5 ✖

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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
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
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
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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