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Enh/setup cleanup #287

Merged
merged 32 commits into from
Dec 21, 2023
Merged

Enh/setup cleanup #287

merged 32 commits into from
Dec 21, 2023

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bzah
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@bzah bzah commented Dec 15, 2023 •
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Pull Request to resolve #259

  • Unit tests cover the changes.
  • These changes were tested on real data.
  • The relevant documentation has been added or updated.
  • A short description of the changes has been added to doc/source/references/release_notes.rst.

Describe the changes you made

TODO:

  • Complete the pyproject.toml with the linter and formatter configuration
    • For now a few rules are disabled (either commented in select or added to ignore in pyproject.toml).
      They should be added step by step and will help improve the code quality.
  • Migrate to ruff for linting
  • Update CI to install requirements from toml file instead of requirement for test, logo generation, API generation and doc generation
  • Remove ICCLIM_VERSION from constants and use icclim.version instead (investigate if that's possible without issues)

Abel Aoun added 2 commits December 15, 2023 09:50
MAINT: Update requirements
852381f
MAINT: Update project structure
c6987c4 
- Moved tests dir to root
- Moved icclim package to a new src dir
  The above are to follow the best practice describe in:
  https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/
  From the Python Packaging Authority.

- Update build and release process to avoid using deprecated features
  Now we will use `flit` and `build` tools to build icclim
  releases.

- Remove setup.py in favor of the more modern pyproject.toml

- Remove requirement.txt and requirement-dev.txt thanks to
  pyproject.toml
bzah
bzah commented Dec 15, 2023
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environment.yml Outdated Show resolved Hide resolved
Abel Aoun added 13 commits December 18, 2023 14:48
MAINT: Update CI
2920ac3
FIX: doc dependencies
738e29e
MAINT: Simplify version number
75d20dc
MAINT: migrate config to ruff
06f9917
MAINT: Apply ruff format
038aa46
MAINT: Apply ruff lint autofix
fce319c
MAINT: Fix some lint issues
8f9d58f
MAINT: More auto fixes
587d127
MAINT: ruff everywhere
e9a8a65
MAINT: Lint TODO comments
5bfdda5
MAINT: Fix some more lint issues
b0f3537
MAINT: Force xarray to read dataset sequentially
83abd6a 
This will avoid getting some segmentation fault.

Context
-------
Since v1.6.1 of netcdf4 py the version used for netcdf-c
release the GIL. However, netcdf-c is not thread safe so
from times to times threads may mess with each other when
we use dask parallelization to open multiple datasets at
once.
Merge remote-tracking branch 'origin/master' into enh/setup-cleanup
a15a5a9
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github-actions bot commented Dec 19, 2023 •
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Coverage

Report
FileStmtsMissCoverMissing
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/icclim
   _generated_api.py178995%17–27
   icclim_logger.py852966%24, 43, 65, 70–95, 105, 111–142, 150–155
   icclim_types.py13130%1–21
   main.py2833488%59–65, 125, 134, 415–419, 502, 528–529, 531–532, 534, 536–537, 539–540, 560–567, 637–642, 727, 734, 738–739
   utils.py40880%14–15, 25–30, 37–41, 43–44
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/icclim/ecad
   xclim_binding.py52885%16–18, 44, 48, 77, 81, 110, 114
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/icclim/generic_indices
   generic_indicators.py4989880%49–55, 68, 72, 89, 93, 97, 110–113, 117, 191, 333–337, 339–343, 389, 420–421, 723–724, 759, 765, 773–774, 794, 958–962, 964–965, 983–989, 993, 1021, 1023, 1091–1092, 1125–1151, 1179–1199, 1215, 1224–1225, 1252–1284, 1290–1293, 1315
   standard_variable.py48198%19
   threshold.py4113492%49–54, 209–210, 234, 238, 286, 302–304, 319–323, 327–331, 411, 553–554, 617–622, 717–718, 913, 936–937, 942, 1016–1017, 1020–1024, 1112–1114
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/icclim/models
   cf_calendar.py35197%20
   climate_variable.py1062180%27–34, 107–113, 168–169, 178, 214–218, 221, 261, 265–269, 296–297, 334
   frequency.py1801592%36–38, 174–177, 321–327, 331, 414–418, 440, 445
   global_metadata.py660%1–9
   index_config.py27581%7–11
   index_group.py35294%33–37
   logical_link.py21195%12
   operator.py31390%10, 15–19
   standard_index.py30680%7–10, 59, 62, 66
   user_index_dict.py20200%1–28
/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/icclim/pre_processing
   in_file_dictionary.py880%1–29
   input_parsing.py2055374%22–28, 81–82, 86–87, 92–97, 111–112, 180, 185–189, 192, 202–203, 214–218, 244, 258, 272, 293–298, 302, 304, 312–317, 322–327, 338–339, 353–360, 369–389, 414
   rechunk.py89693%21–22, 43–44, 48, 136
TOTAL264338186% 

Test results

Tests Skipped Failures Errors Time
189 0 💤 0 ❌ 0 🔥 1m 34s ⏱️

@bzah bzah marked this pull request as ready for review December 21, 2023 12:36
@bzah
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bzah commented Dec 21, 2023 •
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There is a drop of the code coverage in this PR, from 91% to 86%.
It is without consequences because the only statements that are now uncovered are the types declarations.
These are now bypassed at runtime with the addition of if TYPE_CHECKING in imports.

bzah
bzah commented Dec 21, 2023
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tools/build.sh Outdated Show resolved Hide resolved
@bzah bzah merged commit aff2858 into master Dec 21, 2023
5 checks passed
@bzah bzah deleted the enh/setup-cleanup branch December 21, 2023 14:23
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ENH: migrate to project.toml
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