Add conda dev env and pytest settings in `setup.cfg` #784

tomvothecoder · 2021-11-02T16:13:33Z

Related to #774 and #776 (task 4 Add local conda development environment and task 5 Add unit testing infrastructure).

Adds the conda development env for use in local development and in the GH Actions CI/CD workflow(s).
- Usage command: conda env create -f conda-env/dev.yml
- The packages in conda-env/dev.yml reflect those listed in meta.yaml.in from here: https://github.com/PCMDI/pcmdi_metrics/blob/8993d51c23cf8dd7abcc418acc5bbc8ef90fe645/recipe/meta.yaml.in
- In conda envs, packages should be pinned to ensure reproducibility and deterministic behavior.

Adds pytest and pytest-cov (code coverage report tool).

Usage command: pytest
Afterwards, pytest-cov coverage reports are outputted to the console. The reports can also be found under tests_coverage_reports/htmlcov/index.html or tests_coverage_reports/coverage.xml (this one is used for uploading to the Codecov service if desired).
Settings are configured in setup.cfg.
Example output:

  (pcmdi_metrics_test) vo13@ml-9704174 pcmdi_metrics % pytest
  ==================================================== test session starts =====================================================
  platform darwin -- Python 3.9.7, pytest-6.2.5, py-1.10.0, pluggy-1.0.0
  rootdir: /Users/vo13/Documents/Repositories/tomvothecoder/pcmdi_metrics, configfile: setup.cfg
  plugins: anyio-3.3.4, cov-3.0.0
  collected 0 items                                                                                                            
  /opt/miniconda3/envs/pcmdi_metrics_test/lib/python3.9/site-packages/coverage/control.py:761: CoverageWarning: No data was collected. (no-data-collected)
    self._warn("No data was collected.", slug="no-data-collected")
  
  
  ---------- coverage: platform darwin, python 3.9.7-final-0 -----------
  Name                                                                              Stmts   Miss  Cover
  -----------------------------------------------------------------------------------------------------
  pcmdi_metrics/__init__.py                                                            12     12     0%
  pcmdi_metrics/diurnal/__init__.py                                                     2      2     0%
  pcmdi_metrics/diurnal/common.py                                                      32     32     0%
  pcmdi_metrics/diurnal/fourierFFT.py                                                  39     39     0%
  pcmdi_metrics/diurnal/scripts/__init__.py                                             0      0   100%
  pcmdi_metrics/diurnal/scripts/compositeDiurnalStatistics.py                         132    132     0%
  pcmdi_metrics/diurnal/scripts/computeStdOfDailyMeans.py                              87     87     0%
  pcmdi_metrics/diurnal/scripts/fourierDiurnalAllGrid.py                               81     81     0%
  pcmdi_metrics/diurnal/scripts/fourierDiurnalGridpoints.py                           111    111     0%
  pcmdi_metrics/diurnal/scripts/savg_fourier.py                                       166    166     0%
  pcmdi_metrics/diurnal/scripts/std_of_dailymeans.py                                  111    111     0%
  pcmdi_metrics/diurnal/scripts/std_of_hourlyvalues.py                                117    117     0%
  pcmdi_metrics/diurnal/scripts/std_of_meandiurnalcycle.py                            120    120     0%
  pcmdi_metrics/driver/__init__.py                                                      0      0   100%
  pcmdi_metrics/driver/dataset.py                                                     105    105     0%
  pcmdi_metrics/driver/model.py                                                        76     76     0%
  pcmdi_metrics/driver/observation.py                                                 102    102     0%
  pcmdi_metrics/driver/outputmetrics.py                                               191    191     0%
  pcmdi_metrics/driver/pmp_parameter.py                                               160    160     0%
  pcmdi_metrics/driver/pmp_parser.py                                                   22     22     0%
  pcmdi_metrics/enso/__init__.py                                                        0      0   100%
  pcmdi_metrics/enso/enso_driver.py                                                   271    271     0%
  pcmdi_metrics/enso/lib/__init__.py                                                    1      1     0%
  pcmdi_metrics/enso/lib/enso_lib.py                                                  109    109     0%
  pcmdi_metrics/graphics/__init__.py                                                    6      6     0%
  pcmdi_metrics/graphics/bar_chart/__init__.py                                          1      1     0%
  pcmdi_metrics/graphics/bar_chart/bar_chart.py                                        69     69     0%
  pcmdi_metrics/graphics/bar_chart/lib/__init__.py                                      1      1     0%
  pcmdi_metrics/graphics/bar_chart/lib/barChart.py                                     33     33     0%
  pcmdi_metrics/graphics/parallel_coordinate_plot/__init__.py                           0      0   100%
  pcmdi_metrics/graphics/parallel_coordinate_plot/parallel_coordinate_plot_lib.py      84     84     0%
  pcmdi_metrics/graphics/portrait_plot/__init__.py                                      0      0   100%
  pcmdi_metrics/graphics/portrait_plot/portrait_plot_lib.py                           223    223     0%
  pcmdi_metrics/graphics/portraits.py                                                 963    963     0%
  pcmdi_metrics/graphics/share/__init__.py                                              0      0   100%
  pcmdi_metrics/graphics/share/add_logo.py                                             15     15     0%
  pcmdi_metrics/graphics/share/read_json_mean_clim.py                                  96     96     0%
  pcmdi_metrics/io/__init__.py                                                          2      2     0%
  pcmdi_metrics/io/base.py                                                            592    592     0%
  pcmdi_metrics/misc/__init__.py                                                        0      0   100%
  pcmdi_metrics/misc/scripts/__init__.py                                                1      1     0%
  pcmdi_metrics/misc/scripts/get_pmp_data.py                                           35     35     0%
  pcmdi_metrics/misc/scripts/parallel_submitter.py                                     46     46     0%
  pcmdi_metrics/misc/scripts/parallelize_driver.py                                     80     80     0%
  pcmdi_metrics/mjo/__init__.py                                                         0      0   100%
  pcmdi_metrics/mjo/lib/__init__.py                                                     6      6     0%
  pcmdi_metrics/mjo/lib/argparse_functions.py                                          40     40     0%
  pcmdi_metrics/mjo/lib/debug_chk_plot.py                                              23     23     0%
  pcmdi_metrics/mjo/lib/dict_merge.py                                                   8      8     0%
  pcmdi_metrics/mjo/lib/lib_mjo.py                                                    134    134     0%
  pcmdi_metrics/mjo/lib/mjo_metric_calc.py                                             95     95     0%
  pcmdi_metrics/mjo/lib/plot_wavenumber_frequency_power.py                             52     52     0%
  pcmdi_metrics/mjo/lib/post_process_plot.py                                           41     41     0%
  pcmdi_metrics/mjo/lib/post_process_plot_ensemble_mean.py                             46     46     0%
  pcmdi_metrics/monsoon_sperber/__init__.py                                             0      0   100%
  pcmdi_metrics/monsoon_sperber/lib/__init__.py                                         4      4     0%
  pcmdi_metrics/monsoon_sperber/lib/argparse_functions.py                              32     32     0%
  pcmdi_metrics/monsoon_sperber/lib/calc_metrics.py                                    12     12     0%
  pcmdi_metrics/monsoon_sperber/lib/divide_chunks.py                                   57     57     0%
  pcmdi_metrics/monsoon_sperber/lib/model_land_only.py                                 45     45     0%
  pcmdi_metrics/monsoon_wang/__init__.py                                                2      2     0%
  pcmdi_metrics/monsoon_wang/monsoon_precip_index_fncs.py                              50     50     0%
  pcmdi_metrics/monsoon_wang/monsoon_wang_driver.py                                   137    137     0%
  pcmdi_metrics/pcmdi/__init__.py                                                      18     18     0%
  pcmdi_metrics/pcmdi/annual_mean.py                                                    7      7     0%
  pcmdi_metrics/pcmdi/bias_xy.py                                                        7      7     0%
  pcmdi_metrics/pcmdi/bias_xyt.py                                                       7      7     0%
  pcmdi_metrics/pcmdi/cor_xy.py                                                         5      5     0%
  pcmdi_metrics/pcmdi/cor_xyt.py                                                        5      5     0%
  pcmdi_metrics/pcmdi/io.py                                                            67     67     0%
  pcmdi_metrics/pcmdi/mean_climate_metrics_calculations.py                            131    131     0%
  pcmdi_metrics/pcmdi/mean_climate_metrics_driver.py                                  178    178     0%
  pcmdi_metrics/pcmdi/mean_xy.py                                                        6      6     0%
  pcmdi_metrics/pcmdi/meanabs_xy.py                                                     8      8     0%
  pcmdi_metrics/pcmdi/meanabs_xyt.py                                                    8      8     0%
  pcmdi_metrics/pcmdi/pmp_parser.py                                                     6      6     0%
  pcmdi_metrics/pcmdi/rms_0.py                                                          8      8     0%
  pcmdi_metrics/pcmdi/rms_xy.py                                                         5      5     0%
  pcmdi_metrics/pcmdi/rms_xyt.py                                                        5      5     0%
  pcmdi_metrics/pcmdi/rmsc_xy.py                                                        5      5     0%
  pcmdi_metrics/pcmdi/seasonal_mean.py                                                 15     15     0%
  pcmdi_metrics/pcmdi/std_xy.py                                                         5      5     0%
  pcmdi_metrics/pcmdi/std_xyt.py                                                        5      5     0%
  pcmdi_metrics/pcmdi/zonal_mean.py                                                     5      5     0%
  pcmdi_metrics/variability_mode/__init__.py                                            0      0   100%
  pcmdi_metrics/variability_mode/lib/__init__.py                                        7      7     0%
  pcmdi_metrics/variability_mode/lib/argparse_functions.py                             52     52     0%
  pcmdi_metrics/variability_mode/lib/calc_stat.py                                      80     80     0%
  pcmdi_metrics/variability_mode/lib/dict_merge.py                                      6      6     0%
  pcmdi_metrics/variability_mode/lib/eof_analysis.py                                  160    160     0%
  pcmdi_metrics/variability_mode/lib/landmask.py                                       42     42     0%
  pcmdi_metrics/variability_mode/lib/lib_variability_mode.py                           93     93     0%
  pcmdi_metrics/variability_mode/lib/plot_map.py                                       48     48     0%
  pcmdi_metrics/variability_mode/lib/version.py                                         3      3     0%
  pcmdi_metrics/variability_mode/variability_modes_driver.py                          302    302     0%
  pcmdi_metrics/version.py                                                              3      3     0%
  -----------------------------------------------------------------------------------------------------
  TOTAL                                                                              6380   6380     0%
  Coverage HTML written to dir tests_coverage_reports/htmlcov
  Coverage XML written to file tests_coverage_reports/coverage.xml
  
  =================================================== no tests ran in 2.25s ====================================================

Move existing tests to tests/deprecated and ignore with pytest.
- These tests are kept around as reference, but can removed if desired.

conda-env/dev.yml

- These tests are written using Python Unittest, not pytest.

conda-env/dev.yml

tomvothecoder · 2021-11-02T16:23:39Z

Hey @lee1043 @acordonez, this PR is ready for review. You can follow the usage commands to test the changes.

conda-env/dev.yml

setup.cfg

acordonez

Thanks @tomvothecoder. Success with both usage commands. My pytest results look just like yours.

lee1043

I wonder cdat_info and MV should be included in the dev.yml, or they are implicitly installed through cdms2.

acordonez · 2021-11-02T17:16:45Z

@lee1043 which metrics use MV2? Since I've got the environment set up I can try running them and see if they work.

tomvothecoder · 2021-11-02T17:23:46Z

I wonder cdat_info and MV should be included in the dev.yml, or they are implicitly installed through cdms2.

Both packages are installed through cdms2.

An easy way to test:

conda activate pcmdi_metrics_dev
python
>>> import MV2
>>> import cdat_info

Since pcmdi_metrics uses those packages directly, it is best to add them to the meta.yaml and conda-env/dev.yml. I will make these changes.

tomvothecoder · 2021-11-02T17:25:31Z

Actually MV2 is apart of cdms2, not a standalone package. I won't need to add that to the dependencies list.
https://cdms.readthedocs.io/en/latest/cdms2.html#module-cdms2.MV2

lee1043 · 2021-11-02T17:37:56Z

@lee1043 which metrics use MV2? Since I've got the environment set up I can try running them and see if they work.

I think most of metrics use MV2: mean climate, modes of variability, mjo, monsoon_sperber and monsoon_wang.

But good to learn that installing cdms2 implicitly installs MV2 as well.

lee1043 · 2021-11-02T17:39:33Z

@tomvothecoder can this eof package added to the dependency list? it's been used as a part of the modes of variability metric.

It looks like the eofs is on conda-forge: https://anaconda.org/conda-forge/eofs

tomvothecoder · 2021-11-02T17:58:01Z

@lee1043 and @acordonez Thanks for the review, I will go ahead and merge this PR.

tomvothecoder · 2021-11-02T17:59:16Z

Nevermind, I can't merge since the CircleCI checks are required (and I'm not sure if I have admin privilege to merge). Those two checks will need to be disabled in the repo settings.

lee1043 · 2021-11-02T18:00:12Z

@tomvothecoder thanks for this PR. I will disable circle ci requirement and merge the PR.

Add conda dev env and pytest settings in setup.cfg

3f6d865

tomvothecoder commented Nov 2, 2021

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Move existing tests to tests/deprecated

bfe9c8b

- These tests are written using Python Unittest, not pytest.

tomvothecoder commented Nov 2, 2021

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tomvothecoder marked this pull request as ready for review November 2, 2021 16:22

tomvothecoder commented Nov 2, 2021

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Remove unused packages and update to python=3.9.7

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Add cdat_info=8.2.1 to dev.yml

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Add eofs=1.4.0 to dev.yml

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lee1043 merged commit 4aed053 into PCMDI:master Nov 2, 2021

tomvothecoder deleted the devops/776-conda-dev-env branch November 2, 2021 20:36

lee1043 mentioned this pull request Nov 3, 2021

Remove vcs dependencies #785

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Add conda dev env and pytest settings in `setup.cfg` #784

Add conda dev env and pytest settings in `setup.cfg` #784

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Add conda dev env and pytest settings in setup.cfg #784

Add conda dev env and pytest settings in setup.cfg #784

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Add conda dev env and pytest settings in `setup.cfg` #784

Add conda dev env and pytest settings in `setup.cfg` #784

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