diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 3d2eb265..3840f8b7 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -20,11 +20,11 @@ jobs: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: '3.8' + python-version: '3.10' - name: Install dependencies run: | python -m pip install --upgrade python-dateutil requests sphinx \ - sphinx-gallery Pillow sphinx_rtd_theme + sphinx-gallery Pillow sphinx_rtd_theme pandas xarray python -m pip install -r docs/requirements.txt - name: Build docs run: ./.github/jobs/build_documentation.sh diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 44059d18..870e27a6 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -68,11 +68,13 @@ jobs: pytest test_future_warnings.py pytest test_sl1l2.py pytest test_reformatted_for_agg.py + pytest test_diagnostics_land_surface.py coverage run -m pytest test_agg_eclv.py test_agg_ratio.py test_agg_stat.py test_agg_stats_and_boot.py \ test_agg_stats_with_groups.py test_calc_difficulty_index.py test_convert_lon_indices.py \ test_event_equalize.py test_event_equalize_against_values.py test_lon_360_to_180.py \ test_statistics.py test_tost_paired.py test_utils.py test_future_warnings.py \ test_sl1l2.py test_reformatted_for_agg.py + coverage html - name: Archive code coverage results diff --git a/.gitignore b/.gitignore index 09435396..db8aa56f 100644 --- a/.gitignore +++ b/.gitignore @@ -4,9 +4,12 @@ # temp files surrounded by # *#*# +__pycache__/ + # sphinx output docs/_build - +docs/diag_ref/generated +docs/sg_execution_times.rst docs/auto_examples diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 0b538bf5..39a78b05 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -25,3 +25,4 @@ python: sphinx: builder: html configuration: docs/conf.py + fail_on_warning: true diff --git a/docs/Contributors_Guide/index.rst b/docs/Contributors_Guide/index.rst index 1940b4f5..a65abcfb 100644 --- a/docs/Contributors_Guide/index.rst +++ b/docs/Contributors_Guide/index.rst @@ -39,7 +39,7 @@ Python Requirements Coding Standards ================ -METplus has adopted some coding standards for its Python code. Detailed information can be found here: https://metplus.readthedocs.io/en/main_v4.0/Users_Guide/ +METplus has adopted some coding standards for its Python code. Detailed information can be found here: https://metplus.readthedocs.io/en/latest/Contributors_Guide/coding_standards.html Comment the Python code using Python docstrings: https://peps.python.org/pep-0257/ @@ -203,9 +203,9 @@ Create User Documentation * from the command line, run the following commands:: - build clean + make clean - build_html + make html * Verify that there aren’t any warnings or error messages in the output diff --git a/docs/Users_Guide/index.rst b/docs/Users_Guide/index.rst index 66a60f65..545d6b37 100644 --- a/docs/Users_Guide/index.rst +++ b/docs/Users_Guide/index.rst @@ -68,6 +68,7 @@ National Center for Atmospheric Research (NCAR) is sponsored by NSF. aggregation write_mpr release-notes + ../diag_ref/index **Indices and tables** diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst new file mode 100644 index 00000000..1bfebbde --- /dev/null +++ b/docs/_templates/autosummary/module.rst @@ -0,0 +1,61 @@ +{{ fullname | escape | underline}} + +.. automodule:: {{ fullname }} + + {% block attributes %} + {% if attributes %} + .. rubric:: {{ _('Module Attributes') }} + + .. autosummary:: + {% for item in attributes %} + {{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + + {% block functions %} + {% if functions %} + .. rubric:: {{ _('Functions') }} + + .. autosummary:: + :toctree: + {% for item in functions %} + {{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + + {% block classes %} + {% if classes %} + .. rubric:: {{ _('Classes') }} + + .. autosummary:: + {% for item in classes %} + {{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + + {% block exceptions %} + {% if exceptions %} + .. rubric:: {{ _('Exceptions') }} + + .. autosummary:: + {% for item in exceptions %} + {{ item }} + {%- endfor %} + {% endif %} + {% endblock %} + +{% block modules %} +{% if modules %} +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: +{% for item in modules %} + {{ item }} +{%- endfor %} +{% endif %} +{% endblock %} diff --git a/docs/conf.py b/docs/conf.py index 040227cf..12056811 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -12,7 +12,7 @@ # import os import sys -sys.path.insert(0, os.path.abspath('.')) +sys.path.insert(0, os.path.abspath('..')) print(sys.path) @@ -39,10 +39,15 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = ['sphinx.ext.autodoc', + 'sphinx.ext.autosummary', 'sphinx.ext.intersphinx', 'sphinx_gallery.gen_gallery', 'sphinx_design', - 'sphinx_rtd_theme',] + 'sphinx_rtd_theme', + 'sphinx.ext.napoleon',] + +# Turn on sphinx.ext.autosummary +autosummary_generate = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] diff --git a/docs/diag_ref/index.rst b/docs/diag_ref/index.rst new file mode 100644 index 00000000..63c69f56 --- /dev/null +++ b/docs/diag_ref/index.rst @@ -0,0 +1,18 @@ +.. _api-index: + +******************************** +Diagnostic Calculation Reference +******************************** + +This reference contains technical documentation for various diagnostic calculations in METcalcpy. + +.. currentmodule:: metcalcpy.diagnostics + +.. autosummary:: + :toctree: generated/ + :recursive: + + land_surface + +* :ref:`modindex` +* :ref:`genindex` diff --git a/docs/index.rst b/docs/index.rst index ab455bf2..b27ff749 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -121,9 +121,6 @@ To cite this documentation in publications, please refer to the METcalcpy User's Users_Guide/index Contributors_Guide/index - - - Indices ======= diff --git a/docs/requirements.txt b/docs/requirements.txt index acd19d3d..95a6da1f 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -4,3 +4,5 @@ sphinxcontrib-bibtex==2.6.1 sphinx==5.3.0 sphinx-design==0.3.0 sphinx_rtd_theme==1.3.0 +pandas==2.2.1 +xarray==2024.3.0 diff --git a/metcalcpy/diagnostics/__init__.py b/metcalcpy/diagnostics/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/metcalcpy/diagnostics/land_surface.py b/metcalcpy/diagnostics/land_surface.py new file mode 100644 index 00000000..c453ec4c --- /dev/null +++ b/metcalcpy/diagnostics/land_surface.py @@ -0,0 +1,52 @@ +"""Diagnostics relevant to Land/Surface applications""" + +from xarray.core.dataarray import DataArray +from pandas.core.series import Series + +def calc_tci(soil_data,sfc_flux_data,skipna=True): + """ Function for computing the Terrestrial Coupling Index + + Args: + soil_data (Xarray DataArray or Pandas Series): The moisture variable to use for computing TCI. + sfc_flux_data (Xarray DataArray or Pandas Series): The latent heat flux variable to use for computing TCI. + skipna (bool): Skip NA values. Passed to Pandas or Xarray. + + Returns: + Xarray DataArray or float32: If Xarray DataArray's are passed, then an Xarray DataArray + containing the gridded TCI is returned. If a Pandas Series is passed, then a single TCI + value is returned. + + Raises: + TypeError: If an unrecognized object type is passed, or the object types do not match. + + Reference: + Dirmeyer, P. A., 2011: The terrestrial segment of soil moisture-climate coupling. *Geophys. Res. Lett.*, **38**, L16702, doi: 10.1029/2011GL048268. + + """ + + # For Xarray objects, compute the mean + if isinstance(soil_data,DataArray) and isinstance(sfc_flux_data,DataArray): + soil_mean = soil_data.mean(dim='time',skipna=skipna) + soil_count = soil_data.count(dim='time') + sfc_flux_mean = sfc_flux_data.mean(dim='time',skipna=skipna) + soil_std = soil_data.std(dim='time',skipna=skipna) + numer = ((soil_data-soil_mean) * (sfc_flux_data-sfc_flux_mean)).sum(dim='time',skipna=skipna) + + # For Pandas objects, compute the mean + elif isinstance(soil_data,Series) and isinstance(sfc_flux_data,Series): + soil_mean = soil_data.mean(skipna=skipna) + soil_count = soil_data.count() + sfc_flux_mean = sfc_flux_data.mean(skipna=skipna) + soil_std = soil_data.std(skipna=skipna) + numer = ((soil_data-soil_mean) * (sfc_flux_data-sfc_flux_mean)).sum(skipna=skipna) + + # No other object types are supported + else: + raise TypeError("Only Xarray DataArray or Pandas DataFrame Objects are supported. Input objects must be of the same type. Got "+str(type(soil_data))+" for soil_data and "+str(type(sfc_flux_data))+" for sfc_flux_data") + + # Compute the covariance term + covarTerm = numer / soil_count + + # Return the Terrestrial Coupling Index (TCI) + return covarTerm/soil_std + diff --git a/test/data/calc_tci_jja_pandas_input.csv b/test/data/calc_tci_jja_pandas_input.csv new file mode 100644 index 00000000..2512f826 --- /dev/null +++ b/test/data/calc_tci_jja_pandas_input.csv @@ -0,0 +1,2178 @@ +level_0,index,TIMESTAMP,SWC_F_MDS_1,SWC_F_MDS_1_QC,LE_F_MDS,LE_F_MDS_QC,datetime,month,season,station_id +148,152,20000601,43.153,1.0,59.5202,1.0,2000-06-01,06,JJA,DE-Hai +149,153,20000602,42.543,1.0,88.215,0.979167,2000-06-02,06,JJA,DE-Hai +150,154,20000603,42.864,1.0,73.9229,1.0,2000-06-03,06,JJA,DE-Hai +151,155,20000604,45.186,1.0,67.2576,0.9375,2000-06-04,06,JJA,DE-Hai +152,156,20000605,46.062,1.0,47.1207,0.979167,2000-06-05,06,JJA,DE-Hai +153,157,20000606,45.737,1.0,22.5715,1.0,2000-06-06,06,JJA,DE-Hai 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metcalcpy.diagnostics.land_surface import calc_tci +from xarray.testing import assert_equal +import xarray as xr +import pandas as pd +import numpy as np + +__author__ = "Daniel Adriaansen (NCAR)" + +def test_calc_tci(): + """ + Test that the output of the calc_tci function is correct. + + Returns + ------- + None. + """ + + doXarray = True + doPandas = True + + if doXarray: + ###### Xarray DataArray case + # Input data for Xarray case + xr_input = xr.open_dataset('data/calc_tci_jja_xarray_input.nc') + + # Output data for Xarray case + xr_truth_var = '__xarray_dataarray_variable__' + xr_truth = xr.open_dataset('data/calc_tci_jja_xarray_output.nc') + + # Compute TCI + xr_test = calc_tci(xr_input['SOILWATER_10CM'],xr_input['LHFLX']) + + # Validate Xarray case + assert_equal(xr_truth[xr_truth_var],xr_test) + + if doPandas: + ###### Pandas DataFrame case + # Input data for Pandas case + pd_input = pd.read_csv('data/calc_tci_jja_pandas_input.csv') + + # There are three sites in the test data, each should have its own TCI value + pd_test = np.array([]) + for name,site in pd_input.groupby('station_id'): + pd_test = np.append(pd_test,calc_tci(site['SWC_F_MDS_1'],site['LE_F_MDS'])) + + # The truth values + pd_truth = np.array([-1.851168960504201,11.861239905560712,-2.0781980819945076]) + + # Validate Pandas case + for test,truth in tuple(zip(pd_test,pd_truth)): + assert test==truth + +if __name__ == "__main__": + test_calc_tci()