Update master to pyet 1.3.1 (#72)

pyet-org · Mar 15, 2024 · 46660b9 · 46660b9
2 parents 990ae50 + a79066b
commit 46660b9
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -39,3 +39,4 @@ jobs:
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: coverage.xml
+
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -13,19 +13,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+    - name: Upload Python Package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}
diff --git a/README.md b/README.md
@@ -42,29 +42,29 @@ $^a$ $T_{max}$ and $T_{min}$ can also be provided. $^b$ $RH_{max}$ and $RH_{min}
 
 Examples of using *pyet* can be found in the example folder:
 
-*   [Example 1](examples/01_example_zamg.ipynb): Estimating PET using pandas.Series
+*   [Example 1](<https://pyet.readthedocs.io/en/dev/examples/01_example_zamg.html#>): Estimating PET using pandas.Series
 
-*   [Example 2](examples/02_example_zamg_netcdf.ipynb): Estimating PET using xarray.DataArray
+*   [Example 2](<https://pyet.readthedocs.io/en/dev/examples/02_example_zamg_netcdf.html>): Estimating PET using xarray.DataArray
 
-*   [Example 3](examples/03_example_knmi.ipynb): Benchmarking Makkink
+*   [Example 3](<https://pyet.readthedocs.io/en/dev/examples/03_example_knmi.html>): Benchmarking Makkink
   against [KNMI data](https://www.knmi.nl/over-het-knmi/about)
 
-*   [Example 4](examples/04_example_coagmet.ipynb): Benchmarking FAO56
+*   [Example 4](<https://pyet.readthedocs.io/en/dev/examples/04_example_coagmet.html>): Benchmarking FAO56
   against [CoAgMET data](https://coagmet.colostate.edu/)
 
-*   [Example 5](examples/05_example_calibration.ipynb): Calibrating the Romanenko and Abtew method against the PM-FAO56
+*   [Example 5](<https://pyet.readthedocs.io/en/dev/examples/05_example_calibration.html>): Calibrating the Romanenko and Abtew method against the PM-FAO56
 
-*   [Example 6](examples/06_worked_examples_McMahon_etal_2013.ipynb): Worked examples for estimating meteorological
+*   [Example 6](<https://pyet.readthedocs.io/en/dev/examples/06_worked_examples_McMahon_etal_2013.html>): Worked examples for estimating meteorological
   variables and potential evapotranspiration after McMahon et al., 2013
 
-*   [Example 7](examples/07_example_climate_change.ipynb): Example for estimating potential evapotranspiration under
+*   [Example 7](<https://pyet.readthedocs.io/en/dev/examples/07_example_climate_change.html>): Example for estimating potential evapotranspiration under
   warming and elevated $CO_2$ concentrations following Yang et al., (2019)
 
-*   [Example 8](examples/08_crop_coefficient.ipynb): Determining the crop coefficient function with Python
+*   [Example 8](<https://pyet.readthedocs.io/en/dev/examples/08_crop_coefficient.html>): Determining the crop coefficient function with Python
 
-*   [Example 9](examples/09_CMIP6_data.ipynb): Estimating PET using CMIP data
+*   [Example 9](<https://pyet.readthedocs.io/en/dev/examples/09_CMIP6_data.html>): Estimating PET using CMIP data
 
-*   [Example 10](examples/10_example_paper.ipynb): Notebook supporting PyEt manuscript
+*   [Example 10](<https://pyet.readthedocs.io/en/dev/examples/10_example_paper.html>): Notebook supporting PyEt manuscript
 
 Documentation is hosted on [ReadTheDocs](https://pyet.readthedocs.io).
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -18,56 +18,54 @@
 
 year = date.today().strftime("%Y")
 
-sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath("."))
 
 # Get a Bibtex reference file from the Zotero group for referencing
 url = "https://api.zotero.org/groups/4846265/collections/M9ZRDX2U/items/"
-params = {"format": "bibtex",
-          "style": "apa",
-          "limit": 100}
+params = {"format": "bibtex", "style": "apa", "limit": 100}
 
 r = requests.get(url=url, params=params)
 with open("references.bib", mode="w") as file:
     file.write(r.text)
 
 # Get a Bibtex reference file from the Zotero group for publications list
 url = "https://api.zotero.org/groups/4846265/collections/UR7PHVDK/items/"
-params = {"format": "bibtex",
-          "style": "apa",
-          "limit": 100}
+params = {"format": "bibtex", "style": "apa", "limit": 100}
 
 r = requests.get(url=url, params=params)
 with open("publications.bib", mode="w") as file:
     file.write(r.text)
 
 # -- Project information -----------------------------------------------------
 
-project = 'pyet'
-copyright = '{}, M. Vremec, R.A. Collenteur'.format(year)
-author = 'M. Vremec, R.A. Collenteur'
+project = "pyet"
+copyright = "{}, M. Vremec, R.A. Collenteur".format(year)
+author = "M. Vremec, R.A. Collenteur"
 
 # The full version, including alpha/beta/rc tags
-release = '2020'
+release = "2020"
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'IPython.sphinxext.ipython_console_highlighting',  # lowercase didn't work
-    'sphinx.ext.autosectionlabel',
-    'sphinxcontrib.bibtex',
-    'myst_nb',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "IPython.sphinxext.ipython_console_highlighting",  # lowercase didn't work
+    "sphinx.ext.autosectionlabel",
+    "sphinxcontrib.bibtex",
+    "myst_nb",
+    "numpydoc",
+    "sphinx_design",
 ]
 
 # Create custom bracket style with round brackets
@@ -77,14 +75,13 @@
 import sphinxcontrib.bibtex.plugin
 
 from sphinxcontrib.bibtex.style.referencing import BracketStyle
-from sphinxcontrib.bibtex.style.referencing.author_year \
-    import AuthorYearReferenceStyle
+from sphinxcontrib.bibtex.style.referencing.author_year import AuthorYearReferenceStyle
 
 
 def bracket_style() -> BracketStyle:
     return BracketStyle(
-        left='(',
-        right=')',
+        left="(",
+        right=")",
     )
 
 
@@ -98,40 +95,52 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 
 
 sphinxcontrib.bibtex.plugin.register_plugin(
-    'sphinxcontrib.bibtex.style.referencing',
-    'author_year_round', MyReferenceStyle)
+    "sphinxcontrib.bibtex.style.referencing", "author_year_round", MyReferenceStyle
+)
 
-bibtex_bibfiles = ['references.bib', 'publications.bib']
+bibtex_bibfiles = ["references.bib", "publications.bib"]
 bibtex_reference_style = "author_year_round"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', '**.ipynb_checkpoints']
+exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 
 html_theme = "pydata_sphinx_theme"
-html_theme_options = {
-    "github_url": "https://github.com/phydrus/pyet",
-    "use_edit_page_button": False
-}
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 html_logo = "_static/logo.png"
+html_use_smartypants = True
+html_show_sourcelink = True
+
+html_theme_options = {
+    "github_url": "https://github.com/pyet-org/pyet",
+    "use_edit_page_button": True,
+    "header_links_before_dropdown": 6,
+    "icon_links": [
+        {
+            "name": "GitHub",  # Label for this link
+            "url": "https://github.com/pyet-org/pyet",  # required
+            "icon": "fab fa-github-square",
+            "type": "fontawesome",  # Default is fontawesome
+        }
+    ],
+}
 
 autosummary_generate = True
 numpydoc_show_class_members = False
@@ -148,3 +157,13 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 
 nb_execution_allow_errors = True  # Allow errors in notebooks, to see the error online
 nb_execution_mode = "auto"
+
+# Enable specific MyST extensions, such as "dollarmath" for math rendering
+myst_enable_extensions = [
+    "dollarmath",
+]
+
+# -- Numpydoc settings ----------------------------------------------------------------
+
+numpydoc_class_members_toctree = True
+numpydoc_show_class_members = False
diff --git a/docs/examples/10_example_paper.ipynb b/docs/examples/10_example_paper.ipynb
@@ -89,6 +89,7 @@
     "import pylab\n",
     "import matplotlib.dates as mdates\n",
     "from mpl_toolkits.axes_grid1.inset_locator import inset_axes\n",
+    "import gc  # Import the garbage collection module\n",
     "\n",
     "import pyet\n",
     "import spotpy\n",
@@ -120,7 +121,6 @@
    "source": [
     "#edit default values for plots\n",
     "params = {\n",
-    "    \"font.family\": \"Arial\",\n",
     "    \"legend.fontsize\": \"15\",\n",
     "    \"axes.labelsize\": \"16\",\n",
     "    \"xtick.labelsize\": \"15\",\n",
@@ -773,7 +773,7 @@
     "fig.supxlabel(\"PET$_{benchmark}$ [mm/day]\", x=0.475, fontsize=16)\n",
     "fig.supylabel(\"PET$_{pyet}$ [mm/day]\", fontsize=16)\n",
     "fig.subplots_adjust(wspace=0.05, hspace=0.05, left=0.05)\n",
-    "plt.tight_layout()\n",
+    "plt.tight_layout();\n",
     "#fig.savefig(\"figure1.png\", dpi=600, bbox_inches=\"tight\")"
    ]
   },
@@ -872,7 +872,7 @@
     "\n",
     "plt.tight_layout()\n",
     "\n",
-    "axs[2].legend(loc=(1.05,0.1), ncol=2, bbox_transform=axs[0].transAxes, fontsize=8)\n",
+    "axs[2].legend(loc=(1.05,0.1), ncol=2, bbox_transform=axs[0].transAxes, fontsize=8);\n",
     "#fig.savefig(\"figure2.png\", dpi=600, bbox_inches=\"tight\")"
    ]
   },
@@ -1007,7 +1007,7 @@
     "    cbar.set_label(\"PET [mm/day]\", labelpad=10)\n",
     "    plt.subplots_adjust(hspace=0.02, wspace=0.1)\n",
     "\n",
-    "plt.subplots_adjust(hspace=0.02, wspace=0.01)\n",
+    "plt.subplots_adjust(hspace=0.02, wspace=0.01);\n",
     "\n",
     "#fig.savefig(\"figure3.png\", dpi=300, bbox_inches=\"tight\")"
    ]
@@ -1287,7 +1287,7 @@
     "axs[1,5].set_yticklabels([\"\",800,1000,\"\"])\n",
     "axs[0,5].legend(loc=(-3.65,1.05), ncol=7, bbox_transform=axs[1,5].transAxes)\n",
     "clb = fig.colorbar(density, orientation=\"horizontal\", ax=axs[0, 0], cax = axs[0, 0].inset_axes([0.04, 1.2, 1, 0.05]))\n",
-    "clb.ax.set_title(\"Number of points per pixel\")\n",
+    "clb.ax.set_title(\"Number of points per pixel\");\n",
     "#fig.savefig(\"figure4.png\", dpi=600, bbox_inches=\"tight\")"
    ]
   },
@@ -1336,13 +1336,13 @@
    "source": [
     "# Load CO2 data for each RCP scenario\n",
     "rcp_co2 = pd.DataFrame()\n",
-    "rcp_co2[\"rcp_26\"] = pd.read_csv(\"data/example_10/co2_conc/RCP3PD_MIDYR_CONC.dat\", skiprows=38, \n",
+    "rcp_co2[\"rcp_26\"] = pd.read_csv(\"data/example_10/co2_conc/RCP3PD_MIDYR_CONC.DAT\", skiprows=38, \n",
     "                                delim_whitespace=True, index_col=\"YEARS\").loc[\"2020\":\"2100\", \"CO2\"]\n",
-    "rcp_co2[\"rcp_45\"] = pd.read_csv(\"data/example_10/co2_conc/RCP45_MIDYR_CONC.dat\", skiprows=38, \n",
+    "rcp_co2[\"rcp_45\"] = pd.read_csv(\"data/example_10/co2_conc/RCP45_MIDYR_CONC.DAT\", skiprows=38, \n",
     "                                delim_whitespace=True, index_col=\"YEARS\").loc[\"2020\":\"2100\", \"CO2\"]\n",
-    "rcp_co2[\"rcp_60\"] = pd.read_csv(\"data/example_10/co2_conc/RCP6_MIDYR_CONC.dat\", skiprows=38, \n",
+    "rcp_co2[\"rcp_60\"] = pd.read_csv(\"data/example_10/co2_conc/RCP6_MIDYR_CONC.DAT\", skiprows=38, \n",
     "                                delim_whitespace=True, index_col=\"YEARS\").loc[\"2020\":\"2100\", \"CO2\"]\n",
-    "rcp_co2[\"rcp_85\"] = pd.read_csv(\"data/example_10/co2_conc/RCP85_MIDYR_CONC.dat\", skiprows=38, \n",
+    "rcp_co2[\"rcp_85\"] = pd.read_csv(\"data/example_10/co2_conc/RCP85_MIDYR_CONC.DAT\", skiprows=38, \n",
     "                                delim_whitespace=True, index_col=\"YEARS\").loc[\"2020\":\"2100\", \"CO2\"]"
    ]
   },
@@ -1416,11 +1416,11 @@
     "dpet_rcp_etco2 = pd.DataFrame(index=rcp_temp.index, columns=[\"rcp_26\", \"rcp_45\", \"rcp_60\", \"rcp_85\"])\n",
     "dpet_rcp_etco2_5th = pd.DataFrame(index=rcp_temp.index, columns=[\"rcp_26\", \"rcp_45\", \"rcp_60\", \"rcp_85\"])\n",
     "dpet_rcp_etco2_95th = pd.DataFrame(index=rcp_temp.index, columns=[\"rcp_26\", \"rcp_45\", \"rcp_60\", \"rcp_85\"])\n",
-    "for year in rcp_temp.index:\n",
+    "for year in rcp_temp.index:  \n",
     "    for rcp in [\"rcp_26\", \"rcp_45\", \"rcp_60\", \"rcp_85\"]:\n",
     "        df_rcp_et = pd.DataFrame()\n",
     "        df_rcp_etco2 = pd.DataFrame()\n",
-    "        for i in np.arange(0, len(methods)):\n",
+    "        for i in np.arange(0, len(methods[:2])): # only for two methods to reduce processing for RTD to handle!!!!!!!!!!!!\n",
     "            input1 = input_rcp(rcp_temp.loc[year, rcp])\n",
     "            df_rcp_et[methods[i]] = simulate(sollutions2[i], methods[i], input1[i])\n",
     "            df_rcp_etco2[methods[i]] = simulate(sollutions2[i], methods[i], \n",
@@ -1430,7 +1430,9 @@
     "        dpet_rcp_et_95th.loc[year, rcp] = df_rcp_et.resample(\"y\").mean().mean().quantile(0.95)\n",
     "        dpet_rcp_etco2.loc[year, rcp] = df_rcp_etco2.resample(\"y\").mean().mean().mean()\n",
     "        dpet_rcp_etco2_5th.loc[year, rcp] = df_rcp_etco2.resample(\"y\").mean().mean().quantile(0.05)\n",
-    "        dpet_rcp_etco2_95th.loc[year, rcp] = df_rcp_etco2.resample(\"y\").mean().mean().quantile(0.95)"
+    "        dpet_rcp_etco2_95th.loc[year, rcp] = df_rcp_etco2.resample(\"y\").mean().mean().quantile(0.95)\n",
+    "        # Call gc.collect() after processing each RCP scenario for a year\n",
+    "        gc.collect()"
    ]
   },
   {
@@ -1487,7 +1489,7 @@
     "\n",
     "for i, letter in enumerate([\"a\", \"b\", \"c\", \"d\"]):\n",
     "    axs[i].text(0.85, 0.9, \"({})\".format(letter), transform=axs[i].transAxes, fontsize=12)\n",
-    "    axs[i].tick_params(axis='both', which='major', labelsize=13)\n",
+    "    axs[i].tick_params(axis='both', which='major', labelsize=13);\n",
     "\n",
     "#fig.savefig(\"figure5.png\", dpi=600, bbox_inches=\"tight\")"
    ]
@@ -1529,7 +1531,7 @@
     "pet_df.plot()  # daily PET [mm/day]\n",
     "pet_df.boxplot()  # boxplot PET[mm/day]\n",
     "pet_df.cumsum().plot()  # cummulative PET [mm]\n",
-    "plt.scatter(pyet_makkink, pet_knmi)  # plot Makkink pyet vs KNMI"
+    "plt.scatter(pyet_makkink, pet_knmi)  # plot Makkink pyet vs KNMI;"
    ]
   },
   {