some pylint changes

.gitignore

@@ -46,6 +46,10 @@ Thumbs.db
 *.dvi
 *.toc
 
+# Folders created with unit/functional tests
+_build/
+_run/
+
 
 # Old Files
 *~

functional_unit_testing/allometry/AllometryUtils.py → functional_unit_testing/allometry/allometry_utils.py

@@ -20,24 +20,24 @@ def plot_allometry_var(data, varname, units, save_fig, plot_dir=None):
         save_fig (bool): whether or not to write out plot
         plot_dir (str): if saving figure, where to write to
     """
-    df = pd.DataFrame({'dbh': np.tile(data.dbh, len(data.pft)),
+    data_frame = pd.DataFrame({'dbh': np.tile(data.dbh, len(data.pft)),
                        'pft': np.repeat(data.pft, len(data.dbh)),
                        data.name: data.values.flatten()})
 
-    maxdbh = df['dbh'].max()
-    maxvar = round_up(df[data.name].max())
+    maxdbh = data_frame['dbh'].max()
+    maxvar = round_up(data_frame[data.name].max())
 
     colors = get_color_pallete()
 
     plt.figure(figsize=(7, 5))
-    ax = plt.subplot(111)
-    ax.spines["top"].set_visible(False)
-    ax.spines["bottom"].set_visible(False)
-    ax.spines["right"].set_visible(False)
-    ax.spines["left"].set_visible(False)
+    axis = plt.subplot(111)
+    axis.spines["top"].set_visible(False)
+    axis.spines["bottom"].set_visible(False)
+    axis.spines["right"].set_visible(False)
+    axis.spines["left"].set_visible(False)
 
-    ax.get_xaxis().tick_bottom()
-    ax.get_yaxis().tick_left()
+    axis.get_xaxis().tick_bottom()
+    axis.get_yaxis().tick_left()
 
     plt.xlim(0.0, maxdbh)
     plt.ylim(0.0, maxvar)
@@ -47,16 +47,16 @@ def plot_allometry_var(data, varname, units, save_fig, plot_dir=None):
 
     inc = (int(maxvar) - 0)/20
     for i in range(0, 20):
-        y = 0.0 + i*inc
+        y_val = 0.0 + i*inc
         plt.plot(range(math.floor(0), math.ceil(maxdbh)),
-                  [y] * len(range(math.floor(0), math.ceil(maxdbh))),
+                  [y_val] * len(range(math.floor(0), math.ceil(maxdbh))),
                   "--", lw=0.5, color="black", alpha=0.3)
 
     plt.tick_params(bottom=False, top=False, left=False, right=False)
 
-    pfts = np.unique(df.pft.values)
+    pfts = np.unique(data_frame.pft.values)
     for rank, pft in enumerate(pfts):
-        dat = df[df.pft == pft]
+        dat = data_frame[data_frame.pft == pft]
         plt.plot(dat.dbh.values, dat[data.name].values, lw=2, color=colors[rank],
                  label=pft)
 
@@ -66,7 +66,7 @@ def plot_allometry_var(data, varname, units, save_fig, plot_dir=None):
     plt.legend(loc='upper left', title='PFT')
 
     if save_fig:
-        fig_name = os.path.join(plot_dir, f"allometry_plot_{var}.png")
+        fig_name = os.path.join(plot_dir, f"allometry_plot_{data.name}.png")
         plt.savefig(fig_name)
 
 def plot_total_biomass(data, save_fig, plot_dir):
@@ -75,24 +75,25 @@ def plot_total_biomass(data, save_fig, plot_dir):
     Args:
         data (xarray DataSet): the allometry dataset
     """
-    df = pd.DataFrame({'dbh': np.tile(data.dbh, len(data.pft)),
+    data_frame = pd.DataFrame({'dbh': np.tile(data.dbh, len(data.pft)),
                        'pft': np.repeat(data.pft, len(data.dbh)),
                        'total_biomass_parts': data.total_biomass_parts.values.flatten(),
                        'total_biomass_tissues': data.total_biomass_tissues.values.flatten()})
 
     colors = get_color_pallete()
 
     plt.figure(figsize=(7, 5))
-    ax = plt.subplot(111)
-    ax.spines["top"].set_visible(False)
-    ax.spines["bottom"].set_visible(False)
-    ax.spines["right"].set_visible(False)
-    ax.spines["left"].set_visible(False)
+    axis = plt.subplot(111)
+    axis.spines["top"].set_visible(False)
+    axis.spines["bottom"].set_visible(False)
+    axis.spines["right"].set_visible(False)
+    axis.spines["left"].set_visible(False)
 
-    ax.get_xaxis().tick_bottom()
-    ax.get_yaxis().tick_left()
+    axis.get_xaxis().tick_bottom()
+    axis.get_yaxis().tick_left()
 
-    maxbiomass = np.maximum(df['total_biomass_parts'].max(), df['total_biomass_tissues'].max())
+    maxbiomass = np.maximum(data_frame['total_biomass_parts'].max(),
+                            data_frame['total_biomass_tissues'].max())
 
     plt.xlim(0.0, maxbiomass)
     plt.ylim(0.0, maxbiomass)
@@ -101,9 +102,9 @@ def plot_total_biomass(data, save_fig, plot_dir):
     plt.xticks(fontsize=10)
     plt.tick_params(bottom=False, top=False, left=False, right=False)
 
-    pfts = np.unique(df.pft.values)
+    pfts = np.unique(data_frame.pft.values)
     for rank, pft in enumerate(pfts):
-        data = df[df.pft == pft]
+        data = data_frame[data_frame.pft == pft]
         plt.scatter(data.total_biomass_parts.values, data.total_biomass_parts.values,
                  color=colors[rank], label=pft)
 
@@ -117,6 +118,14 @@ def plot_total_biomass(data, save_fig, plot_dir):
         plt.savefig(fig_name)
 
 def plot_allometry_dat(run_dir, out_file, save_figs, plot_dir):
+    """Plots all allometry plots
+
+    Args:
+        run_dir (str): run directory
+        out_file (str): output file name
+        save_figs (bool): whether or not to save the figures
+        plot_dir (str): plot directory to save the figures to
+    """
 
     # read in allometry data
     allometry_dat = xr.open_dataset(os.path.join(run_dir, out_file))
@@ -172,8 +181,8 @@ def plot_allometry_dat(run_dir, out_file, save_figs, plot_dir):
         },
 
     }
-    for plot in plot_dict:
-        plot_allometry_var(allometry_dat[plot], plot_dict[plot]['varname'],
-                           plot_dict[plot]['units'], save_figs, plot_dir)
+    for plot, attributes in plot_dict.items():
+        plot_allometry_var(allometry_dat[plot], attributes['varname'],
+                           attributes['units'], save_figs, plot_dir)
 
-    plot_total_biomass(allometry_dat, save_figs, plot_dir)
+    plot_total_biomass(allometry_dat, save_figs, plot_dir)

functional_unit_testing/build_fortran_tests.py

@@ -1,18 +1,17 @@
+"""
+Builds/compiles any tests within the FATES repository
+"""
 import os
-import sys
 import shutil
-
-_FATES_PYTHON = os.path.join(os.path.dirname(os.path.abspath(__file__)))
-sys.path.insert(1, _FATES_PYTHON)
-
 from utils import add_cime_lib_to_path
+
 add_cime_lib_to_path()
 
-from CIME.utils import get_src_root, run_cmd_no_fail, expect, stringify_bool
-from CIME.build import CmakeTmpBuildDir
-from CIME.XML.machines import Machines
-from CIME.BuildTools.configure import configure, FakeCase
-from CIME.XML.env_mach_specific import EnvMachSpecific
+from CIME.utils import get_src_root, run_cmd_no_fail, expect, stringify_bool # pylint: disable=wrong-import-position,import-error,wrong-import-order
+from CIME.build import CmakeTmpBuildDir # pylint: disable=wrong-import-position,import-error,wrong-import-order
+from CIME.XML.machines import Machines # pylint: disable=wrong-import-position,import-error,wrong-import-order
+from CIME.BuildTools.configure import configure, FakeCase # pylint: disable=wrong-import-position,import-error,wrong-import-order
+from CIME.XML.env_mach_specific import EnvMachSpecific # pylint: disable=wrong-import-position,import-error,wrong-import-order
 
 _CIMEROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../cime")
 
@@ -30,7 +29,8 @@ def run_cmake(name, test_dir, pfunit_path, netcdf_c_path, netcdf_f_path, cmake_a
         print(f"Running cmake for {name}.")
 
         # directory with cmake modules
-        cmake_module_dir = os.path.abspath(os.path.join(_CIMEROOT, "CIME", "non_py", "src", "CMake"))
+        cmake_module_dir = os.path.abspath(os.path.join(_CIMEROOT, "CIME", "non_py",
+                                                        "src", "CMake"))
 
         # directory with genf90
         genf90_dir = os.path.join(_CIMEROOT, "CIME", "non_py", "externals", "genf90")
@@ -64,7 +64,8 @@ def find_library(caseroot, cmake_args, lib_string):
 
     Args:
         caseroot (str): Directory with pfunit macros
-        cmake_args (str): The cmake args used to invoke cmake (so that we get the correct makefile vars)
+        cmake_args (str): The cmake args used to invoke cmake
+        (so that we get the correct makefile vars)
     """
     with CmakeTmpBuildDir(macroloc=caseroot) as cmaketmp:
         all_vars = cmaketmp.get_makefile_vars(cmake_args=cmake_args)
@@ -92,7 +93,7 @@ def prep_build_dir(build_dir, clean):
     # create the build directory
     build_dir_path = os.path.abspath(build_dir)
     if not os.path.isdir(build_dir_path):
-      os.mkdir(build_dir_path)
+        os.mkdir(build_dir_path)
 
     # change into that directory
     os.chdir(build_dir_path)
@@ -116,12 +117,12 @@ def clean_cmake_files():
 
     # Clear contents to do with cmake cache
     for file in cwd_contents:
-      if (
-          file in ("Macros.cmake", "env_mach_specific.xml")
-          or file.startswith("Depends")
-          or file.startswith(".env_mach_specific")
-          ):
-        os.remove(file)
+        if (
+            file in ("Macros.cmake", "env_mach_specific.xml")
+            or file.startswith("Depends")
+            or file.startswith(".env_mach_specific")
+            ):
+            os.remove(file)
 
 def get_extra_cmake_args(build_dir, mpilib):
     """Makes a fake case to grab the required cmake arguments
@@ -152,23 +153,22 @@ def get_extra_cmake_args(build_dir, mpilib):
         os_,
         unit_testing=True,
     )
-    machspecific = EnvMachSpecific(build_dir, unit_testing=True)
+    EnvMachSpecific(build_dir, unit_testing=True)
 
     # make a fake case
-    fake_case = FakeCase(compiler, mpilib, True, "nuopc", threading=False)
-
-    cmake_args = (
-        "{}-DOS={} -DMACH={} -DCOMPILER={} -DDEBUG={} -DMPILIB={} -Dcompile_threaded={} -DCASEROOT={}".format(
-            "",
-            os_,
-            machobj.get_machine_name(),
-            compiler,
-            stringify_bool(True),
-            mpilib,
-            stringify_bool(False),
-            build_dir
-        )
-    )
+    FakeCase(compiler, mpilib, True, "nuopc", threading=False)
+
+    cmake_args_list = [
+      f"-DOS={os_}",
+      f"-DMACH={machobj.get_machine_name()}",
+      f"-DCOMPILER={compiler}",
+      f"-DDEBUG={stringify_bool(True)}",
+      f"-DMPILIB={mpilib}",
+      f"-Dcompile_threaded={stringify_bool(False)}",
+      f"-DCASEROOT={build_dir}"
+    ]
+
+    cmake_args = " ".join(cmake_args_list)
 
     return cmake_args
 
@@ -246,4 +246,3 @@ def build_unit_tests(build_dir, name, cmake_directory, make_j, clean=False):
     # run cmake and make
     run_cmake(name, cmake_directory, pfunit_path, netcdf_c_path, netcdf_f_path, cmake_args)
     run_make(name, make_j, clean=clean)
-

functional_unit_testing/math_utils/math_utils.py

@@ -0,0 +1,52 @@
+"""Utility functions for allometry functional unit tests
+"""
+import os
+import math
+import xarray as xr
+import numpy as np
+import matplotlib.pyplot as plt
+
+from utils import get_color_pallete
+
+def plot_quadratic_dat(run_dir, out_file, save_figs, plot_dir):
+    """Reads in and plots quadratic formula test output
+
+    Args:
+        run_dir (str): run directory
+        out_file (str): output file
+        save_figs (bool): whether or not to save the figures
+        plot_dir (str): plot directory
+    """
+
+    # read in quadratic data
+    quadratic_dat = xr.open_dataset(os.path.join(run_dir, out_file))
+
+    # plot output
+    plot_quad_and_roots(quadratic_dat.a.values, quadratic_dat.b.values,
+                     quadratic_dat.c.values, quadratic_dat.root1.values,
+                     quadratic_dat.root2.values)
+    if save_figs:
+      fig_name = os.path.join(plot_dir, "quadratic_test.png")
+      plt.savefig(fig_name)
+
+def plot_quad_and_roots(a_coeff, b_coeff, c_coeff, root1, root2):
+    """Plots a set of quadratic formulas (ax**2 + bx + c) and their two roots
+
+    Args:
+        a (float array): set of a coefficients
+        b (float array): set of b coefficients
+        c (float array): set of b coefficients
+        r1 (float array): set of first real roots
+        r2 (float array): set of second real roots
+    """
+
+    colors = get_color_pallete()
+
+    plt.figure(figsize=(7, 5))
+    x_vals = np.linspace(-10.0, 10.0, num=20)
+
+    for i in range(len(a_coeff)):
+        y_vals = a_coeff[i]*x_vals**2 + b_coeff[i]*x_vals + c_coeff[i]
+        plt.plot(x_vals, y_vals, lw=2, color=colors[i])
+        plt.scatter(root1[i], root2[i], color=colors[i], s=50)
+        plt.axhline(y=0.0, color='k', linestyle='dotted')