ruff in pre-commit for Python formatting and linting

.pre-commit-config.yaml

@@ -25,4 +25,5 @@ repos:
   rev: v0.1.4 # Ruff version.
   hooks:
     - id: ruff # Run the linter for Python.
+      args: ["--ignore=E402"]  # Ignore E402 error "Module level import not at top of file"
     - id: ruff-format # Run the formatter for Python.

docs/source/conf.py

@@ -1,4 +1,4 @@
-'''
+"""
 ----- CLEO -----
 File: conf.py
 Project: source
@@ -16,7 +16,7 @@
 -----
 File Description:
 configuration for CLEO documentation made using Sphinx
-'''
+"""
 
 
 # Configuration file for the Sphinx documentation builder.
@@ -32,17 +32,18 @@
 
 import pathlib
 import sys
+
 # sys.path.insert(0, os.path.abspath('../..'))
 sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix())
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'CLEO'
-license = 'BSD 3-Clause'
-copyright = '(2023) MPI-M, Clara Bayley'
-author = 'Clara Bayley & Other Developers'
-release = '0.1.0'
+project = "CLEO"
+license = "BSD 3-Clause"
+copyright = "(2023) MPI-M, Clara Bayley"
+author = "Clara Bayley & Other Developers"
+release = "0.1.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -51,21 +52,21 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.duration',
-    'sphinx_copybutton',
-    'sphinx.ext.intersphinx',
-    'sphinxcontrib.bibtex',
-    'breathe',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.duration",
+    "sphinx_copybutton",
+    "sphinx.ext.intersphinx",
+    "sphinxcontrib.bibtex",
+    "breathe",
     "sphinx.ext.viewcode",
 ]
 
 # configuration of citations using bibtex file(s)
-bibtex_bibfiles = ['./references.bib']
-bibtex_reference_style = 'label'
+bibtex_bibfiles = ["./references.bib"]
+bibtex_reference_style = "label"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -74,30 +75,30 @@
 
 # Integrate doxygen with sphinx via breathe
 breathe_projects = {
-    "libs"             : "../build/doxygen/xml/",
-    "runcleo"          : "../build/doxygen/xml/",
-    "superdrops"       : "../build/doxygen/xml/",
-    "zarr"             : "../build/doxygen/xml/",
-    "observers"        : "../build/doxygen/xml/",
-    "initialise"       : "../build/doxygen/xml/",
+    "libs": "../build/doxygen/xml/",
+    "runcleo": "../build/doxygen/xml/",
+    "superdrops": "../build/doxygen/xml/",
+    "zarr": "../build/doxygen/xml/",
+    "observers": "../build/doxygen/xml/",
+    "initialise": "../build/doxygen/xml/",
 }
 
-breathe_default_project = 'proj'
+breathe_default_project = "proj"
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#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 = 'furo'
+html_theme = "furo"
 
 # 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"]
 
 # To include the date of the last visit in Sphinx documentation, use the last
 # updated feature of Sphinx. This feature automatically adds the last modification
 # date of the source file to the rendered HTML output.
-html_last_updated_fmt = '%d %B %Y'
+html_last_updated_fmt = "%d %B %Y"

docs/source/usage/good_coding.rst

@@ -61,7 +61,9 @@ by automated tools such as `Cocogitto-bot <https://github.com/apps/cocogitto-bot
 
 Code Style / Formatting
 -----------------------
-For Python, we obey the PEP 8 style guide.
+For Python, we use `ruff <https://docs.astral.sh/ruff/>`_` for formatting and linting. Ruff checks
+are something like the combination of several Python linters (Flake8, isort, pydocstyle etc.) and
+the black formatter. We obey the default settings of ruff except we ignore E402 errors.
 
 For C++ we obey the Google C++ Style Guide with:
   | IndentWidth: 2

examples/adiabaticparcel/as2017.py

@@ -1,29 +1,27 @@
+"""
+Copyright (c) 2024 MPI-M, Clara Bayley
 
 
-'''
 ----- CLEO -----
 File: as2017.py
 Project: adiabaticparcel
 Created Date: Friday 17th November 2023
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Thursday 18th April 2024
+Last Modified: Tuesday 7th May 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
 https://opensource.org/licenses/BSD-3-Clause
 -----
-Copyright (c) 2023 MPI-M, Clara Bayley
------
 File Description:
-Script generate input files, runs CLEO adia0D executable to
-create data and then creates plots for adiabatic parcel example
-similar to Figure 5 of "On the CCN (de)activation nonlinearities"
-S. Arabas and S. Shima 2017 to show
+Script generate input files, runs CLEO adia0D executable to create data and
+then creates plots for adiabatic parcel example similar to Figure 5 of "On
+the CCN (de)activation nonlinearities" S. Arabas and S. Shima 2017 to show
 example of adaibatic parcel expansion and contraction.
 Note: SD(M) = superdroplet (model)
-'''
+"""
 
 import os
 import sys
@@ -36,25 +34,26 @@
 configfile = sys.argv[3]
 
 sys.path.append(path2CLEO)  # for imports from pySD package
-sys.path.append(path2CLEO+"/examples/exampleplotting/") # for imports from example plotting package
+sys.path.append(
+    path2CLEO + "/examples/exampleplotting/"
+)  # for imports from example plotting package
 
-from plotssrc import pltsds, as2017fig
+from plotssrc import as2017fig
 from pySD import editconfigfile
-from pySD.sdmout_src import sdtracing
-from pySD.sdmout_src import *
-from pySD.initsuperdropsbinary_src import *
+from pySD.sdmout_src import pyzarr, pysetuptxt, pygbxsdat, sdtracing
+from pySD.initsuperdropsbinary_src import rgens, dryrgens, probdists, attrsgen
 from pySD.initsuperdropsbinary_src import create_initsuperdrops as csupers
 from pySD.initsuperdropsbinary_src import read_initsuperdrops as rsupers
 from pySD.gbxboundariesbinary_src import read_gbxboundaries as rgrid
 from pySD.gbxboundariesbinary_src import create_gbxboundaries as cgrid
 
 ############### INPUTS ##################
 # path and filenames for creating SD initial conditions and for running model
-constsfile = path2CLEO+"/libs/cleoconstants.hpp"
-binpath = path2build+"/bin/"
-sharepath = path2build+"/share/"
-initSDsfile = sharepath+"as2017_dimlessSDsinit.dat"
-gridfile = sharepath+"as2017_dimlessGBxboundaries.dat"
+constsfile = path2CLEO + "/libs/cleoconstants.hpp"
+binpath = path2build + "/bin/"
+sharepath = path2build + "/share/"
+initSDsfile = sharepath + "as2017_dimlessSDsinit.dat"
+gridfile = sharepath + "as2017_dimlessGBxboundaries.dat"
 
 # booleans for [making, saving] initialisation figures
 isfigures = [True, True]
@@ -103,42 +102,41 @@
 paramslist = [params1, params2, params3]
 lwdths = [2, 1, 0.5]
 
+
 def displacement(time, w_avg, thalf):
-    '''displacement z given velocity, w, is sinusoidal
+    """displacement z given velocity, w, is sinusoidal
     profile: w = w_avg * pi/2 * np.sin(np.pi * t/thalf)
-    where wmax = pi/2*w_avg and tauhalf = thalf/pi.'''
+    where wmax = pi/2*w_avg and tauhalf = thalf/pi."""
 
     zmax = w_avg / 2 * thalf
     z = zmax * (1 - np.cos(np.pi * time / thalf))
     return z
 
+
 ############### RUN EXAMPLE ##################
 ###  delete any existing datasets
-for run_num in range(len(monors)*len(paramslist)):
-    dataset = binpath+"as2017_sol"+str(run_num)+".zarr"
-    os.system("rm -rf "+dataset)
+for run_num in range(len(monors) * len(paramslist)):
+    dataset = binpath + "as2017_sol" + str(run_num) + ".zarr"
+    os.system("rm -rf " + dataset)
 
 ### ensure build, share and bin directories exist
 if path2CLEO == path2build:
-  raise ValueError("build directory cannot be CLEO")
+    raise ValueError("build directory cannot be CLEO")
 else:
-  Path(path2build).mkdir(exist_ok=True)
-  Path(sharepath).mkdir(exist_ok=True)
-  Path(binpath).mkdir(exist_ok=True)
+    Path(path2build).mkdir(exist_ok=True)
+    Path(sharepath).mkdir(exist_ok=True)
+    Path(binpath).mkdir(exist_ok=True)
 
 ### create file (and plot) for gridbox boundaries
-os.system("rm "+gridfile)
-cgrid.write_gridboxboundaries_binary(gridfile, zgrid, xgrid,
-                                     ygrid, constsfile)
+os.system("rm " + gridfile)
+cgrid.write_gridboxboundaries_binary(gridfile, zgrid, xgrid, ygrid, constsfile)
 rgrid.print_domain_info(constsfile, gridfile)
 if isfigures[0]:
-    rgrid.plot_gridboxboundaries(constsfile, gridfile,
-                                 binpath, isfigures[1])
+    rgrid.plot_gridboxboundaries(constsfile, gridfile, binpath, isfigures[1])
 plt.close()
 
 runnum = 0
 for i in range(len(monors)):
-
     ### create file (and plots) for initial SDs conditions
     monor, numconc = monors[i], numconcs[i]
     # all SDs have the same dryradius = monor [m]
@@ -147,78 +145,84 @@ def displacement(time, w_avg, thalf):
     # monodisperse droplet radii probability distribution
     xiprobdist = probdists.DiracDelta(monor)
 
-    initattrsgen = attrsgen.AttrsGenerator(radiigen, dryradiigen, xiprobdist,
-                                           coord3gen, coord1gen, coord2gen)
-    os.system("rm "+initSDsfile)
-    csupers.write_initsuperdrops_binary(initSDsfile, initattrsgen,
-                                                      configfile, constsfile,
-                                                      gridfile, nsupers, numconc)
+    initattrsgen = attrsgen.AttrsGenerator(
+        radiigen, dryradiigen, xiprobdist, coord3gen, coord1gen, coord2gen
+    )
+    os.system("rm " + initSDsfile)
+    csupers.write_initsuperdrops_binary(
+        initSDsfile, initattrsgen, configfile, constsfile, gridfile, nsupers, numconc
+    )
     rsupers.print_initSDs_infos(initSDsfile, configfile, constsfile, gridfile)
 
     if isfigures[0]:
-        rsupers.plot_initGBxs_distribs(configfile, constsfile, initSDsfile,
-                                              gridfile, binpath, isfigures[1], "all")
+        rsupers.plot_initGBxs_distribs(
+            configfile, constsfile, initSDsfile, gridfile, binpath, isfigures[1], "all"
+        )
         plt.close()
 
     fig, axs = plt.subplots(nrows=3, ncols=1, figsize=(5, 16))
     for params, lwdth in zip(paramslist, lwdths):
-
         ### edit relevant setup file parameters
-        params["zarrbasedir"] = binpath+"as2017_sol"+str(runnum)+".zarr"
-        params["setup_filename"] = binpath+"as2017_setup.txt"
+        params["zarrbasedir"] = binpath + "as2017_sol" + str(runnum) + ".zarr"
+        params["setup_filename"] = binpath + "as2017_setup.txt"
         editconfigfile.edit_config_params(configfile, params)
 
         ### delete any existing dataset
-        os.system("rm -rf "+params["zarrbasedir"])
-        os.system("rm "+params["setup_filename"])
+        os.system("rm -rf " + params["zarrbasedir"])
+        os.system("rm " + params["setup_filename"])
 
         ### run model
         os.chdir(path2build)
-        executable = path2build+"/examples/adiabaticparcel/src/adia0D"
-        print('Executable: '+executable)
-        print('Config file: '+configfile)
+        executable = path2build + "/examples/adiabaticparcel/src/adia0D"
+        print("Executable: " + executable)
+        print("Config file: " + configfile)
         os.system(executable + " " + configfile)
 
         ### load results
-        setupfile = binpath+"as2017_setup.txt"
-        dataset = binpath+"as2017_sol"+str(runnum)+".zarr"
+        setupfile = binpath + "as2017_setup.txt"
+        dataset = binpath + "as2017_sol" + str(runnum) + ".zarr"
 
         ### read in constants and intial setup from setup .txt file
         config = pysetuptxt.get_config(setupfile, nattrs=3, isprint=True)
         consts = pysetuptxt.get_consts(setupfile, isprint=True)
-        gbxs = pygbxsdat.get_gridboxes(gridfile, consts["COORD0"],
-                                       isprint=True)
+        gbxs = pygbxsdat.get_gridboxes(gridfile, consts["COORD0"], isprint=True)
 
         # read in output Xarray data
-        thermo = pyzarr.get_thermodata(dataset, config["ntime"],
-                                       gbxs["ndims"], consts)
+        thermo = pyzarr.get_thermodata(dataset, config["ntime"], gbxs["ndims"], consts)
         supersat = thermo.supersaturation()
         time = pyzarr.get_time(dataset).secs
         sddata = pyzarr.get_supers(dataset, consts)
         zprof = displacement(time, config["W_avg"], config["TAU_half"])
 
         attrs = ["radius", "xi", "msol"]
         sd0 = sdtracing.attributes_for1superdroplet(sddata, 0, attrs)
-        numconc = np.sum(sddata["xi"][0])/gbxs["domainvol"]/1e6  # [/cm^3]
+        numconc = np.sum(sddata["xi"][0]) / gbxs["domainvol"] / 1e6  # [/cm^3]
 
         ### plot results
-        wlab = "<w> = {:.1f}".format(config["W_avg"]*100)+"cm s$^{-1}$"
-        axs = as2017fig.condensation_validation_subplots(axs, time, sd0["radius"],
-                                                   supersat[:, 0, 0, 0],
-                                                   zprof,
-                                                   lwdth=lwdth,
-                                                   lab=wlab)
+        wlab = "<w> = {:.1f}".format(config["W_avg"] * 100) + "cm s$^{-1}$"
+        axs = as2017fig.condensation_validation_subplots(
+            axs, time, sd0["radius"], supersat[:, 0, 0, 0], zprof, lwdth=lwdth, lab=wlab
+        )
 
         runnum += 1
 
     ### save figure
-    as2017fig.plot_kohlercurve_with_criticalpoints(axs[1], sd0["radius"],
-                                                   sd0["msol"][0],
-                                             thermo.temp[0, 0, 0, 0],
-                                             sddata.IONIC, sddata.MR_SOL)
-
-    textlab = "N = "+str(numconc)+"cm$^{-3}$\n" +\
-              "r$_{dry}$ = "+"{:.2g}\u03BCm\n".format(sd0["radius"][0])
+    as2017fig.plot_kohlercurve_with_criticalpoints(
+        axs[1],
+        sd0["radius"],
+        sd0["msol"][0],
+        thermo.temp[0, 0, 0, 0],
+        sddata.IONIC,
+        sddata.MR_SOL,
+    )
+
+    textlab = (
+        "N = "
+        + str(numconc)
+        + "cm$^{-3}$\n"
+        + "r$_{dry}$ = "
+        + "{:.2g}\u03BCm\n".format(sd0["radius"][0])
+    )
     axs[0].legend(loc="lower right", fontsize=10)
     axs[1].legend(loc="upper left")
     axs[0].text(0.03, 0.85, textlab, transform=axs[0].transAxes)
@@ -233,8 +237,9 @@ def displacement(time, w_avg, thalf):
 
     fig.tight_layout()
 
-    savename = "as2017fig_"+str(i)+".png"
-    fig.savefig(binpath+savename, dpi=400,
-                bbox_inches="tight", facecolor='w', format="png")
-    print("Figure .png saved as: "+binpath+savename)
+    savename = "as2017fig_" + str(i) + ".png"
+    fig.savefig(
+        binpath + savename, dpi=400, bbox_inches="tight", facecolor="w", format="png"
+    )
+    print("Figure .png saved as: " + binpath + savename)
     plt.show()