Migrates setup to use pyproject

pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+description = "pyrcel: 0D adiabatic cloud parcel model"
+name = "pyrcel"
+authors = [
+    { name = "Daniel Rothenberg", email = "[email protected]" },
+]
+readme = "README.md"
+requires-python = ">=3.8"
+license = { file = "LICENSE.md" }
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: Unix",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Atmospheric Science",
+]
+dependencies = [
+    "numba",
+    "numpy",
+    "pandas",
+    "pyyaml",
+    "scipy",
+    "setuptools",
+    "setuptools-scm",
+    "xarray",
+]
+dynamic = ["version"]
+
+[project.urls]
+Documentation = "https://pyrcel.readthedocs.io/en/latest/"
+Repository = "https://github.com/darothen/pyrcel"
+
+[tools.setuptools]
+packages = ["pyrcel"]
+
+[tool.setuptools.packages]
+find = {namespaces = false} 
+
+[project.scripts]
+run_parcel = "pyrcel.scripts.run_parcel:run_parcel"
+
+[tool.setuptools_scm]
+version_file = "pyrcel/version.py"

pyrcel/__init__.py

@@ -9,8 +9,9 @@
 """
 
 from importlib.metadata import version as _version
+
 try:
-    __version__ = _version('pyrcel')
+    __version__ = _version("pyrcel")
 except Exception:
     # This is a local copy, or a copy that was not installed via setuptools
     __version__ = "local"

scripts/run_parcel → pyrcel/scripts/run_parcel.py

@@ -12,17 +12,22 @@
 import pyrcel as pm
 import pyrcel.util
 
-parser = ArgumentParser(description=__doc__,
-                        formatter_class=RawDescriptionHelpFormatter)
-parser.add_argument("namelist", type=str, metavar="config.yml",
-                    help="YAML namelist controlling simulation configuration")
+parser = ArgumentParser(
+    description=__doc__, formatter_class=RawDescriptionHelpFormatter
+)
+parser.add_argument(
+    "namelist",
+    type=str,
+    metavar="config.yml",
+    help="YAML namelist controlling simulation configuration",
+)
 
 DIST_MAP = {
-    'lognormal': pm.Lognorm,
+    "lognormal": pm.Lognorm,
 }
 
-if __name__ == "__main__":
 
+def run_parcel():
     # Read command-line arguments
     args = parser.parse_args()
 
@@ -38,56 +43,60 @@
     # Create the aerosol
     aerosol_modes = []
     print("Constructing aerosol modes")
-    for i, aerosol_params in enumerate(y['initial_aerosol'], start=1):
+    for i, aerosol_params in enumerate(y["initial_aerosol"], start=1):
         ap = aerosol_params
 
-        dist = DIST_MAP[ap['distribution']](**ap['distribution_args'])
+        dist = DIST_MAP[ap["distribution"]](**ap["distribution_args"])
 
-        aer = pm.AerosolSpecies(ap['name'], dist,
-                                kappa=ap['kappa'], bins=ap['bins'])
+        aer = pm.AerosolSpecies(ap["name"], dist, kappa=ap["kappa"], bins=ap["bins"])
         print("   {:2d})".format(i), aer)
 
         aerosol_modes.append(aer)
 
     # Set up the model
-    ic = y['initial_conditions']
+    ic = y["initial_conditions"]
     print("Initializing model")
     try:
-        model = pm.ParcelModel(aerosol_modes,
-                               V=ic['updraft_speed'],
-                               T0=ic['temperature'],
-                               S0=-1.*(1.0 - ic['relative_humidity']),
-                               P0=ic['pressure'],
-                               console=True,
-                               truncate_aerosols=True)
+        model = pm.ParcelModel(
+            aerosol_modes,
+            V=ic["updraft_speed"],
+            T0=ic["temperature"],
+            S0=-1.0 * (1.0 - ic["relative_humidity"]),
+            P0=ic["pressure"],
+            console=True,
+            truncate_aerosols=True,
+        )
     except pyrcel.util.ParcelModelError:
         print("Something went wrong setting up the model")
         sys.exit(0)
 
     # Run the model
-    mc = y['model_control']
+    mc = y["model_control"]
     print("Beginning simulation")
     try:
-        par_out, aer_out = model.run(max_steps=2000, solver='cvode',
-                                     output_fmt='dataframes',
-                                     # terminate=True,
-                                     # terminate_depth=10.,
-                                     **mc)
+        par_out, aer_out = model.run(
+            max_steps=2000,
+            solver="cvode",
+            output_fmt="dataframes",
+            # terminate=True,
+            # terminate_depth=10.,
+            **mc,
+        )
     except pyrcel.util.ParcelModelError:
         print("Something went wrong during model run")
         sys.exit(0)
 
     # Output
-    ec = y['experiment_control']
+    ec = y["experiment_control"]
 
-    Smax = par_out['S'].max()
-    T_fin = par_out['T'].iloc[-1]
+    Smax = par_out["S"].max()
+    T_fin = par_out["T"].iloc[-1]
 
     # Make output directory if it doesn't exist
-    if not os.path.exists(ec['output_dir']):
-        os.makedirs(ec['output_dir'])
+    if not os.path.exists(ec["output_dir"]):
+        os.makedirs(ec["output_dir"])
 
-    out_file = os.path.join(ec['output_dir'], ec['name']) + ".nc"
+    out_file = os.path.join(ec["output_dir"], ec["name"]) + ".nc"
     try:
         print("Trying to save output to {}".format(out_file))
         pm.output.write_parcel_output(out_file, parcel=model)
@@ -96,4 +105,8 @@
         sys.exit(0)
 
     # Succesful completion
-    print("Done!")
+    print("Done!")
+
+
+if __name__ == "__main__":
+    run_parcel()

setup.py

@@ -41,51 +41,51 @@ def _write_version_file():
 
 
 # Write version and install
-_write_version_file()
+# _write_version_file()
 
 setup(
-    name="pyrcel",
-    author="Daniel Rothenberg",
-    author_email="[email protected]",
-    maintainer="Daniel Rothenberg",
-    maintainer_email="[email protected]",
-    description="pyrcel: 0D adiabatic cloud parcel model",
-    long_description="""
-        This code implements a relatively simple, adiabatic cloud parcel model for studying aerosol
-        activation. It allows the user to peform and iterate parcel model experiments in a simple
-        fashion through the use of an object-oriented implementation. Furthermore, interfaces for
-        several numerical solvers are built into the model so that users can choose whatever scheme
-        they would like to run with the model.
-    """,
-    license="New BSD (3-clause)",
-    url="https://github.com/darothen/pyrcel",
-    version=VERSION,
-    download_url="https://github.com/darothen/pyrcel",
-    # TODO: Update install requirements and corresponding documentation
-    install_requires=[
-        "numba",
-        "numpy",
-        "pandas",
-        "pyyaml",
-        "scipy",
-        "setuptools",
-        "xarray",
-    ],
-    packages=["pyrcel"],
-    package_data={"pyrcel": ["data/std_atm.csv"]},
-    scripts=["scripts/run_parcel"],
-    ext_modules=extensions,
-    classifiers=[
-        "Development Status :: 5 - Production/Stable",
-        "Environment :: Console",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: BSD License",
-        "Natural Language :: English",
-        "Operating System :: Unix",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Topic :: Scientific/Engineering :: Atmospheric Science",
-    ],
+#     name="pyrcel",
+#     author="Daniel Rothenberg",
+#     author_email="[email protected]",
+#     maintainer="Daniel Rothenberg",
+#     maintainer_email="[email protected]",
+#     description="pyrcel: 0D adiabatic cloud parcel model",
+#     long_description="""
+#         This code implements a relatively simple, adiabatic cloud parcel model for studying aerosol
+#         activation. It allows the user to peform and iterate parcel model experiments in a simple
+#         fashion through the use of an object-oriented implementation. Furthermore, interfaces for
+#         several numerical solvers are built into the model so that users can choose whatever scheme
+#         they would like to run with the model.
+#     """,
+#     license="New BSD (3-clause)",
+#     url="https://github.com/darothen/pyrcel",
+#     version=VERSION,
+#     download_url="https://github.com/darothen/pyrcel",
+#     # TODO: Update install requirements and corresponding documentation
+#     install_requires=[
+#         "numba",
+#         "numpy",
+#         "pandas",
+#         "pyyaml",
+#         "scipy",
+#         "setuptools",
+#         "xarray",
+#     ],
+#     packages=["pyrcel"],
+#     package_data={"pyrcel": ["data/std_atm.csv"]},
+#     scripts=["scripts/run_parcel"],
+#     ext_modules=extensions,
+#     classifiers=[
+#         "Development Status :: 5 - Production/Stable",
+#         "Environment :: Console",
+#         "Intended Audience :: Science/Research",
+#         "License :: OSI Approved :: BSD License",
+#         "Natural Language :: English",
+#         "Operating System :: Unix",
+#         "Programming Language :: Python :: 3.8",
+#         "Programming Language :: Python :: 3.9",
+#         "Programming Language :: Python :: 3.10",
+#         "Programming Language :: Python :: 3.11",
+#         "Topic :: Scientific/Engineering :: Atmospheric Science",
+#     ],
 )