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",
+#  ],
 )