Source code for pysisyphus.config

import argparse
import configparser
from io import StringIO
import os
from pathlib import Path
import shutil
import sys

from pysisyphus import logger

CONFIG_DIR = Path(os.path.abspath(os.path.dirname(__file__)))
BASIS_LIB_DIR = Path(CONFIG_DIR / "basis_library")
LIB_DIR = Path(CONFIG_DIR / "geom_library")
WF_LIB_DIR = Path(CONFIG_DIR / "wf_library")
T_DEFAULT = 298.15  # Kelvin
p_DEFAULT = 101325  # Pascal
OUT_DIR_DEFAULT = "qm_calcs"
LB_MIN_DEG = 175
L_MAX = 4
    # .pysisyphusrc key: command
    "mwfn": "Multiwfn",
    "jmol": "jmol",
    "packmol": "packmol",
    "formchk": "formchk",
    "unfchk": "unfchk",
    "rwfdump": "rwfdump",
    # QC codes
    "orca": "orca",
    "orca5": "orca",
    "gaussian16": "g16",
    "wfoverlap": "wfoverlap.x",
    "openmolcas": "pymolcas",
    "gamess": "rungms",
    "xtb": "xtb",
    "mopac": "mopac",

# First try to read path to .pysisyphusrc from environment variable
    pysisrc_env = os.getenv("PYSISRC", default=None)
    config_fn = Path(pysisrc_env).resolve()
    print(f"Read pysisyphus configuration from '{config_fn}'")
# Fallback to $HOME/.pysisyphusrc
except TypeError:
    config_fn = Path.home() / ".pysisyphusrc"

if not config_fn.is_file():
    print(f"Couldn't find configuration file. Expected it at '{config_fn}'.")

Config = configparser.ConfigParser()
read_fns =

[docs] def get_cmd(section, key="cmd", use_defaults=True): cmd = None msg = f" and no default was specified for '{section}'." # First we try to load the command from .pysisyphusrc try: cmd = Config[section][key] msg = "." # When the command is not available on .pysisyphusrc we check the defaults except KeyError: if use_defaults: default_key = section if key == "cmd" else key try: default_cmd = DEFAULTS[default_key] cmd = shutil.which(default_cmd) # 'msg' will only be printed when 'cmd' is None, so the msg is # always negative. msg = f" and default cmd='{default_cmd}' was not found in $PATH." except KeyError: pass if cmd is None: logger.warning( f"Failed to load '{key}' from [{section}] " f"in ~/.pysisyphusrc{msg}" ) cmd = None return cmd
[docs] def detect_paths(): config = configparser.ConfigParser() for k, v in DEFAULTS.items(): print(f"{k: >16}: ... ", end="") if not (path := shutil.which(v)): print("not found.") else: path = Path(path).resolve() config[k] = {"cmd": str(path)} print(path) fp = StringIO() config.write(fp, space_around_delimiters=False) config_text = return config_text
[docs] def parse_args(args): parser = argparse.ArgumentParser() parser.add_argument( "--out", "-o", help="Filename to which the detected cmds are dumped." ) return parser.parse_args(args)
[docs] def run_detect_paths(): args = parse_args(sys.argv[1:]) out = args.out config_text = detect_paths() if out: print("Dumped detected cmds to '{out}'") with open(out, "w") as handle: handle.write(config_text) else: print("\nExample .pysisyphusrc:\n") print(config_text)