util.py

#
# Utility classes for PyBaMM
#
# The code in this file is adapted from Pints
# (see https://github.com/pints-team/pints)
#
import argparse
import importlib.util
import numbers
import os
import pathlib
import pickle
import subprocess
import sys
import timeit
from platform import system
import difflib
from warnings import warn

import numpy as np
import importlib.metadata

import pybamm

# versions of jax and jaxlib compatible with PyBaMM
JAX_VERSION = "0.4"
JAXLIB_VERSION = "0.4"


def root_dir():
    """return the root directory of the PyBaMM install directory"""
    return str(pathlib.Path(pybamm.__path__[0]).parent)


def get_git_commit_info():
    """
    Get the git commit info for the current PyBaMM version, e.g. v22.8-39-gb25ce8c41
    (version 22.8, commit b25ce8c41)
    """
    try:
        # Get the latest git commit hash
        return str(
            subprocess.check_output(["git", "describe", "--tags"], cwd=root_dir())
            .strip()
            .decode()
        )
    except subprocess.CalledProcessError:  # pragma: no cover
        # Not a git repository so just return the version number
        return f"v{pybamm.__version__}"


class FuzzyDict(dict):
    def get_best_matches(self, key):
        """Get best matches from keys"""
        return difflib.get_close_matches(key, list(self.keys()), n=3, cutoff=0.5)

    def __getitem__(self, key):
        try:
            return super().__getitem__(key)
        except KeyError:
            if key in ["Negative electrode SOC", "Positive electrode SOC"]:
                domain = key.split(" ")[0]
                raise KeyError(
                    f"Variable '{domain} electrode SOC' has been renamed to "
                    f"'{domain} electrode stoichiometry' to avoid confusion "
                    "with cell SOC"
                )
            if "Measured open circuit voltage" in key:
                raise KeyError(
                    "The variable that used to be called "
                    "'Measured open circuit voltage [V]' is now called "
                    "'Surface open-circuit voltage [V]'. There is also another "
                    "variable called 'Bulk open-circuit voltage [V]' which is the"
                    "open-circuit voltage evaluated at the average particle "
                    "concentrations."
                )
            if "Open-circuit voltage at 0% SOC [V]" in key:
                raise KeyError(
                    "Parameter 'Open-circuit voltage at 0% SOC [V]' not found."
                    "In most cases this should be set to be equal to "
                    "'Lower voltage cut-off [V]'"
                )
            if "Open-circuit voltage at 100% SOC [V]" in key:
                raise KeyError(
                    "Parameter 'Open-circuit voltage at 100% SOC [V]' not found."
                    "In most cases this should be set to be equal to "
                    "'Upper voltage cut-off [V]'"
                )
            best_matches = self.get_best_matches(key)
            for k in best_matches:
                if key in k and k.endswith("]"):
                    raise KeyError(
                        f"'{key}' not found. Use the dimensional version '{k}' instead."
                    )
            raise KeyError(f"'{key}' not found. Best matches are {best_matches}")

    def search(self, key, print_values=False):
        """
        Search dictionary for keys containing 'key'. If print_values is True, then
        both the keys and values will be printed. Otherwise just the values will
        be printed. If no results are found, the best matches are printed.
        """
        key_in = key
        key = key_in.lower()

        # Sort the keys so results are stored in alphabetical order
        keys = list(self.keys())
        keys.sort()
        results = {}

        # Check if any of the dict keys contain the key we are searching for
        for k in keys:
            if key in k.lower():
                results[k] = self[k]

        if results == {}:
            # If no results, return best matches
            best_matches = self.get_best_matches(key)
            print(
                f"No results for search using '{key_in}'. "
                f"Best matches are {best_matches}"
            )
        elif print_values:
            # Else print results, including dict items
            print("\n".join("{}\t{}".format(k, v) for k, v in results.items()))
        else:
            # Just print keys
            print("\n".join("{}".format(k) for k in results.keys()))

    def copy(self):
        return FuzzyDict(super().copy())


class Timer(object):
    """
    Provides accurate timing.

    Example
    -------
    timer = pybamm.Timer()
    print(timer.time())

    """

    def __init__(self):
        self._start = timeit.default_timer()

    def reset(self):
        """
        Resets this timer's start time.
        """
        self._start = timeit.default_timer()

    def time(self):
        """
        Returns the time (float, in seconds) since this timer was created,
        or since meth:`reset()` was last called.
        """
        return TimerTime(timeit.default_timer() - self._start)


class TimerTime:
    def __init__(self, value):
        """A string whose value prints in human-readable form"""
        self.value = value

    def __str__(self):
        """
        Formats a (non-integer) number of seconds, returns a string like
        "5 weeks, 3 days, 1 hour, 4 minutes, 9 seconds", or "0.0019 seconds".
        """
        time = self.value
        if time < 1e-6:
            return "{:.3f} ns".format(time * 1e9)
        if time < 1e-3:
            return "{:.3f} us".format(time * 1e6)
        if time < 1:
            return "{:.3f} ms".format(time * 1e3)
        elif time < 60:
            return "{:.3f} s".format(time)
        output = []
        time = int(round(time))
        units = [(604800, "week"), (86400, "day"), (3600, "hour"), (60, "minute")]
        for k, name in units:
            f = time // k
            if f > 0 or output:
                output.append(str(f) + " " + (name if f == 1 else name + "s"))
            time -= f * k
        output.append("1 second" if time == 1 else str(time) + " seconds")
        return ", ".join(output)

    def __repr__(self):
        return f"pybamm.TimerTime({self.value})"

    def __add__(self, other):
        if isinstance(other, numbers.Number):
            return TimerTime(self.value + other)
        else:
            return TimerTime(self.value + other.value)

    def __radd__(self, other):
        return self.__add__(other)

    def __sub__(self, other):
        if isinstance(other, numbers.Number):
            return TimerTime(self.value - other)
        else:
            return TimerTime(self.value - other.value)

    def __rsub__(self, other):
        if isinstance(other, numbers.Number):
            return TimerTime(other - self.value)

    def __mul__(self, other):
        if isinstance(other, numbers.Number):
            return TimerTime(self.value * other)
        else:
            return TimerTime(self.value * other.value)

    def __rmul__(self, other):
        return self.__mul__(other)

    def __truediv__(self, other):
        if isinstance(other, numbers.Number):
            return TimerTime(self.value / other)
        else:
            return TimerTime(self.value / other.value)

    def __rtruediv__(self, other):
        if isinstance(other, numbers.Number):
            return TimerTime(other / self.value)

    def __eq__(self, other):
        return self.value == other.value


def rmse(x, y):
    """
    Calculate the root-mean-square-error between two vectors x and y, ignoring NaNs
    """
    # Check lengths
    if len(x) != len(y):
        raise ValueError("Vectors must have the same length")
    return np.sqrt(np.nanmean((x - y) ** 2))


def load(filename):
    """Load a saved object"""
    with open(filename, "rb") as f:
        obj = pickle.load(f)
    return obj


def get_parameters_filepath(path):
    """Returns path if it exists in current working dir,
    otherwise get it from package dir"""
    if os.path.exists(path):
        return path
    else:
        return os.path.join(pybamm.__path__[0], path)


def have_jax():
    """Check if jax and jaxlib are installed with the correct versions"""
    return (
        (importlib.util.find_spec("jax") is not None)
        and (importlib.util.find_spec("jaxlib") is not None)
        and is_jax_compatible()
    )


def is_jax_compatible():
    """Check if the available version of jax and jaxlib are compatible with PyBaMM"""
    return (
        importlib.metadata.distribution("jax").version.startswith(JAX_VERSION)
        and importlib.metadata.distribution("jaxlib").version.startswith(JAXLIB_VERSION)
    )


def is_constant_and_can_evaluate(symbol):
    """
    Returns True if symbol is constant and evaluation does not raise any errors.
    Returns False otherwise.
    An example of a constant symbol that cannot be "evaluated" is PrimaryBroadcast(0).
    """
    if symbol.is_constant():
        try:
            symbol.evaluate()
            return True
        except NotImplementedError:
            return False
    else:
        return False


def install_jax(arguments=None):  # pragma: no cover
    """
    Install compatible versions of jax, jaxlib.

    Command Line Interface::

        $ pybamm_install_jax

    |   optional arguments:
    |    -h, --help   show help message
    |    -f, --force  force install compatible versions of jax and jaxlib
    """
    parser = argparse.ArgumentParser(description="Install jax and jaxlib")
    parser.add_argument(
        "-f",
        "--force",
        action="store_true",
        help="force install compatible versions of"
        f" jax ({JAX_VERSION}) and jaxlib ({JAXLIB_VERSION})",
    )

    args = parser.parse_args(arguments)

    if system() == "Windows":
        raise NotImplementedError("Jax is not available on Windows")

    # Raise an error if jax and jaxlib are already installed, but incompatible
    # and --force is not set
    elif importlib.util.find_spec("jax") is not None:
        if not args.force and not is_jax_compatible():
            raise ValueError(
                "Jax is already installed but the installed version of jax or jaxlib is"
                " not supported by PyBaMM. \nYou can force install compatible versions"
                f" of jax ({JAX_VERSION}) and jaxlib ({JAXLIB_VERSION}) using the"
                " following command: \npybamm_install_jax --force"
            )

    msg = (
        "pybamm_install_jax is deprecated,"
        " use 'pip install pybamm[jax]' to install jax & jaxlib"
    )
    warn(msg, DeprecationWarning)
    subprocess.check_call(
        [
            sys.executable,
            "-m",
            "pip",
            "install",
            f"jax>={JAX_VERSION}",
            f"jaxlib>={JAXLIB_VERSION}",
        ]
    )