Python path.which函数代码示例

    def run_task(self, fw_spec):

        fw_env = fw_spec.get("_fw_env", {})

        if "mpi_cmd" in fw_env:
            mpi_cmd = fw_spec["_fw_env"]["mpi_cmd"]
        elif which("mpirun"):
            mpi_cmd = "mpirun"
        elif which("aprun"):
            mpi_cmd = "aprun"
        else:
            raise ValueError("No MPI command found!")

        nproc = os.environ['PBS_NP']

        v_exe = shlex.split('{} -n {} {}'.format(mpi_cmd, nproc, fw_env.get("vasp_cmd", "vasp")))
        gv_exe = shlex.split('{} -n {} {}'.format(mpi_cmd, nproc, fw_env.get("gvasp_cmd", "gvasp")))

        # override vasp executable in custodian jobs
        for job in self.jobs:
            job.vasp_cmd = v_exe
            job.gamma_vasp_cmd = gv_exe

        # run the custodian
        c = Custodian(self.handlers, self.jobs, self.max_errors)
        c.run()

        update_spec = {'prev_vasp_dir': os.getcwd(),
                       'prev_task_type': fw_spec['task_type']}

        return FWAction(update_spec=update_spec)

    def run_task(self, fw_spec):

        # write a file containing the formula and task_type for somewhat
        # easier file system browsing
        self._write_formula_file(fw_spec)

        fw_env = fw_spec.get("_fw_env", {})

        if "mpi_cmd" in fw_env:
            mpi_cmd = fw_spec["_fw_env"]["mpi_cmd"]
        elif which("mpirun"):
            mpi_cmd = "mpirun"
        elif which("aprun"):
            mpi_cmd = "aprun"
        else:
            raise ValueError("No MPI command found!")

        nproc = os.environ['PBS_NP']

        v_exe = shlex.split('{} -n {} {}'.format(mpi_cmd, nproc, fw_env.get("vasp_cmd", "vasp")))
        gv_exe = shlex.split('{} -n {} {}'.format(mpi_cmd, nproc, fw_env.get("gvasp_cmd", "gvasp")))

        print 'host:', os.environ['HOSTNAME']

        for job in self.jobs:
            job.vasp_cmd = v_exe
            job.gamma_vasp_cmd = gv_exe

        incar_errors = check_incar(fw_spec['task_type'])
        if incar_errors:
            raise ValueError("Critical error: INCAR does not pass checks: {}".format(incar_errors))

        logging.basicConfig(level=logging.DEBUG)
        c = Custodian(self.handlers, self.jobs, max_errors=self.max_errors, gzipped_output=False, validators=[VasprunXMLValidator()])  # manual gzip
        custodian_out = c.run()

        if self.gzip_output:
            for f in os.listdir(os.getcwd()):
                if not f.lower().endswith("gz") and not f.endswith(".OU") and not f.endswith(".ER"):
                    with open(f, 'rb') as f_in, \
                            GzipFile('{}.gz'.format(f), 'wb') as f_out:
                        f_out.writelines(f_in)
                    os.remove(f)

        all_errors = set()
        for run in custodian_out:
            for correction in run['corrections']:
                all_errors.update(correction['errors'])

        stored_data = {'error_list': list(all_errors)}
        update_spec = {'prev_vasp_dir': os.getcwd(),
                       'prev_task_type': fw_spec['task_type'],
                       'mpsnl': fw_spec['mpsnl'],
                       'snlgroup_id': fw_spec['snlgroup_id'],
                       'run_tags': fw_spec['run_tags'],
                       'parameters': fw_spec.get('parameters')}

        return FWAction(stored_data=stored_data, update_spec=update_spec)

def write_open_notebook(flow, options):
    """
    Generate an ipython notebook and open it in the browser.
    Return system exit code.

    See also:
        http://nbviewer.jupyter.org/github/maxalbert/auto-exec-notebook/blob/master/how-to-programmatically-generate-and-execute-an-ipython-notebook.ipynb
    """
    import nbformat
    nbf = nbformat.v4
    nb = nbf.new_notebook()

    nb.cells.extend([
        #nbf.new_markdown_cell("This is an auto-generated notebook for %s" % os.path.basename(pseudopath)),
        nbf.new_code_cell("""\
##%%javascript
##IPython.OutputArea.auto_scroll_threshold = 9999;

from __future__ import print_function, division, unicode_literals
from abipy import abilab
%matplotlib notebook

import pylab
pylab.rcParams['figure.figsize'] = (25.0, 10.0)
import seaborn as sns"""),

        nbf.new_code_cell("flow = abilab.Flow.pickle_load('%s')" % flow.workdir),
        nbf.new_code_cell("flow.show_dependencies()"),
        nbf.new_code_cell("flow.check_status(show=True, verbose=0)"),
        nbf.new_code_cell("flow.show_inputs(nids=None, wslice=None)"),
        nbf.new_code_cell("flow.inspect(nids=None, wslice=None)"),
        nbf.new_code_cell("flow.show_abierrors()"),
        nbf.new_code_cell("flow.show_qouts()"),
    ])

    # Next, we write it to a file on disk that we can then open as a new notebook.
    # Note: This should be as easy as: nbf.write(nb, fname), but the current api
    # is a little more verbose and needs a real file-like object.
    import tempfile, io
    _, nbpath = tempfile.mkstemp(suffix='.ipynb', text=True)

    with io.open(nbpath, 'wt', encoding="utf8") as f:
        nbformat.write(nb, fh)

    if which("jupyter") is not None:
        return os.system("jupyter notebook %s" % nbpath)

    if which("ipython") is not None:
        return os.system("ipython notebook %s" % nbpath)

    raise RuntimeError("Cannot find neither jupyther nor ipython. Install them with `pip install`")

    def __init__(self, input_str, calc_type, workdir=None):
        super(OncvGenerator, self).__init__(workdir=workdir)
        self._input_str = input_str
        self.calc_type = calc_type

        calctype2exec = {
            "non-relativistic": which("oncvpspnr.x"),
            "scalar-relativistic": which("oncvpsp.x"),
            "fully-relativistic": which("oncvpspr.x")}

        self._executable = calctype2exec[calc_type]
        if self.executable is None:
            msg = "Cannot find executable for oncvpsp is PATH. Use `export PATH=dir_with_executable:$PATH`"
            raise RuntimeError(msg)

def has_abinit(version=None, op=">="):
    """
    True if abinit is in $PATH.
    If version is not None, abinit version op version is evaluated and the result is returned.
    False if condition is not fulfilled or the execution of ``abinit -v`` raised CalledProcessError
    """
    abinit = which("abinit")
    if abinit is None: return False
    if version is None: return abinit is not None

    try:
        abinit_version = str(subprocess.check_output(["abinit", "-v"]))

    except subprocess.CalledProcessError:
        # Some MPI implementations require the mpirunner.
        try:
            abinit_version = subprocess.check_output(["mpirun", "-n", "1", "abinit", "-v"])
        except subprocess.CalledProcessError:
            try:
                abinit_version = subprocess.check_output(["mpiexec", "-n", "1", "abinit", "-v"])
            except subprocess.CalledProcessError as exc:
                logger.warning(exc.output)
                return False

    return cmp_version(abinit_version, version, op=op)

def make_open_notebook(options):
    """
    Generate an ipython notebook and open it in the browser.
    Return system exit code.

    Raise:
        RuntimeError if jupyther is not in $PATH
    """
    import nbformat
    nbf = nbformat.v4
    nb = nbf.new_notebook()

    nb.cells.extend([
        nbf.new_markdown_cell("# This is an auto-generated notebook for %s" % os.path.relpath(filepath)),
        nbf.new_code_cell("""\
from __future__ import print_function, division, unicode_literals, absolute_import
%matplotlib notebook
#import numpy as np
#import seaborn as sns
from abipy import abilab\
"""),

    nbf.new_code_cell("abifile = abilab.abiopen('%s')" % options.filepath)
    ])

    _, nbpath = tempfile.mkstemp(suffix='.ipynb', text=True)

    with io.open(nbpath, 'wt', encoding="utf8") as f:
        nbformat.write(nb, f)

    if which("jupyter") is None:
        raise RuntimeError("Cannot find jupyter in PATH. Install it with `pip install`")
    return os.system("jupyter notebook %s" % nbpath)

    def __init__(self):
        self._figures = collections.OrderedDict()

        self.animate_bin = which("animate")

        if self.animate_bin is None:
            raise RuntimeError("Cannot find animate executable in $PATH.\n Please install the ImageMagick suite of tools.")

def _find_loc(app_name):
    # Try command line version
    path = which(app_name)
    if path is not None: return path

    # Treat Mac OsX applications.
    if is_macosx():

        system_apps = [f.lower() for f in os.listdir("/Applications")]
        try:
            i = system_apps.index(app_name)
            return os.path.join("/Applications", system_apps[i])
        except ValueError:
            try:
                i = system_apps.index(app_name + ".app")
                return os.path.join("/Applications", system_apps[i] + ".app")
            except ValueError:
                pass

        try:
            user_dir = os.path.expanduser("~/Applications/")
            user_apps = [f.lower() for f in os.listdir(user_dir)]
            try:
                i = user_apps.index(app_name)
                return os.path.join(user_dir, user_apps[i])
            except ValueError:
                try:
                    i = user_apps.index(app_name + ".app")
                    return os.path.join("/Applications", user_apps[i] + ".app")
                except ValueError:
                    pass
        except Exception:
            pass

    return None

def has_abinit(version, cmp=">="):
    """
    Return True if abinit is in $PATH and version is cmp version.
    False if condition is not fulfilled or the execution of `abinit -v` 
    raised CalledProcessError 
    """
    if which("abinit") is None:
        return False

    try:
        abiver = str(subprocess.check_output(["abinit", "-v"]))

    except subprocess.CalledProcessError:
        # Some MPI implementations require the mpirunner.
        try:
            abiver = subprocess.check_output(["mpirun", "-n", "1", "abinit", "-v"])
        except subprocess.CalledProcessError:
            try:
                abiver = subprocess.check_output(["mpiexec", "-n", "1", "abinit", "-v"])
            except subprocess.CalledProcessError as exc:
                logger.warning(exc.output)
                return False

    return {">=": abiver.strip() >= version.strip(),
            "==": abiver.strip() == version.strip()}[cmp]

    def __init__(self, username, hostname, workdir, sshfs_mountpoint=None):
        """
        Args:
            username:
                Username used to login on the cluster.
            hostname:
                Name of the host.
            workdir:
                Absolute path (on the remote host) where the `AbinitFlows` will be produced.
            sshfs_mountpoint:
                Absolute path (on the local host) where the file system of 
                the remote host will be mounted via sshfs.
        """
        self.username, self.hostname, self.workdir = username, hostname, workdir

        if not os.path.isabs(self.workdir):
            raise ValueError("Please use an absolute path for the remote workdir")

        self.port = 22    # Port for SSH connection
        self.timeout = 30 # Timeout in seconds.

        self.sshfs_mountpoint = os.path.expanduser(sshfs_mountpoint) if sshfs_mountpoint else None

        if self.sshfs_mountpoint is not None and which("sshfs") is None:
            warnings.warn("Cannot locate sshfs in $PATH, cannot mount remote filesystem without SSHFS")

    def __init__(self, fft_input, executable="fftprof"):
        self.verbose = 1
        self.fft_input = fft_input

        self.executable = which(executable)
        if self.executable is None:
            raise self.Error("Cannot find executable %s in $PATH" % executable)

    def dojo_nbcompare(self, what="all", **kwargs):
        """
        Generate an ipython notebook to compare the results in the dojoreport (calls dojo_compare).
        """
        paths = [p.path for p in self]
        import nbformat
        nbf = nbformat.v4
        nb = nbf.new_notebook()

        nb.cells.extend([
            #nbf.new_markdown_cell("# This is an auto-generated notebook for %s" % os.path.basename(pseudopath)),
            nbf.new_code_cell("""\
from __future__ import print_function, division, unicode_literals
%matplotlib notebook"""),

            nbf.new_code_cell("""\
from pseudo_dojo.core.pseudos import DojoTable
pseudos = DojoTable(%s)""" % str(paths)),
            nbf.new_code_cell("pseudos.dojo_compare(what='%s')" % what),
        ])

        _, nbpath = tempfile.mkstemp(suffix='.ipynb', text=True)

        import io
        with io.open(nbpath, 'wt', encoding="utf8") as f:
            nbformat.write(nb, f)

        if which("jupyter") is None:
            raise RuntimeError("Cannot find jupyter in PATH. Install it with `pip install`")
        return os.system("jupyter notebook %s" % nbpath)

    def make_and_open_notebook(self, nbpath=None, foreground=False):  # pragma: no cover
        """
        Generate an jupyter_ notebook and open it in the browser.

        Args:
            nbpath: If nbpath is None, a temporay file is created.
            foreground: By default, jupyter is executed in background and stdout, stderr are redirected
            to devnull. Use foreground to run the process in foreground

        Return:
            system exit code.

        Raise:
            `RuntimeError` if jupyter_ is not in $PATH
        """
        nbpath = self.write_notebook(nbpath=nbpath)

        if which("jupyter") is None:
            raise RuntimeError("Cannot find jupyter in $PATH. Install it with `conda install jupyter or `pip install jupyter`")

        if foreground:
            return os.system("jupyter notebook %s" % nbpath)
        else:
            fd, tmpname = tempfile.mkstemp(text=True)
            print(tmpname)
            cmd = "jupyter notebook %s" % nbpath
            print("Executing:", cmd)
            print("stdout and stderr redirected to %s" % tmpname)
            import subprocess
            process = subprocess.Popen(cmd.split(), shell=False, stdout=fd, stderr=fd)
            cprint("pid: %s" % str(process.pid), "yellow")
            return 0

        def open_terminal():
            """Try to figure which terminal is available."""
            retcode = 1

            if retcode and which("gnome-terminal") is not None:
                retcode = os.system("gnome-terminal -e 'ssh %s -X'" % cluster.hostname)

            if retcode and which("konsole") is not None:
                retcode = os.system("konsole -e 'ssh %s -X'" % cluster.hostname)

            # This does not work
            #retcode = os.system('open -a Terminal -n --args %s -X" % cluster.hostname")
                
            if retcode: # Fallback to xterm.
                retcode = os.system("xterm -e ssh %s -X" % cluster.hostname)

            return retcode

def abicheck():
    """
    This function tests if the most important ABINIT executables
    can be found in $PATH and whether the python modules needed
    at run-time can be imported.

    Raises:
        RuntimeError if not all the dependencies are fulfilled.
    """
    import os
    # Executables must be in $PATH. Unfortunately we cannot
    # test the version of the binaries.
    # A possible approach would be to execute "exe -v"
    # but supporting argv in Fortran is not trivial.
    # Dynamic linking is tested by calling `ldd exe`
    executables = [
        "abinit",
        "mrgddb",
        "mrggkk",
        "anaddb",
    ]

    has_ldd = which("ldd") is not None

    err_lines = []
    app = err_lines.append
    for exe in executables:
        exe_path = which(exe)

        if exe_path is None:
            app("Cannot find %s in $PATH" % exe)
        else:
            if has_ldd and os.system("ldd %s > /dev/null " % exe_path) != 0:
                app("Missing shared library dependencies for %s" % exe)

    try:    
        software_stack()
    except:
        app(_straceback())

    if err_lines:
        header = "The environment on the local machine is not properly setup\n"
        raise RuntimeError(header + "\n".join(err_lines))

    return 0