Python misc.sage_makedirs函数代码示例

def copy_gz_file(gz_source, bz_destination):
    """
    Decompress a gzipped file and install the bzipped verson.  This is
    used by SloaneEncyclopedia.install_from_gz to install several
    gzipped OEIS database files.

    INPUT:

    - ``gz_source`` - string. The name of the gzipped file.

    - ``bz_destination`` - string.  The name of the newly compressed file.
    """
    import gzip
    from sage.misc.misc import sage_makedirs

    # Read the gzipped input
    try:
        gz_input = gzip.open(gz_source, 'r')
        db_text = gz_input.read()
        gz_input.close()
    except IOError as msg:
        raise IOError("Error reading gzipped input file:\n%s"%msg)

    # Write the bzipped output
    try:
        sage_makedirs(os.path.dirname(bz_destination))
        bz2_output = bz2.BZ2File(bz_destination, 'w')
        bz2_output.write(db_text)
        bz2_output.close()
    except IOError as msg:
        raise IOError("Error writing bzipped output file:\n%s"%msg)

    def is_jvm_available(self):
        """
        Returns True if the Java Virtual Machine is available and False if not.

        EXAMPLES:

        Check that it returns a boolean::

            sage: from sage.interfaces.jmoldata import JmolData
            sage: JData = JmolData()
            sage: type(JData.is_jvm_available())
            <type 'bool'>
        """
        #scratch file for  Jmol errors and status
        jmolscratch = os.path.join(DOT_SAGE, "sage_notebook.sagenb", "jmol_scratch")
        if not os.path.exists(jmolscratch):
            sage_makedirs(jmolscratch)
        scratchout = os.path.join(jmolscratch,"jmolout.txt")
        jout=open(scratchout,'w')
        testjavapath = os.path.join(SAGE_LOCAL, "share", "jmol", "testjava.sh")
        result = subprocess.call([testjavapath],stdout=jout)
        jout.close()
        if (result == 0):
            return (True)
        else:
            return (False)

 def dump_as_dict(self, filename, keys):
     from sage.misc.misc import sage_makedirs
     X = self.as_dict(keys)
     print "Dumping %s..."%filename
     s = cPickle.dumps(X,2)
     dir = "%s/pickles/"%SAGE_DATA
     sage_makedirs(dir)
     open("%s/%s"%(dir,filename), "w").write(s)

 def __init__(self, f, dir='func_persist'):
     from sage.misc.misc import sage_makedirs
     self.__func = f
     self.__dir  = dir
     sage_makedirs(dir)
     self.__doc__ = '%s%s%s'%(\
         f.func_name,
         inspect.formatargspec(*inspect.getargs(f.func_code)),
         f.__doc__)

def citation_dir(app):
    # Split app.outdir in 3 parts: SAGE_DOC/TYPE/TAIL where TYPE
    # is a single directory and TAIL can contain multiple directories.
    # The citation dir is then SAGE_DOC/inventory/TAIL.
    assert app.outdir.startswith(SAGE_DOC)
    rel = app.outdir[len(SAGE_DOC):]
    dirs = rel.split(os.sep)
    # If SAGE_DOC does not end with a slash, rel will start with
    # a slash giving an empty dirs[0]. Remove this:
    if not dirs[0]:
        dirs.pop(0)
    dirs = [SAGE_DOC, "inventory"] + dirs[1:]
    citedir = os.path.join(*dirs)
    sage_makedirs(citedir)
    return citedir

    def _init(self, path):
        """
        Create the database from scratch from the PARI files on John Jones's
        web page, downloaded (e.g., via wget) to a local directory, which
        is specified as path above.

        INPUT:


        -  ``path`` - (default works on William Stein install.)
           path must be the path to Jones's Number_Fields directory
           http://hobbes.la.asu.edu/Number_Fields These files should have
           been downloaded using wget.


        EXAMPLE: This is how to create the database from scratch, assuming
        that the number fields are in the default directory above: From a
        cold start of Sage::

                sage: J = JonesDatabase()
                sage: J._init()   # not tested
                ...

        This takes about 5 seconds.
        """
        from sage.misc.misc import sage_makedirs

        n = 0
        x = PolynomialRing(RationalField(), "x").gen()
        self.root = {}
        self.root[tuple([])] = [x - 1]
        if not os.path.exists(path):
            raise IOError("Path %s does not exist." % path)
        for X in os.listdir(path):
            if X[-4:] == "solo":
                Z = path + "/" + X
                print(X)
                for Y in os.listdir(Z):
                    if Y[-3:] == ".gp":
                        self._load(Z, Y)
        sage_makedirs(JONESDATA)
        save(self.root, JONESDATA + "/jones.sobj")

    def save_preview(self):
        """
        Save the preview PNG image
        
        See :meth:`preview_filename`.

        EXAMPLES::

            sage: from sage.repl.rich_output.backend_sagenb import SageNbOutputSceneJmol
            sage: j = SageNbOutputSceneJmol.example()
            sage: import shutil
            sage: shutil.rmtree('.jmol_images', ignore_errors=True)
            sage: j.save_preview()
            sage: os.listdir('.jmol_images')
            ['sage1-size32.jmol.png']
        """
        from sage.misc.misc import sage_makedirs
        sage_makedirs('.jmol_images')
        self.preview_png.save_as(self.preview_filename())
        world_readable(self.preview_filename())

 def __init__(self, dir=None, debug=False, viewer=None):
     from sage.misc.misc import sage_makedirs
     if dir is None:
         dir = misc.DOT_SAGE + 'log'
     self._time = time.strftime('%Y-%m-%d-%H%M%S')
     dir = os.path.join(os.path.abspath(dir), 'log-' + self._time)
     sage_makedirs(dir)
     self._debug = debug
     self._n = 0
     self._dir = dir
     self._filename = os.path.join(dir, self._filename())
     self._output = __IPYTHON__.output_hist
     self._input  = __IPYTHON__.input_hist_raw
     self._text = ''
     self._after_output = False
     self._init()
     self._input_text  = ''
     self._stopped = False
     self._viewer = viewer
     loggers.append(self)
     print('Now logging to ' + self._filename)
     self._update()
     self.view()

def path():
    from sage.misc.misc import sage_makedirs
    sage_makedirs(PATH)

    def _start(self, alt_message=None, block_during_init=True):
        from sage.misc.misc import sage_makedirs
        self.quit()  # in case one is already running
        global failed_to_start

        self._session_number += 1
        current_path = os.path.abspath('.')
        dir = self.__path
        sage_makedirs(dir)
        os.chdir(dir)

        #If the 'SAGE_PEXPECT_LOG' environment variable is set and
        #the current logfile is None, then set the logfile to be one
        #in .sage/pexpect_logs/
        if self.__logfile is None and 'SAGE_PEXPECT_LOG' in os.environ:
            from sage.env import DOT_SAGE
            logs = '%s/pexpect_logs'%DOT_SAGE
            sage_makedirs(logs)

            filename = '%s/%s-%s-%s-%s.log'%(logs, self.name(), os.getpid(), id(self), self._session_number)
            self.__logfile = open(filename, 'w')

        cmd = self.__command

        if self.__verbose_start:
            print cmd
            print "Starting %s"%cmd.split()[0]

        try:
            if self.__remote_cleaner and self._server:
                c = 'sage-native-execute  ssh %s "nohup sage -cleaner"  &'%self._server
                os.system(c)

            # Unset some environment variables for the children to
            # reduce the chances they do something complicated breaking
            # the terminal interface.
            # See Trac #12221 and #13859.
            pexpect_env = dict(os.environ)
            pexpect_del_vars = ['TERM', 'COLUMNS']
            for i in pexpect_del_vars:
                try:
                    del pexpect_env[i]
                except KeyError:
                    pass
            self._expect = pexpect.spawn(cmd, logfile=self.__logfile, env=pexpect_env)
            if self._do_cleaner():
                cleaner.cleaner(self._expect.pid, cmd)

        except (ExceptionPexpect, pexpect.EOF, IndexError):
            self._expect = None
            self._session_number = BAD_SESSION
            failed_to_start.append(self.name())
            raise RuntimeError("Unable to start %s because the command '%s' failed.\n%s"%(
                self.name(), cmd, self._install_hints()))

        os.chdir(current_path)
        self._expect.timeout = self.__max_startup_time

        #self._expect.setmaxread(self.__maxread)
        self._expect.maxread = self.__maxread
        self._expect.delaybeforesend = 0
        try:
            self._expect.expect(self._prompt)
        except (pexpect.TIMEOUT, pexpect.EOF) as msg:
            self._expect = None
            self._session_number = BAD_SESSION
            failed_to_start.append(self.name())
            raise RuntimeError("Unable to start %s"%self.name())
        self._expect.timeout = None

        # Calling tcsetattr earlier exposes bugs in various pty
        # implementations, see :trac:`16474`. Since we haven't
        # **written** anything so far it is safe to wait with
        # switching echo off until now.
        if not self._terminal_echo:
            self._expect.setecho(0)

        with gc_disabled():
            if block_during_init:
                for X in self.__init_code:
                    self.eval(X)
            else:
                for X in self.__init_code:
                    self._send(X)

    - ``bz_destination`` - string.  The name of the newly compressed file.
    """
    import gzip
    from sage.misc.misc import sage_makedirs
        
    # Read the gzipped input
    try:
        gz_input = gzip.open(gz_source, 'r')
        db_text = gz_input.read()
        gz_input.close()
    except IOError, msg:
        raise IOError, "Error reading gzipped input file:\n%s"%msg

    # Write the bzipped output
    try:
        sage_makedirs(os.path.dirname(bz_destination))
        bz2_output = bz2.BZ2File(bz_destination, 'w')
        bz2_output.write(db_text)
        bz2_output.close()
    except IOError, msg:
        raise IOError, "Error writing bzipped output file:\n%s"%msg


def parse_sequence(text):
    entry = re.compile(r'%(?P<letter>[A-Za-z]) A(?P<num>\d{6}) (?P<body>.*)$')
    unsigned, signed, list = [], [], []
    description = ''
    seqnum = -1

    # Fix broken lines: the next line is indented.
    text = text.replace('\n               ', '');

def path():
    from sage.misc.superseded import deprecation
    deprecation(17653, 'The sage.misc.db module is deprecated, use the load/save functions from sage.structure.sage_object instead')
    from sage.misc.misc import sage_makedirs
    sage_makedirs(PATH)

    def _start(self, alt_message=None, block_during_init=True):
        from sage.misc.misc import sage_makedirs
        self.quit()  # in case one is already running

        self._session_number += 1

        if self.__logfile is None:
            # If the 'SAGE_PEXPECT_LOG' environment variable is set and
            # there is no logfile already defined, then create a
            # logfile in .sage/pexpect_logs/
            if self.__logfilename is None and 'SAGE_PEXPECT_LOG' in os.environ:
                from sage.env import DOT_SAGE
                logs = os.path.join(DOT_SAGE, 'pexpect_logs')
                sage_makedirs(logs)

                self.__logfilename = '%s/%s-%s-%s-%s.log'%(logs, self.name(), os.getpid(), id(self), self._session_number)
            if self.__logfilename is not None:
                self.__logfile = open(self.__logfilename, 'w')

        cmd = self.__command

        if self.__verbose_start:
            print cmd
            print "Starting %s"%cmd.split()[0]

        if self.__remote_cleaner and self._server:
            c = 'sage-native-execute  ssh %s "nohup sage -cleaner"  &'%self._server
            os.system(c)

        # Unset some environment variables for the children to
        # reduce the chances they do something complicated breaking
        # the terminal interface.
        # See Trac #12221 and #13859.
        pexpect_env = dict(os.environ)
        pexpect_del_vars = ['TERM', 'COLUMNS']
        for i in pexpect_del_vars:
            try:
                del pexpect_env[i]
            except KeyError:
                pass

        # Run child from self.__path
        currentdir = os.getcwd()
        os.chdir(self.__path)
        try:
            try:
                self._expect = SageSpawn(cmd,
                        logfile=self.__logfile,
                        timeout=None,  # no timeout
                        env=pexpect_env,
                        name=self._repr_(),
                        quit_string=self._quit_string())
            except (ExceptionPexpect, pexpect.EOF) as e:
                # Change pexpect errors to RuntimeError
                raise RuntimeError("unable to start %s because the command %r failed: %s\n%s" %
                        (self.name(), cmd, e, self._install_hints()))
        except BaseException:
            self._expect = None
            self._session_number = BAD_SESSION
            raise
        finally:
            os.chdir(currentdir)

        if self._do_cleaner():
            cleaner.cleaner(self._expect.pid, cmd)

        self._expect.maxread = self.__maxread
        self._expect.delaybeforesend = 0
        try:
            self._expect.expect(self._prompt)
        except (pexpect.TIMEOUT, pexpect.EOF):
            self._expect = None
            self._session_number = BAD_SESSION
            raise RuntimeError("unable to start %s" % self.name())
        self._expect.timeout = None

        # Calling tcsetattr earlier exposes bugs in various pty
        # implementations, see :trac:`16474`. Since we haven't
        # **written** anything so far it is safe to wait with
        # switching echo off until now.
        if not self._terminal_echo:
            self._expect.setecho(0)

        with gc_disabled():
            if block_during_init:
                for X in self.__init_code:
                    self.eval(X)
            else:
                for X in self.__init_code:
                    self._send(X)

    def export_image(self,
        targetfile,
        datafile, #name (path) of data file Jmol can read or script file telling it what to read or load
        datafile_cmd='script', #"script" or "load"
        image_type ='PNG', #PNG, JPG, GIF
        figsize=5,
        **kwds):
        r"""
        This executes JmolData.jar to make an image file.

        INPUT:

        - targetfile -- the full path to the file where the image
          should be written.

        - datafile -- full path to the data file Jmol can read or
          text of a script telling Jmol what to read or load.

        - datafile_cmd -- (default ``'script'``)  ``'load'`` or ``'script'``
          should be ``"load"`` for a data file.

        - image_type -- (default ``"PNG"``) ``'PNG'`` ``'JPG'`` or ``'GIF'``

        - figsize -- number (default 5) equal to (pixels/side)/100

        OUTPUT:

        Image file, .png, .gif or .jpg (default .png)

        .. note::

            Examples will generate an error message if a functional Java Virtual Machine (JVM)
            is not installed on the machine the Sage instance is running on.

        .. warning::

            Programmers using this module should check that the JVM is
            available before making calls to avoid the user getting
            error messages.  Check for the JVM using the function
            :meth:`is_jvm_available`, which returns True if a JVM is available.

        EXAMPLES:

        Use Jmol to load a pdb file containing some DNA from a web data
        base and make an image of the DNA. If you execute this in the
        notebook, the image will appear in the output cell::

            sage: from sage.interfaces.jmoldata import JmolData
            sage: JData = JmolData()
            sage: script = "load =1lcd;display DNA;moveto 0.0 { -473 -713 -518 59.94} 100.0 0.0 0.0 {21.17 26.72 27.295} 27.544636 {0.0 0.0 0.0} -25.287832 64.8414 0.0;"
            sage: testfile = tmp_filename(ext="DNA.png")
            sage: JData.export_image(targetfile=testfile,datafile=script,image_type="PNG") # optional -- internet
            sage: print os.path.exists(testfile) # optional -- internet
            True

        Use Jmol to save an image of a 3-D object created in Sage.
        This method is used internally by plot3d to generate static images.
        This example doesn't have correct scaling::

            sage: from sage.interfaces.jmoldata import JmolData
            sage: JData = JmolData()
            sage: D=dodecahedron()
            sage: from sage.misc.misc import SAGE_TMP
            sage: archive_name=os.path.join(SAGE_TMP, "archive.jmol.zip")
            sage: D.export_jmol(archive_name)  #not scaled properly...need some more steps.
            sage: testfile = os.path.join(SAGE_TMP, "testimage.png")
            sage: script = 'set defaultdirectory "%s"\n script SCRIPT\n'%archive_name
            sage: JData.export_image(targetfile =testfile,datafile = script, image_type="PNG") # optional -- java
            sage: print os.path.exists(testfile) # optional -- java
            True

         """
        if (self.is_jvm_available()):
            # Set up paths, file names and scripts
            jmolpath = os.path.join(SAGE_LOCAL, "share", "jmol", "JmolData.jar")
            launchscript = ""
            if (datafile_cmd!='script'):
                launchscript = "load "
            launchscript = launchscript + datafile
            #print launchscript
            imagescript = "write "+ image_type +" "+targetfile+"\n"
            #print imagescript

            sizeStr = "%sx%s" %(figsize*100,figsize*100)
            #scratch file for  Jmol errors and status
            jmolscratch = os.path.join(DOT_SAGE, "sage_notebook.sagenb", "jmol_scratch")
            if not os.path.exists(jmolscratch):
                sage_makedirs(jmolscratch)
            scratchout = os.path.join(jmolscratch,"jmolout.txt")
            jout=open(scratchout,'w')
            #now call the java application and write the file.
            result = subprocess.call(["java","-Xmx512m","-Djava.awt.headless=true","-jar",jmolpath,"-iox","-g",sizeStr,"-J",launchscript,"-j",imagescript],stdout=jout)
            jout.close()
        else:
            errStr = "Java Virtual Machine not available.\n"
            errStr +="This should be checked before calling JmolData().export_image().\n"
            errStr +="Use JmolData().is_jvm_available() to check.\n"
            errStr +="Administrator should install JVM."
            raise JmolDataError(errStr)

    def _start(self, alt_message=None, block_during_init=True):
        from sage.misc.misc import sage_makedirs
        self.quit()  # in case one is already running
        global failed_to_start

        self._session_number += 1
        current_path = os.path.abspath('.')
        dir = self.__path
        sage_makedirs(dir)
        os.chdir(dir)

        #If the 'SAGE_PEXPECT_LOG' environment variable is set and
        #the current logfile is None, then set the logfile to be one
        #in .sage/pexpect_logs/
        if self.__logfile is None and 'SAGE_PEXPECT_LOG' in os.environ:
            from sage.misc.all import DOT_SAGE
            logs = '%s/pexpect_logs'%DOT_SAGE
            sage_makedirs(logs)

            filename = '%s/%s-%s-%s-%s.log'%(logs, self.name(), os.getpid(), id(self), self._session_number)
            self.__logfile = open(filename, 'w')

        cmd = self.__command

        if self.__verbose_start:
            print cmd
            print "Starting %s"%cmd.split()[0]
            
        try:
            if self.__remote_cleaner and self._server:
                c = 'sage-native-execute  ssh %s "nohup sage -cleaner"  &'%self._server
                os.system(c)

            # Unset $TERM for the children to reduce the chances they do
            # something complicated breaking the terminal interface.
            # See Trac #12221.
            pexpect_env = dict(os.environ)
            try:
                del pexpect_env["TERM"]
            except KeyError:
                pass
            self._expect = pexpect.spawn(cmd, logfile=self.__logfile, env=pexpect_env)
            if self._do_cleaner():
                cleaner.cleaner(self._expect.pid, cmd)
            
        except (ExceptionPexpect, pexpect.EOF, IndexError):
            self._expect = None
            self._session_number = BAD_SESSION
            failed_to_start.append(self.name())
            raise RuntimeError, "Unable to start %s because the command '%s' failed.\n%s"%(
                self.name(), cmd, self._install_hints())

        os.chdir(current_path)
        self._expect.timeout = self.__max_startup_time
            
        #self._expect.setmaxread(self.__maxread)
        self._expect.maxread = self.__maxread
        self._expect.delaybeforesend = 0
        try:
            self._expect.expect(self._prompt)
        except (pexpect.TIMEOUT, pexpect.EOF), msg:
            self._expect = None
            self._session_number = BAD_SESSION
            failed_to_start.append(self.name())
            raise RuntimeError, "Unable to start %s"%self.name()