Merge branch 'xraypy:master' into struct2xasV2407

larch/apps.py

@@ -1,13 +1,12 @@
 """
 main Larch Applications
 """
-import os
 import sys
 import locale
 import inspect
 import shutil
 from argparse import ArgumentParser
-
+from  pathlib import Path
 
 import matplotlib
 from pyshortcuts import make_shortcut, ico_ext, get_desktop
@@ -53,17 +52,16 @@ def __init__(self, name, script, icon=None, description=None,
     def make_desktop_shortcut(self, folder='Larch'):
         """make (or remake) desktop shortcuts for Larch apps"""
         bindir = 'Scripts' if uname == 'win' else 'bin'
-        bindir = os.path.join(sys.prefix, bindir)
+        bindir = Path(sys.prefix, bindir).absolute()
         script = self.script
         if not self.script.startswith('_'):
-            script = os.path.normpath(os.path.join(bindir, self.script))
-
+            script = Path(bindir, self.script).absolute()
 
-        icon = os.path.join(icondir, self.icon)
+        icon = Path(icondir, self.icon)
         if isinstance(ico_ext, (list, tuple)):
             for ext in ico_ext:
                 ticon = f"{self.icon:s}.{ext:s}"
-                if os.path.exists(ticon):
+                if Path(ticon).exists():
                     icon = ticon
 
         make_shortcut(script, name=self.name, folder=folder, icon=icon,
@@ -83,7 +81,7 @@ def prep_cli(self):
         args = parser.parse_args()
         self.filename = None
         if 'filename' in args and args.filename is not None:
-            self.filename = os.path.abspath(args.filename)
+            self.filename = Path(args.filename).absolute()
         self.wx_inspect = args.wx_inspect
         self.run_mode = args.run_mode
         if self.is_wxapp:
@@ -237,8 +235,8 @@ def run_larch():
 
     # create desktop icons
     if args.makeicons:
-        larchdir = os.path.join(get_desktop(), 'Larch')
-        if os.path.exists(larchdir):
+        larchdir = Path(get_desktop(), 'Larch').absolute()
+        if Path(larchdir).exists():
             shutil.rmtree(larchdir)
 
         for n, app in LarchApps.items():

larch/inputText.py

@@ -4,6 +4,7 @@
 
 from __future__ import print_function
 import os
+from pathlib import Path
 import sys
 import time
 from collections import deque
@@ -152,7 +153,7 @@ def clear(self):
     def load(self, filename=None):
         if filename is not None:
             self.filename = filename
-        if os.path.exists(self.filename):
+        if Path(filename).exists():
             self.clear()
             text = read_textfile(filename).split('\n')
             for hline in text:

larch/interpreter.py

@@ -7,6 +7,7 @@
 numpy functions are imported if available and used.
 """
 import os
+from pathlib import Path
 import sys
 import types
 import ast
@@ -400,7 +401,7 @@ def show_errors(self):
 
     def run_init_scripts(self):
         for fname in site_config.init_files:
-            if os.path.exists(fname):
+            if Path(fname).exists():
                 try:
                     self.runfile(fname)
                 except:
@@ -1048,7 +1049,7 @@ def import_module(self, name, asname=None,
         """
         st_sys = self.symtable._sys
         for idir in st_sys.path:
-            if idir not in sys.path and os.path.exists(idir):
+            if idir not in sys.path and Path(idir).exists():
                 sys.path.append(idir)
 
         # step 1  import the module to a global location
@@ -1066,11 +1067,11 @@ def import_module(self, name, asname=None,
             islarch = False
             larchname = "%s.lar" % name
             for dirname in st_sys.path:
-                if not os.path.exists(dirname):
+                if not Path(dirname).exists():
                     continue
                 if larchname in sorted(os.listdir(dirname)):
                     islarch = True
-                    modname = os.path.abspath(os.path.join(dirname, larchname))
+                    modname = Path(dirname, larchname).absolute()
                     try:
                         thismod = self.runfile(modname, new_module=name)
                     except:

larch/io/__init__.py

@@ -8,8 +8,7 @@
 
 from .fileutils import (increment_filename, new_filename, new_dirname,
                         fix_filename, fix_varname, pathOf, unixpath,
-                        winpath, nativepath, strip_quotes, get_timestamp,
-                        asciikeys)
+                        strip_quotes, get_timestamp, asciikeys)
 
 from .columnfile import (read_ascii, write_ascii, write_group, set_array_labels,
                          guess_filereader, look_for_nans, read_fdmnes, sum_fluor_channels)
@@ -58,8 +57,6 @@ def read_tiff(fname, *args, **kws):
                    fix_varname=fix_varname,
                    pathOf=pathOf,
                    unixpath=unixpath,
-                   winpath=winpath,
-                   nativepath=nativepath,
                    strip_quotes=strip_quotes,
                    get_timestamp=get_timestamp,
                    asciikeys=asciikeys,

larch/io/athena_project.py

@@ -4,12 +4,12 @@
 
 """
 
-import os
 import io
 import sys
 import time
 import json
 import platform
+from pathlib import Path
 from fnmatch import fnmatch
 from gzip import GzipFile
 from copy import deepcopy
@@ -18,7 +18,7 @@
 
 from larch import Group, repr_value
 from larch import __version__ as larch_version
-from larch.utils.strutils import bytes2str, str2bytes, fix_varname, asfloat
+from larch.utils import bytes2str, str2bytes, fix_varname, asfloat, unixpath
 
 from xraydb import guess_edge
 import asteval
@@ -49,7 +49,7 @@ def _read_raw_athena(filename):
     # try gzip
     text = None
     try:
-        fh = GzipFile(filename)
+        fh = GzipFile(unixpath(filename))
         text = bytes2str(fh.read())
     except Exception:
         errtype, errval, errtb = sys.exc_info()
@@ -624,7 +624,7 @@ def __init__(self, filename=None):
         self.journal = None
         self.filename = filename
         if filename is not None:
-            if os.path.exists(filename) and is_athena_project(filename):
+            if Path(filename).exists() and is_athena_project(filename):
                 self.read(filename)
 
     def add_group(self, group, signal=None):
@@ -711,10 +711,8 @@ def save(self, filename=None, use_gzip=True):
         buff.extend(["", "@journal = {};", "", "1;", "", "",
                      "# Local Variables:", "# truncate-lines: t",
                      "# End:", ""])
-        fopen =open
-        if use_gzip:
-            fopen = GzipFile
-        fh = fopen(self.filename, 'w')
+        fopen = GzipFile if use_gzip else open
+        fh = fopen(unixpath(self.filename), 'w')
         fh.write(str2bytes("\n".join([bytes2str(t) for t in buff])))
         fh.close()
 
@@ -756,12 +754,12 @@ def read(self, filename=None, match=None, do_preedge=True, do_bkg=False,
         """
         if filename is not None:
             self.filename = filename
-        if not os.path.exists(self.filename):
+        if not Path(self.filename).exists():
             raise IOError("%s '%s': cannot find file" % (ERR_MSG, self.filename))
 
         from larch.xafs import pre_edge, autobk, xftf
 
-        if not os.path.exists(filename):
+        if not Path(filename).exists():
             raise IOError("file '%s' not found" % filename)
 
         text = _read_raw_athena(filename)
@@ -927,7 +925,7 @@ def read_athena(filename, match=None, do_preedge=True, do_bkg=False,
            zn_data = read_athena('Zn on Stuff.prj', match='*merge*', do_bkg=True, do_fft=True)
 
     """
-    if not os.path.exists(filename):
+    if not Path(filename).exists():
         raise IOError("%s '%s': cannot find file" % (ERR_MSG, filename))
 
     aprj = AthenaProject()

larch/io/columnfile.py

@@ -6,13 +6,14 @@
 import sys
 import time
 import string
+from pathlib import Path
 from collections import namedtuple
 import numpy as np
 from dateutil.parser import parse as dateparse
 from math import log10
 from larch import Group
 from larch.symboltable import isgroup
-from ..utils import read_textfile, format_exception
+from ..utils import read_textfile, format_exception, gformat
 from .fileutils import fix_varname
 from .xafs_beamlines import guess_beamline
 
@@ -121,48 +122,6 @@ def colname(txt):
     return fix_varname(txt.strip().lower()).replace('.', '_')
 
 
-def lformat(val, length=12):
-    """Format a number with fixed-length format, somewhat like '%g' except that
-
-        a) the length of the output string will be the requested length.
-        b) positive numbers will have a leading blank.
-        b) the precision will be as high as possible.
-        c) trailing zeros will not be trimmed.
-
-    The precision will typically be length-7, but may be better than
-    that for values with absolute value between 1.e-5 and 1.e8.
-
-    Arguments:
-    val       value to be formatted
-    length    length of output string
-
-    Returns
-    -------
-    string of specified length.
-
-    Notes
-    ------
-     Positive values will have leading blank.
-
-    """
-    try:
-        expon = int(log10(abs(val)))
-    except (OverflowError, ValueError):
-        expon = 0
-    length = max(length, 7)
-    form = 'e'
-    prec = length - 7
-    if abs(expon) > 99:
-        prec -= 1
-    elif ((expon > 0 and expon < (prec+4)) or
-          (expon <= 0 and -expon < (prec-1))):
-        form = 'f'
-        prec += 4
-        if expon > 0:
-            prec -= expon
-    fmt = '{0: %i.%i%s}' % (length, prec, form)
-    return fmt.format(val)
-
 def parse_labelline(labelline, header):
     """
     parse the 'label line' for an ASCII file.
@@ -333,7 +292,7 @@ def read_ascii(filename, labels=None, simple_labels=False,
         read_xdi, write_ascii
 
     """
-    if not os.path.isfile(filename):
+    if not Path(filename).is_file():
         raise OSError("File not found: '%s'" % filename)
     if os.stat(filename).st_size > MAX_FILESIZE:
         raise OSError("File '%s' too big for read_ascii()" % filename)
@@ -402,11 +361,11 @@ def read_ascii(filename, labels=None, simple_labels=False,
                 header_attrs[key] = words[1].strip()
 
 
-    path, fname = os.path.split(filename)
+    fpath = Path(filename).absolute()
+    filename = fpath.as_posix()
     attrs = {'filename': filename}
     group = Group(name='ascii_file %s' % filename,
-                  path=filename,
-                  filename=fname,
+                  path=filename, filename=fpath.name,
                   header=headers, data=[], array_labels=[])
 
     if len(data) == 0:
@@ -597,7 +556,7 @@ def write_ascii(filename, *args, commentchar='#', label=None, header=None):
 
     arrays = np.array(arrays)
     for i in range(arraylen):
-        w = [" %s" % lformat(val[i], length=14) for val in arrays]
+        w = [" %s" % gformat(val[i], length=14) for val in arrays]
         buff.append('  '.join(w))
     buff.append('')
 

larch/io/save_restore.py

@@ -11,8 +11,8 @@
 # from lmfit.minimizer import Minimizer, MinimizerResult
 
 from larch import Group, isgroup, __date__, __version__, __release_version__
-from ..utils import (isotime, bytes2str, str2bytes, fix_varname, is_gzip,
-                     read_textfile, unique_name, format_exception)
+from ..utils import (isotime, bytes2str, str2bytes, fix_varname,
+                     read_textfile, unique_name, format_exception, unixpath)
 from ..utils.jsonutils import encode4js, decode4js
 
 SessionStore = namedtuple('SessionStore', ('config', 'command_history', 'symbols'))
@@ -43,7 +43,7 @@ def save_groups(fname, grouplist):
 
     buff.append("")
 
-    fh = GzipFile(fname, "w")
+    fh = GzipFile(unixpath(fname), "w")
     fh.write(str2bytes("\n".join(buff)))
     fh.close()
 
@@ -175,7 +175,7 @@ def save_session(fname=None, symbols=None, histbuff=None,
     buff.append("##</Symbols>")
     buff.append("")
 
-    fh = GzipFile(fname, "w")
+    fh = GzipFile(unixpath(fname), "w")
     fh.write(str2bytes("\n".join(buff)))
     fh.close()
 

larch/io/xafs_beamlines.py

@@ -28,8 +28,6 @@
 
 """
 
-import re
-
 import numpy as np
 from .fileutils import fix_varname