Merge branch 'rename-to-apps'

* rename subpackage `applications` --> `apps`
* support old import name `applications`

Resolve #34.

Author: pavoljuhas

.coveragerc

@@ -20,4 +20,6 @@ exclude_lines =
 omit =
     ## Exclude from codecov report:
     */tests/debug.py
+    */apps/*.py
+    # TODO remove in version 3.1
     */applications/*.py

conda-recipe/meta.yaml

@@ -43,15 +43,16 @@ test:
   imports:
     - diffpy.structure
     - diffpy.structure.parsers
-    - diffpy.structure.applications
+    - diffpy.structure.apps
     - diffpy.structure.expansion
     - diffpy.structure.tests
     # legacy imports
     - diffpy.Structure
     - diffpy.Structure.Parsers
-    - diffpy.Structure.applications
+    - diffpy.Structure.apps
     - diffpy.Structure.expansion
     - diffpy.Structure.tests
+    - diffpy.structure.applications
 
   # commands:
     # You can put test commands to be run here.  Use this to test that the

doc/manual/source/diffpy.structure.applications.rst

@@ -0,0 +1,30 @@
+diffpy.structure.apps package
+=============================
+
+Submodules
+----------
+
+diffpy.structure.apps.anyeye module
+-----------------------------------
+
+.. automodule:: diffpy.structure.apps.anyeye
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.structure.apps.transtru module
+-------------------------------------
+
+.. automodule:: diffpy.structure.apps.transtru
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: diffpy.structure.apps
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/manual/source/diffpy.structure.apps.rst

@@ -14,7 +14,7 @@ Submodules
     mod_lattice
     mod_spacegroup
     diffpy.structure.parsers
-    diffpy.structure.applications
+    diffpy.structure.apps
     diffpy.structure.expansion
 
 

doc/manual/source/package.rst

@@ -1,17 +1,29 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# diffpy.structure  by DANSE Diffraction group
-#                   Simon J. L. Billinge
-#                   (c) 2006 trustees of the Michigan State University.
+# diffpy.structure  Complex Modeling Initiative
+#                   (c) 2019 Brookhaven Science Associates,
+#                   Brookhaven National Laboratory.
 #                   All rights reserved.
 #
 # File coded by:    Pavol Juhas
 #
 # See AUTHORS.txt for a list of people who contributed.
-# See LICENSE_DANSE.txt for license information.
+# See LICENSE.txt for license information.
 #
 ##############################################################################
 
-"""Script applications that use the diffpy.structure package.
 """
+Import support for renamed subpackage diffpy.structure.applications.
+
+This module is deprecated and will be removed in version 3.1.
+"""
+
+# TODO remove this module in version 3.1.
+
+from warnings import warn
+
+
+warn("Module 'diffpy.structure.applications' is deprecated.  "
+     "Import 'diffpy.structure.apps' instead.",
+     DeprecationWarning, stacklevel=2)

src/diffpy/structure/applications/__init__.py

@@ -1,252 +1,14 @@
 #!/usr/bin/env python
-##############################################################################
-#
-# diffpy.structure  by DANSE Diffraction group
-#                   Simon J. L. Billinge
-#                   (c) 2006 trustees of the Michigan State University.
-#                   All rights reserved.
-#
-# File coded by:    Pavol Juhas
-#
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE_DANSE.txt for license information.
-#
-##############################################################################
 
-"""anyeye    view structure file in atomeye
-Usage: anyeye [options] strufile
-
-anyeye understands more structure formats than atomeye.  It converts strufile
-to a temporary XCFG file which is opened in atomeye.  Supported file formats:
-  inputFormats
-
-Options:
-  -f, --formula     override chemical formula in strufile, formula defines
-                    elements in the same order as in strufile, e.g, Na4Cl4
-  -w, --watch       watch input file for changes
-  --viewer=VIEWER   the structure viewer program, by default "atomeye".
-                    The program will be executed as "VIEWER structurefile"
-  --formats=FORMATS comma separated list of file formats that are understood
-                    by the VIEWER, by default "xcfg,pdb".  Files of other
-                    formats will be converted to the first listed format.
-  -h, --help        display this message and exit
-  -V, --version     show script version and exit
 """
+Temporary support for old import name.
 
-from __future__ import print_function
-
-import sys
-import os
-import re
-import signal
-from diffpy.structure import StructureFormatError
-
-# parameter dictionary
-pd = {  'formula' : None,
-        'watch' : False,
-        'viewer' : 'atomeye',
-        'formats' : ['xcfg', 'pdb'],
-}
-
-
-def usage(style = None):
-    """show usage info, for style=="brief" show only first 2 lines"""
-    import os.path
-    myname = os.path.basename(sys.argv[0])
-    msg = __doc__.replace("anyeye", myname)
-    if style == 'brief':
-        msg = msg.split("\n")[1] + "\n" + \
-                "Try `%s --help' for more information." % myname
-    else:
-        from diffpy.structure.parsers import inputFormats
-        fmts = [ f for f in inputFormats() if f != 'auto' ]
-        msg = msg.replace("inputFormats", " ".join(fmts))
-    print(msg)
-    return
-
-
-def version():
-    from diffpy.structure import __version__
-    print("anyeye", __version__)
-    return
-
-
-def loadStructureFile(filename, format="auto"):
-    """Load structure from specified file.
-
-    Return a tuple of (Structure, fileformat).
-    """
-    from diffpy.structure import Structure
-    stru = Structure()
-    p = stru.read(filename, format)
-    fileformat = p.format
-    return (stru, fileformat)
-
-
-def convertStructureFile(pd):
-    # make temporary directory on the first pass
-    if 'tmpdir' not in pd:
-        from tempfile import mkdtemp
-        pd['tmpdir'] = mkdtemp()
-    strufile = pd['strufile']
-    tmpfile = os.path.join(pd['tmpdir'], os.path.basename(strufile))
-    pd['tmpfile'] = tmpfile
-    # speed up file processing in the watch mode
-    fmt = pd.get('format', 'auto')
-    stru = None
-    if fmt == 'auto':
-        stru, fmt = loadStructureFile(strufile)
-        pd['fmt'] = fmt
-    # if fmt is recognized by the viewer, use as is
-    if fmt in pd['formats'] and pd['formula'] is None:
-        import shutil
-        shutil.copyfile(strufile, tmpfile+'.tmp')
-        os.rename(tmpfile+'.tmp', tmpfile)
-        return
-    # otherwise convert to the first recognized viewer format
-    if stru is None:
-        stru = loadStructureFile(strufile, fmt)[0]
-    if pd['formula']:
-        formula = pd['formula']
-        if len(formula) != len(stru):
-            emsg = "Formula has %i atoms while structure %i" % (
-                            len(formula), len(stru) )
-            raise RuntimeError(emsg)
-        for a, el in zip(stru, formula):
-            a.element = el
-    elif format == "rawxyz":
-        for a in stru:
-            if a.element == "": a.element = "C"
-    stru.write(tmpfile+'.tmp', pd['formats'][0])
-    os.rename(tmpfile+'.tmp', tmpfile)
-    return
-
-
-def watchStructureFile(pd):
-    from time import sleep
-    strufile = pd['strufile']
-    tmpfile  = pd['tmpfile']
-    while pd['watch']:
-        if os.path.getmtime(tmpfile) < os.path.getmtime(strufile):
-            convertStructureFile(pd)
-        sleep(1)
-    return
-
-
-def cleanUp(pd):
-    if 'tmpfile' in pd:
-        os.remove(pd['tmpfile'])
-        del pd['tmpfile']
-    if 'tmpdir' in pd:
-        os.rmdir(pd['tmpdir'])
-        del pd['tmpdir']
-    return
-
-
-def parseFormula(formula):
-    """parse chemical formula and return a list of elements"""
-    # remove all blanks
-    formula = re.sub(r'\s', '', formula)
-    if not re.match('^[A-Z]', formula):
-        raise RuntimeError("InvalidFormula '%s'" % formula)
-    elcnt = re.split('([A-Z][a-z]?)', formula)[1:]
-    ellst = []
-    try:
-        for i in range(0, len(elcnt), 2):
-            el = elcnt[i]
-            cnt = elcnt[i+1]
-            cnt = (cnt == "") and 1 or int(cnt)
-            ellst.extend(cnt*[el])
-    except ValueError:
-        emsg = "Invalid formula, %r is not valid count" % elcnt[i+1]
-        raise RuntimeError(emsg)
-    return ellst
-
-
-def die(exit_status=0, pd={}):
-    cleanUp(pd)
-    sys.exit(exit_status)
-
-
-def signalHandler(signum, stackframe):
-    # revert to default handler
-    signal.signal(signum, signal.SIG_DFL)
-    if signum == signal.SIGCHLD:
-        pid, exit_status = os.wait()
-        exit_status = (exit_status >> 8) + (exit_status & 0x00ff)
-        die(exit_status, pd)
-    else:
-        die(1, pd)
-    return
-
+This module is deprecated and will be removed in version 3.1.
+"""
 
-def main():
-    import getopt
-    # default parameters
-    pd['watch'] = False
-    try:
-        opts, args = getopt.getopt(sys.argv[1:], "f:whV",
-                ["formula=", "watch", "viewer=", "formats=",
-                "help", "version"])
-    except getopt.GetoptError as errmsg:
-        print(errmsg, file=sys.stderr)
-        die(2)
-    # process options
-    for o, a in opts:
-        if o in ("-f", "--formula"):
-            try:
-                pd['formula'] = parseFormula(a)
-            except RuntimeError as msg:
-                print(msg, file=sys.stderr)
-                die(2)
-        elif o in ("-w", "--watch"):
-            pd['watch'] = True
-        elif o == "--viewer":
-            pd['viewer'] = a
-        elif o == "--formats":
-            pd['formats'] = [w.strip() for w in a.split(',')]
-        elif o in ("-h", "--help"):
-            usage()
-            die()
-        elif o in ("-V", "--version"):
-            version()
-            die()
-    if len(args) < 1:
-        usage('brief')
-        die()
-    elif len(args) > 1:
-        print("too many structure files", file=sys.stderr)
-        die(2)
-    pd['strufile'] = args[0]
-    # trap the following signals
-    signal.signal(signal.SIGHUP, signalHandler)
-    signal.signal(signal.SIGQUIT, signalHandler)
-    signal.signal(signal.SIGSEGV, signalHandler)
-    signal.signal(signal.SIGTERM, signalHandler)
-    signal.signal(signal.SIGINT, signalHandler)
-    env = os.environ.copy()
-    if os.path.basename(pd['viewer']).startswith('atomeye'):
-        env['XLIB_SKIP_ARGB_VISUALS'] = "1"
-    # try to run the thing:
-    try:
-        convertStructureFile(pd)
-        spawnargs = (pd['viewer'], pd['viewer'], pd['tmpfile'], env)
-        # load strufile in atomeye
-        if pd['watch']:
-            signal.signal(signal.SIGCLD, signalHandler)
-            os.spawnlpe(os.P_NOWAIT, *spawnargs)
-            watchStructureFile(pd)
-        else:
-            status = os.spawnlpe(os.P_WAIT, *spawnargs)
-            die(status, pd)
-    except IOError as e:
-        print("%s: %s" % (args[0], e.strerror), file=sys.stderr)
-        die(1, pd)
-    except StructureFormatError as e:
-        print("%s: %s" % (args[0], e), file=sys.stderr)
-        die(1, pd)
-    return
+# TODO remove this module in version 3.1.
 
+from diffpy.structure.apps.anyeye import main
 
 if __name__ == "__main__":
     main()