new zip file script and python3 fixes

dbfile.py

@@ -357,7 +357,9 @@ def __iter__(self):
         >>> [x for x in db][:3]
         ['napht', 'plusminus', 'fluorbenz']
         """
-        return iter(self.databases.keys())
+        # return iter(self.databases.keys()) #python2
+        return iter(list(self.databases.keys()))
+
 
     def list_fragments(self):
         # type: () -> list

elements.py

@@ -210,7 +210,7 @@ def nominalmass(self):
         """Return mass number of most abundant natural stable isotope."""
         nominalmass = 0
         maxabundance = 0
-        for massnum, iso in self.isotopes.items():
+        for massnum, iso in list(self.isotopes.items()):
             if iso.abundance > maxabundance:
                 maxabundance = iso.abundance
                 nominalmass = massnum
@@ -224,7 +224,7 @@ def neutrons(self):
     @lazyattr
     def exactmass(self):
         """Return relative atomic mass calculated from isotopic composition."""
-        return sum(iso.mass * iso.abundance for iso in self.isotopes.values())
+        return sum(iso.mass * iso.abundance for iso in list(self.isotopes.values()))
 
     @lazyattr
     def eleconfig_dict(self):
@@ -241,7 +241,7 @@ def eleconfig_dict(self):
     def eleshells(self):
         """Return number of electrons in shell as tuple."""
         eleshells = [0, 0, 0, 0, 0, 0, 0]
-        for key, val in self.eleconfig_dict.items():
+        for key, val in list(self.eleconfig_dict.items()):
             eleshells[key[0] - 1] += val
         return tuple(ele for ele in eleshells if ele)
 
@@ -266,7 +266,7 @@ def validate(self):
 
         mass = 0.0
         frac = 0.0
-        for iso in self.isotopes.values():
+        for iso in list(self.isotopes.values()):
             mass += iso.abundance * iso.mass
             frac += iso.abundance
         if abs(mass - self.mass) > 0.03:

misc.py

@@ -103,6 +103,42 @@ def check_file_exist(filename):
     return status
 
 
+def walkdir(rootdir, include="", exclude=""):
+    """
+    Returns a list of files in all subdirectories with full path.
+    :param rootdir: base path from which walk should start
+    :param filter: list of file endings to include only e.g. ['.py', '.res']
+    :return: list of files
+
+    >>> walkdir("./setup/debian-package") #doctest: +REPORT_NDIFF +NORMALIZE_WHITESPACE +ELLIPSIS
+    ['./setup/debian-package/.DS_Store', './setup/debian-package/howto.txt',
+    './setup/debian-package/DEBIAN/postinst', './setup/debian-package/DEBIAN/control']
+    >>> walkdir("./modpath.iss")
+    ['./modpath.iss']
+    >>> walkdir("./modpath.iss", exclude=['.iss'])
+    []
+    >>> walkdir("./setup/debian-package", exclude=['.txt']) #doctest: +REPORT_NDIFF +NORMALIZE_WHITESPACE +ELLIPSIS
+    ['./setup/debian-package/.DS_Store',
+    './setup/debian-package/DEBIAN/postinst', './setup/debian-package/DEBIAN/control']
+    """
+    results = []
+    if not os.path.isdir(rootdir):
+        if os.path.splitext(rootdir)[1] in exclude:
+            return []
+        return [rootdir]
+    for root, subFolders, files in os.walk(rootdir):
+        for file in files:
+            fullfilepath = os.path.join(root, file)
+            if exclude:
+                if os.path.splitext(fullfilepath)[1] in exclude:
+                    continue
+            if include:
+                if os.path.splitext(fullfilepath)[1] in include:
+                    results.append(fullfilepath)
+            else:
+                results.append(fullfilepath)
+    return results
+
 def pairwise(iterable):
     """
      s -> (s0,s1), (s2,s3), (s4, s5), ...

scripts/mac_package.py

@@ -4,7 +4,6 @@
 import misc
 import selfupdate
 
-
 try:  # Python2:
     # noinspection PyCompatibility
     import urllib2
@@ -13,10 +12,10 @@
     import urllib
     http_error = IOError
 
-version = "205"  # define the .dmg release version
+version = "207"  # define the .dmg release version
 
 volname = "DSR-"+version
-inputfile = "/Users/daniel/Downloads/DSR-{}.tar.gz".format(version, version)
+inputfile = "../setup/Output/DSR-{}.tar.gz".format(version, version)
 dmgname = os.path.abspath("../setup/Output/{}.dmg".format(volname))
 skeldmg = os.path.abspath("../setup/Output/DSR-skel-rw.dmg")
 finaltmpdmg = os.path.abspath("../setup/Output/DSR-tmp-rw.dmg")
@@ -33,7 +32,7 @@
 subprocess.Popen(unmountcommmand, stderr=subprocess.PIPE)
 
 print('Mounting .dmg file for mac deployment')
-print(finaltmpdmg+"\n")
+print('Mounting: ', finaltmpdmg, '\n')
 subprocess.call(mountcommmand)
 
 """
@@ -52,7 +51,7 @@
 # use instead of webserver stuff above
 tmpdir = tempfile.mkdtemp()  # a temporary directory
 misc.extract_tarfile(inputfile, tmpdir)
-selfupdate.move_dir(tmpdir+"/DSR-{}".format(version), '/Volumes/DSR-install/DSR')
+selfupdate.move_dir(os.path.join(tmpdir, "DSR-{}".format(version)), '/Volumes/DSR-install/DSR/')
 # end
 
 #########################################################

setup/make_zipfile.py

@@ -0,0 +1,75 @@
+"""
+Creates a zip file with the content of the StructureDB program.
+"""
+from tarfile import TarFile
+
+import os
+
+from dsr import VERSION
+from misc import copy_file, remove_file, walkdir
+
+version = VERSION
+
+files = [
+    "afix.py",
+    "README",
+    "atomhandling.py",
+    "atoms.py",
+    "constants.py",
+    "dbfile.py",
+    "dsr.py",
+    "dsrparse.py",
+    "export.py",
+    "misc.py",
+    "elements.py",
+    "options.py",
+    "resfile.py",
+    "restraints.py",
+    "cf3fit.py",
+    "selfupdate.py",
+    "terminalsize.py",
+    "resi.py",
+    "refine.py",
+    "pyperclip.py",
+    "dsr_db.txt",
+    "manuals/DSR-manual.pdf",
+    "setup/dsr.sh",
+    "setup/dsr-mac",
+    "setup/dsr-linux",
+    "dsr",
+    "example/p21c.hkl",
+    "example/p21c.res",
+    "example/p21c_step0.res",
+    "example/p21c_step1.res",
+    "example/p21c_step2.ins",
+    "example/p21c_step3.res",
+    "example/p21c_final.res",
+    "example/p21n_cf3.hkl",
+    "example/p21n_cf3.res",
+    "networkx",
+    "mpmath"
+    ]
+
+
+def make_zip(filelist):
+    """
+    :type filelist: list
+    """
+    os.chdir('../')
+    zipfilen = 'setup/Output/DSR-{}.tar.gz'.format(version)
+    remove_file(zipfilen)
+    with TarFile(zipfilen, mode='w') as myzip:
+        for f in filelist:
+            print("Adding {}".format(f))
+            for file in walkdir(f, exclude=['.pyc']):
+                try:
+                    myzip.add(file)
+                except FileNotFoundError as e:
+                    print(e)
+                    print("#####################")
+                    return False
+    #copy_file(zipfilen, 'StructureFinder/scripts/Output/')
+    print("File written to {}".format(zipfilen))
+
+if __name__ == "__main__":
+    make_zip(files)

sql_export.py

@@ -168,7 +168,7 @@ def get_picture(name):
 
 
 def export_database():
-    for fid, fragment in enumerate(db.keys(), 1):
+    for fid, fragment in enumerate(list(db.keys()), 1):
         Name = gl.get_fragment_name(fragment)
         print("Exporting {}: {}: {}".format(fid, fragment, Name))
         head = db[fragment]['restraints']