Tweak metadata and fix pip install

stefsmeets · Feb 15, 2023 · 7c1509e · 7c1509e
1 parent 12e9c57
commit 7c1509e
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Showing 4 changed files with 229 additions and 235 deletions.
diff --git a/CITATION.cff b/CITATION.cff
@@ -13,9 +13,9 @@ keywords:
     - "Topas"
     - "Structure refinement"
     - "Profile refinement"
-license: "GPL-2.0"
+license: "MIT"
 message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/stefsmeets/topas_tools"
 title: topas_tools
-version: "1.0.0"
+version: "1.0.1"
 ...
diff --git a/setup.cfg b/setup.cfg
@@ -25,7 +25,7 @@ project_urls =
     Bug Tracker = https://github.com/stefsmeets/topas_tools/issues
     Documentation = https://github.com/stefsmeets/topas_tools
 url = https://github.com/stefsmeets/topas_tools
-version = 1.0.0
+version = 1.0.1
 
 
 [options]
@@ -52,9 +52,9 @@ console_scripts =
   topasrestraints = topas_tools.topas_restraints:main
   topas_ndxan = topas_tools.topas_ndxan:main
   restraints_statistics = topas_tools.restraints_statistics:main
-  cif2patterson = topas_tools.cif2patterson
+  cif2patterson = topas_tools.cif2patterson:main
   cif2topas = topas_tools.cif2topas:main
-  expandcell = topas_tools.expandcell
+  expandcell = topas_tools.expandcell:main
   stripcif = topas_tools.stripcif:main
   topasdiff = topas_tools.topasdiff:main
   make_superflip = topas_tools.make_superflip:main

diff --git a/topas_tools/cif2patterson.py b/topas_tools/cif2patterson.py
@@ -24,90 +24,88 @@ def read_cif(f):
         val.show_summary().show_scatterers()
     return structures
 
+def main():
+    usage = """cif2patterson structure.cif"""
 
-usage = """cif2patterson structure.cif"""
+    description = """Notes: Takes any cif file and generated patterson map
+    """
 
-description = """Notes: Takes any cif file and generated patterson map
-"""
+    parser = argparse.ArgumentParser(  # usage=usage,
+        description=description,
+        formatter_class=argparse.RawDescriptionHelpFormatter)
 
-parser = argparse.ArgumentParser(  # usage=usage,
-    description=description,
-    formatter_class=argparse.RawDescriptionHelpFormatter)
 
+    parser.add_argument("args",
+                        type=str, metavar="FILE",
+                        help="Path to input cif")
 
-parser.add_argument("args",
-                    type=str, metavar="FILE",
-                    help="Path to input cif")
 
+    parser.set_defaults(
+        spgr="P1"
+    )
 
-parser.set_defaults(
-    spgr="P1"
-)
+    options = parser.parse_args()
 
-options = parser.parse_args()
+    cif = options.args
+    s = list(read_cif(cif).values())[0]
+    s = s.expand_to_p1()
+    print(f"Expanded to P1 => {s.scatterers().size()} atoms")
+    print()
 
-cif = options.args
-s = list(read_cif(cif).values())[0]
-s = s.expand_to_p1()
-print(f"Expanded to P1 => {s.scatterers().size()} atoms")
-print()
+    root, ext = os.path.splitext(cif)
 
-root, ext = os.path.splitext(cif)
+    uc = s.unit_cell()
 
-uc = s.unit_cell()
+    scatterers = s.scatterers()
 
-scatterers = s.scatterers()
+    fout1 = open("patterson_dists.txt", 'w')
+    fout2 = open("patterson_full.txt", 'w')
 
-fout1 = open("patterson_dists.txt", 'w')
-fout2 = open("patterson_full.txt", 'w')
+    distances_all = []
 
-distances_all = []
+    verbose = False
+    for atom1 in scatterers:
+        x1, y1, z1 = atom1.site
 
-verbose = False
-for atom1 in scatterers:
-    x1, y1, z1 = atom1.site
-
-    if verbose:
-        print()
-        atom1.show()
-    distances = []
-    for atom2 in scatterers:
         if verbose:
-            atom2.show()
-
-        x2, y2, z2 = atom2.site
+            print()
+            atom1.show()
+        distances = []
+        for atom2 in scatterers:
+            if verbose:
+                atom2.show()
 
-        dx, dy, dz = x1-x2, y1-y2, z1-z2
+            x2, y2, z2 = atom2.site
 
-        dx = dx % 1
-        dy = dy % 1
-        dz = dz % 1
+            dx, dy, dz = x1-x2, y1-y2, z1-z2
 
-        length = uc.length((dx, dy, dz))
+            dx = dx % 1
+            dy = dy % 1
+            dz = dz % 1
 
-        distances.append((atom2.label, dx, dy, dz, length))
+            length = uc.length((dx, dy, dz))
 
-        if verbose:
-            print(f' --> {atom2.label:>4s} {dx:9.5f} {dy:9.5f} {dz:9.5f}  {length:9.5f}')
+            distances.append((atom2.label, dx, dy, dz, length))
 
-        # print atom1.label, '-->', atom2.label, '=', uc.length((dx,dy,dz))
+            if verbose:
+                print(f' --> {atom2.label:>4s} {dx:9.5f} {dy:9.5f} {dz:9.5f}  {length:9.5f}')
 
-    distances_all.extend(distances)
+            # print atom1.label, '-->', atom2.label, '=', uc.length((dx,dy,dz))
 
-    atom1.show(fout2)
-    for label, dx, dy, dz, distance in sorted(distances, key=lambda x: x[-1]):
-        print(' --> {:>4s} {:9.5f} {:9.5f} {:9.5f}  {:9.5f}'.format(
-            label, dx, dy, dz, distance), file=fout2)
-    print(file=fout2)
+        distances_all.extend(distances)
 
-print('Wrote file', fout2.name)
+        atom1.show(fout2)
+        for label, dx, dy, dz, distance in sorted(distances, key=lambda x: x[-1]):
+            print(' --> {:>4s} {:9.5f} {:9.5f} {:9.5f}  {:9.5f}'.format(
+                label, dx, dy, dz, distance), file=fout2)
+        print(file=fout2)
 
-for label, dx, dy, dz, distance in sorted(distances_all, key=lambda x: x[-1]):
-    print(f'{distance:9.5f}', file=fout1)
+    print('Wrote file', fout2.name)
 
-print('Wrote file', fout1.name)
+    for label, dx, dy, dz, distance in sorted(distances_all, key=lambda x: x[-1]):
+        print(f'{distance:9.5f}', file=fout1)
 
-fout1.close()
-fout2.close()
+    print('Wrote file', fout1.name)
 
-sys.exit()
+    fout1.close()
+    fout2.close()