Merge branch 'develop' into update-test-paths

Author: brockdyer03

nexus/nexus/basisset.py

@@ -154,6 +154,7 @@ def read(self,filepath=None):
         #end if
         file = TextFile(filepath)
         self.read_file(file)
+        file.close()
     #end def read
 
     def read_file(self,file):
@@ -319,7 +320,8 @@ def read(self,filepath,format=None):
         #end if
         #self.name = split_delims(os.path.split(filepath)[1])[0]
         self.name = os.path.split(filepath)[1].split('.')[0]
-        text = open(filepath,'r').read()
+        with open(filepath, "r") as f:
+            text = f.read()
         self.read_text(text,format)
     #end def read
 

nexus/nexus/bin/eshdf

@@ -6,6 +6,16 @@ import sys
 from pathlib import Path
 from optparse import OptionParser
 
+if sys.version_info[0:3] < (3, 10, 0):
+    v = sys.version_info[0:3]
+    print(
+       f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n"
+        "To use Nexus, please install at least Python 3.10.0 or higher!\n\n"
+        "If you already have a higher version installed, ensure that your Python\n"
+        "environment is properly activated and your $PATH is set correctly."
+    )
+    sys.exit(1)
+
 # Non-standard Python library imports
 import numpy as np
 

nexus/nexus/bin/nxs-redo

@@ -1,9 +1,20 @@
 #! /usr/bin/env python3
 
 import os
+import sys
 from pathlib import Path
 from optparse import OptionParser
 
+if sys.version_info[0:3] < (3, 10, 0):
+    v = sys.version_info[0:3]
+    print(
+       f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n"
+        "To use Nexus, please install at least Python 3.10.0 or higher!\n\n"
+        "If you already have a higher version installed, ensure that your Python\n"
+        "environment is properly activated and your $PATH is set correctly."
+    )
+    sys.exit(1)
+
 # Copied from qmca. Modification must done on qmca first
 # Locate and import the closely coupled Nexus module
 search_basepath = Path(__file__).resolve().parent.parent

nexus/nexus/bin/nxs-sim

@@ -1,9 +1,20 @@
 #! /usr/bin/env python3
 
 import os
+import sys
 from pathlib import Path
 from optparse import OptionParser
 
+if sys.version_info[0:3] < (3, 10, 0):
+    v = sys.version_info[0:3]
+    print(
+       f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n"
+        "To use Nexus, please install at least Python 3.10.0 or higher!\n\n"
+        "If you already have a higher version installed, ensure that your Python\n"
+        "environment is properly activated and your $PATH is set correctly."
+    )
+    sys.exit(1)
+
 # Copied from qmca. Modification must done on qmca first
 # Locate and import the closely coupled Nexus module
 search_basepath = Path(__file__).resolve().parent.parent

nexus/nexus/bin/nxs-test

@@ -12,6 +12,16 @@ for development.
 
 import sys
 
+if sys.version_info[0:3] < (3, 10, 0):
+    v = sys.version_info[0:3]
+    print(
+       f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n"
+        "To use Nexus, please install at least Python 3.10.0 or higher!\n\n"
+        "If you already have a higher version installed, ensure that your Python\n"
+        "environment is properly activated and your $PATH is set correctly."
+    )
+    sys.exit(1)
+
 try:
     import pytest
 except ImportError:

nexus/nexus/bin/qdens

@@ -2,9 +2,20 @@
 
 import gc
 import os
+import sys
 from pathlib import Path
 from optparse import OptionParser
 
+if sys.version_info[0:3] < (3, 10, 0):
+    v = sys.version_info[0:3]
+    print(
+       f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n"
+        "To use Nexus, please install at least Python 3.10.0 or higher!\n\n"
+        "If you already have a higher version installed, ensure that your Python\n"
+        "environment is properly activated and your $PATH is set correctly."
+    )
+    sys.exit(1)
+
 # Copied from qmca. Modification must done on qmca first
 # Locate and import the closely coupled Nexus module
 search_basepath = Path(__file__).resolve().parent.parent

nexus/nexus/bin/qdens-radial

@@ -2,6 +2,17 @@
 
 from pathlib import Path
 from optparse import OptionParser
+import sys
+
+if sys.version_info[0:3] < (3, 10, 0):
+    v = sys.version_info[0:3]
+    print(
+       f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n"
+        "To use Nexus, please install at least Python 3.10.0 or higher!\n\n"
+        "If you already have a higher version installed, ensure that your Python\n"
+        "environment is properly activated and your $PATH is set correctly."
+    )
+    sys.exit(1)
 
 # Copied from qmca. Modification must done on qmca first
 # Locate and import the closely coupled Nexus module

nexus/nexus/bin/qmc-fit

@@ -5,6 +5,16 @@ import sys
 import argparse
 from pathlib import Path
 
+if sys.version_info[0:3] < (3, 10, 0):
+    v = sys.version_info[0:3]
+    print(
+       f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n"
+        "To use Nexus, please install at least Python 3.10.0 or higher!\n\n"
+        "If you already have a higher version installed, ensure that your Python\n"
+        "environment is properly activated and your $PATH is set correctly."
+    )
+    sys.exit(1)
+
 try:
     import numpy as np
 except:

nexus/nexus/bin/qmca

@@ -5,6 +5,15 @@ from pathlib import Path
 import sys
 from optparse import OptionParser
 
+if sys.version_info[0:3] < (3, 10, 0):
+    v = sys.version_info[0:3]
+    print(
+       f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n"
+        "To use Nexus, please install at least Python 3.10.0 or higher!\n\n"
+        "If you already have a higher version installed, ensure that your Python\n"
+        "environment is properly activated and your $PATH is set correctly."
+    )
+    sys.exit(1)
 
 # Gold implementation. All the Nexus scripts need to be updated once modified.
 # Locate and import the closely coupled Nexus module

nexus/nexus/fileio.py

@@ -30,6 +30,7 @@
 from .periodic_table import Elements
 from .unit_converter import convert
 from . import numpy_extensions as npe
+from .utilities import path_string
 
 class TextFile(DevBase):
     # interface to mmap files
@@ -39,11 +40,13 @@ def __init__(self,filepath=None):
         self.mm = None
         self.f  = None
         if filepath is not None:
+            filepath = path_string(filepath)
             self.open(filepath)
         #end if
     #end def __init__
 
     def open(self,filepath):
+        filepath = path_string(filepath)
         if not os.path.exists(filepath):
             self.error('cannot open non-existent file: {0}'.format(filepath))
         #end if
@@ -243,7 +246,8 @@ class StandardFile(DevBase):
     def __init__(self,filepath=None):
         if filepath is None:
             None
-        elif isinstance(filepath, (str, Path)):
+        elif isinstance(filepath, str | bytes | Path):
+            filepath = path_string(filepath)
             self.read(filepath)
         else:
             self.error('unsupported input: {0}'.format(filepath))
@@ -255,7 +259,9 @@ def read(self,filepath):
         if not os.path.exists(filepath):
             self.error('read failed\nfile does not exist: {0}'.format(filepath))
         #end if
-        self.read_text(open(filepath,'r').read())
+        with open(filepath, "r") as f:
+            self.read_text(f.read())
+
         self.check_valid('read failed')
     #end def read
 
@@ -264,7 +270,8 @@ def write(self,filepath=None):
         self.check_valid('write failed')
         text = self.write_text()
         if filepath is not None:
-            open(filepath,'w').write(text)
+            with open(filepath, "w") as f:
+                f.write(text)
         #end if
         return text
     #end def write