Initial copy of commit 5ed0da5 of arbdmodel package

https://gitlab.engr.illinois.edu/tbgl/tools/arbdmodel

mrdna/arbdmodel/LICENSE

+../LICENSE
\ No newline at end of file

mrdna/arbdmodel/README.md

+../README.md
\ No newline at end of file

mrdna/arbdmodel/__init__.py

 # -*- coding: utf-8 -*-
-import abc
+from pathlib import Path
+
+from .version import get_version
+__version__ = get_version() 
+
 import numpy as np
 from copy import copy, deepcopy
 from inspect import ismethod
-
-# from datetime import datetime
-# from math import pi,sqrt,exp,floor
-# from scipy.special import erf
-# import scipy.optimize as opt
 import os, sys, subprocess
 
 
@@ -1175,3 +1174,4 @@ run {num_steps:d}
         self.writePsf( output_name + ".psf" )
         self.write_namd_configuration( output_name, output_directory = output_directory )
         os.sync()
+

mrdna/arbdmodel/version.py

+# -*- coding: utf-8 -*-
+# Author: Douglas Creager <dcreager@dcreager.net>
+# This file is placed into the public domain.
+
+# Calculates the current version number.  If possible, this is the
+# output of “git describe”, modified to conform to the versioning
+# scheme that setuptools uses.  If “git describe” returns an error
+# (most likely because we're in an unpacked copy of a release tarball,
+# rather than in a git working copy), then we fall back on reading the
+# contents of the RELEASE-VERSION file.
+#
+# To use this script, simply import it your setup.py file, and use the
+# results of get_git_version() as your package version:
+#
+# from version import *
+#
+# setup(
+#     version=get_git_version(),
+#     .
+#     .
+#     .
+# )
+#
+#
+# This will automatically update the RELEASE-VERSION file, if
+# necessary.  Note that the RELEASE-VERSION file should *not* be
+# checked into git; please add it to your top-level .gitignore file.
+#
+# You'll probably want to distribute the RELEASE-VERSION file in your
+# sdist tarballs; to do this, just create a MANIFEST.in file that
+# contains the following line:
+#
+#   include RELEASE-VERSION
+
+__all__ = ("get_version")
+
+from pathlib import Path
+import subprocess
+from subprocess import Popen, PIPE
+
+_version_file = Path(__file__).parent / "RELEASE-VERSION"
+
+
+def check_git_repository():
+    try:
+        remotes = subprocess.check_output(['git', 'remote', '-v'], stderr=subprocess.STDOUT)
+        return b'arbdmodel.git' in remotes
+    except:
+        return False   
+
+def call_git_describe(abbrev):
+    try:
+        p = Popen(['git', 'describe', '--tags', '--abbrev=%d' % abbrev],
+                  stdout=PIPE, stderr=PIPE)
+        p.stderr.close()
+        line = p.stdout.readlines()[0]
+        return line.strip().decode('utf-8')
+
+    except:
+        return None
+
+
+def is_dirty():
+    try:
+        p = Popen(["git", "diff-index", "--name-only", "HEAD"],
+                  stdout=PIPE, stderr=PIPE)
+        p.stderr.close()
+        lines = p.stdout.readlines()
+        return len(lines) > 0
+    except:
+        return False
+
+
+def read_release_version():
+    try:
+        f = open(_version_file, "r")
+
+        try:
+            version = f.readlines()[0]
+            return version.strip()
+
+        finally:
+            f.close()
+
+    except:
+        return None
+
+
+def write_release_version(version):
+    f = open(_version_file, "w")
+    f.write("%s\n" % version)
+    f.close()
+
+def get_version(abbrev=7):
+    # Read in the version that's currently in RELEASE-VERSION.
+
+    
+    release_version = read_release_version()
+
+    if not check_git_repository():
+        return release_version
+        # raise Exception(__function__ +" called from outside a version controlled source repository")
+
+
+    # First try to get the current version using “git describe”.
+
+    split_version = call_git_describe(abbrev).split("-")
+    version = split_version[0]
+    if len(split_version) > 1 and int(split_version[-2]) > 0:
+        version += ".dev{}".format(int(split_version[-2]))
+
+
+    # If that doesn't work, fall back on the value that's in
+    # RELEASE-VERSION.
+
+    if version is None:
+        version = release_version
+
+    # If we still don't have anything, that's an error.
+
+    if version is None:
+        raise ValueError("Cannot find the version number!")
+
+    # If the current version is different from what's in the
+    # RELEASE-VERSION file, update the file to be current.
+
+    if version != release_version:
+        write_release_version(version)
+
+    # Finally, return the current version.
+
+    return version
+
+
+if __name__ == "__main__":
+    print( get_version() )
+
+def read_version_file(filename):
+    with open(filename) as fh:
+        version = fh.readlines()[0].strip()
+    return version
+        
+
+try:
+    version = read_version_file(_version_file)
+except:
+    try:
+        version = read_version_file(_version_file)
+    except:
+        version = "Unknown"