Fixed formatting errors, and wrong path in _version.py.

.gitignore

@@ -1,8 +1,85 @@
+# -*- mode: gitignore; -*-
+
+## emacs: https://github.com/github/gitignore/blob/master/Global/Emacs.gitignore
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+dist/
+
+# Flycheck
+flycheck_*.el
+
+# server auth directory
+/server/
+
+# projectiles files
+.projectile
+
+# directory configuration
+.dir-locals.el
+
+# network security
+/network-security.data
+## end of emacs
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
 
+## macOS useful to ignore https://github.com/github/gitignore/blob/master/Global/macOS.gitignore
+*.DS_Store
+.AppleDouble
+.LSOverride
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+## end of macOS
+
 # C extensions
 *.so
 
@@ -55,8 +132,18 @@ coverage.xml
 # Sphinx documentation
 docs/_build/
 
+# IntelliJ Idea family of suites
+.idea
+*.iml
+## File-based project format:
+*.ipr
+*.iws
+## mpeltonen/sbt-idea plugin
+.idea_modules/
+
 # PyBuilder
 target/
 
-# pyenv python configuration file
-.python-version
+# Cookiecutter
+output/
+python_boilerplate/

.yapfignore

@@ -0,0 +1,2 @@
+setup.py
+seamm_util/_version.py

seamm_util/_version.py

@@ -1,4 +1,3 @@
-
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -43,7 +42,7 @@ def get_config():
     cfg.style = "pep440"
     cfg.tag_prefix = ""
     cfg.parentdir_prefix = "None"
-    cfg.versionfile_source = "packmol_step/_version.py"
+    cfg.versionfile_source = "seamm_util/_version.py"
     cfg.verbose = False
     return cfg
 
@@ -58,28 +57,34 @@ class NotThisMethod(Exception):
 
 def register_vcs_handler(vcs, method):  # decorator
     """Decorator to mark a method as the handler for a particular VCS."""
+
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
             HANDLERS[vcs] = {}
         HANDLERS[vcs][method] = f
         return f
+
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
+def run_command(
+    commands, args, cwd=None, verbose=False, hide_stderr=False, env=None
+):
     """Call the given command(s)."""
     assert isinstance(commands, list)
     p = None
     for c in commands:
         try:
             dispcmd = str([c] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
-                                 stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
+            p = subprocess.Popen(
+                [c] + args,
+                cwd=cwd,
+                env=env,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None)
+            )
             break
         except EnvironmentError:
             e = sys.exc_info()[1]
@@ -116,16 +121,22 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     for i in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
+            return {
+                "version": dirname[len(parentdir_prefix):],
+                "full-revisionid": None,
+                "dirty": False,
+                "error": None,
+                "date": None
+            }
         else:
             rootdirs.append(root)
             root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print("Tried directories %s but none started with prefix %s" %
-              (str(rootdirs), parentdir_prefix))
+        print(
+            "Tried directories %s but none started with prefix %s" %
+            (str(rootdirs), parentdir_prefix)
+        )
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -201,16 +212,23 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
             r = ref[len(tag_prefix):]
             if verbose:
                 print("picking %s" % r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+                "date": date
+            }
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+        "date": None
+    }
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
@@ -225,19 +243,23 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                          hide_stderr=True)
+    out, rc = run_command(
+        GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True
+    )
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
         raise NotThisMethod("'git rev-parse --git-dir' returned error")
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
-                                          "--always", "--long",
-                                          "--match", "%s*" % tag_prefix],
-                                   cwd=root)
+    describe_out, rc = run_command(
+        GITS, [
+            "describe", "--tags", "--dirty", "--always", "--long", "--match",
+            "%s*" % tag_prefix
+        ],
+        cwd=root
+    )
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
@@ -269,8 +291,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
+            pieces["error"] = (
+                "unable to parse git-describe output: '%s'" % describe_out
+            )
             return pieces
 
         # tag
@@ -279,8 +302,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
+            pieces["error"] = (
+                "tag '%s' doesn't start with prefix '%s'" %
+                (full_tag, tag_prefix)
+            )
             return pieces
         pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
@@ -293,8 +318,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                    cwd=root)
+        count_out, rc = run_command(
+            GITS, ["rev-list", "HEAD", "--count"], cwd=root
+        )
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
@@ -330,8 +356,7 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -445,11 +470,13 @@ def render_git_describe_long(pieces):
 def render(pieces, style):
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+            "date": None
+        }
 
     if not style or style == "default":
         style = "pep440"  # the default
@@ -469,9 +496,13 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+        "date": pieces.get("date")
+    }
 
 
 def get_versions():
@@ -485,8 +516,9 @@ def get_versions():
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
-                                          verbose)
+        return git_versions_from_keywords(
+            get_keywords(), cfg.tag_prefix, verbose
+        )
     except NotThisMethod:
         pass
 
@@ -498,10 +530,13 @@ def get_versions():
         for i in cfg.versionfile_source.split('/'):
             root = os.path.dirname(root)
     except NameError:
-        return {"version": "0+unknown", "full-revisionid": None,
-                "dirty": None,
-                "error": "unable to find root of source tree",
-                "date": None}
+        return {
+            "version": "0+unknown",
+            "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to find root of source tree",
+            "date": None
+        }
 
     try:
         pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
@@ -515,6 +550,10 @@ def get_versions():
     except NotThisMethod:
         pass
 
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to compute version", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+        "date": None
+    }