Set up versioneer (mdtraj#1909)

* Set up versioneer

* remove pdb version import

* remove all from mdtraj import veresion errors

* try import version later

* xyz mdtraj.version

* typo

* use mdtraj._version instead

* use mdtraj.__version__

* Skip un-used version check in docs

* Help sphinx along

---------

Co-authored-by: Jeremy M. G. Leung <[email protected]>

.gitattributes

@@ -0,0 +1 @@
+mdtraj/_version.py export-subst

basesetup.py

@@ -272,41 +272,6 @@ def _minimal_ext_cmd(cmd):
     return GIT_REVISION
 
 
-def write_version_py(version, isreleased, filename):
-    cnt = """
-# This file is generated in setup.py at build time.
-version = '{version}'
-short_version = '{short_version}'
-full_version = '{full_version}'
-git_revision = '{git_revision}'
-release = {release}
-"""
-    # git_revision
-    if os.path.exists(".git"):
-        git_revision = git_version()
-    else:
-        git_revision = "Unknown"
-
-    # short_version, full_version
-    if isreleased:
-        full_version = version
-        short_version = version
-    else:
-        full_version = f"{version}+{git_revision}"
-        short_version = version
-
-    with open(filename, "w") as f:
-        f.write(
-            cnt.format(
-                version=version,
-                short_version=short_version,
-                full_version=full_version,
-                git_revision=git_revision,
-                release=isreleased,
-            ),
-        )
-
-
 def copy_same_file_pass(source, destination):
     try:
         # Try to copy

docs/conf.py

@@ -18,7 +18,7 @@
 import msmb_theme
 import sphinx_rtd_theme
 
-import mdtraj.version
+from mdtraj import __version__
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -37,12 +37,12 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.mathjax",
-    'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
     "numpydoc",
     "notebook_sphinxext",
     "nbsphinx",
-    "nbsphinx_link"
+    "nbsphinx_link",
 ]
 
 autosummary_generate = True
@@ -70,10 +70,11 @@
 # built documents.
 #
 
+# versions which Sphinx uses for default html_title
 # The short X.Y version.
-version = mdtraj.version.short_version
+version = __version__
 # The full version, including alpha/beta/rc tags.
-release = mdtraj.version.version
+release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -115,12 +116,12 @@
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
 # keep_warnings = False
- 
+
 # -- Options for NBsphinx --------------------------------------------------
 
 # nbsphinx specific options
 nbsphinx_allow_errors = True  # Continue through Jupyter errors
-nbsphinx_execute = 'never'  # Never execute cells
+nbsphinx_execute = "never"  # Never execute cells
 
 
 # -- Options for HTML output ----------------------------------------------
@@ -334,4 +335,4 @@
     __ https://github.com/mdtraj/mdtraj/tree/master/
         """
     + r"{{ docpath }}"
-)
+)

mdtraj/__init__.py

@@ -116,6 +116,10 @@
 from ._lprmsd import lprmsd
 from ._rmsd import rmsd, rmsf
 
+from . import _version
+
+__version__ = _version.get_versions()["version"]
+
 __all__ = (
     "reporters",
     "lprmsd",