skpkg: linelength fixes and some copyright updates

Author: cadenmyers13

doc/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# diffpy.pdffit2 documentation build configuration file, created by
+# diffpy.pdffit2 documentation build configuration file, created by  # noqa: E501
 # sphinx-quickstart on Thu Jan 30 15:49:41 2014.
 #
 # This file is execfile()d with the current directory set to its
@@ -18,6 +18,12 @@
 from importlib.metadata import version
 from pathlib import Path
 
+# Attempt to import the version dynamically from GitHub tag.
+try:
+    fullversion = version("diffpy.pdffit2")
+except Exception:
+    fullversion = "No version found. The correct version will appear in the released 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
 # documentation root, use Path().resolve() to make it absolute, like shown here.
@@ -26,7 +32,7 @@
 sys.path.insert(0, str(Path("../../src").resolve()))
 
 # abbreviations
-ab_authors = "Billinge Group members and community contributors"
+ab_authors = "Billinge group and community members."
 
 # -- General configuration ------------------------------------------------
 
@@ -43,6 +49,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
     "sphinx_rtd_theme",
+    "sphinx_copybutton",
     "m2r",
 ]
 
@@ -88,6 +95,11 @@
 # substitute YEAR in the copyright string
 copyright = copyright.replace("%Y", year)
 
+# For sphinx_copybutton extension.
+# Do not copy "$" for shell commands in code-blocks.
+copybutton_prompt_text = r"^\$ "
+copybutton_prompt_is_regexp = True
+
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = ["build"]
@@ -123,6 +135,14 @@
 #
 html_theme = "sphinx_rtd_theme"
 
+html_context = {
+    "display_github": True,
+    "github_user": "diffpy",
+    "github_repo": "diffpy.pdffit2",
+    "github_version": "main",
+    "conf_py_path": "/doc/source/",
+}
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
@@ -221,7 +241,13 @@
 # (source start file, target name, title,
 # author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ("index", "diffpy.pdffit2.tex", "diffpy.pdffit2 Documentation", ab_authors, "manual"),
+    (
+        "index",
+        "diffpy.pdffit2.tex",
+        "diffpy.pdffit2 Documentation",
+        ab_authors,
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -249,7 +275,15 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "diffpy.pdffit2", "diffpy.pdffit2 Documentation", ab_authors, 1)]
+man_pages = [
+    (
+        "index",
+        "diffpy.pdffit2",
+        "diffpy.pdffit2 Documentation",
+        ab_authors,
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False

src/diffpy/pdffit2/pdffit.py

@@ -138,7 +138,8 @@ def _exportAll(self, namespace):
         public = [
             a
             for a in dir(self)
-            if "__" not in a and a not in ["_handle", "_exportAll", "selalias", "FCON", "Sctp"]
+            if "__" not in a
+            and a not in ["_handle", "_exportAll", "selalias", "FCON", "Sctp"]
         ]
         for funcname in public:
             namespace[funcname] = getattr(self, funcname)
@@ -234,12 +235,16 @@ def read_data_string(self, data, stype, qmax, qdamp, name=""):
         qdamp   -- instrumental Q-resolution factor
         name    -- tag with which to label data
         """
-        pdffit2.read_data_string(self._handle, data, stype.encode(), qmax, qdamp, name)
+        pdffit2.read_data_string(
+            self._handle, data, stype.encode(), qmax, qdamp, name
+        )
         name = data
         self.data_files.append(name)
         return
 
-    def read_data_lists(self, stype, qmax, qdamp, r_data, Gr_data, dGr_data=None, name="list"):
+    def read_data_lists(
+        self, stype, qmax, qdamp, r_data, Gr_data, dGr_data=None, name="list"
+    ):
         """read_data_lists(stype, qmax, qdamp, r_data, Gr_data, dGr_data =
         None, name = "list") --> Read pdf data into memory from lists.
 
@@ -255,7 +260,16 @@ def read_data_lists(self, stype, qmax, qdamp, r_data, Gr_data, dGr_data=None, na
 
         Raises: ValueError when the data lists are of different length
         """
-        pdffit2.read_data_arrays(self._handle, stype.encode(), qmax, qdamp, r_data, Gr_data, dGr_data, name)
+        pdffit2.read_data_arrays(
+            self._handle,
+            stype.encode(),
+            qmax,
+            qdamp,
+            r_data,
+            Gr_data,
+            dGr_data,
+            name,
+        )
         self.data_files.append(name)
         return
 
@@ -296,7 +310,9 @@ def alloc(self, stype, qmax, qdamp, rmin, rmax, bin):
             ValueError for bad input values
             pdffit.unassignedError when no structure has been loaded
         """
-        pdffit2.alloc(self._handle, stype.encode(), qmax, qdamp, rmin, rmax, bin)
+        pdffit2.alloc(
+            self._handle, stype.encode(), qmax, qdamp, rmin, rmax, bin
+        )
         return
 
     def calc(self):
@@ -876,8 +892,13 @@ def blen(self, *args):
             ij = (args[0], args[1])
             # indices were already checked in bond_length_atoms call
             assert (0 <= min(ij) - 1) and (max(ij) - 1 < len(atom_symbols))
-            symij = (atom_symbols[ij[0] - 1].upper(), atom_symbols[ij[1] - 1].upper())
-            print(_format_bond_length(dij, ddij, ij, symij), file=output.stdout)
+            symij = (
+                atom_symbols[ij[0] - 1].upper(),
+                atom_symbols[ij[1] - 1].upper(),
+            )
+            print(
+                _format_bond_length(dij, ddij, ij, symij), file=output.stdout
+            )
         # second form
         elif len(args) == 4:
             a1, a2, lb, ub = args
@@ -892,7 +913,12 @@ def blen(self, *args):
                 return
             # arguments are OK here, get bond length dictionary
             bld = pdffit2.bond_length_types(self._handle, a1, a2, lb, ub)
-            s = "(%s,%s) bond lengths in [%gA,%gA] for current phase :" % (a1, a2, lb, ub)
+            s = "(%s,%s) bond lengths in [%gA,%gA] for current phase :" % (
+                a1,
+                a2,
+                lb,
+                ub,
+            )
             print(s, file=output.stdout)
             atom_symbols = self.get_atoms()
             npts = len(bld["dij"])

src/diffpy/pdffit2/version.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
@@ -38,7 +38,9 @@ def get_pypi_release_date(package_name, timeout=5):
         installed_version = version(package_name)
         release_data = data["releases"].get(installed_version, [])
         if not release_data:
-            raise ValueError(f"No release data found for version {installed_version}")
+            raise ValueError(
+                f"No release data found for version {installed_version}"
+            )
 
         release_date_str = release_data[-1]["upload_time"]
         release_date = datetime.datetime.fromisoformat(release_date_str).date()
@@ -48,7 +50,9 @@ def get_pypi_release_date(package_name, timeout=5):
 
     except (ValueError, OSError) as e:
         print(f"Warning: Could not fetch release date from PyPI: {e}")
-        release_date = datetime.datetime.fromtimestamp(package_file.stat().st_ctime).isoformat()
+        release_date = datetime.datetime.fromtimestamp(
+            package_file.stat().st_ctime
+        ).isoformat()
 
     return str(release_date)