style: fix pre-commit (codespell typos, black/isort, exclude vendored cxxtest and data)

Author: cadenmyers13

.codespell/ignore_words.txt

@@ -6,3 +6,9 @@ mater
 
 ;; Frobenius norm used in np.linalg.norm
 fro
+
+;; variable name for a pair type multiplicity in BaseDebyeSum.cpp
+multipl
+
+;; custom scattering factor label used in TestScatteringFactorTable.hpp
+ccustom

.github/workflows/check-news-item.yml

@@ -3,7 +3,7 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-      - main  # GitHub does not evaluate expressions in trigger filters; edit this value if your base branch is not main
+      - main # GitHub does not evaluate expressions in trigger filters; edit this value if your base branch is not main
 
 jobs:
   check-news-item:

.pre-commit-config.yaml

@@ -9,6 +9,12 @@ ci:
   autoupdate_schedule: monthly
   skip: [no-commit-to-branch]
   submodules: false
+# Leave the vendored CxxTest SCons tool and the data tables untouched.
+exclude: |
+  (?x)^(
+    site_scons/site_tools/cxxtest\.py|
+    .*\.(cif|dat)
+  )$
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0

news/docs-migration.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* Library overview from the old manual on the ``docs/`` index page.
+
+**Changed:**
+
+* Moved the Sphinx documentation from ``doc/manual/`` to the scikit-package ``docs/`` layout.
+* Read the documentation version from git tags through ``site_scons/libdiffpybuildutils.py``.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* Old ``doc/manual/`` Sphinx project.
+* Python ``automodule`` API page, which cannot document a C++ library.
+
+**Fixed:**
+
+* Pre-commit hooks now pass: fixed spelling in C++ comments, reformatted ``site_scons`` helpers, and excluded the vendored CxxTest tool and data tables.
+
+**Security:**
+
+* <news item>

site_scons/fallback_version.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 
-'''
-Definition of FALLBACK_VERSION.  Use it when git repository is
-not available for example, when building from git zip archive.
+"""Definition of FALLBACK_VERSION.
+
+Use it when git repository is not available for example, when building
+from git zip archive.
 
 Update FALLBACK_VERSION when tagging a new release.
-'''
+"""
 
-FALLBACK_VERSION = '1.4.0.post0'
+FALLBACK_VERSION = "1.4.0.post0"

site_scons/libdiffpybuildutils.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
-'''Utility functions used by scons and sphinx for version extraction.
-'''
+"""Utility functions used by scons and sphinx for version extraction."""
 
 import os
 import re
@@ -21,79 +20,81 @@
 
 
 def gitinfo():
-    'Extract dictionary of version data from git records.'
-    from subprocess import Popen, PIPE
+    "Extract dictionary of version data from git records."
+    from subprocess import PIPE, Popen
+
     global _cached_gitinfo
     if _cached_gitinfo is not None:
         return _cached_gitinfo
-    nullfile = open(os.devnull, 'w')
-    kw = dict(stdout=PIPE, stderr=nullfile, cwd=MYDIR,
-              universal_newlines=True)
-    proc = Popen(['git', 'describe', '--match=v[[:digit:]]*'], **kw)
+    nullfile = open(os.devnull, "w")
+    kw = dict(stdout=PIPE, stderr=nullfile, cwd=MYDIR, universal_newlines=True)
+    proc = Popen(["git", "describe", "--match=v[[:digit:]]*"], **kw)
     desc = proc.stdout.read()
     if proc.wait():
         _cached_gitinfo = {}
         return gitinfo()
-    proc = Popen(['git', 'log', '-1', '--format=%H %ci'], **kw)
+    proc = Popen(["git", "log", "-1", "--format=%H %ci"], **kw)
     glog = proc.stdout.read()
-    words = desc.strip().split('-')
-    vtag = words[0].lstrip('v')
-    vnum = int((words[1:2] or ['0'])[0])
+    words = desc.strip().split("-")
+    vtag = words[0].lstrip("v")
+    vnum = int((words[1:2] or ["0"])[0])
     rv = {}
-    rv['commit'], rv['date'] = glog.strip().split(None, 1)
-    rv['patchnumber'] = vnum
-    rv['version'] = vtag
+    rv["commit"], rv["date"] = glog.strip().split(None, 1)
+    rv["patchnumber"] = vnum
+    rv["version"] = vtag
     if vnum:
-        rv['version'] += '.post' + str(vnum)
+        rv["version"] += ".post" + str(vnum)
     _cached_gitinfo = rv
     return gitinfo()
 
+
 _cached_gitinfo = None
 
 
 def getversion():
     """Extract version from gitinfo and/or gitarchive.cfg file.
 
-    Process gitinfo first and make sure it matches FALLBACK_VERSION
-    in gitarchive.cfg.  Use expanded data from gitarchive.cfg when
-    these sources are from git archive bundle.
+    Process gitinfo first and make sure it matches FALLBACK_VERSION in
+    gitarchive.cfg.  Use expanded data from gitarchive.cfg when these
+    sources are from git archive bundle.
     """
     from fallback_version import FALLBACK_VERSION
-    gitarchivecfgfile = os.path.join(MYDIR, 'gitarchive.cfg')
+
+    gitarchivecfgfile = os.path.join(MYDIR, "gitarchive.cfg")
     assert os.path.isfile(gitarchivecfgfile)
     with open(gitarchivecfgfile) as fp:
         gacontent = fp.read()
-    gaitems = re.findall(r'^(\w+) *= *(\S.*?)\s*$', gacontent, re.M)
+    gaitems = re.findall(r"^(\w+) *= *(\S.*?)\s*$", gacontent, re.M)
     ga = dict(gaitems)
     gi = gitinfo()
     rv = {}
     if gi:
         afb = FALLBACK_VERSION
-        gfb = gi['version'].split('.post')[0] + '.post0'
+        gfb = gi["version"].split(".post")[0] + ".post0"
         if gfb != afb:
             raise RuntimeError(EMSG_BAD_FALLBACK_VERSION.format(afb, gfb))
         rv.update(gi)
     else:
         # Not a git repository.  Require that gitarchive.cfg is expanded.
-        if '$Format:' in ga['commit']:
+        if "$Format:" in ga["commit"]:
             raise RuntimeError(EMSG_GIT_MISSING)
-        rv['commit'] = ga['commit']
-        rv['date'] = ga['date']
+        rv["commit"] = ga["commit"]
+        rv["date"] = ga["date"]
         # First assume we have an undetermined post-release.  Keep version
         # suffix as ".post0", but set patchnumber to ensure we are post
         # FALLBACK_VERSION.
-        rv['version'] = FALLBACK_VERSION
-        rv['patchnumber'] = 1
+        rv["version"] = FALLBACK_VERSION
+        rv["patchnumber"] = 1
         # If we are at version tag turn this to regular release.
-        mx = re.search(r'\btag: v(\d[^,]*)', ga['refnames'])
+        mx = re.search(r"\btag: v(\d[^,]*)", ga["refnames"])
         if mx:
-            rv['version'] = mx.group(1)
-            rv['patchnumber'] = 0
+            rv["version"] = mx.group(1)
+            rv["patchnumber"] = 0
     # rv['version'] is resolved, let's parse its subfields.
-    vbase = rv['version'].split('.post')[0]
-    mx = re.match(r'^(\d+)\.(\d+)(?:\.(\d+))?((?:[ab]|rc)\d*)?', vbase)
-    rv['major'] = int(mx.group(1))
-    rv['minor'] = int(mx.group(2))
-    rv['micro'] = int(mx.group(3) or 0)
-    rv['prerelease'] = mx.group(4)
+    vbase = rv["version"].split(".post")[0]
+    mx = re.match(r"^(\d+)\.(\d+)(?:\.(\d+))?((?:[ab]|rc)\d*)?", vbase)
+    rv["major"] = int(mx.group(1))
+    rv["minor"] = int(mx.group(2))
+    rv["micro"] = int(mx.group(3) or 0)
+    rv["prerelease"] = mx.group(4)
     return rv

src/diffpy/HasClassRegistry.hpp

@@ -16,7 +16,7 @@
 *   functions that produce derived classes.  To be used as a base for a
 *   specific class branch.  For a proper function, the HasClassRegistry
 *   template must be instantiated in just one cpp file that includes the
-*   implementatios in HasClassRegistry.ipp.
+*   implementations in HasClassRegistry.ipp.
 *
 *   A Base class with registry should be declared as
 *     class Base : public HasClassRegistry<Base>
@@ -62,7 +62,7 @@ class HasClassRegistry
 
         /// Clear registration of the specified type under its standard name
         /// or any alias.  Return the number of unset names and aliases or
-        /// 0 if the specifed string type was not registered.
+        /// 0 if the specified string type was not registered.
         static int deregisterType(const std::string& tp);
 
         /// Create new instance of a specified string type.

src/diffpy/srreal/PairQuantity.cpp

@@ -448,7 +448,7 @@ void PairQuantity::updateMaskData()
         // rebuild minvertpairmask according to mtypemask
         minvertpairmask.clear();
         TypeMaskStorage::const_iterator tpmsk;
-        // build a list of type masks with all-masks at the begining
+        // build a list of type masks with all-masks at the beginning
         list< pair<string,string> > orderedpairs;
         for (tpmsk = mtypemask.begin(); tpmsk != mtypemask.end(); ++tpmsk)
         {

src/diffpy/srreal/PeakProfile.hpp

@@ -13,7 +13,7 @@
 ******************************************************************************
 *
 * class PeakProfile -- base class for calculation of peak profiles.
-*     When possible total integrated area of the profile should eqaul 1.
+*     When possible total integrated area of the profile should equal 1.
 *     The operator()(x, fwhm) returns amplitude of a zero-centered profile.
 *     Methods xboundlo(fwhm), xboundhi(fwhm) return low and high x-boundaries,
 *     where amplitude relative to the maximum becomes smaller than precision

src/diffpy/srreal/PointsInSphere.cpp

@@ -14,7 +14,7 @@
 *
 * classes PointsInSphere, ReflectionsInQminQmax, ReflectionsInDmaxDmin
 *
-* Comments: sequencers for lattice points insided 3D sphere
+* Comments: sequencers for lattice points inside 3D sphere
 *
 *****************************************************************************/
 
@@ -117,7 +117,7 @@ void PointsInSphere::rewind()
     mHalfSpan = Rmax()*latpar.ar;
     hi_m = int(ceil(mHalfSpan));
     this->_m = -hi_m;
-    // make indices n, o invalid, reset the neares point
+    // make indices n, o invalid, reset the nearest point
     this->_n = hi_n = 0;
     this->_o = hi_o = outside_o = 0;
     n0plane = o0plane = o0line = 0.0;