Merge pull request #135 from cadenmyers13/pre-commit-codespell

sbillinge · web-flow · commit d47b71993559 · 2025-06-11T16:57:54.000-04:00
skpkg: pre-commit codespell fixes
diff --git a/.codespell/ignore_words.txt b/.codespell/ignore_words.txt
@@ -4,14 +4,24 @@
 ;; abbreviation for "materials" often used in a journal title
 mater
 
-;; alternative use of socioeconomic
-socio-economic
-
 ;; Frobenius norm used in np.linalg.norm
 fro
 
 ;; class name within distutils module
 ccompiler
 
+;; dum as a C variable
+dum
+
+;; gaus used for gaussian
+gaus
+
 ;; structure file format
-discus
+DISCUS
+
+;; Periodic table elements
+Te
+Nd
+
+;; Ois
+Ois
diff --git a/CODE_OF_CONDUCT.rst b/CODE_OF_CONDUCT.rst
@@ -8,7 +8,7 @@ Our Pledge
 We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 
diff --git a/environment.yml b/environment.yml
diff --git a/news/pre-commit-codespell.rst b/news/pre-commit-codespell.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Fix misspelled words in source code comments.
+
+**Security:**
+
+* <news item>
diff --git a/src/extensions/libpdffit2/PointsInSphere.cc b/src/extensions/libpdffit2/PointsInSphere.cc
@@ -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));
     m = -hi_m;
-    // make indices n, o invalid, reset the neares point
+    // make indices n, o invalid, reset the nearest point
     n = hi_n = 0;
     o = hi_o = outside_o = 0;
     n0plane = o0plane = o0line = 0.0;
diff --git a/src/extensions/libpdffit2/fit.cc b/src/extensions/libpdffit2/fit.cc
@@ -15,7 +15,7 @@
 * Mixed definitions of several DataSet, Fit and PdfFit methods
 *
 * Comments: Up to date with 1.3.10 Fortran version.
-*	    What a spagetti.
+*	    What a spaghetti.
 *
 ***********************************************************************/
 
diff --git a/src/extensions/libpdffit2/metric.cc b/src/extensions/libpdffit2/metric.cc
@@ -302,7 +302,7 @@ void Phase::dtensor(double vec[3], double win[3], double dten[3][3],
 }
 
 /********************************************************
-  Calulates the SCALARPRODUCT of two vectors
+  Calculates the SCALARPRODUCT of two vectors
   1/D**2 = H(I)*K(J)*RTEN(I,J)
   uses the phase's metric
  *********************************************************/
diff --git a/src/extensions/libpdffit2/nrutil.cc b/src/extensions/libpdffit2/nrutil.cc
@@ -12,7 +12,7 @@
 *
 ************************************************************************
 *
-* Utilities from numerical recipies.
+* Utilities from numerical recipes.
 *
 * Comments:
 *
diff --git a/src/extensions/libpdffit2/nrutil.h b/src/extensions/libpdffit2/nrutil.h
@@ -12,7 +12,7 @@
 *
 ************************************************************************
 *
-* Utilities from numerical recipies.
+* Utilities from numerical recipes.
 *
 * Comments:
 *
diff --git a/src/extensions/libpdffit2/pdf.cc b/src/extensions/libpdffit2/pdf.cc
@@ -15,7 +15,7 @@
 * Mixed methods for PDF calculation from PdfFit, DataSet and Phase
 *
 * Comments: Up to date with 1.3.10 Fortran version.
-*	    What a spagetti.
+*	    What a spaghetti.
 *
 ***********************************************************************/
 
@@ -1387,7 +1387,7 @@ bool isRegular(Iterator first, Iterator last)
 
 /* Wed Oct 12 2005 - CLF
  * Using read_data_arrays adds functionality
- * to pdffit2, allowing one to read data that is alread stored as arrays.
+ * to pdffit2, allowing one to read data that is already stored as arrays.
  */
 void DataSet::read_data_arrays(int _iset, char tp, double _qmax, double _qdamp,
         int length, double * r_data, double * Gr_data,
diff --git a/src/extensions/libpdffit2/pdflsmin.cc b/src/extensions/libpdffit2/pdflsmin.cc
@@ -65,7 +65,7 @@ void PdfFit::mrqmin(vector<double> &a, vector<int> &ia, matrix<double> &covar,
 // Levenberg-Marquardt method, attempting to reduce the value Chi2 of a fit
 // between a set of data points x[1..ndata], y[1..ndata] with individual
 // standard deviations sig[1..ndata], and a nonlinear function dependent on ma
-// coeffcients a[1..ma].  The input array ia[1..ma] indicates by nonzero
+// coefficients a[1..ma].  The input array ia[1..ma] indicates by nonzero
 // entries those components of a that should be fitted for, and by zero entries
 // those components that should be held fixed at their input values. The
 // program re- turns current best-fit values for the parameters a[1..ma], and
diff --git a/src/extensions/libpdffit2/stru.cc b/src/extensions/libpdffit2/stru.cc
@@ -106,7 +106,7 @@ string lstrip(const string &line)
     return naked;
 }
 
-// substitute all occurences of literal pattern with new string
+// substitute all occurrences of literal pattern with new string
 void substitute(string& s, const string& pat, const string& sub)
 {
     string::size_type p;
@@ -230,7 +230,7 @@ void Phase::read_struct_stream(int _iphase, istream& fstruct)
 /******************************************************************
     This subroutine reads the header of a structure file
     Wed Oct 12 2005 - CLF
-    Changed ifstream to istream to accomodate stringstreams
+    Changed ifstream to istream to accommodate stringstreams
     as well.
 ********************************************************************/
 
diff --git a/src/extensions/pdffit2module/misc.cc b/src/extensions/pdffit2module/misc.cc
@@ -1381,8 +1381,8 @@ char pypdffit2_bond_length_types__doc__[] =
     "\n"
     "Return a dictionary of distance data containing:\n"
     "\n"
-    "dij  : list of bond lenghts within given bounds\n"
-    "ddij : list of bond legnth standard deviations\n"
+    "dij  : list of bond lengths within given bounds\n"
+    "ddij : list of bond length standard deviations\n"
     "ij0  : list of tupled pairs of indices starting at 0\n"
     "ij1  : list of tupled pairs of indices starting at 1";
 char pypdffit2_bond_length_types__name__[] = "bond_length_types";

Original file line number	Diff line number	Diff line change
`@@ -14,7 +14,7 @@`
`14`	`14`	`*`
`15`	`15`	`* classes PointsInSphere, ReflectionsInQminQmax, ReflectionsInDmaxDmin`
`16`	`16`	`*`
`17`		`-* Comments: sequencers for lattice points insided 3D sphere`
	`17`	`+* Comments: sequencers for lattice points inside 3D sphere`
`18`	`18`	`*`
`19`	`19`	`***********************************************************************/`
`20`	`20`
`@@ -117,7 +117,7 @@ void PointsInSphere::rewind()`
`117`	`117`	`mHalfSpan = Rmax*latpar.ar;`
`118`	`118`	`hi_m = int(ceil(mHalfSpan));`
`119`	`119`	`m = -hi_m;`
`120`		`- // make indices n, o invalid, reset the neares point`
	`120`	`+ // make indices n, o invalid, reset the nearest point`
`121`	`121`	`n = hi_n = 0;`
`122`	`122`	`o = hi_o = outside_o = 0;`
`123`	`123`	`n0plane = o0plane = o0line = 0.0;`
Original file line number	Diff line number	Diff line change
`@@ -15,7 +15,7 @@`
`15`	`15`	`* Mixed definitions of several DataSet, Fit and PdfFit methods`
`16`	`16`	`*`
`17`	`17`	`* Comments: Up to date with 1.3.10 Fortran version.`
`18`		`-* What a spagetti.`
	`18`	`+* What a spaghetti.`
`19`	`19`	`*`
`20`	`20`	`***********************************************************************/`
`21`	`21`
Original file line number	Diff line number	Diff line change
`@@ -302,7 +302,7 @@ void Phase::dtensor(double vec[3], double win[3], double dten[3][3],`
`302`	`302`	`}`
`303`	`303`
`304`	`304`	`/********************************************************`
`305`		`- Calulates the SCALARPRODUCT of two vectors`
	`305`	`+ Calculates the SCALARPRODUCT of two vectors`
`306`	`306`	`1/D*2 = H(I)K(J)*RTEN(I,J)`
`307`	`307`	`uses the phase's metric`
`308`	`308`	`*********************************************************/`
Original file line number	Diff line number	Diff line change
`@@ -12,7 +12,7 @@`
`12`	`12`	`*`
`13`	`13`	`************************************************************************`
`14`	`14`	`*`
`15`		`-* Utilities from numerical recipies.`
	`15`	`+* Utilities from numerical recipes.`
`16`	`16`	`*`
`17`	`17`	`* Comments:`
`18`	`18`	`*`