chore: fix typos and spelling inconsistency

Signed-off-by: Eisuke Kawashima <[email protected]>

avogadro/calc/chargemodel.h

@@ -51,14 +51,14 @@ class AVOGADROCALC_EXPORT ChargeModel
   virtual ChargeModel* newInstance() const = 0;
 
   /**
-   * @brief A unique identifier, used to retrieve models programatically.
+   * @brief A unique identifier, used to retrieve models programmatically.
    * EEM2, NPA, etc. A runtime warning will be generated if the identifier
    * is not unique.
    */
   virtual std::string identifier() const = 0;
 
   /**
-   * @brief A user-visibile name of the model (e.g., "Natural Population
+   * @brief A user-visible name of the model (e.g., "Natural Population
    * Analysis")
    */
   virtual std::string name() const = 0;

avogadro/io/fileformat.h

@@ -191,7 +191,7 @@ class AVOGADROIO_EXPORT FileFormat
   virtual FileFormat* newInstance() const = 0;
 
   /**
-   * @brief A unique identifier, used to retrieve formats programatically.
+   * @brief A unique identifier, used to retrieve formats programmatically.
    * CML, XYZ, PDB etc. A runtime warning will be generated if the identifier
    * is not unique.
    */

avogadro/io/hdf5dataformat.h

@@ -28,7 +28,7 @@ namespace Io {
  *
  * This class is intended to supplement an existing format reader/writer by
  * providing the option to write large data to an HDF5 file store. The purpose
- * is to keep text format files at a managable size.
+ * is to keep text format files at a manageable size.
  *
  * To use this class, open or create an HDF5 file with the openFile method,
  * using the appropriate OpenMode for the intended operation. Data can be

avogadro/molequeue/inputgenerator.h

@@ -191,7 +191,7 @@ namespace MoleQueue {
 }
 ~~~
  * This will result in a QCheckBox in the dynamically generated GUI, with
- * the inital check state shown in `default`.
+ * the initial check state shown in `default`.
  *
  * Special Parameters
  * ------------------

avogadro/qtgui/colorbutton.h

@@ -26,7 +26,7 @@ namespace QtGui {
  * When clicked by the user, it brings up a color picker to select a new
  * color.
  *
- * The widget has a default minimium size of 35x20 pixels.
+ * The widget has a default minimum size of 35x20 pixels.
  */
 
 class AVOGADROQTGUI_EXPORT ColorButton : public QAbstractButton
@@ -38,7 +38,7 @@ class AVOGADROQTGUI_EXPORT ColorButton : public QAbstractButton
   explicit ColorButton(const QColor& initial, QWidget* parent = 0);
 
   /**
-   *  Redraw the widget (i.e., refresh the colored rectange)
+   *  Redraw the widget (i.e., refresh the colored rectangle)
    */
   void paintEvent(QPaintEvent*);
 

avogadro/qtgui/interfacescript.h

@@ -190,7 +190,7 @@ class PythonScript;
 }
 ~~~
  * This will result in a QCheckBox in the dynamically generated GUI, with
- * the inital check state shown in `default`.
+ * the initial check state shown in `default`.
  *
  * Special Parameters
  * ------------------

avogadro/qtgui/jsonwidget.cpp

@@ -165,7 +165,7 @@ void JsonWidget::buildOptionGui()
       m_currentLayout = layout;
     } else if (m_options["userOptions"].isObject()) {
       userOptions = m_options["userOptions"].toObject();
-      // don't need to set layout, we aready did that
+      // don't need to set layout, we already did that
     } else {
       break;
     }

avogadro/qtgui/pluginlayermanager.h

@@ -62,10 +62,10 @@ class AVOGADROQTGUI_EXPORT PluginLayerManager : protected Core::LayerManager
   /** set active layer @p enable */
   void setEnabled(bool enable);
 
-  /** @return @p atom layer enabled globaly and in plugin */
+  /** @return @p atom layer enabled globally and in plugin */
   bool atomEnabled(Index atom) const;
 
-  /** @return @p atom layer enabled globaly, in plugin and in @p layer */
+  /** @return @p atom layer enabled globally, in plugin and in @p layer */
   bool atomEnabled(size_t layer, Index atom) const;
 
   /** @return if @p atom1 or @p atom2 is enabled */

avogadro/qtplugins/coloropacitymap/vtkChartHistogram.cpp

@@ -147,7 +147,7 @@ void vtkChartHistogram::SetHistogramInputData(vtkTable* table,
     this->GetAxis(vtkAxis::LEFT)->SetRange(0, 1.0);
     this->GetAxis(vtkAxis::BOTTOM)->SetRange(0, 255);
 
-    // Set visiblity of items
+    // Set visibility of items
     setItemsVisible(false);
 
     return;

avogadro/qtplugins/coordinateeditor/coordinateeditordialog.cpp

@@ -459,7 +459,7 @@ void CoordinateEditorDialog::validateInputWorker()
           if (!isReal)
             m_ui->text->markInvalid(tokenCursor, tr("Invalid coordinate."));
           else
-            m_ui->text->markValid(tokenCursor, tr("'c' coordinate."));
+            m_ui->text->markValid(tokenCursor, tr("'c' lattice coordinate."));
           break;
         }
 

avogadro/qtplugins/qtaim/qtaimcubature.cpp

@@ -122,7 +122,7 @@
  scratch as part of a larger code-cleanup, and in order to have
  a single code path for the vectorized and non-vectorized APIs.  I
  subsequently implemented the algorithm by Gladwell to extract
- even more parallelism by evalutating many hypercubes at once.)
+ even more parallelism by evaluating many hypercubes at once.)
 
  TODO:
 
@@ -1872,7 +1872,7 @@ QList<QVariant> QTAIMEvaluatePropertyTP(QList<QVariant> variantList)
   ode.setBetaSpheres(betaSpheres);
 
   // Determine radial basin limit via bisection
-  // Bisection Algorithm courtesey of Wikipedia
+  // Bisection Algorithm courtesy of Wikipedia
 
   qint64 thisBasin = basinList.at(0);
   Matrix<qreal, 3, 1> origin;

avogadro/qtplugins/scriptfileformats/fileformatscript.h

@@ -62,7 +62,7 @@ namespace QtPlugins {
  * - `outputFormat` indicates the format that the script can convert to from the
  *   implemented format by the `--read` command. Allowed values are `"cml"`,
  *   `"cjson"`, `"sdf"`, `"pdb"` or `"xyz"`. See the `--read` documentation for more detail.
- * - `operations` specifies the scripts capabilies. The array should contain
+ * - `operations` specifies the scripts capabilities. The array should contain
  *   `"read"` if the script implements the `--read` option, and/or `"write"` if
  *   `--write` is available.
  * - `identifier` is a unique identifier. The value must only be unique amongst

avogadro/qtplugins/selectiontool/selectiontool.cpp

@@ -311,7 +311,7 @@ bool SelectionTool::toggleAtom(const Index& atom)
 
 bool SelectionTool::shouldClean(QMouseEvent* e)
 {
-  // acumulate the selection if shift or ctrl are presset
+  // accumulate the selection if shift or ctrl are presset
   if (!(e->modifiers() & Qt::ControlModifier) &&
       !(e->modifiers() & Qt::ShiftModifier)) {
     clearAtoms();

avogadro/quantumio/gaussianfchk.h

@@ -31,7 +31,7 @@ class AVOGADROQUANTUMIO_EXPORT GaussianFchk : public Io::FileFormat
   std::string name() const override { return "Gaussian FCHK"; }
   std::string description() const override
   {
-    return "Guassian formatted checkpoint reader.";
+    return "Gaussian formatted checkpoint reader.";
   }
 
   std::string specificationUrl() const override

avogadro/rendering/cartoongeometry.cpp

@@ -59,7 +59,7 @@ float arrowFunction(float t)
   const float maxPoint = 0.7f;
   if (t < maxPoint) {
     // normalize t using max point and scale it so that adding will be between
-    // [minimunRadius, 1]
+    // [minimumRadius, 1]
     result = t / maxPoint;
   } else {
     // starting with 1 and go decreassing

avogadro/rendering/cartoongeometry.h

@@ -18,8 +18,8 @@ enum CartoonType
   Undefined = -1, // constant small radius
   Body = 0,       // constant big radius
   Arrow = 3,      // arrow head
-  Head = 2,       // decreassing
-  Tail = 1        // increassing
+  Head = 2,       // decreasing
+  Tail = 1        // increasing
 };
 
 class AVOGADRORENDERING_EXPORT Cartoon : public BSplineGeometry
@@ -33,7 +33,7 @@ class AVOGADRORENDERING_EXPORT Cartoon : public BSplineGeometry
                 size_t id, Core::Residue::SecondaryStructure sec);
 
 protected:
-  // create an elipse and adapt it to the affine A
+  // create an ellipsis and adapt it to the affine A
   std::vector<ColorNormalVertex> computeCirclePoints(const Eigen::Affine3f& a,
                                                      const Eigen::Affine3f& b,
                                                      bool flat) const override;

avogadro/rendering/sphere_ao_bake_fs.glsl

@@ -15,7 +15,7 @@
 varying vec3 v_pos;
 // the sphere radius
 varying float v_radius;
-// streched corner: [-1.x, 1.x] (see below)
+// stretched corner: [-1.x, 1.x] (see below)
 varying vec2 v_corner;
 
 //

avogadro/rendering/sphere_ao_bake_vs.glsl

@@ -26,7 +26,7 @@ attribute vec2 a_tileOffset;
 varying vec3 v_pos;
 // the sphere radius
 varying float v_radius;
-// streched corner: [-1.x, 1.x] (see below)
+// stretched corner: [-1.x, 1.x] (see below)
 varying vec2 v_corner;
 
 //

avogadro/rendering/textlabelbase.cpp

@@ -47,7 +47,7 @@ class TextLabelBase::RenderImpl
   Array<PackedVertex> vertices;
   BufferObject vbo;
 
-  // Sentinals:
+  // Sentinels:
   bool shadersInvalid;
   bool textureInvalid;
   bool vboInvalid;

avogadro/rendering/textlabelbase_vs.glsl

@@ -41,7 +41,7 @@ void main(void)
   // Apply radius;
   eyeAnchor += vec4(0., 0., radius, 0.);
 
-  // Tranform to clip coordinates
+  // Transform to clip coordinates
   vec4 clipAnchor = proj * eyeAnchor;
 
   // Move the anchor to a pixel center:

avogadro/rendering/texture2d.h

@@ -144,7 +144,7 @@ class AVOGADRORENDERING_EXPORT Texture2D
    * use std::vector or Avogadro::Core::Array):
    * - ContainerT must have tightly packed values of ContainerT::value_type
    * - elements must be accessible by reference via ContainerT::operator[].
-   * - ContainterT::size() must return the number of elements in the container
+   * - ContainerT::size() must return the number of elements in the container
    *   as integral type ContainerT::size_type.
    */
   template <class ContainerT>

cmake/CompilerFlags.cmake

@@ -2,7 +2,7 @@ if(CMAKE_COMPILER_IS_GNUCXX)
 
   include(CheckCXXCompilerFlag)
 
-  # Addtional warnings for GCC
+  # Additional warnings for GCC
   set(CMAKE_CXX_FLAGS_WARN "-Wnon-virtual-dtor -Wno-long-long -Wcast-align -Wchar-subscripts -Wall -Wpointer-arith -Wformat-security -Woverloaded-virtual -fno-check-new -fno-common")
 
   # This flag is useful as not returning from a non-void function is an error

scripts/extractrc.sh

@@ -252,7 +252,7 @@ for my $file_name ( @ARGV )
              push @atts, [$ectx_att, $aval];
            }
          }
-         # Kill all tags in element-context with level higer or equal to this,
+         # Kill all tags in element-context with level higher or equal to this,
          # and add it to the end.
          my $clevel = ECTX_SPEC->{$ectx_ext}{$tag}[0];
          for ( my $i = 0; $i < @ectx; ++$i )
@@ -350,7 +350,7 @@ for my $file_name ( @ARGV )
              for my $agr ( @{$tgr->[2]} )
              {
                #push @attr_gr, "$agr->[0]=$agr->[1]";
-               push @attr_gr, "$agr->[1]"; # no real nead for attribute name
+               push @attr_gr, "$agr->[1]"; # no real need for attribute name
              }
              my $attr = join(", ", @attr_gr);
              push @tag_gr, "$tgr->[1] ($attr)" if $attr;

tests/core/moleculetest.cpp

@@ -158,7 +158,7 @@ TEST_F(MoleculeTest, addBond)
   EXPECT_EQ(bondBC.index(), static_cast<Index>(1));
   EXPECT_EQ(bondBC.order(), static_cast<unsigned char>(2));
 
-  // try to lookup nonexistant bond
+  // try to lookup nonexistent bond
   Bond bond = molecule.bond(a, c);
   EXPECT_FALSE(bond.isValid());
 

tests/qtgui/moleculetest.cpp

@@ -157,7 +157,7 @@ TEST_F(MoleculeTest, addBond)
   EXPECT_EQ(bondBC.index(), static_cast<Index>(1));
   EXPECT_EQ(bondBC.order(), static_cast<unsigned char>(2));
 
-  // try to lookup nonexistant bond
+  // try to lookup nonexistent bond
   Bond bond = molecule.bond(a, c);
   EXPECT_FALSE(bond.isValid());
 

thirdparty/gif-h/gif.h

@@ -425,7 +425,7 @@ void GifDitherImage( const uint8_t* lastFrame, const uint8_t* nextFrame, uint8_t
             int32_t bestDiff = 1000000;
             int32_t bestInd = kGifTransIndex;
 
-            // Search the palete
+            // Search the palette
             GifGetClosestPaletteColor(pPal, rr, gg, bb, &bestInd, &bestDiff, 1);
 
             // Write the result to the temp buffer

thirdparty/libgwavi/gwavi.c

@@ -60,12 +60,12 @@
  * FourCC is a sequence of four chars used to uniquely identify data formats.
  * For more information, you can visit www.fourcc.org.
  * @param fps Number of frames per second of your video. It needs to be > 0.
- * @param audio This parameter is optionnal. It is used for the audio track. If
+ * @param audio This parameter is optional. It is used for the audio track. If
  * you do not want to add an audio track to your AVI file, simply pass NULL for
  * this argument.
  *
  * @return Structure containing required information in order to create the AVI
- * file. If an error occured, NULL is returned.
+ * file. If an error occurred, NULL is returned.
  */
 struct gwavi_t* gwavi_open(const char* filename, unsigned int width,
                            unsigned int height, const char* fourcc,

thirdparty/nlohmann/detail/input/binary_reader.hpp

@@ -866,7 +866,7 @@ class binary_reader
 
     @return whether conversion completed
 
-    @note This function needs to respect the system's endianess, because
+    @note This function needs to respect the system's endianness, because
           bytes in CBOR, MessagePack, and UBJSON are stored in network order
           (big endian) and therefore need reordering on little endian systems.
     */

thirdparty/nlohmann/detail/output/binary_writer.hpp

@@ -683,7 +683,7 @@ class binary_writer
     @param[in] n number of type @a NumberType
     @tparam NumberType the type of the number
 
-    @note This function needs to respect the system's endianess, because bytes
+    @note This function needs to respect the system's endianness, because bytes
           in CBOR, MessagePack, and UBJSON are stored in network order (big
           endian) and therefore need reordering on little endian systems.
     */

thirdparty/tinycolormap/include/tinycolormap.hpp

@@ -205,7 +205,7 @@ inline double QuantizeArgument(double x, unsigned int num_levels) {
   const double interval_length = 255.0 / num_levels;
 
   // Calculate index of the interval to which the given x belongs to.
-  // Substracting eps prevents getting out of bounds index.
+  // Subtracting eps prevents getting out of bounds index.
   constexpr double eps = 0.0005;
   const unsigned int index =
       static_cast<unsigned int>((x * 255.0 - eps) / interval_length);