Merge branch 'main' into version-0.4.0

Author: chrisrichardson

.gitignore

@@ -36,3 +36,9 @@ joss/paper.pdf
 *.egg-info
 _skbuild
 dist
+
+*.png
+*.jpg
+*.svg
+!joss/img/*.png
+!joss/img/*.svg

cpp/CMakeLists.txt

@@ -26,7 +26,7 @@ add_feature_info(BUILD_SHARED_LIBS BUILD_SHARED_LIBS "Build Basix with shared li
 option(DOWNLOAD_XTENSOR_LIBS "Download xtl and xtensor. Requires git." OFF)
 add_feature_info(DOWNLOAD_XTENSOR_LIBS DOWNLOAD_XTENSOR_LIBS "Download xtl and xtensor. Requires git.")
 
-# Enable xtensor with target-specific optimization, i.e. -march=native
+# Enable xtensor with target-specific optimization, ie -march=native
 option(XTENSOR_OPTIMIZE "Enable xtensor target-specific optimization" OFF)
 add_feature_info(XTENSOR_OPTIMIZE XTENSOR_OPTIMIZE "Enable architecture-specific optimizations as defined by xtensor.")
 

cpp/basix/finite-element.h

@@ -245,7 +245,7 @@ class FiniteElement
   FiniteElement& operator=(FiniteElement&& element) = default;
 
   /// Check if two elements are the same
-  /// @note This operator compares the element properties, e.g. family,
+  /// @note This operator compares the element properties, eg family,
   /// degree, etc, and not computed numerical data
   /// @return True if elements are the same
   bool operator==(const FiniteElement& e) const;
@@ -275,7 +275,7 @@ class FiniteElement
   /// @return The basis functions (and derivatives). The shape is
   /// (derivative, point, basis fn index, value index).
   /// - The first index is the derivative, with higher derivatives are
-  /// stored in triangular (2D) or tetrahedral (3D) ordering, i.e. for
+  /// stored in triangular (2D) or tetrahedral (3D) ordering, ie for
   /// the (x,y) derivatives in 2D: (0,0), (1,0), (0,1), (2,0), (1,1),
   /// (0,2), (3,0)... The function basix::indexing::idx can be used to find the
   /// appropriate derivative.
@@ -299,7 +299,7 @@ class FiniteElement
   /// value_size). The function `FiniteElement::tabulate_shape` can be
   /// used to get the required shape.
   /// - The first index is the derivative, with higher derivatives are
-  /// stored in triangular (2D) or tetrahedral (3D) ordering, i.e. for
+  /// stored in triangular (2D) or tetrahedral (3D) ordering, ie for
   /// the (x,y) derivatives in 2D: (0,0), (1,0), (0,1), (2,0), (1,1),
   /// (0,2), (3,0)... The function basix::indexing::idx can be used to
   /// find the appropriate derivative.
@@ -321,7 +321,7 @@ class FiniteElement
   /// @return Polynomial degree
   int degree() const;
 
-  /// The element value tensor shape, e.g. returning {} for scalars, {3}
+  /// The element value tensor shape, eg returning {} for scalars, {3}
   /// for vectors in 3D, {2, 2} for a rank-2 tensor in 2D.
   /// @return Value shape
   const std::vector<int>& value_shape() const;
@@ -693,7 +693,7 @@ class FiniteElement
   void apply_inverse_dof_transformation_to_transpose(
       const xtl::span<T>& data, int block_size, std::uint32_t cell_info) const;
 
-  /// Return the interpolation points, i.e. the coordinates on the
+  /// Return the interpolation points, ie the coordinates on the
   /// reference element where a function need to be evaluated in order
   /// to interpolate it in the finite element space.
   /// @return Array of coordinate with shape `(num_points, tdim)`
@@ -895,7 +895,7 @@ class FiniteElement
 
   // Shape function coefficient of expansion sets on cell. If shape
   // function is given by @f$\psi_i = \sum_{k} \phi_{k}
-  // \alpha^{i}_{k}@f$, then _coeffs(i, j) = @f$\alpha^i_k@f$. i.e.,
+  // \alpha^{i}_{k}@f$, then _coeffs(i, j) = @f$\alpha^i_k@f$. ie
   // _coeffs.row(i) are the expansion coefficients for shape function i
   // (@f$\psi_{i}@f$).
   xt::xtensor<double, 2> _coeffs;

cpp/basix/lattice.h

@@ -67,7 +67,7 @@ enum class simplex_method
 /// optionally including the outer surface points
 ///
 /// For a given celltype, this creates a set of points on a regular grid
-/// which covers the cell, e.g. for a quadrilateral, with n=2, the points are:
+/// which covers the cell, eg for a quadrilateral, with n=2, the points are:
 /// [0,0],[0.5,0],[1,0],[0,0.5],[0.5,0.5],[1,0.5],[0,1],[0.5,1],[1,1]
 /// If the parameter exterior is set to false, the points lying on the external
 /// boundary are omitted, in this case for a quadrilateral with n=2, the points

cpp/basix/loguru.cpp

@@ -989,7 +989,7 @@ bool add_file(const char* path_in, FileMode mode, Verbosity verbosity)
         Any logging message with a verbosity lower or equal to
         the given verbosity will be included.
 
-        This works for Unix like systems (i.e. Linux/Mac)
+        This works for Unix like systems (ie Linux/Mac)
         There is no current implementation for Windows (as I don't know the
         equivalent calls or have a way to test them). If you know please
         add and send a pull request.
@@ -2026,7 +2026,7 @@ EcEntryBase::~EcEntryBase() { get_thread_ec_head_ref() = _previous; }
 Text ec_to_text(const char* value)
 {
   // Add quotes around the string to make it obvious where it begin and ends.
-  // This is great for detecting erroneous leading or trailing spaces in e.g. an
+  // This is great for detecting erroneous leading or trailing spaces in eg an
   // identifier.
   auto str = "\"" + std::string(value) + "\"";
   return Text{STRDUP(str.c_str())};

cpp/basix/loguru.hpp

@@ -392,7 +392,7 @@ struct Message
 /* Everything with a verbosity equal or greater than g_stderr_verbosity will be
 written to stderr. You can set this in code or via the -v argument.
 Set to loguru::Verbosity_OFF to write nothing to stderr.
-Default is 0, i.e. only log ERROR, WARNING and INFO are written to stderr.
+Default is 0, ie only log ERROR, WARNING and INFO are written to stderr.
 */
 LOGURU_EXPORT extern Verbosity g_stderr_verbosity;
 LOGURU_EXPORT extern bool g_colorlogtostderr;      // True by default.
@@ -530,7 +530,7 @@ void init(int& argc, char* argv[], const Options& options = {});
 LOGURU_EXPORT
 void shutdown();
 
-// What ~ will be replaced with, e.g. "/home/your_user_name/"
+// What ~ will be replaced with, eg "/home/your_user_name/"
 LOGURU_EXPORT
 const char* home_dir();
 
@@ -553,19 +553,19 @@ const char* current_dir();
 LOGURU_EXPORT
 const char* filename(const char* path);
 
-// e.g. "foo/bar/baz.ext" will create the directories "foo/" and "foo/bar/"
+// eg "foo/bar/baz.ext" will create the directories "foo/" and "foo/bar/"
 LOGURU_EXPORT
 bool create_directories(const char* file_path_const);
 
-// Writes date and time with millisecond precision, e.g. "20151017_161503.123"
+// Writes date and time with millisecond precision, eg "20151017_161503.123"
 LOGURU_EXPORT
 void write_date_time(char* buff, unsigned buff_size);
 
 // Helper: thread-safe version strerror
 LOGURU_EXPORT
 Text errno_as_text();
 
-/* Given a prefix of e.g. "~/loguru/" this might return
+/* Given a prefix of eg "~/loguru/" this might return
    "/home/your_username/loguru/app_name/20151017_161503.123.log"
 
    where "app_name" is a sanitized version of argv[0].
@@ -1132,14 +1132,14 @@ some.cpp:
         namespace loguru {
                 Text ec_to_text(MySmallType small_value)
                 {
-                        // Called only when needed, i.e. on a crash.
+                        // Called only when needed, ie on a crash.
                         std::string str = small_value.as_string(); // Format
 'small_value' here somehow. return Text{STRDUP(str.c_str())};
                 }
 
                 Text ec_to_text(const MyBigType* big_value)
                 {
-                        // Called only when needed, i.e. on a crash.
+                        // Called only when needed, ie on a crash.
                         std::string str = big_value->as_string(); // Format
 'big_value' here somehow. return Text{STRDUP(str.c_str())};
                 }