Merge pull request #245 from FloatingArrayDesign/dev

Release 2.3.6

Author: sanguinariojoe

.github/workflows/python-wheels-emulated.yml

@@ -24,7 +24,7 @@ jobs:
         os: ${{ fromJSON(inputs.os) }}
     env:
       # Skip 32-bit windows wheels builds.
-      CIBW_SKIP: "*-win32* *musllinux*"
+      CIBW_SKIP: "*-win32* *musllinux* pp38* pp39* pp310*"
       CIBW_ARCHS: ${{inputs.arch}}
       CIBW_ENVIRONMENT_LINUX: "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/project/install/lib"
       CIBW_BEFORE_ALL_LINUX: >
@@ -38,15 +38,20 @@ jobs:
         fi &&
         cmake -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=install -DEXTERNAL_EIGEN:BOOL=OFF -DPYTHON_WRAPPER:BOOL=OFF -DFORTRAN_WRAPPER:BOOL=OFF -DRUST_WRAPPER:BOOL=OFF -DUSE_VTK=ON -DVTK_DIR=$VTK_DIR -DMOORDYN_PACKAGE_IGNORE_VTK_DEPENDENCY=ON -DBUILD_TESTING=OFF &&
         cmake --build build --config Release &&
-        cmake --install build --config Release
+        cmake --install build --config Release &&
+        rm -rf docs extern source tests
+      CIBW_BEFORE_BUILD_WINDOWS: "pip install delvewheel"
       CIBW_BEFORE_ALL_WINDOWS: >
-        cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/install -DEXTERNAL_EIGEN:BOOL=OFF -DPYTHON_WRAPPER:BOOL=OFF -DFORTRAN_WRAPPER:BOOL=OFF -DRUST_WRAPPER:BOOL=OFF -DUSE_VTK=ON -DVTK_DIR=${{github.workspace}}/vtk/lib/cmake/vtk-9.2/ -DMOORDYN_PACKAGE_IGNORE_VTK_DEPENDENCY=ON -DBUILD_TESTING=OFF &&
-        cmake --build ${{github.workspace}}/build --config Release &&
-        cmake --install ${{github.workspace}}/build --config Release
+        cmake -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=install -DEXTERNAL_EIGEN:BOOL=OFF -DPYTHON_WRAPPER:BOOL=OFF -DFORTRAN_WRAPPER:BOOL=OFF -DRUST_WRAPPER:BOOL=OFF -DUSE_VTK=ON -DVTK_DIR=vtk/lib/cmake/vtk-9.2/ -DMOORDYN_PACKAGE_IGNORE_VTK_DEPENDENCY=ON -DBUILD_TESTING=OFF &&
+        cmake --build build --config Release &&
+        cmake --install build --config Release &&
+        rm -rf docs extern source tests
+      CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair --add-path install/bin -w {dest_dir} {wheel}"
       CIBW_BEFORE_ALL_MACOS: >
-        cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/install -DEXTERNAL_EIGEN:BOOL=OFF -DPYTHON_WRAPPER:BOOL=OFF -DFORTRAN_WRAPPER:BOOL=OFF -DRUST_WRAPPER:BOOL=OFF -DUSE_VTK=ON -DMOORDYN_PACKAGE_IGNORE_VTK_DEPENDENCY=ON -DBUILD_TESTING=OFF -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 &&
-        cmake --build ${{github.workspace}}/build --config Release &&
-        cmake --install ${{github.workspace}}/build --config Release
+        cmake -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=install -DEXTERNAL_EIGEN:BOOL=OFF -DPYTHON_WRAPPER:BOOL=OFF -DFORTRAN_WRAPPER:BOOL=OFF -DRUST_WRAPPER:BOOL=OFF -DUSE_VTK=ON -DMOORDYN_PACKAGE_IGNORE_VTK_DEPENDENCY=ON -DBUILD_TESTING=OFF -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 &&
+        cmake --build build --config Release &&
+        cmake --install build --config Release &&
+        rm -rf docs extern source tests
       
     steps:
       - uses: actions/checkout@v4

CHANGELOG.md

@@ -1,3 +1,16 @@
+## [](https://github.com/core-marine-dev/MoorDyn/compare/v2.3.5...v) (2024-08-14)
+
+### Bug Fixes
+
+* **python-wheels:** {project} placeholder seems to be ignored/invalid ([0a97f4d](https://github.com/core-marine-dev/MoorDyn/commit/0a97f4dcff2bfa1f83c0b943f0c1695b71e33f69))
+* **python-wheels:** Add the DLL path to delvewheel ([9310754](https://github.com/core-marine-dev/MoorDyn/commit/9310754b965ee3602db579e22fd1f242970dff05))
+* **python-wheels:** Remove the useless folders after installing ([e6aa341](https://github.com/core-marine-dev/MoorDyn/commit/e6aa341be866183266afacd996accf0afde30837))
+* **python-wheels:** Temporary disable pypy3.10, which is not working on the CI ([49dd580](https://github.com/core-marine-dev/MoorDyn/commit/49dd5805db58c21a09a7012cdf6cce685ceeaf72))
+* **python-wheels:** Temporary disable pypy3.8, which is not working on the CI ([27166f6](https://github.com/core-marine-dev/MoorDyn/commit/27166f6575586727d2893bc9094eb3fb121aed05))
+* **python-wheels:** Temporary disable pypy3.9, which is not working on the CI ([b5b4003](https://github.com/core-marine-dev/MoorDyn/commit/b5b400327b9ec1debeab328c57a314715b0740d9))
+* **python-wheels:** Use delvewheel on Windows ([89b5ddc](https://github.com/core-marine-dev/MoorDyn/commit/89b5ddcbc5f64404ff902c8a536e304052ab580a))
+* **python-wheels:** Use the installed headers ([ad18025](https://github.com/core-marine-dev/MoorDyn/commit/ad18025c6ff5353f4c99fa7bd58a988c5016c9cd))
+* resolves typos and warnings thrown at compiling ([e4a8f08](https://github.com/core-marine-dev/MoorDyn/commit/e4a8f08195e031cbfecfd30574edaad08b15a4d0))
 ## [](https://github.com/core-marine-dev/MoorDyn/compare/v2.3.3...v) (2024-08-07)
 
 ### Features

CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.10)
 set(MOORDYN_MAJOR_VERSION 2)
 set(MOORDYN_MINOR_VERSION 3)
-set(MOORDYN_PATCH_VERSION 5)
+set(MOORDYN_PATCH_VERSION 6)
 set(MOORDYN_VERSION ${MOORDYN_MAJOR_VERSION}.${MOORDYN_MINOR_VERSION})
 project(Moordyn VERSION ${MOORDYN_VERSION})
 

docs/compiling.rst

@@ -30,24 +30,78 @@ Pre-Compiled Releases
 ---------------------
 .. _releases:
 
-Pre-compiled releases can be found at the
-`releases page <https://github.com/FloatingArrayDesign/MoorDyn/releases>`_. These releases contain the 
-libraries and header files required by driver scripts. These provide the same libraries as compiling 
-as a :ref:`simple library <compile_simple>` and as compiling with :ref:`cmake <CMake_compile>`. Typically 
-if you are just looking for the compiled libraries, this is the easiest way to obtain them.
+Typically if you are just looking for the compiled libraries,
+either because it is a dependency of some other software,
+or because you are integrating it on your C/C++ project,
+this is the easiest way to obtain them.
 
-The lastest release corresponds to the current state of the master branch of MoorDyn. The releases 
-contain the source code, as well as three executables (OS dependent) that install the libraries and 
-header files. The executables correspond to the following OS:
+Depending on your OS, you have several options to download and install
+precompiled packages.
+No matter the way you install it, the precompiled package will provide you with
+the same libraries, headers and CMake project files as compiling with
+:ref:`cmake <CMake_compile>`.
 
-* Windows: Moordyn-X.Y.Z-win64.exe (with X.Y.Z replaced by the specific version)
-* Linux: Moordyn-X.Y.Z-Linux.sh 
-* MacOS: Moordyn-X.Y.Z-Darwin.sh
+Windows
+^^^^^^^
+
+An installer for each released version can be found at the
+`releases page <https://github.com/FloatingArrayDesign/MoorDyn/releases>`_.
+Just select/expand the latest release, download the file named
+"Moordyn-X.Y.Z-win64.exe" (with X.Y.Z the specific version you chosen) and
+execute it.
+
+MacOS
+^^^^^
+
+Similarly to Windows, just head your browser to the
+`releases page <https://github.com/FloatingArrayDesign/MoorDyn/releases>`_,
+select/expand the latest release, download the file named
+"Moordyn-X.Y.Z-Darwin.sh" (with X.Y.Z the specific version you chosen) and
+execute it.
+
+NOTE: The self-extracting file you have downloaded cannot be executed until you
+give it execution permissions.
+This can be done by executing the following command:
+
+.. code-block:: bash
+   
+   chmod u=rwx <executable name>
+
+Linux
+^^^^^
+
+Some GNU/Linux distributions have already packages deployed for their package
+managers, which would make your life way easier.
+Otherwise, a self-extracting package is also provided.
+
+Arch
+""""
+
+There is an AUR package that you can easily install on your system, just typing
+
+.. code-block:: bash
+   
+   yay -S moordyn
+
+This is also valid for Arch derivatives, like Manjaro or Endeavour OS.
+
+Others
+""""""
+
+On other Linux distributions you can give a shot to the self-extracting
+package.
+However, it is strongly recommended to compile it yourself with
+:ref:`cmake <CMake_compile>`.
 
-To install the MoorDyn libraries, download the appropriate executable for your library and execute it.  
+To use the self-extracting package head your browser to the
+`releases page <https://github.com/FloatingArrayDesign/MoorDyn/releases>`_,
+select/expand the latest release, download the file named
+"Moordyn-X.Y.Z-Linux.sh" (with X.Y.Z the specific version you chosen) and
+execute it.
 
-NOTE: When you download the self-extracting files for Linux and MacOS they
-cannot be launched until you give them execution permissions. This can be done by executing the following command:
+NOTE: The self-extracting file you have downloaded cannot be executed until you
+give it execution permissions.
+This can be done by executing the following command:
 
 .. code-block:: bash
    

source/Body.cpp

@@ -108,7 +108,7 @@ Body::setup(int number_in,
 	rPointRel.clear();
 	r6RodRel.clear();
 
-	// set up body initial mass matrix (excluding any rods or attachements)
+	// set up body initial mass matrix (excluding any rods or attachments)
 	mat6 Mtemp = mat6::Zero();
 	Mtemp(Eigen::seqN(0, 3), Eigen::seqN(0, 3)) = mat::Identity() * bodyM;
 	Mtemp(Eigen::seqN(3, 3), Eigen::seqN(3, 3)) = bodyI.asDiagonal();

source/Body.hpp

@@ -63,7 +63,7 @@ class Rod;
 /** @class Body Body.hpp
  * @brief A rigid body
  *
- * Some really basic dynamics are implemented for rigid bodiesout of the box,
+ * Some really basic dynamics are implemented for rigid bodies out of the box,
  * which can be extended through the usage of coupled ones.
  *
  * In the configuration file the options are:
@@ -144,7 +144,7 @@ class Body final : public io::IO, public SuperCFL
 	/// total body mass + added mass matrix including all elements
 	mat6 M;
 	/// starting mass and added mass matrix (6x6) of body without any rod
-	/// elements in inertital orientation
+	/// elements in inertial orientation
 	mat6 M0;
 
 	/// orientation matrix of body (rotation matrix that gets it to its current

source/IO.cpp

@@ -91,7 +91,7 @@ pack754(long double f, unsigned bits, unsigned expbits)
 	}
 	fnorm = fnorm - 1.0;
 
-	// calculate the binary form (non-float) of the significand data
+	// calculate the binary form (non-float) of the significant data
 	significand = fnorm * ((1LL << significandbits) + 0.5f);
 
 	// get the biased exponent

source/IO.hpp

@@ -53,7 +53,7 @@ namespace moordyn {
 namespace io {
 
 /** @class IO IO.hpp
- * @brief A base class for all the entitites that must save/load data to/from
+ * @brief A base class for all the entities that must save/load data to/from
  * disk
  *
  * @note Since this class already publicly inherits moordyn::LogUser, all the
@@ -108,91 +108,91 @@ class IO : public LogUser
 	virtual uint64_t* Deserialize(const uint64_t* data) = 0;
 
   protected:
-	/** @brief Pack an unsigned integer to make it writtable
+	/** @brief Pack an unsigned integer to make it writable
 	 * @param i The unsigned integer number
 	 * @return The packed number
 	 */
 	uint64_t Serialize(const uint64_t& i);
 
-	/** @brief Pack an integer to make it writtable
+	/** @brief Pack an integer to make it writable
 	 * @param i The integer number
 	 * @return The packed number
 	 */
 	uint64_t Serialize(const int64_t& i);
 
-	/** @brief Pack a float to make it writtable
+	/** @brief Pack a float to make it writable
 	 * @param f The float number
 	 * @return The packed number
 	 */
 	uint64_t Serialize(const real& f);
 
-	/** @brief Pack a 3D vector to make it writtable
+	/** @brief Pack a 3D vector to make it writable
 	 * @param m The matrix
 	 * @return The packed matrix
 	 */
 	std::vector<uint64_t> Serialize(const vec& m);
 
-	/** @brief Pack a 6D vector to make it writtable
+	/** @brief Pack a 6D vector to make it writable
 	 * @param m The matrix
 	 * @return The packed matrix
 	 */
 	std::vector<uint64_t> Serialize(const vec6& m);
 
-	/** @brief Pack a 3x3 matrix to make it writtable
+	/** @brief Pack a 3x3 matrix to make it writable
 	 * @param m The matrix
 	 * @return The packed matrix
 	 */
 	std::vector<uint64_t> Serialize(const mat& m);
 
-	/** @brief Pack a 6x6 matrix to make it writtable
+	/** @brief Pack a 6x6 matrix to make it writable
 	 * @param m The matrix
 	 * @return The packed matrix
 	 */
 	std::vector<uint64_t> Serialize(const mat6& m);
 
-	/** @brief Pack a quaternion to make it writtable
+	/** @brief Pack a quaternion to make it writable
 	 * @param m The quaternion
 	 * @return The packed quaternion
 	 */
 	std::vector<uint64_t> Serialize(const quaternion& m);
 
-	/** @brief Pack an XYZQuat to make it writtable
+	/** @brief Pack an XYZQuat to make it writable
 	 * @param m The XYZQuat
 	 * @return The packed XYZQuat
 	 */
 	std::vector<uint64_t> Serialize(const XYZQuat& m);
 
-	/** @brief Pack a list of floating point numbers to make it writtable
+	/** @brief Pack a list of floating point numbers to make it writable
 	 * @param l The list
 	 * @return The packed list
 	 */
 	std::vector<uint64_t> Serialize(const std::vector<real>& l);
 
-	/** @brief Pack a list of 3D vectors to make it writtable
+	/** @brief Pack a list of 3D vectors to make it writable
 	 * @param l The list
 	 * @return The packed list
 	 */
 	std::vector<uint64_t> Serialize(const std::vector<vec>& l);
 
-	/** @brief Pack a list of 6D vectors to make it writtable
+	/** @brief Pack a list of 6D vectors to make it writable
 	 * @param l The list
 	 * @return The packed list
 	 */
 	std::vector<uint64_t> Serialize(const std::vector<vec6>& l);
 
-	/** @brief Pack a list of 3x3 matrices to make it writtable
+	/** @brief Pack a list of 3x3 matrices to make it writable
 	 * @param l The list
 	 * @return The packed list
 	 */
 	std::vector<uint64_t> Serialize(const std::vector<mat>& l);
 
-	/** @brief Pack a list of 6x6 matrices to make it writtable
+	/** @brief Pack a list of 6x6 matrices to make it writable
 	 * @param l The list
 	 * @return The packed list
 	 */
 	std::vector<uint64_t> Serialize(const std::vector<mat6>& l);
 
-	/** @brief Pack a list of lists to make it writtable
+	/** @brief Pack a list of lists to make it writable
 	 * This function might act recursively
 	 * @param l The list
 	 * @return The packed list

source/Line.cpp

@@ -552,7 +552,7 @@ Line::GetLineOutput(OutChanProps outChan)
 	else if (outChan.QType == VelZ)
 		return rd[outChan.NodeID][2];
 	else if (outChan.QType == Ten) {
-		if ((outChan.NodeID == 0) || (outChan.NodeID == N))
+		if ((outChan.NodeID == 0) || (outChan.NodeID == (int)N))
 			return getNodeForce(outChan.NodeID).norm();
 		return getNodeTen(outChan.NodeID).norm();
 	}
@@ -775,7 +775,7 @@ Line::getStateDeriv()
 	// NOTE:
 	// Jose Luis Cercos-Pita: This is by far the most consuming function of the
 	// whole library, just because it is called every single time substep and
-	// it shall makecomputations in every single line node. Thus it is worthy
+	// it shall make computations in every single line node. Thus it is worthy
 	// to invest effort on keeping it optimized.
 
 	// attempting error handling <<<<<<<<

source/Line.h

@@ -281,7 +281,7 @@ extern "C"
 	 * the water density, \f$F(i)\f$ the portion of the segment submerged and
 	 * \f$\bar{g}\f$ the gravity acceleration.
 	 *
-	 * The weight and bounyancy force at any internal node is computed as the
+	 * The weight and buoyancy force at any internal node is computed as the
 	 * average of the surrounding segments, while on the line-ends \b half of
 	 * the associated ending segment weight force is returned.
 	 *