Merge pull request #99 from jhu-cisst/rc-1.2.1

1.2.1

.github/workflows/macos-11.0.yml → .github/workflows/macos-latest.yml

@@ -1,4 +1,4 @@
-name: macOS 11.0
+name: macOS latest
 
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
@@ -11,7 +11,7 @@ on:
 jobs:
   build:
 
-    runs-on: macos-11.0
+    runs-on: macos-latest
 
     steps:
     - uses: actions/checkout@v2
@@ -29,7 +29,7 @@ jobs:
     - name: Build cisstNetlib
       working-directory: ${{github.workspace}}/cisstNetlib-build
       run: |
-        cmake ${{github.workspace}}/cisstNetlib-source -DCMAKE_Fortran_COMPILER=gfortran-9
+        cmake ${{github.workspace}}/cisstNetlib-source -DcisstNetlib_LANGUAGE=C
         cmake --build . --config Release
         sudo cmake --build . --target install
 

CHANGELOG.md

@@ -1,6 +1,20 @@
 Change log
 ==========
 
+
+1.2.1 (2022-12-29)
+==================
+
+* API changes:
+  * CMake find_package now uses CMake `COMPATIBILITY` `SameMajorVersion`, older code used custom version check equivalent to `SameMinorVersion`
+* Deprecated features:
+  * cisstNumerical: polynomial is not compiled by default, set `CISST_NMR_COMPILE_POLYNOMIALS` if these are needed. We plan to remove this code in later releases 
+* Bug fixes:
+  * cisstDataGenerator: fixed export for enums and static methods
+  * cisstNumerical: for OS requiring CLAPACK, cisstNetlib now uses a fork that has been updated to support recent C/C++ compilers
+  * Fixed some GitHub actions/workflows
+
+
 1.2.0 (2022-11-21)
 ==================
 

CMakeLists.txt

@@ -1,7 +1,7 @@
 ## -*- Mode: CMAKE; tab-width: 2; indent-tabs-mode: nil; c-basic-offset: 2 -*-
 
 #
-# (C) Copyright 2005-2021 Johns Hopkins University (JHU), All Rights Reserved.
+# (C) Copyright 2005-2023 Johns Hopkins University (JHU), All Rights Reserved.
 #
 # --- begin cisst license - do not edit ---
 #
@@ -13,10 +13,10 @@
 
 
 # Backward compatibility
-cmake_minimum_required (VERSION 3.0)
+cmake_minimum_required (VERSION 3.10)
 
 # cisst (Computer Integrated Surgical Systems and Technology)
-project (cisst VERSION 1.2.0)
+project (cisst VERSION 1.2.1)
 
 # cisst compiler settings
 include (cmake/cisstSettings.cmake)
@@ -545,8 +545,8 @@ install (FILES "${cisst_BINARY_DIR}/cisst-config.cmake-to-be-installed"
 
 # CMake use cisst file
 set (CISST_CMAKE_FILES_TO_COPY
-     Usecisst.cmake cisstSettings.cmake cisstMacros.cmake cisstConfigVersion.cmake.in
-     sawRevision.h.in sawConfig.cmake.in sawConfigVersion.cmake.in)
+     Usecisst.cmake cisstSettings.cmake cisstMacros.cmake
+     sawRevision.h.in sawConfig.cmake.in)
 foreach (cmake_file_to_copy ${CISST_CMAKE_FILES_TO_COPY})
   # copy to build for users not installing
   configure_file ("${CISST_CMAKE_SOURCE_DIR}/${cmake_file_to_copy}"

cisstMultiTask/applications/cisstComponentManager/CMakeLists.txt

@@ -1,6 +1,5 @@
 #
-#
-# (C) Copyright 2011-2012 Johns Hopkins University (JHU), All Rights Reserved.
+# (C) Copyright 2011-2023 Johns Hopkins University (JHU), All Rights Reserved.
 #
 # --- begin cisst license - do not edit ---
 #
@@ -11,9 +10,9 @@
 # --- end cisst license ---
 
 # name of project and executable
-project (cisstComponentManager)
+project (cisstComponentManager VERSION ${cisst_VERSION})
 
-cmake_minimum_required (VERSION 2.6)
+cmake_minimum_required (VERSION 3.10)
 
 # create a list of libraries needed for this project
 set (REQUIRED_CISST_LIBRARIES cisstCommon cisstOSAbstraction cisstMultiTask)

cisstNumerical/CMakeLists.txt

@@ -19,6 +19,8 @@ else ()
   option (CISST_HAS_CISSTNETLIB "Use the netlib.org sets of numerical methods in Fortran (provided on cisst.org)." OFF)
 endif ()
 
+option (CISST_NMR_COMPILE_POLYNOMIALS "Compile the cisstNumerical polynomial classes (deprecated)" OFF)
+
 if (CISST_HAS_CISSTNETLIB)
   find_package (CisstNetlib REQUIRED)
   cisst_set_package_settings (cisstNumerical cisstNetlib INCLUDE_DIRECTORIES CISSTNETLIB_INCLUDE_DIR)

cisstNumerical/code/CMakeLists.txt

@@ -1,7 +1,7 @@
 #
 # CMakeLists for cisstNumerical
 #
-# (C) Copyright 2003-2021 Johns Hopkins University (JHU), All Rights Reserved.
+# (C) Copyright 2003-2023 Johns Hopkins University (JHU), All Rights Reserved.
 #
 # --- begin cisst license - do not edit ---
 #
@@ -15,36 +15,44 @@ project (cisstNumerical)
 
 # all source files
 set (SOURCE_FILES
-     nmrBernsteinPolynomial.cpp
-     nmrBernsteinPolynomialLineIntegral.cpp
      nmrGaussJordanInverse.cpp
-     nmrMultiIndexCounter.cpp
-     nmrMultiVariablePowerBasis.cpp
-     nmrPolynomialBase.cpp
-     nmrPolynomialTermPowerIndex.cpp
-     nmrSingleVariablePowerBasis.cpp
-     nmrStandardPolynomial.cpp
      )
 
-
 # all header files
 set (HEADER_FILES
-     nmrBernsteinPolynomial.h
-     nmrBernsteinPolynomialLineIntegral.h
-     nmrDynAllocPolynomialContainer.h
      nmrExport.h
      nmrGaussJordanInverse.h
      nmrIsOrthonormal.h
      nmrLinearRegression.h
-     nmrMultiIndexCounter.h
-     nmrMultiVariablePowerBasis.h
-     nmrPolynomialBase.h
-     nmrPolynomialContainer.h
-     nmrPolynomialTermPowerIndex.h
-     nmrSingleVariablePowerBasis.h
-     nmrStandardPolynomial.h
      )
 
+if (CISST_NMR_COMPILE_POLYNOMIALS)
+  set (SOURCE_FILES
+    ${SOURCE_FILES}
+    nmrBernsteinPolynomial.cpp
+    nmrBernsteinPolynomialLineIntegral.cpp
+    nmrMultiIndexCounter.cpp
+    nmrMultiVariablePowerBasis.cpp
+    nmrPolynomialBase.cpp
+    nmrPolynomialTermPowerIndex.cpp
+    nmrSingleVariablePowerBasis.cpp
+    nmrStandardPolynomial.cpp
+    )
+  set (HEADER_FILES
+    ${HEADER_FILES}
+    nmrBernsteinPolynomial.h
+    nmrBernsteinPolynomialLineIntegral.h
+    nmrDynAllocPolynomialContainer.h
+    nmrMultiIndexCounter.h
+    nmrMultiVariablePowerBasis.h
+    nmrPolynomialBase.h
+    nmrPolynomialContainer.h
+    nmrPolynomialTermPowerIndex.h
+    nmrSingleVariablePowerBasis.h
+    nmrStandardPolynomial.h
+    )
+endif (CISST_NMR_COMPILE_POLYNOMIALS)
+
 if (CISST_HAS_CISSTNETLIB)
   set (SOURCE_FILES
        ${SOURCE_FILES}

cisstNumerical/code/cisstNumericalBuild.cmake.in

@@ -1,13 +1,10 @@
 #
-# $Id$
-#
 # CMake configuration file for the installed version of cisstNumerical
 #
 # Author(s):  Anton Deguet
 # Created on: 2011-09-21
 #
-# (C) Copyright 2011-2012 Johns Hopkins University (JHU), All Rights
-# Reserved.
+# (C) Copyright 2011-2023 Johns Hopkins University (JHU), All Rights Reserved.
 #
 # --- begin cisst license - do not edit ---
 #
@@ -17,4 +14,6 @@
 #
 # --- end cisst license ---
 
-set (CISST_HAS_CISSTNETLIB @CISST_HAS_CISSTNETLIB_CONFIG@)
+set (CISST_HAS_CISSTNETLIB @CISST_HAS_CISSTNETLIB@)
+
+set (CISST_NMR_COMPILE_POLYNOMIALS @CISST_NMR_COMPILE_POLYNOMIALS@)

cisstNumerical/nmrConfig.h.in

@@ -2,22 +2,18 @@
 /* ex: set filetype=cpp softtabstop=4 shiftwidth=4 tabstop=4 cindent expandtab: */
 
 /*
-$Id$
-
-Author(s): Anton Deguet
-Created on: 2011-09-22
-
-(C) Copyright 2011 Johns Hopkins University (JHU), All Rights
-Reserved.
+  Author(s): Anton Deguet
+  Created on: 2011-09-22
 
+  (C) Copyright 2011-2023 Johns Hopkins University (JHU), All Rights Reserved.
+  
 --- begin cisst license - do not edit ---
 
 This software is provided "as is" under an open source license, with
 no warranty. The complete license can be found in license.txt and
 http://www.cisst.org/cisst/license.txt.
 
 --- end cisst license ---
-
 */
 
 #ifndef _nmrConfig_h
@@ -28,4 +24,6 @@ http://www.cisst.org/cisst/license.txt.
 // Do we have cisstNetlib
 #cmakedefine01 CISST_HAS_CISSTNETLIB
 
+#cmakedefine01 CISST_NMR_COMPILE_POLYNOMIALS
+
 #endif // _nmrConfig_h

cisstNumerical/nmrNetlib.h

@@ -2,12 +2,10 @@
 /* ex: set filetype=cpp softtabstop=4 shiftwidth=4 tabstop=4 cindent expandtab: */
 
 /*
-
   Author(s): Anton Deguet, Simon Leonard
   Created on: 2005-11-24
 
-  (C) Copyright 2005-2010 Johns Hopkins University (JHU), All Rights
-  Reserved.
+  (C) Copyright 2005-2023 Johns Hopkins University (JHU), All Rights Reserved.
 
 --- begin cisst license - do not edit ---
 
@@ -36,14 +34,21 @@ no warranty.  The complete license can be found in license.txt and
 /*! Check if cisstNetlib has a version, i.e. it has for versions
   greater or equal to 2.  In Version 2 we introduced typedefs to make
   sure we use the correct Fortran types. */
-#ifndef CISSTNETLIB_VERSION
+#ifndef cisstNetlib_VERSION
 typedef long int CISSTNETLIB_INTEGER;
 typedef long int CISSTNETLIB_LOGICAL;
 typedef float CISSTNETLIB_FLOAT;
 typedef double CISSTNETLIB_DOUBLE;
 #endif // CISSTNETLIB_VERSION
 
+// for backward compatibility
+#ifndef CISSTNETLIB_VERSION
+#define CISSTNETLIB_VERSION cisstNetlib_VERSION
+#endif
+#ifndef CISSTNETLIB_VERSION_MAJOR
+#define CISSTNETLIB_VERSION_MAJOR cisstNetlib_VERSION_MAJOR
+#endif
+
 #endif // CISST_HAS_CISSTNETLIB
 
 #endif // _nmrNetlib_h
-

cisstNumerical/tests/CMakeLists.txt

@@ -1,8 +1,5 @@
 #
-# CMakeLists for cisstNumerical tests
-#
-# (C) Copyright 2004-2014 Johns Hopkins University (JHU), All Rights
-# Reserved.
+# (C) Copyright 2004-2023 Johns Hopkins University (JHU), All Rights Reserved.
 #
 # --- begin cisst license - do not edit ---
 #
@@ -14,31 +11,38 @@
 
 # all source files
 set (SOURCE_FILES
-     nmrBernsteinPolynomialTest.cpp
-     nmrBernsteinPolynomialLineIntegralTest.cpp
-     nmrDynAllocPolynomialContainerTest.cpp
-     nmrGaussJordanInverseTest.cpp
-     nmrLinearRegressionTest.cpp
-     nmrMultiIndexCounterTest.cpp
-     nmrPolynomialBaseTest.cpp
-     nmrPolynomialTermPowerIndexTest.cpp
-     nmrStandardPolynomialTest.cpp
-     )
+  nmrGaussJordanInverseTest.cpp
+  nmrLinearRegressionTest.cpp
+  )
 
 # all header files
 set (HEADER_FILES
-     nmrBernsteinPolynomialTest.h
-     nmrBernsteinPolynomialLineIntegralTest.h
-     nmrDynAllocPolynomialContainerTest.h
-     nmrGaussJordanInverseTest.h
-     nmrLinearRegressionTest.h
-     nmrMultiIndexCounterTest.h
-     nmrPolynomialBaseTest.h
-     nmrPolynomialTermPowerIndexTest.h
-     nmrStandardPolynomialTest.h
-     )
+  nmrGaussJordanInverseTest.h
+  nmrLinearRegressionTest.h
+  )
+
+if (CISST_NMR_COMPILE_POLYNOMIALS)
+  set (SOURCE_FILES
+    ${SOURCE_FILES}
+    nmrBernsteinPolynomialTest.cpp
+    nmrBernsteinPolynomialLineIntegralTest.cpp
+    nmrDynAllocPolynomialContainerTest.cpp
+    nmrMultiIndexCounterTest.cpp
+    nmrPolynomialBaseTest.cpp
+    nmrPolynomialTermPowerIndexTest.cpp
+    nmrStandardPolynomialTest.cpp
+    )
+  set (HEADER_FILES
+    nmrBernsteinPolynomialTest.h
+    nmrBernsteinPolynomialLineIntegralTest.h
+    nmrDynAllocPolynomialContainerTest.h
+    nmrMultiIndexCounterTest.h
+    nmrPolynomialBaseTest.h
+    nmrPolynomialTermPowerIndexTest.h
+    nmrStandardPolynomialTest.h
+    )
+endif (CISST_NMR_COMPILE_POLYNOMIALS)
 
-# Added tests available for cisstNetlib
 if (CISST_HAS_CISSTNETLIB)
   set (SOURCE_FILES
        ${SOURCE_FILES}
@@ -81,22 +85,6 @@ if (CISST_HAS_CISSTNETLIB)
        )
 endif (CISST_HAS_CISSTNETLIB)
 
-# add files if cnetlib is used
-# IF(CISST_HAS_CNETLIB)
-#  SET(SOURCE_FILES
-#      ${SOURCE_FILES}
-#      nmrLSEISolverTest.cpp
-#      nmrNonLinSolverTest.cpp
-#      )
-
-#  SET(HEADER_FILES
-#      ${HEADER_FILES}
-#      nmrLSEISolverTest.h
-#      nmrNonLinSolverTest.h
-#      )
-#
-# ENDIF(CISST_HAS_CNETLIB)
-
 # paths for headers/libraries
 cisst_set_directories (cisstCommon cisstVector cisstOSAbstraction cisstNumerical cisstTestsDriver)
 

cisstOSAbstraction/osaSerialPort.h

@@ -75,6 +75,10 @@ class CISST_EXPORT osaSerialPort: public cmnGenericObject
                        BaudRate230400 = CBR_230400,
                        BaudRate460800 = CBR_460800};
 #else
+    // MacOS doesn't define some of the baud rates
+    #ifndef B460800
+    #define B460800 460800
+    #endif
     enum BaudRateType {BaudRate300 = B300,
                        BaudRate1200 = B1200,
                        BaudRate9600 = B9600,