Merge branch 'f-macos' into f-final-review

.docker/Dockerfile

@@ -7,8 +7,8 @@ RUN mkdir build
 WORKDIR /libcaosdb/build
 RUN conan create .. -s "compiler.libcxx=libstdc++11"
 
-RUN apt-get install -y octave-common/buster-backports liboctave7/buster-backports octave/buster-backports
-RUN apt-get install -y liboctave-dev/buster-backports
+RUN apt-get install -y octave-common liboctave8 octave
+RUN apt-get install -y liboctave-dev
 RUN apt-get install -y unzip
 RUN apt-get install -y wget
 

CMakeLists.txt

@@ -30,7 +30,10 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 # dependency management with conan
 include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
-conan_basic_setup()
+conan_basic_setup(KEEP_RPATHS)
+
+# remove path-like elements from CONAN_LIBS, relevant on MacOS
+string(REGEX REPLACE ";/[^;]+" "" CONAN_LIBS "${CONAN_LIBS}")
 
 # fix grpc - remove unsecure (no-op ssl implementations)
 string(REGEX REPLACE ";grpc\\+?\\+?_unsecure" "" CONAN_LIBS_GRPC
@@ -75,6 +78,7 @@ execute_process(COMMAND mkoctfile -p OCTAVE_LIBS
     OUTPUT_VARIABLE OCTLIBS
     )
 string(REGEX REPLACE "\n" "" OCTLIBS "${OCTLIBS}")
+string(REGEX REPLACE "-l" "" OCTLIBS "${OCTLIBS}")
 string(REGEX REPLACE " " ";" OCTLIBS "${OCTLIBS}")
 
 set(MAOXDB_DIR "${PROJECT_SOURCE_DIR}/src/lib")
@@ -101,7 +105,8 @@ file(MAKE_DIRECTORY ${PKG_INST_DIR})
 string(REGEX REPLACE ";" ";-I" _MKOCTFILE_INCLUDES "-I${CONAN_INCLUDE_DIRS};${MAOXDB_DIR}")
 string(REGEX REPLACE ";" ";-L" _MKOCTFILE_LIB_DIRS "-L${CONAN_LIB_DIRS};${_MAOX_LIB_DIR}")
 string(REGEX REPLACE ";" ";-l" _MKOCTFILE_LIBS "-lmaoxdb;${CONAN_LIBS}")
-string(REGEX REPLACE ";" ":" _MKOCTFILE_RPATH "${CONAN_LIB_DIRS}")
+# Needs this in front: -Wl,-rpath,
+string(REGEX REPLACE ";" ",-rpath," _MKOCTFILE_RPATH "${CONAN_LIB_DIRS}")
 set(_MKOCTFILE_OPTIONS "-Wl,-rpath,${_MKOCTFILE_RPATH}" "--mex" "-std=gnu++17"
     "-L/usr/local/lib" ${_MKOCTFILE_INCLUDES} ${_MKOCTFILE_LIB_DIRS} ${_MKOCTFILE_LIBS})
 
@@ -212,9 +217,8 @@ if(TEST)
             ${OCTINCLUDEDIR}
             ${MAOXDB_DIR})
         target_link_libraries(${test_case_name} PUBLIC
-            maoxdb ${CONAN_LIBS_CAOSDB} ${CONAN_LIBS_GTEST} ${CONAN_LIBS_BOOST})
+            maoxdb ${OCTLIBS} ${CONAN_LIBS_CAOSDB} ${CONAN_LIBS_GTEST} ${CONAN_LIBS_BOOST})
         target_link_directories(${test_case_name} PUBLIC ${OCTLIBDIR})
-        target_link_options(${test_case_name} PUBLIC ${OCTLIBS})
         message(STATUS "CMAKE_CURRENT_BINARY_DIR: ${CMAKE_CURRENT_BINARY_DIR}")
         gtest_discover_tests(${test_case_name}
             WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"

Makefile

@@ -29,6 +29,17 @@ help:
 	@echo "    test - run unit tests."
 	@echo "    doc - create the documentation."
 
+###############################################################################
+#                        Environment dependent options                        #
+###############################################################################
+
+TAR_OPTS := undefined
+ifeq "$(shell tar --version | head -n 1 | grep -o -i gnu | tr '[:upper:]' '[:lower:]')" 'gnu'
+	TAR_OPTS := --exclude-ignore-recursive=.gitignore --transform 's,^\.,caosdb,'
+else
+	TAR_OPTS := --exclude-from=.gitignore -s '/^\./caosdb/'
+endif
+
 .PHONY: doc
 doc:
 	$(MAKE) -C doc html
@@ -85,6 +96,7 @@ linting_cpp:
 
 test: install
 	$(MAKE) -C test test
+	@echo "All tests successfully passed."
 .PHONY: test
 
 test_octave: install
@@ -108,6 +120,10 @@ install: pkg
 
 .PHONY: caosdb.tar.gz
 dist/caosdb.tar.gz: dist/
+# For GNU tar:
+# [...] --exclude-ignore-recursive=.gitignore --transform 's,^\.,caosdb,' [...]
+# For POSIX tar:
+# [...] --exclude-from=.gitignore -s '/^\./caosdb/' [...]
 	tar -czf dist/caosdb.tar.gz \
 	--exclude=.git* \
 	--exclude=env* \
@@ -116,8 +132,8 @@ dist/caosdb.tar.gz: dist/
 	--exclude=.docker* \
 	--exclude=dist* \
 	--exclude=inst* \
-	--exclude-ignore-recursive=.gitignore \
-	--transform 's,^\.,caosdb,' .
+	$(TAR_OPTS) \
+	.
 
 .PHONY: dist/
 dist/:

README_SETUP.md

@@ -5,12 +5,12 @@
 This package requires the following software:
 
 - conan: `pip install conan`
-- Create a local conan package libcaosdb: See https://gitlab.indiscale.com/caosdb/src/caosdb-cpplib for
-  further instructions.
+- Create a local *libcaosdb* conan package: See
+  https://gitlab.indiscale.com/caosdb/src/caosdb-cpplib for further instructions.
 - For running this library, a valid libcaosdb configuration is needed, for example a
   `.caosdb_client.json` file in your home directory or current working directory.  Please look at
   [`README_SETUP.md` in caosdb-cpplib](https://gitlab.indiscale.com/caosdb/src/caosdb-cpplib/-/blob/main/README_SETUP.md) for more information.
-* MOxUnit for unit tests, see below.
+- For unit tests, MOxUnit is required, see below.
 
 ## Install and Load
 
@@ -21,6 +21,12 @@ This package requires the following software:
     * `pkg install dist/caosdb.tar.gz`
     * `pkg load caosdb;`
 
+### Notes for installing on MacOS ###
+
+On MacOS, installation should work the same as on Linux.  *libcaosdb* should be installed with conan
+as described in [its documentation](https://gitlab.indiscale.com/caosdb/src/caosdb-cpplib).  Octave must of course also be installed, the developers
+tested it with the [homebrew version](https://formulae.brew.sh/formula/octave).
+
 ## Run Unit Tests
 
 * run `make test`

dev-requirements.txt

-attrs==21.2.0
+alabaster==0.7.12
+Babel==2.9.1
 bottle==0.12.19
-certifi==2021.10.8
-chardet==4.0.0
-charset-normalizer==2.0.7
+certifi==2021.5.30
+charset-normalizer==2.0.1
 colorama==0.4.4
-conan==1.41.0
-deprecation==2.1.0
-distro==1.6.0
+conan==1.43.0
+deprecation==2.0.7
+distro==1.5.0
+docutils==0.16
 fasteners==0.16.3
 future==0.18.2
 idna==3.2
+imagesize==1.2.0
 Jinja2==2.11.3
-jsonschema==4.1.0
 MarkupSafe==2.0.1
+miss-hit==0.9.24
+miss-hit-core==0.9.24
 node-semver==0.6.1
 packaging==21.0
 patch-ng==1.17.4
 pluginbase==1.0.1
-Pygments==2.10.0
+Pygments==2.9.0
 PyJWT==1.7.1
 pyparsing==2.4.7
-pyrsistent==0.18.0
 python-dateutil==2.8.2
+pytz==2021.1
 PyYAML==5.4.1
 requests==2.26.0
-six==1.16.0
-tqdm==4.62.3
-urllib3==1.26.7
+six==1.15.0
+snowballstemmer==2.1.0
+Sphinx==4.1.0
+sphinx-rtd-theme==0.5.2
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+tqdm==4.61.2
+urllib3==1.26.6

src/configure

@@ -2,10 +2,47 @@
 
 set -e
 
-# See https://octave.org/doc/interpreter/Creating-Packages.html
+###############################################################################
+## Package generation script                                                 ##
+## See https://octave.org/doc/interpreter/Creating-Packages.html             ##
+###############################################################################
 
 echo "Octave CaosDB SRC_DIR: $PWD"
 
+# Environment specific settings ###############################################
+
+CONAN_SETTINGS="compiler.libcxx=libstdc++11"
+
+# OS specific handling, with code by Ken Jackson and oHo,
+# from https://stackoverflow.com/a/52062069/232888 and
+# https://stackoverflow.com/a/14777895/232888
+if [[ $PATH == *";"* ]] ; then
+	DETECTED_OS=Windows
+else
+	DETECTED_OS=$(uname 2>/dev/null || echo Unknown)
+	DETECTED_OS="${DETECTED_OS//CYGWIN%/Cygwin}"
+	DETECTED_OS="${DETECTED_OS//MSYS%/MSYS}"
+	DETECTED_OS="${DETECTED_OS//MINGW%/MSYS}"
+fi
+
+if [[ $DETECTED_OS == Darwin ]]; then  # Test if we are on MacOS
+	CONAN_SETTINGS="compiler.cppstd=17"
+fi
+
+# Functions for systems without coreutils (such as MacOS) #####################
+
+# realpath
+# Copied from https://stackoverflow.com/a/45420776/232888 by user
+# [mattes](https://stackoverflow.com/users/2142441/mattes)
+if ! which realpath > /dev/null; then
+   realpath () {
+       python -c 'import os, sys; print(os.path.realpath(sys.argv[1]))' "$1"
+   }
+fi
+
+###############################################################################
+# The real script starts here #################################################
+
 # clean-up
 INST_DIR="$(realpath ../inst)"
 echo "Octave CaosDB INST_DIR: $INST_DIR"
@@ -30,7 +67,7 @@ fi
 
 # conan install .. -s "compiler.libcxx=libstdc++11"
 # cmake -G "Unix Makefiles" -D CMAKE_BUILD_TYPE=Release -D AUTOFORMATTING=OFF ..
-conan install .. -s "compiler.libcxx=libstdc++11" -s build_type="${BUILD_TYPE}"
+conan install .. -s $CONAN_SETTINGS -s build_type="${BUILD_TYPE}"
 cmake -G "Unix Makefiles" -D CMAKE_BUILD_TYPE="${BUILD_TYPE}" -D AUTOFORMATTING=OFF ..
 
 popd

src/lib/maoxdb.hpp

@@ -303,7 +303,7 @@ inline auto mxEmptyCell() -> mxArray * {
  * @details Valgrind complains when duplicating empty sparse arrays.  This implementation works
  * around the bug, but does not care about sparse arrays inside cell arrays yet.
  */
-auto mxDuplicateArrayAlsoSparse(mxArray *array) -> mxArray*;
+auto mxDuplicateArrayAlsoSparse(mxArray *array) -> mxArray *;
 
 /**
  * @brief      Get the value of a scalar array.

test/Makefile

@@ -23,6 +23,24 @@
 #
 # Specifically, the libraries must have be installed with Conan.
 
+CONAN_SETTINGS = "compiler.libcxx=libstdc++11"
+
+# OS specific handling, with code by Ken Jackson and oHo,
+# from https://stackoverflow.com/a/52062069/232888 and
+# https://stackoverflow.com/a/14777895/232888
+ifeq '$(findstring ;,$(PATH))' ';'
+	DETECTED_OS := Windows
+else
+	DETECTED_OS := $(shell uname 2>/dev/null || echo Unknown)
+	DETECTED_OS := $(patsubst CYGWIN%,Cygwin,$(DETECTED_OS))
+	DETECTED_OS := $(patsubst MSYS%,MSYS,$(DETECTED_OS))
+	DETECTED_OS := $(patsubst MINGW%,MSYS,$(DETECTED_OS))
+endif
+ifeq ($(DETECTED_OS),Darwin)  # Test if we are on MacOS
+	CONAN_SETTINGS := "compiler.cppstd=17"
+endif
+
+
 .PHONY: help
 help:
 	@echo "Targets:"
@@ -46,9 +64,9 @@ test_octave:
 
 # && make test || echo "Test(s) failed."; exit 1
 test_cpp:
-	$(eval BUILD_DIR ::= $(shell mktemp -d build_test_XXXXXXXX))
+	$(eval BUILD_DIR := $(shell mktemp -d build_test_XXXXXXXX))
 	cd $(BUILD_DIR)                                                \
-    && conan install ../.. -s "compiler.libcxx=libstdc++11"      \
+    && conan install ../.. -s $(CONAN_SETTINGS)                  \
     && cmake -D TEST=On ../..                                    \
     && make test_detailed                                        \
     || (echo "Test(s) failed."; exit 1)

test/Run_Test.m

-% (C) Copyright 2021 IndiScale GmbH <info@indiscale.com>
-% (C) Copyright 2021 Timm FItschen <t.fitschen@indiscale.com>
+% Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
+% Copyright (C) 2021 Daniel Hornung <d.hornung@indiscale.com>
+% Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
 %
 % This file is a part of the CaosDB Project.
 %

test/test_caosdb_conversion.cpp

@@ -100,7 +100,7 @@ TEST(caosdb_conversion, value_Bool) {
 }
 
 TEST(caosdb_conversion, value_Integer) {
-  auto value_contents = generateValues<long>();
+  auto value_contents = generateValues<int64_t>();
   test_value_native(value_contents);
 }
 

test/test_utilities.cpp

@@ -165,7 +165,7 @@ TEST(utilities, duplicateArray) {
 
   // Simple double array
   auto number_array = mxCreateDoubleMatrix(2, 2, mxREAL);
-  double number_data[4] = {0.0, 1.0, 0.0/0.0, 3.14};
+  double number_data[4] = {0.0, 1.0, 0.0 / 0.0, 3.14};
   mxSetData(number_array, number_data);
   auto number_dup = mxDuplicateArrayAlsoSparse(number_array);
   auto number_data_dup = static_cast<double *>(mxGetData(number_dup));
@@ -174,7 +174,7 @@ TEST(utilities, duplicateArray) {
   EXPECT_EQ(mxGetNumberOfElements(number_array), mxGetNumberOfElements(number_dup));
 
   // Struct array
-  auto fields = std::vector<const char*>{"role", "value", "errors"};
+  auto fields = std::vector<const char *>{"role", "value", "errors"};
   auto errors_cell = mxCreateCellMatrix(1, 2);
   mxSetCell(errors_cell, 0, mxScalarINT64(23));
   mxSetCell(errors_cell, 1, mxCreateString("twenty three"));
@@ -190,7 +190,6 @@ TEST(utilities, duplicateArray) {
   EXPECT_EQ(struct_data_value_dup, 23.42);
   EXPECT_EQ(mxGetScalarValue<int64_T>(mxGetCell(struct_data_errors_dup, 0)), 23);
   EXPECT_EQ(mxGetStdString(mxGetCell(struct_data_errors_dup, 1)), "twenty three");
-
 }
 
 /**