Merge pull request #1735 from bennibbelink/update-dependencies

CHANGELOG.rst

@@ -43,7 +43,7 @@ Since last release
 * Changed README.rst installation instructions, tested on fresh Ubuntu-22.04 system with Python 3.11 (#1617, #1644)
 * Resolved various compilation warnings due to use of deprecated APIs (#1671)
 * Update version management in CMake build (#1696)
-* Changed dependency versions in README.rst, INSTALL.rst, and DEPENDENCIES.rst (#1703)
+* Changed dependency versions in README.rst, INSTALL.rst, and DEPENDENCIES.rst (#1703, #1735)
 * Updated minor documentation about updating CHANGELOG.rst, fix formatting for rendering 
   hyperlinks, and change branch name in README instructions on forking for development (#1715)
 

CMakeLists.txt

@@ -306,13 +306,16 @@ IF(NOT CYCLUS_DOC_ONLY)
     # Cython & Python Bindings
     #
     # Use new Python library finder
-    find_package (Python3 COMPONENTS Interpreter Development NumPy)
+    find_package (Python3 REQUIRED COMPONENTS Interpreter Development)
 
     execute_process(COMMAND "${Python3_EXECUTABLE}" -m site --user-site
                     OUTPUT_VARIABLE PYTHON_SITE_PACKAGES
                     OUTPUT_STRIP_TRAILING_WHITESPACE)
     message("-- PYTHON_EXECUTABLE: ${Python3_EXECUTABLE}")
     message("-- PYTHON_SITE_PACKAGES: ${PYTHON_SITE_PACKAGES}")
+    IF (NOT APPLE)
+        set(LIBS ${LIBS} ${Python3_LIBRARIES})
+    ENDIF (NOT APPLE)
 
     # Include the CMake script UseCython.cmake.  This defines add_cython_module().
     # Instruction for use can be found at the top of cmake/UseCython.cmake.
@@ -325,7 +328,7 @@ IF(NOT CYCLUS_DOC_ONLY)
           message(FATAL_ERROR "Cython version is too old, must be 0.25+.")
         endif()
         include(UseCython)
-
+        find_package (Python3 REQUIRED COMPONENTS NumPy)
         find_package(Jinja2 REQUIRED)
         find_package(Pandas REQUIRED)
 
@@ -341,9 +344,6 @@ IF(NOT CYCLUS_DOC_ONLY)
 
         # make sure we know about having python
         add_definitions(-DCYCLUS_WITH_PYTHON)
-        IF (NOT APPLE)
-            set(LIBS ${LIBS} ${Python3_LIBRARIES})
-        ENDIF (NOT APPLE)
         INCLUDE_DIRECTORIES("${CMAKE_CURRENT_BINARY_DIR}/cyclus")
     else(Cython_FOUND)
         # If we don't have Python bindings, we may try to find tcmalloc.
@@ -365,6 +365,7 @@ IF(NOT CYCLUS_DOC_ONLY)
     # NOTE: for some reason, adding quotes around
     # ${Glibmm_INCLUDE_DIRS} breaks Ubuntu 12.04
     set(inc_dirs
+        "${Python3_INCLUDE_DIRS}"
         "${LIBXML2_INCLUDE_DIR}"
         "${LIBXMLXX_INCLUDE_DIRS}"
         "${Glibmm_INCLUDE_DIRS}"
@@ -378,7 +379,6 @@ IF(NOT CYCLUS_DOC_ONLY)
     ENDIF()
     message("-- Include Directories: ${inc_dirs}")
 
-
     if(Cython_FOUND)
         INCLUDE_DIRECTORIES(AFTER "${Python3_INCLUDE_DIRS}" "${_Python3_NumPy_INCLUDE_DIR}")
     endif(Cython_FOUND)

DEPENDENCIES.rst

@@ -22,45 +22,41 @@ In order to facilitate future compatibility with multiple platforms,
 Cyclus is built using ``CMake``. A full list of the Cyclus package
 dependencies is shown below:
 
-====================   ==================
-Package                Minimum Version
-====================   ==================
-``CMake``                3.16.3
-``boost``                1.71.0
-``libxml2``              2.9.10+
-``libxml++``             2.40.1
-``python``               3.8.10
-``sqlite3``              3.31.1
-``HDF5``                 1.10.4+
-``Coin-Cbc``             2.10.3
-``Coin-Clp``             1.17.5
-``zlib``                 1.2.11
-====================   ==================
+====================      ==================
+Package                   Minimum Version
+====================      ==================
+``CMake``                 3.16.3
+``pkg-config``            0.29.1
+``boost``                 1.71.0
+``libxml2``               2.9.10
+``libxml++``              2.40.1
+``python``                3.8.10
+``sqlite3``               3.31.1
+``HDF5``                  1.10.4
+``LAPACK``                3.9.0
+====================      ==================
 
 .. website_include_end
 
-
-
 And a few optional dependencies:
 
-====================   ==================
-Package                Minimum Version
-====================   ==================
-doxygen (for docs)     1.7.6.1
-tcmalloc (for speed)   any
-Cython                 0.29+
-Python (dev version)   3.8+
-Jinja2                 any
-NumPy                  1.9+
-Pandas                 any
-====================   ==================
+====================   ==================  =============================================  ==================        
+Package                Minimum Version     Purpose                                        Notes
+====================   ==================  =============================================  ==================  
+``Coin-Cbc``           2.10.3              Enables use of Branch-and-Cut solver           Cyclus must be built with ``--allow-milps`` flag
+``Coin-Clp``           1.17.5              Enables use of Linear Programming solver       Cyclus must be built with ``--allow-milps`` flag
+``doxygen``            1.7.6.1             Building documentation                         N/A
+``TCMmalloc``          any                 Improves performance                           Only used if Cython is not present
+``Cython``             0.29                Enables use of Python agents and input files   N/A
+``Jinja2``             2.10.1              Enables use of Python agents and input files   Only needed if Cython is installed
+``NumPy``              1.9                 Enables use of Python agents and input files   Only needed if Cython is installed
+``pandas``             0.25.3              Enables use of Python agents and input files   Only needed if Cython is installed
+``pip``                20.0.2              Enables use of Python agents and input files   Only needed if Cython is installed
+====================   ==================  =============================================  ==================
 
 *Note that the Debian/Ubuntu package ``libtcmalloc`` is NOT discovered correctly
 by our build system.  Instead use ``libgoogle-perftools-dev``.*
 
-*Also note that the development version of Python, Jinja2, NumPy, and Pandas are
-only needed if Cython is installed.*
-
 ***********************
 Installing Dependencies
 ***********************
@@ -88,31 +84,30 @@ required library package names is:
 
 #. make
 #. cmake
+#. pkg-config
 #. libboost-all-dev (see note below)
 #. libxml2-dev
 #. libxml++2.6-dev
+#. python3-dev
 #. libsqlite3-dev
-#. libhdf5-serial-dev
-#. libbz2-dev
-#. coinor-libcbc-dev
-#. coinor-libcoinutils-dev
-#. coinor-libosi-dev
-#. coinor-libclp-dev
-#. coinor-libcgl-dev
+#. libhdf5-dev
+#. liblapack-dev
+
 
 and (optionally):
 
 #. doxygen
-#. g++
-#. libblas-dev
-#. liblapack-dev
 #. libgoogle-perftools-dev
-#. python3-dev
+#. coinor-libcbc-dev
+#. coinor-libcoinutils-dev
+#. coinor-libosi-dev
+#. coinor-libclp-dev
 #. python3-tables
 #. python3-pandas
 #. python3-numpy
-#. python3-nose
+#. python3-pytest
 #. python3-jinja2
+#. python3-pip
 #. cython3       (see note below)
 
 For example, in order to install libxml++ (and libxml2) on your system, type:
@@ -126,19 +121,17 @@ If you'd prefer to copy/paste, the following line will install all **required**
 
 .. code-block:: bash
 
-   sudo apt-get install -y cmake make libboost-all-dev libxml2-dev libxml++2.6-dev \
-   libsqlite3-dev libhdf5-serial-dev libbz2-dev coinor-libcbc-dev coinor-libcoinutils-dev \
-   coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev
+   sudo apt-get install -y cmake make pkg-config libboost-all-dev libxml2-dev libxml++2.6-dev \
+   python3-dev libsqlite3-dev libhdf5-dev liblapack-dev
 
 And to install all *Cyclus* dependencies (**required and optional**):
 
 .. code-block:: bash
 
-   sudo apt-get install -y cmake make libboost-all-dev libxml2-dev libxml++2.6-dev \
-   libsqlite3-dev libhdf5-serial-dev libbz2-dev coinor-libcbc-dev coinor-libcoinutils-dev \
-   coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev libblas-dev liblapack-dev g++ \
-   libgoogle-perftools-dev python3-dev python3-tables python3-pandas python3-numpy python3-nose \
-   python3-jinja2 cython3
+   sudo apt-get install -y cmake make pkg-config libboost-all-dev libxml2-dev libxml++2.6-dev \
+   python3-dev libsqlite3-dev libhdf5-dev liblapack-dev coinor-libcbc-dev coinor-libcoinutils-dev \
+   coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev doxygen libgoogle-perftools-dev python3-tables \
+   python3-pandas python3-numpy python3-pytest python3-jinja2 cython3
 
 To determine which version of Python is already installed on your computer, run:
 

README.rst

@@ -99,7 +99,7 @@ To install Cyclus and its dependencies onto a clean Ubuntu machine (tested on 18
 
 - ``conda activate cyclus``
 
-- ``conda install -y openssh gxx_linux-64 gcc_linux-64 cmake make docker-pycreds git xo python-json-logger glib glibmm zlib libxml2 libxmlpp libxmlpp-4.0 libblas libcblas liblapack pkg-config coincbc boost-cpp hdf5 sqlite pcre gettext bzip2 xz setuptools pytest pytables pandas jinja2 "cython<3" websockets pprintpp``
+- ``conda install -y gxx_linux-64 gcc_linux-64 cmake make git glib libxml2 libxmlpp-4.0 liblapack pkg-config coincbc boost-cpp hdf5 sqlite pcre setuptools pytest pytables pandas jinja2 cython websockets pprintpp pip``
 
 - ``conda install -y --force-reinstall libsqlite``
 

docker/Dockerfile

@@ -9,14 +9,12 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 FROM common-base as apt-deps
 
 RUN apt update -y && apt install -y \
-        libssh-dev \
         g++ \
         gcc \
         cmake \
         make \
         libxml2-dev \
         libxml++2.6-dev \
-        libblas-dev \
         liblapack-dev \
         pkg-config \
         coinor-libcbc-dev \
@@ -27,8 +25,6 @@ RUN apt update -y && apt install -y \
         libhdf5-dev \
         libsqlite3-dev \
         libpcre2-dev \
-        gettext-base \
-        xz-utils \
         python3-setuptools \
         python3-pytest \ 
         python3-tables \
@@ -68,30 +64,21 @@ RUN conda uninstall -y conda-libmamba-solver
 RUN conda config --set solver classic
 RUN conda update -y --all && \
     mamba install -y \
-               openssh \
                gxx_linux-64 \
                gcc_linux-64 \
                cmake \
                make \
-               docker-pycreds \
                git \
-               xo \
-               python-json-logger \
                glib \
                libxml2 \
                libxmlpp-4.0 \
-               libblas \
-               libcblas \
                liblapack \
                pkg-config \
                coincbc \
                boost-cpp \
                hdf5 \
                sqlite \
                pcre \
-               gettext \
-               bzip2 \
-               xz \
                setuptools \
                pytest \
                pytables \

docker/Rocky.dockerfile

@@ -19,7 +19,6 @@ RUN alternatives --install /usr/bin/python python /bin/python3.11 10 && \
 
 FROM rocky-${rocky_version}-config as dnf-deps
 RUN dnf update -y && dnf install -y \
-        wget \
         which \
         git \
         gcc \
@@ -29,10 +28,8 @@ RUN dnf update -y && dnf install -y \
         hdf5-devel \
         libxml2-devel \
         boost-devel \
-        blas-devel \
         lapack-devel \
         sqlite-devel \
-        gettext \
         xz \
         python3.11-devel \
         python3.11-setuptools \
@@ -43,7 +40,7 @@ RUN dnf update -y && dnf install -y \
 RUN mkdir -p $(python -m site --user-site) && python -m pip install pandas tables cython jinja2
 
 FROM dnf-deps as libxmlpp
-RUN dnf update -y && dnf install -y m4 doxygen perl-open perl-XML-Parser diffutils pcre-cpp pcre-devel  && \
+RUN dnf update -y && dnf install -y wget m4 doxygen perl-open perl-XML-Parser diffutils pcre-cpp pcre-devel  && \
     python -m pip install meson ninja packaging && \
     wget https://github.com/libxmlplusplus/libxmlplusplus/releases/download/4.0.3/libxml++-4.0.3.tar.xz && \
     tar xf libxml++-4.0.3.tar.xz && \

src/CMakeLists.txt

@@ -201,8 +201,9 @@ list(REMOVE_ITEM cc_files ${CMAKE_CURRENT_SOURCE_DIR}/coin_helpers.cc)
 list(REMOVE_ITEM cc_files ${CMAKE_CURRENT_SOURCE_DIR}/prog_translator.cc)
 # The cython modules are built as their own shared libraries
 # We don't want them to be included in libcyclus.so
-list(REMOVE_ITEM cc_files ${CythonModuleSrc})
-
+if(Cython_FOUND)
+  list(REMOVE_ITEM cc_files ${CythonModuleSrc})
+endif()
 SET(CYCLUS_CORE_SRC ${CYCLUS_CORE_SRC} ${cc_files})
 
 # Add Cyclus source files that use COIN, if we have COIN

tests/toolkit/infile_converters_tests.cc

@@ -2,6 +2,7 @@
 
 #include "cyclus.h"
 
+
 std::string MakeInput() {
   return std::string(
           "<simulation>"
@@ -81,6 +82,8 @@ TEST(InfileConverters, JsonXmlRoundTrip) {
   EXPECT_STREQ(x1.c_str(), x2.c_str());
 }
 
+#ifdef CYCLUS_WITH_PYTHON
+
 TEST(InfileConverters, JsonPyRoundTrip) {
   using std::string;
   cyclus::PyStart();
@@ -109,3 +112,5 @@ TEST(InfileConverters, PyXmlRoundTrip) {
   EXPECT_STREQ(p1.c_str(), p2.c_str());
   EXPECT_STREQ(x1.c_str(), x2.c_str());
 }
+
+#endif // CYCLUS_WITH_PYTHON