Merge pull request cyclus#1747 from bennibbelink/python3

CHANGELOG.rst

@@ -10,6 +10,7 @@ Since last release
 **Changed:**
 
 * Changed README.rst installation instructions, tested on fresh Ubuntu-22.04 system with Python3.11 (#1744)
+* Rely on `python3` in environment instead of `python` (#1747)
 
 **Removed:**
 

INSTALL.rst

@@ -31,7 +31,7 @@ Run the install script:
 
 .. code-block:: bash
   
-  python install.py
+  python3 install.py
 
 If you successfully followed the instruction above, the cyclus binary has been
 generated and placed in the  ``~/.local/`` in your home directory. 
@@ -47,7 +47,7 @@ On MacOSX you also need to add ~/.local/lib/pythonX.Y/site-packages to your
 
 .. code-block:: bash
 
-  echo "export PYTHONPATH=\"\$HOME/.local/lib/python`python -c 'import sys; \
+  echo "export PYTHONPATH=\"\$HOME/.local/lib/python`python3 -c 'import sys; \
   print(".".join(map(str, sys.version_info[:2])))'`/site-packages:\$PYTHONPATH\"" >> ~/.bashrc
   source ~/.bashrc
 
@@ -128,7 +128,7 @@ installation flag. The otherwise identical process would look like:
 
 .. code-block:: bash
 
-    .../cyclus$  python install.py --coin_root=path/to/coin
+    .../cyclus$  python3 install.py --coin_root=path/to/coin
 
 
 CMake Cyclus Installation

README.rst

@@ -134,7 +134,7 @@ simulations, first download Cycamore
   https://github.com/cyclus/cycamore.git``,
 
 - Install in the same location you installed Cyclus (eg. in ``~/.local/``):
-  ``python install.py`` from the ``cycamore`` folder.
+  ``python3 install.py`` from the ``cycamore`` folder.
 
 
 **************

cli/cycpp.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """The cyclus preprocessor.
 
 cycpp is a 3-pass preprocessor which adds reflection-like semantics to cyclus

cli/cycstub

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 from __future__ import print_function
 

cli/post-process-cython.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 from __future__ import print_function, unicode_literals
 import re
 

cmake/UseCython.cmake

@@ -284,7 +284,7 @@ function( cython_add_standalone_executable _name )
   set( other_module_sources "" )
   set( main_module "" )
   cmake_parse_arguments( cython_arguments "" "MAIN_MODULE" "" ${ARGN} )
-  include_directories( ${PYTHON_INCLUDE_DIRS} )
+  include_directories( ${Python3_INCLUDE_DIRS} )
   foreach( _file ${cython_arguments_UNPARSED_ARGUMENTS} )
     if( ${_file} MATCHES ".*\\.py[x]?$" )
       get_filename_component( _file_we ${_file} NAME_WE )
@@ -310,5 +310,5 @@ function( cython_add_standalone_executable _name )
   set( CYTHON_FLAGS ${CYTHON_FLAGS} --embed )
   compile_pyx( "${main_module_we}_static" generated_file ${main_module} )
   add_executable( ${_name} ${generated_file} ${pyx_module_sources} ${other_module_sources} )
-  target_link_libraries( ${_name} ${PYTHON_LIBRARIES} ${pyx_module_libs} )
+  target_link_libraries( ${_name} ${Python3_LIBRARIES} ${pyx_module_libs} )
 endfunction()

cyclus/CMakeLists.txt

@@ -8,7 +8,7 @@ INCLUDE_DIRECTORIES(${CYCLUS_CORE_INCLUDE_DIRS})
 # First things first, code-generation
 #
 message(STATUS "Generating Type System API for Python")
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/gentypesystem.py
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/gentypesystem.py
     "--src-dir=${CMAKE_CURRENT_SOURCE_DIR}"
     "--data-model-version=${DATA_MODEL_VERSION}"
     "--verbose"

cyclus/gentypesystem.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """Generates Cyclus Type System bindings.
 
 Module history:

cyclus/server.py

@@ -175,18 +175,18 @@
 ======================
 You may launch the cyclus server by running::
 
-    $ python -m cyclus.server input.xml
+    $ python3 -m cyclus.server input.xml
 
 Most of the arguments are relatively self-explanatory. However, the CLI here
 also allows you to load initial and repeating actions. The syntax for this
 is an event name followed by parameter tokens (which must contain an equals
 sign)::
 
-    $ python -m cyclus.server input.xml --repeating-actions sleep n=1
+    $ python3 -m cyclus.server input.xml --repeating-actions sleep n=1
 
 You may load many actions by repeating the name-params pattern:
 
-    $ python -m cyclus.server input.xml --repeating-actions \
+    $ python3 -m cyclus.server input.xml --repeating-actions \
         sleep n=1 \
         table_data table="TimeSeriesPower"
 

docker/Dockerfile

@@ -37,8 +37,7 @@ RUN apt update -y && apt install -y \
 RUN apt install -y python3-pprintpp; exit 0
 RUN apt clean -y all
 
-RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10
-RUN mkdir -p `python -m site --user-site`
+RUN mkdir -p `python3 -m site --user-site`
 
 FROM common-base as conda-deps
 
@@ -91,7 +90,7 @@ RUN conda update -y --all && \
                && \
     mamba install -y --force-reinstall libsqlite && \
     conda clean -y --all
-RUN mkdir -p `python -m site --user-site`
+RUN mkdir -p `python3 -m site --user-site`
 ENV CC /opt/conda/bin/x86_64-conda_cos6-linux-gnu-gcc
 ENV CXX /opt/conda/bin/x86_64-conda_cos6-linux-gnu-g++
 ENV CPP /opt/conda/bin/x86_64-conda_cos6-linux-gnu-cpp
@@ -110,12 +109,12 @@ ARG make_cores=2
 COPY . /cyclus
 WORKDIR /cyclus
 
-RUN python install.py -j ${make_cores} --allow-milps --code_coverage
+RUN python3 install.py -j ${make_cores} --allow-milps --code_coverage
 ENV PATH /root/.local/bin:$PATH
 ENV LD_LIBRARY_PATH /root/.local/lib:/root/.local/lib/cyclus
 RUN lcov -c -d /cyclus -o initial_coverage.info --gcov-tool ${GCOV} --initial --no-external && \
     cyclus_unit_tests && \
-    cd tests && python -m pytest && cd .. && \
+    cd tests && python3 -m pytest && cd .. && \
     lcov -c -d /cyclus -o test_coverage.info --gcov-tool ${GCOV} --no-external && \
     lcov --add-tracefile initial_coverage.info --add-tracefile test_coverage.info -o total_coverage.info && \
     mkdir -p html && genhtml total_coverage.info --output-directory html
@@ -135,7 +134,7 @@ WORKDIR /cyclus
 
 # You may add the option "--cmake-debug" to the following command
 # for further CMake debugging.
-RUN python install.py -j ${make_cores} --allow-milps
+RUN python3 install.py -j ${make_cores} --allow-milps
 ENV PATH /root/.local/bin:$PATH
 
 FROM cyclus as deb-generation
@@ -151,4 +150,4 @@ RUN cyclus_unit_tests
 
 FROM cyclus-test as cyclus-pytest
 
-RUN cd tests && python -m pytest
+RUN cd tests && python3 -m pytest

docker/Rocky.dockerfile

@@ -8,13 +8,11 @@ RUN dnf update -y && \
     dnf install -y python3.11 epel-release
 
 FROM common-base as rocky-8-config
-RUN alternatives --set python /usr/bin/python3.11 && \
-    alternatives --set python3 /usr/bin/python3.11 && \
+RUN alternatives --set python3 /usr/bin/python3.11 && \
     dnf config-manager --set-enabled powertools
 
 FROM common-base as rocky-9-config
-RUN alternatives --install /usr/bin/python python /bin/python3.11 10 && \
-    alternatives --install /usr/bin/python3 python3 /bin/python3.11 10 && \
+RUN alternatives --install /usr/bin/python3 python3 /bin/python3.11 10 && \
     dnf config-manager --set-enabled crb
 
 FROM rocky-${rocky_version}-config as dnf-deps
@@ -37,11 +35,11 @@ RUN dnf update -y && dnf install -y \
         python3.11-pytest \
     && dnf clean all
 
-RUN mkdir -p $(python -m site --user-site) && python -m pip install pandas tables cython jinja2
+RUN mkdir -p $(python3 -m site --user-site) && python3 -m pip install pandas tables cython jinja2
 
 FROM dnf-deps as libxmlpp
 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 && \
+    python3 -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 && \
     cd libxml++-4.0.3 && \
@@ -72,7 +70,7 @@ WORKDIR /cyclus
 
 # You may add the option "--cmake-debug" to the following command
 # for further CMake debugging.
-RUN python install.py -j ${make_cores} -D Python3_EXECUTABLE=/usr/bin/python3.11
+RUN python3 install.py -j ${make_cores} -D Python3_EXECUTABLE=/usr/bin/python3.11
 ENV PATH /root/.local/bin:$PATH
 ENV LD_LIBRARY_PATH /root/.local/lib:/root/.local/lib/cyclus
 
@@ -82,5 +80,5 @@ RUN cyclus_unit_tests
 
 FROM cyclus-test as cyclus-pytest
 
-RUN cd tests && python -m pytest
+RUN cd tests && python3 -m pytest
 

setup.py

@@ -57,8 +57,7 @@ def run_setup(ver):
         url='http://fuelcycle.org',
         platforms=['posix'],
         classifiers=['Operating System :: POSIX',
-                     'Programming Language :: Python :: 3',
-                     'Programming Language :: Python :: 2'],
+                     'Programming Language :: Python :: 3'],
         packages=['cyclus'],
         package_dir={'cyclus': 'cyclus'},
         package_data={'cyclus': ['*.pxd', '*.so', '*.dylib']},

share/CMakeLists.txt

@@ -20,7 +20,7 @@ CONFIGURE_FILE(
     COPYONLY
     )
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/dbtypes_gen.py ${DATA_MODEL_VERSION} OUTPUT_VARIABLE DBTYPES_JSON_ENTRIES RESULT_VARIABLE res_var)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/dbtypes_gen.py ${DATA_MODEL_VERSION} OUTPUT_VARIABLE DBTYPES_JSON_ENTRIES RESULT_VARIABLE res_var)
 IF(NOT "${res_var}" STREQUAL "0")
   message(FATAL_ERROR "Process dbtypes_gen.py failed, res_var = '${res_var}'")
 ENDIF()

share/dbtypes_gen.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 from __future__ import print_function
 import os
 import re

src/CMakeLists.txt

@@ -33,7 +33,7 @@ CONFIGURE_FILE(
     @ONLY
     )
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "VAL_TO_BUF_H" OUTPUT_VARIABLE HDF5_BACK_CC_VAL_TO_BUF_H RESULT_VARIABLE res_var_h)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "VAL_TO_BUF_H" OUTPUT_VARIABLE HDF5_BACK_CC_VAL_TO_BUF_H RESULT_VARIABLE res_var_h)
 IF(NOT "${res_var_h}" STREQUAL "0")
   message(FATAL_ERROR "Process hdf5_back_gen.py 'VAL_TO_BUF_H' failed, result = '${res_var_h}'")
 ENDIF()
@@ -48,37 +48,37 @@ copy_when_diff(
     "${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back.h"
     )
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "QUERY" OUTPUT_VARIABLE HDF5_BACK_CC_QUERY RESULT_VARIABLE res_var_q)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "QUERY" OUTPUT_VARIABLE HDF5_BACK_CC_QUERY RESULT_VARIABLE res_var_q)
 IF(NOT "${res_var_q}" STREQUAL "0")
   message(FATAL_ERROR "Process hdf5_back_gen.py 'QUERY' failed, result = '${res_var_q}'")
 ENDIF()
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "CREATE" OUTPUT_VARIABLE HDF5_BACK_CC_CREATE RESULT_VARIABLE res_var_c)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "CREATE" OUTPUT_VARIABLE HDF5_BACK_CC_CREATE RESULT_VARIABLE res_var_c)
 IF(NOT "${res_var_c}" STREQUAL "0")
   message(FATAL_ERROR "Process hdf5_back_gen.py 'CREATE' failed, result = '${res_var_c}'")
 ENDIF()
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "VL_DATASET" OUTPUT_VARIABLE HDF5_BACK_CC_VL_DATASET RESULT_VARIABLE res_var_v)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "VL_DATASET" OUTPUT_VARIABLE HDF5_BACK_CC_VL_DATASET RESULT_VARIABLE res_var_v)
 IF(NOT "${res_var_v}" STREQUAL "0")
   message(FATAL_ERROR "Process hdf5_back_gen.py 'VL_DATASET' failed, result = '${res_var_v}'")
 ENDIF()
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "FILL_BUF" OUTPUT_VARIABLE HDF5_BACK_CC_FILL_BUF RESULT_VARIABLE res_var_f)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "FILL_BUF" OUTPUT_VARIABLE HDF5_BACK_CC_FILL_BUF RESULT_VARIABLE res_var_f)
 IF(NOT "${res_var_f}" STREQUAL "0")
   message(FATAL_ERROR "Process hdf5_back_gen.py 'FILL_BUF' failed, result = '${res_var_f}'")
 ENDIF()
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "WRITE" OUTPUT_VARIABLE HDF5_BACK_CC_WRITE RESULT_VARIABLE res_var_w)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "WRITE" OUTPUT_VARIABLE HDF5_BACK_CC_WRITE RESULT_VARIABLE res_var_w)
 IF(NOT "${res_var_w}" STREQUAL "0")
   message(FATAL_ERROR "Process hdf5_back_gen.py 'WRITE' failed, result = '${res_var_w}'")
 ENDIF()
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "VAL_TO_BUF" OUTPUT_VARIABLE HDF5_BACK_CC_VAL_TO_BUF RESULT_VARIABLE res_var_vb)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "VAL_TO_BUF" OUTPUT_VARIABLE HDF5_BACK_CC_VAL_TO_BUF RESULT_VARIABLE res_var_vb)
 IF(NOT "${res_var_vb}" STREQUAL "0")
   message(FATAL_ERROR "Process hdf5_back_gen.py 'VAL_TO_BUF' failed, result = '${res_var_vb}'")
 ENDIF()
 
-EXECUTE_PROCESS(COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "BUF_TO_VAL" OUTPUT_VARIABLE HDF5_BACK_CC_BUF_TO_VAL RESULT_VARIABLE res_var_bv)
+EXECUTE_PROCESS(COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/hdf5_back_gen.py "BUF_TO_VAL" OUTPUT_VARIABLE HDF5_BACK_CC_BUF_TO_VAL RESULT_VARIABLE res_var_bv)
 IF(NOT "${res_var_bv}" STREQUAL "0")
   message(FATAL_ERROR "Process hdf5_back_gen.py 'BUF_TO_VAL' failed, result = '${res_var_bv}'")
 ENDIF()

src/hdf5_back_gen.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """This module generates HDF5 backend code found in src/hdf5_back.cc
 
 There are 8 distinct code generation options, one of which must be passed
@@ -14,7 +14,7 @@
 -------
 To generate the code found in src/hdf5_back.cc::Query, use
 
-    $ python hdf5_back_gen.py QUERY
+    $ python3 hdf5_back_gen.py QUERY
 
 """
 import os

tests/CMakeLists.txt

@@ -95,7 +95,7 @@ set(tgt "cyclus_unit_tests")
 add_custom_target(
     ${tgt}-post-build
     DEPENDS ${tgt}
-    COMMAND python "${CMAKE_CURRENT_SOURCE_DIR}/generate_gtest_macros.py"
+    COMMAND ${Python3_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/generate_gtest_macros.py"
     "--executable=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${tgt}"
     "--output=${CYCLUS_BINARY_DIR}/CTestTestfile.cmake"
     COMMENT "adding tests from ${tgt}"

tests/test_stubs.py

@@ -28,7 +28,7 @@ def test_stubs():
         inst = os.path.join(d, 'baz')
 
         stub_cmd = 'cycstub --type {0} {1}:{1}:{2}'
-        inst_cmd = 'python install.py --build_dir {0} --prefix {1}'
+        inst_cmd = 'python3 install.py --build_dir {0} --prefix {1}'
         tst_cmd = './bin/{}_unit_tests'
 
         log = 'stub_test.log'