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schwede
ProMod3
Commits
fbdfe1ff
Commit
fbdfe1ff
authored
Nov 19, 2020
by
Studer Gabriel
Browse files
Merge branch 'release-3.2.0'
parents
3c0b431e
50a4df6c
Changes
85
Hide whitespace changes
Inline
Side-by-side
CHANGELOG
View file @
fbdfe1ff
...
...
@@ -5,6 +5,18 @@
Changelog
================================================================================
Release 3.2.0
--------------------------------------------------------------------------------
* Remove outdated configuration scripts (Fedora 19 / ancient Mac)
* Construct CB atoms if only N,CA and C atoms are present in
ReconstructSidechains input structure.
* Detect Python using functionality provided by CMake instead of our own code.
You might have to adapt CMake flags when building ProMod3 to variables
specified here: https://cmake.org/cmake/help/latest/module/FindPython.html
* Several minor bug fixes, improvements, and speed-ups.
Release 3.1.1
--------------------------------------------------------------------------------
...
...
CMakeLists.txt
View file @
fbdfe1ff
...
...
@@ -24,8 +24,8 @@ include(PROMOD3)
# versioning info
set
(
PROMOD3_VERSION_MAJOR 3
)
set
(
PROMOD3_VERSION_MINOR
1
)
set
(
PROMOD3_VERSION_PATCH
1
)
set
(
PROMOD3_VERSION_MINOR
2
)
set
(
PROMOD3_VERSION_PATCH
0
)
set
(
PROMOD3_VERSION_STRING
${
PROMOD3_VERSION_MAJOR
}
.
${
PROMOD3_VERSION_MINOR
}
)
set
(
PROMOD3_VERSION_STRING
${
PROMOD3_VERSION_STRING
}
.
${
PROMOD3_VERSION_PATCH
}
)
...
...
@@ -87,21 +87,23 @@ file(MAKE_DIRECTORY ${STAGE_DIR}
setup_compiler_flags
()
# Python needed before Boost
find_package
(
Python 3.6 REQUIRED
)
find_package
(
Python 3.6 REQUIRED
COMPONENTS Interpreter Development
)
# Split version string
string
(
REPLACE
"."
";"
_python_version_list
${
PYTHON_VERSION
}
)
list
(
GET _python_version_list 0 PYTHON_VERSION_MAJOR
)
list
(
GET _python_version_list 1 PYTHON_VERSION_MINOR
)
string
(
REPLACE
"."
";"
_python_version_list
${
Python_VERSION
}
)
list
(
GET _python_version_list 0 Python_VERSION_MAJOR
)
list
(
GET _python_version_list 1 Python_VERSION_MINOR
)
# where Python modules live
set
(
PYTHON_MODULE_PATH
"python
${
Python_VERSION_MAJOR
}
.
${
Python_VERSION_MINOR
}
/site-packages/"
)
setup_boost
()
if
(
NOT DISABLE_DOCUMENTATION
)
find_package
(
Sphinx REQUIRED
)
set
(
PYTHON_DOC_URL
"https://docs.python.org/
${
P
YTHON
_VERSION
}
"
)
set
(
PYTHON_DOC_URL
"https://docs.python.org/
${
P
ython_VERSION_MAJOR
}
.
${
Python
_VERSION
_MINOR
}
"
)
# this URL should always point to the latest version of OST
set
(
OST_DOC_URL
"https://www.openstructure.org/docs"
)
endif
()
find_package
(
OPENSTRUCTURE 2.
1
.0 REQUIRED
find_package
(
OPENSTRUCTURE 2.
2
.0 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm
)
if
(
CMAKE_COMPILER_IS_GNUCXX
)
...
...
@@ -125,7 +127,7 @@ endif()
# This is somewhat experimental: Checking if Boost is compiled with the same
# Python version used for Promod3. The very same macro is disabled in OST so
# it may fail at some point.
#promod3_match_boost_python_version(${P
YTHON
_LIBRARIES})
#promod3_match_boost_python_version(${P
ython
_LIBRARIES})
# basic environment
include_directories
(
${
Boost_INCLUDE_DIRS
}
...
...
@@ -162,5 +164,5 @@ message(STATUS "${PROJECT_NAME} will be built with the following options:\n"
" OpenStructure (-DOST_ROOT) :
${
OST_ROOT
}
\n
"
" Compound library (-DCOMPOUND_LIB):
${
occp
}
\n
"
" Optimized (-DOPTIMIZE) :
${
_OPT
}
\n
"
" Python :
${
P
YTHON_BINARY
}
\n
"
" Python :
${
P
ython_EXECUTABLE
}
\n
"
" Eigen3 :
${
EIGEN3_INCLUDE_DIR
}
\n
"
)
cmake_support/FindOPENSTRUCTURE.cmake
View file @
fbdfe1ff
...
...
@@ -27,7 +27,7 @@ macro(find_OPENSTRUCTURE OST_ROOT HEADER_NAMES PYMOD_NAME)
set
(
FOUND_LIB FOUND_LIB-NOTFOUND
)
find_library
(
FOUND_LIB
NAMES ost_
${
LIB
}
HINTS
"
${
P
YTHON
_ROOT
}
"
HINTS
"
${
P
ython
_ROOT
_DIR
}
"
PATH
${
OST_ROOT
}
PATH_SUFFIXES lib lib64
NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
...
...
cmake_support/FindPython.cmake
deleted
100644 → 0
View file @
3c0b431e
#-------------------------------------------------------------------------------
# Check for Python Libraries
#
# PYTHON_IGNORE_FRAMEWORKS if set, do not check for python frameworks.
# has meaning on MacOS X only
# PYTHON_ROOT Prefix for python libraries
# PYTHON_MIN_VERSION minimal python version required
#
# When Python is found, the result is placed in the following variables:
#
# PYTHON_LIBRARIES is set to the library and linker flags used to
# link against python
# PYTHON_VERSION is set to the version of python
# PYTHON_INCLUDE_PATH is set to the path that contains Python.h
# PYTHON_BINARY is set to the path to the python executable
# PYTHON_MODULE_PATH is set as path-component where modules should live
#
# Author: Marco Biasini/ Stefan Bienert
#-------------------------------------------------------------------------------
set
(
PYTHON_VERSIONS 3.8 3.7 3.6
)
set
(
PYTHON_MIN_VERSION 3.6.0
)
#-------------------------------------------------------------------------------
# check for python framework
# this macro honours the values of PYTHON_ROOT
#-------------------------------------------------------------------------------
macro
(
check_for_python_framework
)
set
(
_FRAMEWORK_SEARCH_PATHS /Library/Frameworks/ /System/Library/Frameworks
)
if
(
PYTHON_ROOT
)
set
(
_FRAMEWORK_SEARCH_PATHS
${
PYTHON_ROOT
}
/Library/Frameworks
)
endif
()
foreach
(
_PATH
${
_FRAMEWORK_SEARCH_PATHS
}
)
set
(
_FULL_FRAMEWORK_NAME
"
${
_PATH
}
/Python.framework"
)
if
(
EXISTS
${
_FULL_FRAMEWORK_NAME
}
)
set
(
PYTHON_FRAMEWORK ON
)
set
(
PYTHON_INCLUDE_PATH
"
${
_FULL_FRAMEWORK_NAME
}
/Headers"
)
set
(
PYTHON_FRAMEWORK_PATH
"
${
_FULL_FRAMEWORK_NAME
}
/Python"
)
endif
()
endforeach
()
endmacro
()
macro
(
_find_python PYTHON_ROOT VERSION
)
string
(
REPLACE
"."
""
_VERSION_NO_DOTS
"
${
VERSION
}
"
)
if
(
PYTHON_ROOT
)
find_library
(
PYTHON_LIBRARIES
NAMES
"python
${
_VERSION_NO_DOTS
}
"
"python
${
VERSION
}
"
"python
${
_VERSION_NO_DOTS
}
m"
"python
${
VERSION
}
m"
HINTS
"
${
PYTHON_ROOT
}
"
PATH_SUFFIXES lib libs
NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
)
find_path
(
PYTHON_INCLUDE_PATH
NAMES Python.h
HINTS
"
${
PYTHON_ROOT
}
/include"
PATH_SUFFIXES include
"python
${
_VERSION_NO_DOTS
}
"
"python
${
VERSION
}
"
"python
${
_VERSION_NO_DOTS
}
m"
"python
${
VERSION
}
m"
NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
)
else
()
find_library
(
PYTHON_LIBRARIES
NAMES
"python
${
_VERSION_NO_DOTS
}
"
"python
${
VERSION
}
"
"python
${
_VERSION_NO_DOTS
}
m"
"python
${
VERSION
}
m"
PATH_SUFFIXES lib
)
find_path
(
PYTHON_INCLUDE_PATH
NAMES Python.h
PATH_SUFFIXES include
"python
${
_VERSION_NO_DOTS
}
"
"python
${
VERSION
}
"
"python
${
_VERSION_NO_DOTS
}
m"
"python
${
VERSION
}
m"
)
endif
()
endmacro
()
macro
(
_find_python_bin PYTHON_ROOT VERSION
)
string
(
REPLACE
"."
""
_VERSION_NO_DOTS
"
${
VERSION
}
"
)
if
(
PYTHON_ROOT
)
find_program
(
PYTHON_BINARY
NAMES
"python
${
_VERSION_NO_DOTS
}
"
"python
${
VERSION
}
"
python.exe
HINTS
"
${
PYTHON_ROOT
}
"
PATH_SUFFIXES bin
NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
)
else
()
find_program
(
PYTHON_BINARY
NAMES
"python
${
_VERSION_NO_DOTS
}
"
"python
${
VERSION
}
"
HINTS
"
${
CMAKE_PREFIX_PATH
}
"
PATH_SUFFIXES bin
)
endif
()
endmacro
()
#-------------------------------------------------------------------------------
# check for python lib
#
# this macro honours the values of PYTHON_ROOT and PYTHON_VERSION
#-------------------------------------------------------------------------------
macro
(
check_for_python_lib
)
if
(
PYTHON_VERSION
)
_find_python
(
"
${
PYTHON_ROOT
}
"
"
${
PYTHON_VERSION
}
"
)
else
()
foreach
(
_VERSION
${
PYTHON_VERSIONS
}
)
if
((
${
PYTHON_MIN_VERSION
}
VERSION_LESS
${
_VERSION
}
)
OR
(
${
PYTHON_MIN_VERSION
}
VERSION_EQUAL
${
_VERSION
}
))
_find_python
(
"
${
PYTHON_ROOT
}
"
"
${
_VERSION
}
"
)
if
(
PYTHON_LIBRARIES
)
set
(
PYTHON_VERSION
"
${
_VERSION
}
"
)
break
()
endif
()
endif
()
endforeach
()
endif
()
# fallback to non-versioned naming scheme
if
(
NOT $PYTHON_LIBRARIES
)
_find_python
(
"
${
PYTHON_ROOT
}
"
""
)
endif
()
endmacro
()
macro
(
check_for_python_binary
)
if
(
PYTHON_VERSION
)
_find_python_bin
(
"
${
PYTHON_ROOT
}
"
"
${
PYTHON_VERSION
}
"
)
else
()
foreach
(
_VERSION
${
PYTHON_VERSIONS
}
)
if
((
${
PYTHON_MIN_VERSION
}
VERSION_LESS
${
_VERSION
}
)
OR
(
${
PYTHON_MIN_VERSION
}
VERSION_EQUAL
${
_VERSION
}
))
_find_python_bin
(
"
${
PYTHON_ROOT
}
"
"
${
_VERSION
}
"
)
if
(
PYTHON_BINARY
)
set
(
PYTHON_VERSION
"
${
_VERSION
}
"
)
# disallow all versions except for the one we just found. This makes
# sure we don't mismatch the python binary and the libraries.
set
(
PYTHON_VERSIONS
"
${
_VERSION
}
"
)
break
()
endif
()
endif
()
endforeach
()
endif
()
if
(
NOT PYTHON_BINARY
)
_find_python
(
"
${
PYTHON_ROOT
}
"
""
)
endif
()
endmacro
()
if
(
NOT PYTHON_ROOT
)
if
(
WIN32
)
set
(
PYTHON_ROOT
"
${
CMAKE_PREFIX_PATH
}
"
)
else
()
set
(
PYTHON_ROOT
"/usr"
)
endif
()
endif
()
if
(
APPLE AND NOT PYTHON_IGNORE_FRAMEWORKS
)
check_for_python_framework
()
endif
()
# first check for python binary.
check_for_python_binary
()
if
(
NOT PYTHON_FRAMEWORK_FOUND
)
check_for_python_lib
()
endif
()
set
(
PYTHON_MODULE_PATH
"python
${
PYTHON_VERSION
}
/site-packages/"
)
mark_as_advanced
(
PYTHON_LIBRARIES
PYTHON_INCLUDE_PATH
PYTHON_VERSION
PYTHON_BINARY
PYTHON_MODULE_PATH
)
if
(
PYTHON_LIBRARIES
)
if
(
PYTHON_FRAMEWORK
)
set
(
PYTHON_LIBRARIES
"
${
PYTHON_FRAMEWORK_PATH
}
"
CACHE FILEPATH
"Python Libraries"
FORCE
)
else
()
set
(
PYTHON_LIBRARIES
"
${
PYTHON_LIBRARIES
}
"
CACHE FILEPATH
"Python Libraries"
FORCE
)
endif
()
set
(
PYTHON_INCLUDE_PATH
"
${
PYTHON_INCLUDE_PATH
}
"
CACHE FILEPATH
"Python Include Path"
FORCE
)
endif
()
if
(
PYTHON_BINARY
)
set
(
PYTHON_VERSION
"
${
PYTHON_VERSION
}
"
CACHE STRING
"Python Version"
FORCE
)
set
(
PYTHON_BINARY
"
${
PYTHON_BINARY
}
"
CACHE FILEPATH
"Python Binary"
FORCE
)
endif
()
cmake_support/FindSphinx.cmake
View file @
fbdfe1ff
IF
(
P
YTHON_BINARY
)
EXEC_PROGRAM
(
"
${
P
YTHON_BINARY
}
"
IF
(
P
ython_EXECUTABLE
)
EXEC_PROGRAM
(
"
${
P
ython_EXECUTABLE
}
"
ARGS
"-c 'import sphinx; print(sphinx.__version__)'"
OUTPUT_VARIABLE VERSION_STRING
RETURN_VALUE SPHINX_NOT_FOUND
)
...
...
@@ -9,13 +9,13 @@ IF(PYTHON_BINARY)
set
(
SPHINX_FOUND TRUE
)
set
(
SPHINX_VERSION
${
VERSION_STRING
}
)
endif
(
SPHINX_NOT_FOUND
)
ENDIF
(
P
YTHON_BINARY
)
ENDIF
(
P
ython_EXECUTABLE
)
if
(
SPHINX_FOUND
)
message
(
STATUS
"Sphinx version: "
${
SPHINX_VERSION
}
)
else
(
SPHINX_FOUND
)
if
(
Sphinx_FIND_REQUIRED
)
message
(
FATAL_ERROR
"Could not import sphinx in "
${
P
YTHON_BINARY
}
message
(
FATAL_ERROR
"Could not import sphinx in "
${
P
ython_EXECUTABLE
}
" make it available or disable documentation with -DDISABLE_DOCUMENTATION"
)
endif
(
Sphinx_FIND_REQUIRED
)
endif
(
SPHINX_FOUND
)
...
...
cmake_support/PROMOD3.cmake
View file @
fbdfe1ff
...
...
@@ -70,7 +70,7 @@ endmacro(check_architecture)
#
# Set variable VAR (in parent scope) to an updated PYTHONPATH env. variable
# which includes OST and PM3 paths. This can then be used to call python scripts
# with commands such as: sh -c "PYTHONPATH=${VAR} ${P
YTHON_BINARY
} ..."
# with commands such as: sh -c "PYTHONPATH=${VAR} ${P
ython_EXECUTABLE
} ..."
#-------------------------------------------------------------------------------
macro
(
get_python_path VAR
)
set
(
${
VAR
}
$ENV{PYTHONPATH}
)
...
...
@@ -521,7 +521,7 @@ macro(pymod)
set
(
_PARENT_LIB_NAME
"
${
_PARENT_NAME
}
"
)
endif
()
target_link_libraries
(
"_
${
_ARG_NAME
}
"
${
_PARENT_LIB_NAME
}
${
P
YTHON
_LIBRARIES
}
${
BOOST_PYTHON_LIBRARIES
}
)
${
P
ython
_LIBRARIES
}
${
BOOST_PYTHON_LIBRARIES
}
)
set_target_properties
(
"_
${
_ARG_NAME
}
"
PROPERTIES LIBRARY_OUTPUT_DIRECTORY
${
PYMOD_STAGE_DIR
}
)
if
(
NOT ENABLE_STATIC
)
...
...
@@ -589,7 +589,7 @@ macro(pymod)
add_custom_target
(
"
${
_ARG_NAME
}
_
${
_trans_py_source
}
_pymod"
ALL DEPENDS
${
_trans_py_file_to
}
)
add_dependencies
(
"
${
_ARG_NAME
}
_pymod"
"
${
_ARG_NAME
}
_
${
_trans_py_source
}
_pymod"
)
add_dependencies
(
"_
${
_ARG_NAME
}
"
"
${
_ARG_NAME
}
_pymod"
)
include_directories
(
${
P
YTHON
_INCLUDE_
PATH
}
)
include_directories
(
${
P
ython
_INCLUDE_
DIRS
}
)
install
(
FILES
${
_trans_py_file_to
}
DESTINATION
"
${
LIB_DIR
}
/
${
PYMOD_DIR
}
"
)
if
(
NOT DISABLE_DOCUMENTATION
)
add_doc_dependency
(
NAME
${
_ARG_NAME
}
DEP
"
${
_ARG_NAME
}
_
${
_trans_py_source
}
_pymod"
)
...
...
@@ -641,7 +641,7 @@ macro(pymod)
copy_if_different
(
"./"
"
${
PYMOD_STAGE_DIR
}
"
"
${
_ABS_PY_FILES
}
"
"TARGETS"
"
${
_ARG_NAME
}
_pymod"
)
add_dependencies
(
"_
${
_ARG_NAME
}
"
"
${
_ARG_NAME
}
_pymod"
)
include_directories
(
${
P
YTHON
_INCLUDE_
PATH
}
)
include_directories
(
${
P
ython
_INCLUDE_
DIRS
}
)
install
(
FILES
${
_PY_FILES
}
DESTINATION
"
${
LIB_DIR
}
/
${
PYMOD_DIR
}
"
)
endif
()
endif
()
...
...
@@ -798,7 +798,7 @@ macro(promod3_unittest)
message
(
FATAL_ERROR
"Python test script does not exist:
${
py_twp
}
"
)
endif
()
get_python_path
(
python_path
)
set
(
PY_TESTS_CMD
"PYTHONPATH=
${
python_path
}
${
P
YTHON_BINARY
}
"
)
set
(
PY_TESTS_CMD
"PYTHONPATH=
${
python_path
}
${
P
ython_EXECUTABLE
}
"
)
add_custom_target
(
"
${
py_test
}
_run"
sh -c
"
${
PY_TESTS_CMD
}
${
py_twp
}
"
WORKING_DIRECTORY
${
CMAKE_CURRENT_BINARY_DIR
}
...
...
@@ -863,8 +863,8 @@ endmacro(add_unit_test_data_target)
#-------------------------------------------------------------------------------
macro
(
promod3_find_python_module MODULE
)
if
(
NOT PYTHON_MODULE_
${
MODULE
}
)
message
(
STATUS
"Searching for python module
${
MODULE
}
for
${
P
YTHON_BINARY
}
"
)
execute_process
(
COMMAND
${
P
YTHON_BINARY
}
-c
"import
${
MODULE
}
"
message
(
STATUS
"Searching for python module
${
MODULE
}
for
${
P
ython_EXECUTABLE
}
"
)
execute_process
(
COMMAND
${
P
ython_EXECUTABLE
}
-c
"import
${
MODULE
}
"
OUTPUT_QUIET ERROR_QUIET
RESULT_VARIABLE _IMPORT_ERROR
)
if
(
_IMPORT_ERROR
)
...
...
@@ -900,9 +900,9 @@ macro(promod3_match_boost_python_version)
list
(
GET _BOOST_PYTHON_LIBRARY
${
_LIB_INDEX
}
_BP_LIB_PATH
)
set
(
_BOOST_PYTHON_LIBRARY
${
_BP_LIB_PATH
}
)
endif
()
set
(
CMAKE_REQUIRED_FLAGS
"-I
${
P
YTHON
_INCLUDE_
PATH
}
"
)
set
(
CMAKE_REQUIRED_FLAGS
"-I
${
P
ython
_INCLUDE_
DIRS
}
"
)
set
(
CMAKE_REQUIRED_FLAGS
"
${
CMAKE_REQUIRED_FLAGS
}
-I
${
Boost_INCLUDE_DIR
}
"
)
set
(
CMAKE_REQUIRED_FLAGS
"
${
CMAKE_REQUIRED_FLAGS
}
${
P
YTHON
_LIBRARIES
}
"
)
set
(
CMAKE_REQUIRED_FLAGS
"
${
CMAKE_REQUIRED_FLAGS
}
${
P
ython
_LIBRARIES
}
"
)
set
(
CMAKE_REQUIRED_FLAGS
"
${
CMAKE_REQUIRED_FLAGS
}
${
_BOOST_PYTHON_LIBRARY
}
"
)
check_cxx_source_runs
(
"#include <boost/python.hpp>
...
...
@@ -1016,12 +1016,12 @@ set(_BOOST_MIN_VERSION 1.53)
macro
(
setup_boost
)
# starting with CMake 3.11 we could use the following instead of the foreach
# find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS
# python${P
YTHON
_VERSION_MAJOR}${P
YTHON
_VERSION_MINOR} REQUIRED)
# python${P
ython
_VERSION_MAJOR}${P
ython
_VERSION_MINOR} REQUIRED)
# set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
# see https://cmake.org/cmake/help/v3.11/module/FindBoost.html
foreach
(
_python_lib_name python
${
P
YTHON
_VERSION_MAJOR
}${
P
YTHON
_VERSION_MINOR
}
python
${
P
YTHON
_VERSION_MAJOR
}
.
${
P
YTHON
_VERSION_MINOR
}
python
${
P
YTHON
_VERSION_MAJOR
}
foreach
(
_python_lib_name python
${
P
ython
_VERSION_MAJOR
}${
P
ython
_VERSION_MINOR
}
python
${
P
ython
_VERSION_MAJOR
}
.
${
P
ython
_VERSION_MINOR
}
python
${
P
ython
_VERSION_MAJOR
}
python
)
find_package
(
Boost
${
_BOOST_MIN_VERSION
}
COMPONENTS
${
_python_lib_name
}
QUIET
)
if
(
Boost_FOUND
)
...
...
@@ -1331,7 +1331,7 @@ macro(convert_module_data)
# setup python call
set
(
_PY_PATH
"
${
CMAKE_CURRENT_SOURCE_DIR
}
/
${
_ARG_SCRIPT
}
"
)
set
(
_PY_CMD
"
${
P
YTHON_BINARY
}
'
${
_PY_PATH
}
' '
${
_SRC_PATH
}
' '
${
_TRG_PATH
}
'
${
_ARG_ARGS
}
"
)
set
(
_PY_CMD
"
${
P
ython_EXECUTABLE
}
'
${
_PY_PATH
}
' '
${
_SRC_PATH
}
' '
${
_TRG_PATH
}
'
${
_ARG_ARGS
}
"
)
# set command to run (depends on _MODULE (pymod-target), FILE and SCRIPT)
# -> here we also make sure "import promod3" is ready
...
...
conf-scripts/bc2-conf
deleted
100755 → 0
View file @
3c0b431e
#!/bin/sh
# This script is aware of out-of-source builds. Just call it from within the
# build directory. Does not work from top-level dir.
# Meant to work on bc2 cluster (and probably nowhere else)!
function
usage_centos6
{
echo
'usage:'
echo
' bc2-conf [OPTIONS]'
echo
' If no OPTIONS given, a default OST module is loaded.'
echo
' If any OPTIONS given, they must contain one special option:'
echo
' -DOST_ROOT=<PATH TO OST/stage>, which points to a specific OST path.'
echo
' In that case, you must have all dependencies of OST loaded as modules'
echo
' before calling this function!'
echo
' Other valid options are anything that CMake accepts.'
exit
1
}
NUM_PARAMS
=
$#
CENTOS_RELEASE
=
$(
lsb_release
-r
|awk
{
'print $2'
}
)
CENTOS_MAJOR
=(
${
CENTOS_RELEASE
//./
}
)
PROMOD3_SRC
=
$(
cd
`
dirname
$0
`
;
pwd
)
# Going up one level is intentionally, please go out of source. Just create
# a directory at your repository root, prefixed 'build'. Change into it and
# call script from there.
PROMOD3_SRC
=
${
PROMOD3_SRC
}
/..
if
test
"
$CENTOS_MAJOR
"
==
"6"
;
then
# configuration for the new environment
# checking to switch OST_ROOT
cmd_params
=
if
test
"
$NUM_PARAMS
"
-gt
"0"
;
then
IFS
=
" "
for
opt
in
$@
;
do
if
test
${
opt
:0:11
}
==
"-DOST_ROOT="
;
then
EBROOTOPENSTRUCTURE
=
$(
cd
${
opt
:11
}
;
pwd
)
else
cmd_params
=
"
${
cmd_params
}
${
opt
}
"
fi
done
else
module load OpenStructure/.1.7.0-RC-goolf-1.4.10_20170822
fi
# load required modules
module load git/1.8.5.6-goolf-1.4.10
\
CMake/2.8.12-goolf-1.4.10
\
Python/2.7.5-goolf-1.4.10
\
Eigen/3.3.1
\
Boost/1.53.0-goolf-1.4.10-Python-2.7.5
# run cmake
cmake
$PROMOD3_SRC
\
-DOST_ROOT
=
$EBROOTOPENSTRUCTURE
\
-DPYTHON_ROOT
=
$EBROOTPYTHON
\
-DEIGEN3_INCLUDE_DIR
=
"
${
EBROOTEIGEN
}
/include"
\
-DBOOST_ROOT
=
$EBROOTBOOST
\
-DDISABLE_DOCUMENTATION
=
ON
\
-DOPTIMIZE
=
1
-DENABLE_SSE
=
1
\
$cmd_params
else
echo
'Only the CentOS 6 version of bc2 is supported'
# TODO: update for CentOS 7
fi
## Emacs magic
# Local Variables:
# mode: shell-script
# End:
# LocalWords: SRC OST promod CMake NUM PARAMS lt fi cd dir centos bc EIGEN
# LocalWords: pwd dirname cmake DPYTHON DBOOST conf Eigen DEIGEN
conf-scripts/fedora-19-conf
deleted
100755 → 0
View file @
3c0b431e
#!/bin/sh
# To find out your version of Fedora, run 'cat /etc/issue'.
# This script is aware of out-of-source builds. Just call it from within the
# build directory. Does not work from top-level dir.
function
usage
{
echo
'usage:'
echo
' fedora-19-conf <OST_ROOT> [OPTIONS]'
echo
' OST_ROOT is the staging directory of OST.'
echo
' Valid options are anything that CMake accepts.'
exit
}
NUM_PARAMS
=
$#
if
[[
"
$NUM_PARAMS
"
-lt
"1"
]]
;
then
echo
'You must specify the locations of OST.'
;
usage
fi
OST_ROOT
=
$(
cd
$1
;
pwd
)
shift
PROMOD3_SRC
=
$(
cd
`
dirname
$0
`
;
pwd
)
# Going up one level is intentionally, please go out of source. Just create a
# directory at your repository root, prefixed 'build'. Change into it and call
# script from there.
PROMOD3_SRC
=
${
PROMOD3_SRC
}
/..
cmake
$PROMOD3_SRC
-DOST_ROOT
=
$OST_ROOT
\
-DPYTHON_ROOT
=
/usr
\
$@
## Emacs magic
# Local Variables:
# mode: shell-script
# End:
# LocalWords: OSX MacPorts uname SRC OST promod CMake NUM PARAMS lt fi cd
# LocalWords: pwd dirname cmake DPYTHON DBOOST conf
conf-scripts/osx-11.4.2-conf
deleted
100755 → 0
View file @
3c0b431e
#!/bin/sh
# For OSX we assume that all missing dependencies are built with MacPorts
# and are located in '/opt/local'.
# To find out your version of OSX, run 'uname -r'.
# This script is aware of out-of-source builds. Just call it from within the
# build directory. Does not work from top-level dir.
function
usage
{
echo
'usage:'
echo
' osx-11.4.2-conf <OST_ROOT> [OPTIONS]'
echo
' OST_ROOT is the staging directory of OST.'
echo
' Valid options are anything that CMake accepts.'
exit
}
NUM_PARAMS
=
$#
if
[[
"
$NUM_PARAMS
"
-lt
"1"
]]
;
then
echo
'You must specify the locations of OST.'
;
usage
fi
OST_ROOT
=
$(
cd
$1
;
pwd
)
shift
PROMOD3_SRC
=
$(
cd
`
dirname
$0
`
;
pwd
)
# Going up one level is intentionally, please go out of source. Just create a
# directory at your repository root, prefixed 'build'. Change into it and call
# script from there.
PROMOD3_SRC
=
${
PROMOD3_SRC
}
/..
cmake
$PROMOD3_SRC
-DOST_ROOT
=
$OST_ROOT
\
-DPYTHON_ROOT
=
/opt/local
\
-DBOOST_ROOT
=
/opt/local
\
-DPYTHON_INCLUDE_PATH
=
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/
\
-DPYTHON_LIBRARIES
=
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib
\
$@
## Emacs magic
# Local Variables:
# mode: shell-script
# End:
# LocalWords: OSX MacPorts uname SRC OST promod CMake NUM PARAMS lt fi cd
# LocalWords: pwd dirname cmake DPYTHON DBOOST
container/Dockerfile
View file @
fbdfe1ff
ARG
OPENSTRUCTURE_IMAGE_TAG="2.
1
.0-
bionic
"
ARG
OPENSTRUCTURE_IMAGE_TAG="2.
2
.0-
focal
"
FROM
registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
# ARGUMENTS
###########
ARG
PROMOD_VERSION="3.
1.1
"
ARG
PROMOD_VERSION="3.
2.0
"
ARG
SRC_FOLDER="/usr/local/src"
...
...
@@ -24,7 +24,6 @@ RUN cd ${SRC_FOLDER} && \
cd ${SRC_FOLDER}/promod-${PROMOD_VERSION}/build && \
# Build and install ProMod3
cmake .. -DOST_ROOT=/usr/local \
-DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
-DOPTIMIZE=1 \
-DENABLE_SSE=1 \
-DDISABLE_DOCUMENTATION=1 && \
...
...
container/Singularity
View file @
fbdfe1ff
BootStrap: docker
From: registry.scicore.unibas.ch/schwede/promod3:3.
1.1
-OST2.
1
.0-
bionic
From: registry.scicore.unibas.ch/schwede/promod3:3.
2.0
-OST2.
2
.0-
focal
%post
##############################################################################
# POST
...
...
@@ -42,7 +42,7 @@ cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
"-m", "ipykernel",
"-f", "{connection_file}",
"--InteractiveShellApp.exec_PYTHONSTARTUP=False",
"--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.
6
/site-packages/ost/ost_startup.py']"
"--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.
8
/site-packages/ost/ost_startup.py']"
],
"env": {
}
...
...
@@ -200,7 +200,7 @@ and goes to CWD. Thus this sould work as expected out of the box.
# NOTEBOOK ENV
##############################################################################
export DNG_ROOT=$OST_ROOT
export DNG_INITDIR=${DNG_ROOT}/lib64/python3.
6
/site-packages/ost
export DNG_INITDIR=${DNG_ROOT}/lib64/python3.
8
/site-packages/ost
%apprun IPython
...
...
doc/CMakeLists.txt
View file @
fbdfe1ff
...
...
@@ -144,7 +144,7 @@ set(_SPHINX_INDEX_HTML "${_SPHINX_HTML_DIR}/index.html")
add_custom_command
(
OUTPUT
${
_SPHINX_INDEX_HTML
}
DEPENDS doc_wait_for_rst
"
${
_SPHINX_CONF_PY
}
"
${
_RST_DEPS
}
${
_DOC_MODULE_DEPS
}
doc_wait_for_modules
COMMAND
"
${
P
YTHON_BINARY
}
"
-m sphinx -b html -c
"
${
_RST_SOURCE_DIR
}
"
COMMAND
"
${
P
ython_EXECUTABLE
}
"
-m sphinx -b html -c
"
${
_RST_SOURCE_DIR
}
"
"
${
_RST_SOURCE_DIR
}
"
"
${
_SPHINX_HTML_DIR
}
"
)
add_custom_target
(
html DEPENDS
${
_SPHINX_INDEX_HTML
}
)
...
...
@@ -156,7 +156,7 @@ set(_SPHINX_INDEX_JSON "${_SPHINX_JSON_DIR}/index.fjson")
add_custom_command
(
OUTPUT
${
_SPHINX_INDEX_JSON
}
DEPENDS doc_wait_for_rst
"
${
_SPHINX_CONF_PY
}
"
${
_RST_DEPS
}
${
_DOC_MODULE_DEPS
}
doc_wait_for_modules
COMMAND
"
${
P
YTHON_BINARY
}
"
-m sphinx -b json -c
"
${
_RST_SOURCE_DIR
}
"
COMMAND
"
${
P
ython_EXECUTABLE
}
"
-m sphinx -b json -c
"
${
_RST_SOURCE_DIR
}
"
"
${
_RST_SOURCE_DIR
}
"
"
${
_SPHINX_JSON_DIR
}
"
)
add_custom_target
(
json DEPENDS
${
_SPHINX_INDEX_JSON
}
)
...
...
@@ -167,7 +167,7 @@ set(_SPHINX_MAN "${_SPHINX_MAN_DIR}/promod3.1")
add_custom_command
(
OUTPUT
${
_SPHINX_MAN
}
DEPENDS doc_wait_for_rst
"
${
_SPHINX_CONF_PY
}
"
${
_RST_DEPS
}
${
_DOC_MODULE_DEPS
}
doc_wait_for_modules
COMMAND
"
${
P
YTHON_BINARY
}
"
-m sphinx -b man -c
"
${
_RST_SOURCE_DIR
}
"
COMMAND
"
${
P
ython_EXECUTABLE
}
"
-m sphinx -b man -c
"
${
_RST_SOURCE_DIR
}
"
"
${
_RST_SOURCE_DIR
}
"
"
${
_SPHINX_MAN_DIR
}
"
)
add_custom_target
(
man DEPENDS
${
_SPHINX_MAN
}
)
...
...
@@ -180,7 +180,7 @@ add_dependencies(doc man)
set
(
_SPHINX_LINKCHECK_DIR
"
${
CMAKE_CURRENT_BINARY_DIR
}
/linkcheck"
)
file
(
MAKE_DIRECTORY
${
_SPHINX_LINKCHECK_DIR
}
)
