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https://github.com/TREX-CoE/qmckl.git
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Out of source build of python
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parent
c531feeb54
commit
7651d19f22
37
Makefile.am
37
Makefile.am
@ -65,7 +65,7 @@ AM_CPPFLAGS += -DQMCKL_TEST_DIR=\"$(QMCKL_TEST_DIR)\"
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lib_LTLIBRARIES = src/libqmckl.la
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src_libqmckl_la_SOURCES = $(qmckl_h) $(src_qmckl_f) $(C_FILES) $(F_FILES) $(H_PRIVATE_FUNC_FILES) $(H_PRIVATE_TYPE_FILES)
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src_libqmckl_la_LDFLAGS = $(LDFLAGS)
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src_libqmckl_la_LDFLAGS = $(LDFLAGS)
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CLEANFILES+=$(test_qmckl_fo) $(src_qmckl_fo) $(test_qmckl_o) $(src_qmckl_o) $(FH_TYPE_FILES) $(FH_FUNC_FILES)
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@ -172,26 +172,39 @@ cppcheck.out: $(qmckl_h)
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setup_py = $(srcdir)/python/setup.py
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process_header_py = $(srcdir)/python/src/process_header.py
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qmckl_py = $(srcdir)/python/qmckl.py
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test_py = $(srcdir)/python/test/test_api.py
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qmckl_wrap_c = $(srcdir)/python/src/qmckl_wrap.c
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pyqmckl_i = $(srcdir)/python/src/pyqmckl.i
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pyqmckl_include_i = $(srcdir)/python/src/pyqmckl_include.i
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qmckl_i = $(srcdir)/python/src/qmckl.i
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numpy_i = $(srcdir)/python/src/numpy.i
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qmckl_wrap_c = python/src/qmckl_wrap.c
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qmckl_include_i = python/src/qmckl_include.i
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qmckl_py = python/qmckl/qmckl.py
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$(qmckl_include_i): $(qmckl_h) $(process_header_py)
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$(MKDIR_P) python/src
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python $(process_header_py) $(qmckl_h)
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mv qmckl_include.i $(qmckl_include_i)
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python-install: $(qmckl_h) $(pyqmckl_i) $(process_header_py) $(setup_py)
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cp $(qmckl_h) $(srcdir)/python/src/
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cd $(srcdir)/python/ && \
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./pip_install_pyqmckl.sh
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$(qmckl_py): $(qmckl_i) $(qmckl_include_i)
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swig -Iinclude -Ipython/src -python -py3 -builtin -o $(qmckl_wrap_c) $(qmckl_i)
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$(qmckl_wrap_c): $(qmckl_py)
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python-install: $(qmckl_h) $(qmckl_i) $(setup_py) $(qmckl_py) $(qmckl_wrap_c)
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$(MKDIR_P) python/src
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cd python ; \
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[[ ! -f pyproject.toml ]] && \
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cp $(abs_srcdir)/python/{pyproject.toml,requirements.txt,README.md,setup.py} . ; \
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cp src/qmckl.py . ; \
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pip install .
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python-test: $(test_py)
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cd $(srcdir)/python/test/ && \
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cd $(abs_srcdir)/python/test/ && \
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python test_api.py
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CLEANFILES += $(qmckl_wrap_c) \
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$(qmckl_py) \
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$(pyqmckl_include_i)
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$(qmckl_include_i) \
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$(qmckl_py)
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.PHONY: cppcheck python-test python-install
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@ -12,31 +12,31 @@
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## Manual installation
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1. Install the QMCkl library (see upstream instructions)
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2. `./manual_install_pyqmckl.sh` which should do the following
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3. Copy the produced `_pyqmckl.so` and `pyqmckl.py` files into your working directory and do not forget to `import pyqmckl` in your Python scripts
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2. `./manual_install_qmckl.sh` which should do the following
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3. Copy the produced `_qmckl.so` and `qmckl.py` files into your working directory and do not forget to `import qmckl` in your Python scripts
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The second step executes the following under the hood:
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1. `./build_pyqmckl.sh`
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2. `<c-compiler> -I/usr/include/python3.8 -c -fPIC pyqmckl_wrap.c` to compile the wrapper code into an object file using the `<c-compiler>` (replace with your C compiler, e.g. `gcc`) on your machine
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3. `<c-compiler> -shared pyqmckl_wrap.o -lqmckl -o _pyqmckl.so` to produce the final C extension (this requires the `qmckl` library to be installed and present in the linking paths together with all its dependencies like `trexio`)
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1. `./build_qmckl.sh`
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2. `<c-compiler> -I/usr/include/python3.8 -c -fPIC qmckl_wrap.c` to compile the wrapper code into an object file using the `<c-compiler>` (replace with your C compiler, e.g. `gcc`) on your machine
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3. `<c-compiler> -shared qmckl_wrap.o -lqmckl -o _qmckl.so` to produce the final C extension (this requires the `qmckl` library to be installed and present in the linking paths together with all its dependencies like `trexio`)
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## Python-ic installation (recommended)
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1. Install the QMCkl library (see upstream instructions)
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2. `./pip_install_pyqmckl.sh`
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2. `./pip_install_qmckl.sh`
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The last step runs `./build_pyqmckl.sh`, copies the result into the `pyqmckl/` directory and
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then runs `pip install .` to install the `pyqmckl` Python package in your environment.
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The last step runs `./build_qmckl.sh`, copies the result into the `qmckl/` directory and
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then runs `pip install .` to install the `qmckl` Python package in your environment.
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## SWIG pre-processing
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Both aforementioned steps call `build_pyqmckl.sh` script which does the following pre-processing for SWIG
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Both aforementioned steps call `build_qmckl.sh` script which does the following pre-processing for SWIG
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1. Copy the latest `qmckl.h` file fron `include/` into the `src/` directory
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2. `python process_header.py` to generate `pyqmckl_include.i` list of SWIG patterns
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3. `swig -python -py3 -builtin -threads -o pyqmckl_wrap.c pyqmckl.i` to generate the SWIG wrapper code in C and `pyqmckl.py` module in Python.
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**Note:** for this to work three files have to be present in the working directory: `pyqmckl.i`, `pyqmckl_include.i` and `numpy.i`.
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2. `python process_header.py` to generate `qmckl_include.i` list of SWIG patterns
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3. `swig -python -py3 -builtin -threads -o qmckl_wrap.c qmckl.i` to generate the SWIG wrapper code in C and `qmckl.py` module in Python.
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**Note:** for this to work three files have to be present in the working directory: `qmckl.i`, `qmckl_include.i` and `numpy.i`.
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@ -1,33 +0,0 @@
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#!/bin/bash
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set -e
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set -x
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#cp ../include/qmckl.h src/
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cd src/
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# check if qmckl header exists
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if [[ ! -f 'qmckl.h' ]]; then
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echo "qmckl.h NOT FOUND in the src/ directory"
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exit 1
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fi
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# process the qmckl header file to get patterns for SWIG
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python process_header.py
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# check if SWIG files exist
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SWIG_LIST='pyqmckl.i pyqmckl_include.i numpy.i'
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for file in $SWIG_LIST; do
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if [[ ! -f $file ]]; then
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echo "$file NOT FOUND in the src/ directory"
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exit 1
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fi
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done
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# run SWIG interface file to produce the Python wrappers
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# `-threads` to release GIL before the call to C functions (for multi-threading)
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# `-builtin` to activate Python-ic built-in types
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swig -python -py3 -builtin -o qmckl_wrap.c pyqmckl.i
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cd ..
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@ -4,7 +4,7 @@ set -x
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set -e
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# swig pre-processing
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./build_pyqmckl.sh
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./build_qmckl.sh
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cd src/
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@ -12,7 +12,7 @@ cd src/
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cc -c -fPIC `pkg-config --cflags qmckl` -I/usr/include/python3.8 qmckl_wrap.c -o qmckl_wrap.o
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# link against the previously installed QMCkl library (as detected by pkg-config)
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cc -shared pyqmckl_wrap.o `pkg-config --libs qmckl` -o _qmckl.so
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cc -shared qmckl_wrap.o `pkg-config --libs qmckl` -o _qmckl.so
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cd ..
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@ -1,14 +0,0 @@
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#!/bin/bash
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set -x
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set -e
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./build_pyqmckl.sh
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# copy swig-produced pyqmckl.py module into the pyqmckl/ folder
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#cp src/qmckl.py qmckl/
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cp src/qmckl.py ./
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# install using pip
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pip install .
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@ -14,8 +14,8 @@ with open("README.md", "r") as fh:
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# Define the name of the Python package
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MODULE_NAME = "qmckl"
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# Define pyqmckl extension module based on SWIG interface file (requires qmckl.h)
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pyqmckl_module = Extension(name = "._" + MODULE_NAME,
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# Define qmckl extension module based on SWIG interface file (requires qmckl.h)
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qmckl_module = Extension(name = "._" + MODULE_NAME,
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sources = [ join("src", MODULE_NAME + "_wrap.c") ],
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#include_dirs = [numpy_includedir],
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#library_dirs = [],
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@ -34,7 +34,7 @@ setup(name = MODULE_NAME,
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description = """Python API of the QMCkl library""",
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long_description = long_description,
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long_description_content_type = "text/markdown",
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ext_modules = [pyqmckl_module],
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ext_modules = [qmckl_module],
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py_modules = [MODULE_NAME],
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url = "https://github.com/TREX-CoE/qmckl",
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license = "BSD",
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@ -1,6 +1,9 @@
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#!/usr/bin/env python3
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import os
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import sys
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qmckl_h = sys.argv[1]
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collect = False
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process = False
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@ -13,9 +16,9 @@ numbers = {}
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qmckl_public_api = []
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qmckl_errors = []
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with open("qmckl.h", 'r') as f_in:
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with open(qmckl_h, 'r') as f_in:
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for line in f_in:
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# get the errors but without the type cast because SWIG does not recognize it
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if '#define' in line and 'qmckl_exit_code' in line:
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qmckl_errors.append(line.strip().replace('(qmckl_exit_code)',''))
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@ -62,11 +65,11 @@ with open("qmckl.h", 'r') as f_in:
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# print(pattern)
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continue
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# if size_max is not provided then the function should deal with numbers or string
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# if size_max is not provided then the function should deal with numbers or string
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#elif 'num' in line and 'get' in func_name:
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elif ';' in line and 'get' in func_name:
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# special case
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if 'size_max' in line:
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# special case
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if 'size_max' in line:
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continue
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#print(line)
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@ -145,7 +148,7 @@ processed = list(arrays.keys()) + list(numbers.keys())
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# print(v)
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with open("pyqmckl_include.i", 'w') as f_out:
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with open("qmckl_include.i", 'w') as f_out:
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# write the list of errors as constants without the type cast
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for e in qmckl_errors:
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@ -154,7 +157,7 @@ with open("pyqmckl_include.i", 'w') as f_out:
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swig_type = ''
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for v in numbers.values():
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if 'int' in v['datatype']:
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swig_type = 'int'
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elif 'float' in v['datatype'] or 'double' in v['datatype']:
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