diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..74449ff --- /dev/null +++ b/.gitattributes @@ -0,0 +1,12 @@ +*.f90 linguist-language=fortran +*.fypp linguist-language=fortran + +doc/** linguist-documentation +docs/** linguist-documentation +example/** linguist-vendored +include/** linguist-vendored +capi/** linguist-vendored +media/** linguist-vendored +pywrapper/** linguist-vendored +py/** linguist-vendored + diff --git a/.gitignore b/.gitignore index f65032a..02cb9b7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,34 +1,42 @@ -*.o +#API: an (incompatible) API change +#BENCH: changes to the benchmark suite +#BLD: change related to building numpy +#BUG: bug fix +#DEP: deprecate something, or remove a deprecated object +#DEV: development tool or utility +#DOC: documentation +#ENH: enhancement +#MAINT: maintenance commit (refactoring, typos, etc.) +#REV: revert an earlier commit +#STY: style fix (whitespace, PEP8) +#TST: addition or modification of tests +#REL: related to releasing + +.idea/ +bin/ +build/ +docs/build/ +dist/ +local/ +API-doc/ +.vscode/ *.obj -*.exe -*.out -*.pyd -*.lib -*.cmake +*.o *.mod -*.dylib -*.dll +*.pyd *.dll.a -*.so *.a +*.dll +*.so +*.dylib -.idea -.vscode - -build/ *.egg-info - -.DS_Store - -dist/ - __pycache__ +*.so -generator* +.DS_Store -pywrapper/src/pyecx/ecx*.h -pywrapper/src/pyecx/*.dylib -pywrapper/src/pyecx/*.so -pywrapper/src/pyecx/*.dll -pywrapper/src/pyecx/*.dll.a -pywrapper/wheelhouse/ +py/wheelhouse/ +py/src/pyecx/bin/ +py/src/pyecx/include/ +py/src/pyecx/lib/ diff --git a/API-doc-FORD-file.md b/API-doc-FORD-file.md new file mode 100644 index 0000000..a6bf191 --- /dev/null +++ b/API-doc-FORD-file.md @@ -0,0 +1,41 @@ +--- +project: ecx +summary: ECX - Electrochemistry +project_github: https://github.com/MilanSkocic/ecx +project_download: https://github.com/MilanSkocic/ecx/releases +project_website: https://milanskocic.github.io/ecx/index.html +author: Milan Skocic +email: milan.skocic@icloud.com +github: https://github.com/MilanSkocic +src_dir: ./src +include: ./include +media_dir: ./media +page_dir: ./doc +output_dir: API-doc +exclude_dir: ./example + ./test +display: public + protected +source: true +proc_internals: true +sort: permission-alpha +print_creation_date: true +md_extensions: markdown.extensions.toc + markdown.extensions.smarty +fpp_extensions: fypp +preprocess: true +preprocessor: fypp +graph: true +graph_maxnodes: 250 +graph_maxdepth: 5 +coloured_edges: true +license: by-sa +favicon: media/logo.ico +--- + +![ecx](./media/logo.png) + +[TOC] + +{!README.md!} + diff --git a/CHANGELOG.md b/CHANGELOG.md index b209c49..c160f1a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,3 +5,5 @@ * Documentation with sphinx. Full changelog available at [github](https://github.com/MilanSkocic/ecx/releases) + +**Note released yet** diff --git a/LICENSE b/LICENSE index 26425f5..5ec1f2a 100644 --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,4 @@ -Copyright (c) 2021-2024 Milan Skocic +Copyright (c) Milan Skocic Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the diff --git a/Makefile b/Makefile index b3fb4ab..00b4e5d 100644 --- a/Makefile +++ b/Makefile @@ -10,19 +10,23 @@ else btype=release endif +SRC_FYPP=$(wildcard ./src/*.fypp) + +.PHONY: build doc docs + all: $(LIBNAME) $(LIBNAME): build copy_a shared -.PHONY: build build: fpm build --profile=$(btype) test: build fpm test --profile=$(btype) - + example: build - fpm run --profile=$(btype) --example example_in_f example_in_c + fpm run --profile=$(btype) --example example_in_f + fpm run --profile=$(btype) --example example_in_c copy_a: cp -f $(shell find ./build/gfortran* -type f -name $(LIBNAME).a) $(BUILD_DIR) @@ -38,18 +42,14 @@ shared_darwin: shared_windows: $(FC) -shared $(FPM_LDFLAGS) -o $(BUILD_DIR)/$(LIBNAME).dll -Wl,--out-implib=$(BUILD_DIR)/$(LIBNAME).dll.a,--export-all-symbols,--enable-auto-import,--whole-archive $(BUILD_DIR)/$(LIBNAME).a -Wl,--no-whole-archive -clean: - fpm clean --all - rm -f src/*.mod - install: install_dirs install_$(PLATFORM) install_dirs: mkdir -p $(install_dir)/bin mkdir -p $(install_dir)/include mkdir -p $(install_dir)/lib - fpm install --prefix=$(install_dir) - cp -f ./include/*.h $(install_dir)/include + fpm install --prefix=$(install_dir) --profile=$(btype) + cp -f $(INCLUDE_DIR)/$(NAME)*.h $(install_dir)/include install_linux: cp -f $(BUILD_DIR)/$(LIBNAME).so $(install_dir)/lib @@ -59,14 +59,31 @@ install_darwin: install_windows: cp -f $(BUILD_DIR)/$(LIBNAME).dll.a $(install_dir)/lib + cp -f $(BUILD_DIR)/$(LIBNAME).dll $(install_dir)/lib cp -f $(BUILD_DIR)/$(LIBNAME).dll $(install_dir)/bin uninstall: - rm -f $(install_dir)/include/$(HEADER_PREFIX)*.h - rm -f $(install_dir)/include/$(HEADER_PREFIX)*.mod + rm -f $(install_dir)/include/$(NAME)*.h + rm -f $(install_dir)/include/$(NAME)*.mod rm -f $(install_dir)/lib/$(LIBNAME).a rm -f $(install_dir)/lib/$(LIBNAME).so rm -f $(install_dir)/lib/$(LIBNAME).dylib rm -f $(install_dir)/lib/$(LIBNAME).dll.a + rm -f $(install_dir)/lib/$(LIBNAME).dll rm -f $(install_dir)/bin/$(LIBNAME).dll +clean: + fpm clean --all + make -C py clean + rm -rf API-doc/* + +doc: + ford API-doc-FORD-file.md + +docs: + rm -rf docs/* + cp -rf API-doc/* ./docs/ + +logo: + make -C media + diff --git a/VERSION b/VERSION new file mode 100644 index 0000000..6e8bf73 --- /dev/null +++ b/VERSION @@ -0,0 +1 @@ +0.1.0 diff --git a/configure.sh b/configure.sh index c9400ce..aee8672 100755 --- a/configure.sh +++ b/configure.sh @@ -1,5 +1,9 @@ +#!/bin/bash + LIBNAME="libecx" -HEADER_PREFIX="ecx" +NAME="ecx" +PYNAME="py$NAME" +PY_SRC="./src/$PYNAME" # environment variables FC=gfortran @@ -10,21 +14,31 @@ FPM_CFLAGS="-std=c11 -pedantic -Wall -Wextra" FPM_LDFLAGS="" DEFAULT_INSTALL_DIR="$HOME/.local" PLATFORM="linux" +EXT=".so" if [[ "$OSTYPE" == "msys" ]]; then DEFAULT_INSTALL_DIR="${APPDATA//\\//}/local" PLATFORM="windows" + ROOT=$ROOTWINDOWS + EXT=".dll" + LIBS=( "${LIBSWINDOWS[@]}" ) fi if [[ "$OSTYPE" == "darwin"* ]];then PLATFORM="darwin" + ROOT=$ROOTDARWIN + EXT=".dylib" + LIBS=( "${LIBSDARWIN[@]}" ) fi +cp -f VERSION ./py/VERSION +cp -f LICENSE ./py/LICENSE + export LIBNAME echo "LIBNAME=" $LIBNAME -export HEADER_PREFIX -echo "HEADER_PREFIX=" $HEADER_PREFIX +export NAME +echo "NAME=" $NAME export PLATFORM echo "PLATFORM=" $PLATFORM @@ -47,5 +61,9 @@ echo "BUILD DIR=" $BUILD_DIR export INCLUDE_DIR echo "INCLUDE_DIR=" $INCLUDE_DIR +export PY_SRC +echo "PY_SRC=" $PY_SRC + export FC echo "FC=" $FC + diff --git a/example/example_in_c.c b/example/example.c similarity index 100% rename from example/example_in_c.c rename to example/example.c diff --git a/example/example_in_f.f90 b/example/example.f90 old mode 100755 new mode 100644 similarity index 100% rename from example/example_in_f.f90 rename to example/example.f90 diff --git a/example/example_in_py.py b/example/example.py similarity index 100% rename from example/example_in_py.py rename to example/example.py diff --git a/fpm.toml b/fpm.toml index 2476f43..170ea80 100644 --- a/fpm.toml +++ b/fpm.toml @@ -1,9 +1,9 @@ name = "ecx" version = "0.1.0" -license = "GNU General Public License v3 (GPLv3)" +license = "MIT" author = "Milan Skocic" maintainer = "milan.skocic@icloud.com" -copyright = "Copyright 2021-2024, Milan Skocic" +copyright = "Copyright, Milan Skocic" categories =["Science"] keywords = ["electrochemistry", "impedance", "photoelectrochemistry"] homepage = "https://milanskocic.github.io/ecx/index.html" @@ -28,11 +28,11 @@ library = true [[example]] name="example_in_f" -main="example_in_f.f90" +main="example.f90" [[example]] name="example_in_c" -main="example_in_c.c" +main="example.c" [[test]] name="test_core" diff --git a/include/ecx.h b/include/ecx.h index 2745f2e..8c4e236 100644 --- a/include/ecx.h +++ b/include/ecx.h @@ -1,15 +1,53 @@ -/** - * @file - * @brief C API - Main C header for the ecx library. - */ #ifndef ECX_H #define ECX_H +#include +#if _MSC_VER + #define ADD_IMPORT __declspec(dllimport) + typedef _Dcomplex ecx_cdouble; + #define ecx_cbuild(real, imag) (_Cbuild(real, imag)) +#else + #define ADD_IMPORT + typedef double _Complex ecx_cdouble; + #define ecx_cbuild(real, imag) (real+I*imag) +#endif + +extern char* ecx_get_version(void); + + +/* ---------------------------------------------------------------------------------------------- */ +ADD_IMPORT extern const double ecx_core_PI; +ADD_IMPORT extern const double ecx_core_T_K; +void ecx_core_nm2eV(double *lambda, double *E, size_t n); +void ecx_core_kTe(double *U, double *kTE, size_t n); +/* ---------------------------------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------------------------------- */ +extern double ecx_kinetics_capi_nernst(double E0, int z, + double *aox, double *vox, size_t nox, + double *ared, double *vred, size_t nred, + double T); + +extern void ecx_kinetics_capi_sbv(double *U, double OCV, double j0, + double aa, double ac, double za, double zc, + double A, double T, double *i, size_t n); + +extern void ecx_kinetics_capi_bv(double *U, double OCV, double j0, double jdla, double jdlc, + double aa, double ac, double za, double zc, + double A, double T, double *i, size_t n); +/* ---------------------------------------------------------------------------------------------- */ + -#include "ecx_core.h" -#include "ecx_eis.h" -#include "ecx_pec.h" -#include "ecx_kinetics.h" -#include "ecx_version.h" +/* ---------------------------------------------------------------------------------------------- */ +extern void ecx_capi_zr(double *w, double R, size_t n, ecx_cdouble *Z); +extern void ecx_capi_zc(double *w, double C, size_t n, ecx_cdouble *Z); +extern void ecx_capi_zl(double *w, double L, size_t n, ecx_cdouble *Z); +extern void ecx_capi_zcpe(double *w, double Q, double a, size_t n, ecx_cdouble *Z); +extern void ecx_capi_zw(double *w, double s, size_t n, ecx_cdouble *Z); +extern void ecx_eis_z(double *p, double *w, ecx_cdouble *z, + char e, size_t k, size_t n, + int *errstat, char *(*errmsg)); +/* ---------------------------------------------------------------------------------------------- */ #endif diff --git a/include/ecx_core.h b/include/ecx_core.h deleted file mode 100644 index 464f1de..0000000 --- a/include/ecx_core.h +++ /dev/null @@ -1,18 +0,0 @@ -/** - * @file - * @brief C API - core - */ -#ifndef ECX_CORE_H -#define ECX_CORE_H -#if _MSC_VER -#define ADD_IMPORT __declspec(dllimport) -#else -#define ADD_IMPORT -#endif -#include "ecx_types.h" -ADD_IMPORT extern const double ecx_core_PI; /**< PI */ -ADD_IMPORT extern const double ecx_core_T_K; /**< 0°C in Kelvin */ -void ecx_core_nm2eV(double *lambda, double *E, size_t n); /**< Convert wavelength (nm) to energy (eV)*/ -void ecx_core_kTe(double *U, double *kTE, size_t n); /**< Compute the thermal voltage (V) from temperature (°C)*/ - -#endif diff --git a/include/ecx_eis.h b/include/ecx_eis.h deleted file mode 100644 index 5146592..0000000 --- a/include/ecx_eis.h +++ /dev/null @@ -1,30 +0,0 @@ -/** - * @file - * @brief CAPI - EIS - */ -#ifndef ECX_EIS_CAPI_H -#define ECX_EIS_CAPI_H -#include "ecx_types.h" -#include "ecx_core.h" - -extern void ecx_capi_zr(double *w, double R, size_t n, ecx_cdouble *Z); -extern void ecx_capi_zc(double *w, double C, size_t n, ecx_cdouble *Z); -extern void ecx_capi_zl(double *w, double L, size_t n, ecx_cdouble *Z); -extern void ecx_capi_zcpe(double *w, double Q, double a, size_t n, ecx_cdouble *Z); -extern void ecx_capi_zw(double *w, double s, size_t n, ecx_cdouble *Z); - -/** - * @brief C API - Compute the complex impedance for the given element - * @details @ref ecx__eis::capi_z - * @param[in] p Parameters. - * @param[in] w Angular frequencies in rad.s-1 - * @param[in] zout Complex impedances in Ohms. - * @param[in] e Electrochemical element: R, C, L, Q, O, T, G - * @param[in] k Size of p - * @param[in] n Size of w - * @param[in] errstat Error status - * @param[in] errmsg Error message - */ -extern void ecx_eis_z(double *p, double *w, ecx_cdouble *z, char e, size_t k, size_t n, int *errstat, char *(*errmsg)); - -#endif diff --git a/include/ecx_kinetics.h b/include/ecx_kinetics.h deleted file mode 100644 index 07ad24b..0000000 --- a/include/ecx_kinetics.h +++ /dev/null @@ -1,24 +0,0 @@ -/** - * @file - * @brief C API - kinetics. - * @details Kinetics - */ -#ifndef ECX_KINETICS_CAPI_H -#define ECX_KINETICS_CAPI_H -#include "ecx_types.h" -#include "ecx_core.h" - -extern double ecx_kinetics_capi_nernst(double E0, int z, - double *aox, double *vox, size_t nox, - double *ared, double *vred, size_t nred, - double T); - -extern void ecx_kinetics_capi_sbv(double *U, double OCV, double j0, - double aa, double ac, double za, double zc, - double A, double T, double *i, size_t n); - -extern void ecx_kinetics_capi_bv(double *U, double OCV, double j0, double jdla, double jdlc, - double aa, double ac, double za, double zc, - double A, double T, double *i, size_t n); - -#endif diff --git a/include/ecx_pec.h b/include/ecx_pec.h deleted file mode 100644 index f190bb4..0000000 --- a/include/ecx_pec.h +++ /dev/null @@ -1,11 +0,0 @@ -/** - * @file - * @brief C API - PEC. - */ -#ifndef ECX_PEC_CAPI_H -#define ECX_PEC_CAPI_H -#include "ecx_types.h" -#include "ecx_core.h" - - -#endif diff --git a/include/ecx_types.h b/include/ecx_types.h deleted file mode 100644 index 836ce95..0000000 --- a/include/ecx_types.h +++ /dev/null @@ -1,19 +0,0 @@ -/** - * @file - * @brief C API - Types - * @details Compatibilty layer for handling complex numbers with MSC. - * It is imported by all headers for each submodule. - */ -#ifndef ECX_TYPES_H -#define ECX_TYPES_H - -#include -#if _MSC_VER -typedef _Dcomplex ecx_cdouble; /**< Cross platform complex type. */ -#define ecx_cbuild(real, imag) (_Cbuild(real, imag))/**< Cross platform complex type constructor*/ -#else -typedef double _Complex ecx_cdouble; /**< Cross platform complex type. */ -#define ecx_cbuild(real, imag) (real+I*imag) /**< Cross platform complex type constructor*/ -#endif - -#endif diff --git a/include/ecx_version.h b/include/ecx_version.h deleted file mode 100644 index 6e0d1be..0000000 --- a/include/ecx_version.h +++ /dev/null @@ -1,9 +0,0 @@ -/** -* @file -* @brief C API - Version -*/ -#ifndef ecx_VERSION_H -#define ecx_VERSION_H -extern char* ecx_get_version(void); -#endif - diff --git a/media/logo-ecx.png b/media/logo.png similarity index 100% rename from media/logo-ecx.png rename to media/logo.png diff --git a/media/logo-ecx.svg b/media/logo.svg similarity index 100% rename from media/logo-ecx.svg rename to media/logo.svg diff --git a/py/LICENSE b/py/LICENSE new file mode 100644 index 0000000..5ec1f2a --- /dev/null +++ b/py/LICENSE @@ -0,0 +1,20 @@ +Copyright (c) Milan Skocic + +Permission is hereby granted, free of charge, to any person obtaining +a copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE +LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION +OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION +WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/py/MANIFEST.in b/py/MANIFEST.in new file mode 100644 index 0000000..11b2040 --- /dev/null +++ b/py/MANIFEST.in @@ -0,0 +1,8 @@ +include README.md +include LICENSE +include VERSION +include pyproject.toml +include setup.py +include src/pyecx/*.c +include src/pyecx/*.h + diff --git a/pywrapper/Makefile b/py/Makefile similarity index 84% rename from pywrapper/Makefile rename to py/Makefile index 58a2c0b..a964df4 100644 --- a/pywrapper/Makefile +++ b/py/Makefile @@ -56,14 +56,14 @@ clean: rm -rf *.egg-info rm -rf __pycache__ rm -rf wheelhouse - rm -rf $(PYW_SRC)/__pycache__ - -cleanall: clean - - rm -f $(PYW_SRC)/$(HEADER_PREFIX)*.h - rm -f $(PYW_SRC)/*.a - rm -f $(PYW_SRC)/*.so - rm -f $(PYW_SRC)/*.dylib - rm -f $(PYW_SRC)/*.dll - rm -f $(PYW_SRC)/*.dll.a - rm -f $(PYW_SRC)/*.pyd + rm -rf $(PY_SRC)/__pycache__ + rm -f $(PY_SRC)/$(NAME)*.h + rm -f $(PY_SRC)/*.a + rm -f $(PY_SRC)/*.so + rm -f $(PY_SRC)/*.dylib + rm -f $(PY_SRC)/*.dll + rm -f $(PY_SRC)/*.dll.a + rm -f $(PY_SRC)/*.pyd + rm -rf $(PY_SRC)/bin + rm -rf $(PY_SRC)/include + rm -rf $(PY_SRC)/lib diff --git a/py/README.md b/py/README.md new file mode 100644 index 0000000..4957cc7 --- /dev/null +++ b/py/README.md @@ -0,0 +1,51 @@ +# Introduction + +Python wrapper around the +[Fortran ecx library](https://milanskocic.github.io/ecx/index.html). +The Fortran library does not need to be installed, the python wrapper embeds all needed dependencies for Windows and MacOS. +On linux, you might have to install `libgfortran` if it is not distributed with your linux distribution. + +All functions that operate on arrays, more precisely on objects with the buffer protocol, return memory views +in order to avoid compilation dependencies on 3rd party packages. + + +# Installation + +In a terminal, enter: + +```python +pip install pyecx +``` + + +# Usage + +```python +import numpy as np +from pyecx import eis +import matplotlib.pyplot as plt + +R = 100 +C = 1e-6 +w = np.logspace(6, -3, 100) + +zr = np.asarray(eis.zr(w, R)) +zc = np.asarray(eis.zc(w, C)) +zrc = zr*zc / (zr+zc) +print("finish") + +fig = plt.figure() +ax = fig.add_subplot(111) + +ax.set_aspect("equal") +ax.plot(zrc.real, zrc.imag, "g.", label="R/C") + +ax.invert_yaxis() + +plt.show() +``` + + +# License + +MIT diff --git a/py/VERSION b/py/VERSION new file mode 100644 index 0000000..6e8bf73 --- /dev/null +++ b/py/VERSION @@ -0,0 +1 @@ +0.1.0 diff --git a/pywrapper/pyproject.toml b/py/pyproject.toml similarity index 80% rename from pywrapper/pyproject.toml rename to py/pyproject.toml index 1b83673..0411263 100644 --- a/pywrapper/pyproject.toml +++ b/py/pyproject.toml @@ -4,15 +4,15 @@ build-backend = "setuptools.build_meta" [project] name = "pyecx" -version = "0.1.0" +dynamic=["version"] authors = [{name = "Milan Skocic", email = "milan.skocic@icloud.com"}] description = "pyecx: electrochemistry for Python." -readme = "README.rst" +readme = "README.md" requires-python = ">=3.8" -license = {text = "GNU General Public License v3 (GPLv3)"} +license = {text = "MIT"} classifiers=["Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", - "License :: OSI Approved :: GNU General Public License v3 (GPLv3)"] + "License :: OSI Approved :: MIT License"] [project.urls] Documentation = "https://milanskocic.github.io/ecx/index.html" diff --git a/pywrapper/run.py b/py/run.py similarity index 100% rename from pywrapper/run.py rename to py/run.py diff --git a/py/setup.py b/py/setup.py new file mode 100644 index 0000000..42c3986 --- /dev/null +++ b/py/setup.py @@ -0,0 +1,130 @@ +r"""Setup.""" +import platform +import shutil +import pathlib +import subprocess +from setuptools import setup, Extension + +LIBSDARWIN = ("libgfortran.5", "libquadmath.0", "libgcc_s.1.1") +LIBSWINDOWS = ("libgfortran-5", "libquadmath-0", "libgcc_s_seh-1", "libwinpthread-1") +LIBSLINUX = [] +ROOTLINUX = "/usr/lib/" +ROOTDARWIN = "/usr/local/opt/gcc/lib/gcc/current" +ROOTWINDOWS = "C:/msys64/mingw64/bin" +ROOT = ROOTLINUX +LIBS = LIBSLINUX + +name = "ecx" +libraries = None +library_dirs = None +runtime_library_dirs = None +extra_objects = None +ext = [".so"] + + +if platform.system() == "Linux": + libraries = [name] + library_dirs = [f"./src/py{name:s}/lib/"] + runtime_library_dirs = ["$ORIGIN"] + ext = [".so"] +if platform.system() == "Windows": + extra_objects = [f"./src/py{name:s}/lib/lib{name:s}.dll.a"] + src = pathlib.Path(f"./src/py{name:s}/lib/lib{name:s}.dll") + dest = pathlib.Path(f"./src/py{name:s}/lib{name:s}.dll") + if not src.exists(): + raise ValueError(f"The library {name} was not installed. Run in the root folder: make install prefix=./py/src/py{name:s}") + shutil.copy(src, dest) + ext = [".dll", ".dll.a"] + ROOT = ROOTWINDOWS + LIBS = LIBSWINDOWS +if platform.system() == "Darwin": + libraries = [name] + library_dirs = [f"./src/py{name:s}/lib/"] + runtime_library_dirs = ["@loader_path"] + ext = [".dylib"] + ROOT = ROOTDARWIN + LIBS = LIBSDARWIN + +# Headers +root_src = pathlib.Path(f"./src/py{name:s}/include/") +root_dest = pathlib.Path(f"./src/py{name:s}/") +files = [f"{name:s}.h"] +for file in files: + src = root_src / file + dest = root_dest / file + try: + print(f"copying {str(src):s} -> {str(dest.parent):s}.") + shutil.copy(src, dest) + except: + print(f"{file:s} was not found.") + +# Libs +root_src = pathlib.Path(f"./src/py{name:s}/lib/") +root_dest = pathlib.Path(f"./src/py{name:s}/") +files = list(map(lambda s: f"lib{name:s}"+s, ext)) +for file in files: + src = root_src / file + dest = root_dest / file + try: + print(f"copying {str(src):s} -> {str(dest.parent):s}.") + shutil.copy(src, dest) + except: + print(f"{file:s} was not found.") + +# gfortran libs +root_src = pathlib.Path(ROOT) +root_dest = pathlib.Path(f"./src/py{name:s}/") +files = LIBS +for file in files: + src = root_src / (file + ext[0]) + dest = root_dest / (file + ext[0]) + cmd = ["install_name_tool", "-change", f"{str(src):s}", f"@loader_path/{src.name}", f"./src/py{name:s}/lib{name:s}{ext[0]:s}"] + try: + print(f"copying {str(src):s} -> {str(dest.parent):s}.") + shutil.copy(src, dest) + if platform.system() == "Darwin": + print(f"changing rpath for {str(file):s}") + subprocess.check_call(cmd) + except subprocess.CalledProcessError: + print(" ".join(cmd) + " was not successful.") + except: + print(f"{file:s} was not found.") + +# check rpaths for Darwin +if platform.system() == "Darwin": + cmd = ["otool", "-L", f"./src/py{name:s}/lib{name:s}{ext[0]:s}"] + try: + print(f"checking rpaths") + subprocess.check_call(cmd) + except subprocess.CalledProcessError: + print(" ".join(cmd) + " was not successful.") + +version = None +with open("./VERSION", "r") as f: + version = f.read().strip() + + +if __name__ == "__main__": + + mod_version = Extension(name="pyecx.version", + sources=["./src/pyecx/cpy_version.c"], + libraries=libraries, + library_dirs=library_dirs, + runtime_library_dirs=runtime_library_dirs, + extra_objects=extra_objects) + mod_eis = Extension(name="pyecx.eis", + sources=["./src/pyecx/cpy_eis.c", "./src/pyecx/cpy_common.c"], + libraries=libraries, + library_dirs=library_dirs, + runtime_library_dirs=runtime_library_dirs, + extra_objects=extra_objects) + mod_core = Extension(name="pyecx.core", + sources=["./src/pyecx/cpy_core.c", "./src/pyecx/cpy_common.c"], + libraries=libraries, + library_dirs=library_dirs, + runtime_library_dirs=runtime_library_dirs, + extra_objects=extra_objects) + + setup(version=version, + ext_modules=[mod_version, mod_core, mod_eis]) + diff --git a/pywrapper/src/pyecx/__init__.py b/py/src/pyecx/__init__.py similarity index 100% rename from pywrapper/src/pyecx/__init__.py rename to py/src/pyecx/__init__.py diff --git a/pywrapper/src/pyecx/cpy_common.c b/py/src/pyecx/cpy_common.c similarity index 100% rename from pywrapper/src/pyecx/cpy_common.c rename to py/src/pyecx/cpy_common.c diff --git a/pywrapper/src/pyecx/cpy_common.h b/py/src/pyecx/cpy_common.h similarity index 100% rename from pywrapper/src/pyecx/cpy_common.h rename to py/src/pyecx/cpy_common.h diff --git a/pywrapper/src/pyecx/cpy_core.c b/py/src/pyecx/cpy_core.c similarity index 100% rename from pywrapper/src/pyecx/cpy_core.c rename to py/src/pyecx/cpy_core.c diff --git a/pywrapper/src/pyecx/cpy_eis.c b/py/src/pyecx/cpy_eis.c similarity index 100% rename from pywrapper/src/pyecx/cpy_eis.c rename to py/src/pyecx/cpy_eis.c diff --git a/pywrapper/src/pyecx/cpy_kinetics.c b/py/src/pyecx/cpy_kinetics.c similarity index 100% rename from pywrapper/src/pyecx/cpy_kinetics.c rename to py/src/pyecx/cpy_kinetics.c diff --git a/pywrapper/src/pyecx/cpy_version.c b/py/src/pyecx/cpy_version.c similarity index 100% rename from pywrapper/src/pyecx/cpy_version.c rename to py/src/pyecx/cpy_version.c diff --git a/py/src/pyecx/ecx.h b/py/src/pyecx/ecx.h new file mode 100644 index 0000000..8c4e236 --- /dev/null +++ b/py/src/pyecx/ecx.h @@ -0,0 +1,54 @@ +#ifndef ECX_H +#define ECX_H +#include +#if _MSC_VER + #define ADD_IMPORT __declspec(dllimport) + typedef _Dcomplex ecx_cdouble; + #define ecx_cbuild(real, imag) (_Cbuild(real, imag)) +#else + #define ADD_IMPORT + typedef double _Complex ecx_cdouble; + #define ecx_cbuild(real, imag) (real+I*imag) +#endif + +extern char* ecx_get_version(void); + + +/* ---------------------------------------------------------------------------------------------- */ +ADD_IMPORT extern const double ecx_core_PI; +ADD_IMPORT extern const double ecx_core_T_K; +void ecx_core_nm2eV(double *lambda, double *E, size_t n); +void ecx_core_kTe(double *U, double *kTE, size_t n); +/* ---------------------------------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------------------------------- */ +extern double ecx_kinetics_capi_nernst(double E0, int z, + double *aox, double *vox, size_t nox, + double *ared, double *vred, size_t nred, + double T); + +extern void ecx_kinetics_capi_sbv(double *U, double OCV, double j0, + double aa, double ac, double za, double zc, + double A, double T, double *i, size_t n); + +extern void ecx_kinetics_capi_bv(double *U, double OCV, double j0, double jdla, double jdlc, + double aa, double ac, double za, double zc, + double A, double T, double *i, size_t n); +/* ---------------------------------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------------------------------- */ +extern void ecx_capi_zr(double *w, double R, size_t n, ecx_cdouble *Z); +extern void ecx_capi_zc(double *w, double C, size_t n, ecx_cdouble *Z); +extern void ecx_capi_zl(double *w, double L, size_t n, ecx_cdouble *Z); +extern void ecx_capi_zcpe(double *w, double Q, double a, size_t n, ecx_cdouble *Z); +extern void ecx_capi_zw(double *w, double s, size_t n, ecx_cdouble *Z); +extern void ecx_eis_z(double *p, double *w, ecx_cdouble *z, + char e, size_t k, size_t n, + int *errstat, char *(*errmsg)); +/* ---------------------------------------------------------------------------------------------- */ + +#endif + + diff --git a/pywrapper/test/__init__.py b/py/test/__init__.py similarity index 100% rename from pywrapper/test/__init__.py rename to py/test/__init__.py diff --git a/pywrapper/test/test.py b/py/test/test.py similarity index 100% rename from pywrapper/test/test.py rename to py/test/test.py diff --git a/pywrapper/INSTALL.rst b/pywrapper/INSTALL.rst deleted file mode 100644 index 812bdc4..0000000 --- a/pywrapper/INSTALL.rst +++ /dev/null @@ -1,3 +0,0 @@ -.. code-block:: bash - - pip install pyecx \ No newline at end of file diff --git a/pywrapper/LICENSE.txt b/pywrapper/LICENSE.txt deleted file mode 100644 index 3877ae0..0000000 --- a/pywrapper/LICENSE.txt +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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But first, please read -. diff --git a/pywrapper/MANIFEST.in b/pywrapper/MANIFEST.in deleted file mode 100644 index 08b428b..0000000 --- a/pywrapper/MANIFEST.in +++ /dev/null @@ -1,5 +0,0 @@ -include INSTALL.rst -include LICENSE.TXT -include MANIFEST.in -include README.rst -include requirements.txt diff --git a/pywrapper/README.rst b/pywrapper/README.rst deleted file mode 100644 index b638a4a..0000000 --- a/pywrapper/README.rst +++ /dev/null @@ -1,25 +0,0 @@ -Introduction -============== - - .. readme_inclusion_start - -Python wrapper around the `Fortran ecx library <./ecx.html>`_. -The Fortran library does not need to be installed, the python wrapper embeds all needed fortran dependencies. -On linux, you might have to install `libgfortran` if it is not distributed by default with your linux distribution. - -.. readme_inclusion_end - - -Installation -=================== -See ``INSTALL.txt``. - -Dependencies -================ - -See ``requirements.txt``. - - -License information -=========================== -See ``LICENSE.txt``. diff --git a/pywrapper/configure.sh b/pywrapper/configure.sh deleted file mode 100755 index 2ea20f2..0000000 --- a/pywrapper/configure.sh +++ /dev/null @@ -1,86 +0,0 @@ -PYW_SRC="./src/py$HEADER_PREFIX" -LIB_INCLUDE_DIR="../include" -LIB_BUILD_DIR="../build" - -EXT=".so" - -LIBS=("libgfortran.5" "libquadmath.0" "libgcc_s.1.1") -LIBSWINDOWS=("libwinpthread") - -ROOTLINUX=/usr/lib/ -ROOTDARWIN=/usr/local/opt/gcc/lib/gcc/current -ROOTWINDOWS=/C/msys64/mingw64/bin -ROOT=$ROOTLINUX - -export PYW_SRC -echo "PYW_SRC=" $PYW_SRC - -export LIB_INCLUDE_DIR -echo "LIB_INCLUDE_DIR=" $LIB_INCLUDE_DIR - -export LIB_BUILD_DIR -echo "LIB_BUILD_DIR=" $LIB_BUILD_DIR - - -if [ "$PLATFORM" = "darwin" ]; then - ROOT=$ROOTDARWIN - EXT=".dylib" -fi - -if [ "$PLATFORM" = "windows" ]; then - ROOT=$ROOTWINDOWS - EXT=".dll" - LIBS+=$LIBSWINDOWS -fi - -if ! [ -z $1 ]; then - ROOT=$1 -fi - -# LIBRARY -echo "$LIBNAME folder: $LIB_BUILD_DIR" -fpath=$LIB_BUILD_DIR/$LIBNAME$EXT -if [ -f $fpath ]; then - echo -n " $fpath exists." - cp $fpath $PYW_SRC - echo " Copied." - if [ "$PLATFORM" = "windows" ]; then - cp $fpath.a $PYW_SRC - fi -else - echo " $fpath does not exist." -fi - - -# C HEADERS -echo "Include folder: $LIB_INCLUDE_DIR" -for header in "$LIB_INCLUDE_DIR"/*; do - echo -n " $header." - cp $LIB_INCLUDE_DIR/$header $PYW_SRC - echo " Copied." -done - - -# GFORTRAN LIBRARIES -echo "Gfortran libraries: $ROOT" -for lib in ${LIBS[@]}; do - fpath=$ROOT/$lib$EXT - if [ -f "$fpath" ]; then - echo -n " $fpath exists." - cp "$fpath" $PYW_SRC - if [ "$PLATFORM" = "darwin" ]; then - install_name_tool -change "$fpath" "@loader_path/$lib$EXT" $PYW_SRC/$LIBNAME$EXT - echo " Copied. Changed rpath in $LIBNAME$EXT." - else - echo " Copied." - fi - else - echo " $fpath does not exist." - fi -done - - -if [ "$PLATFORM" = "darwin" ]; then - echo "Check rpaths:" - otool -L $PYW_SRC/$LIBNAME$EXT -fi diff --git a/pywrapper/requirements.txt b/pywrapper/requirements.txt deleted file mode 100644 index e69de29..0000000 diff --git a/pywrapper/setup.py b/pywrapper/setup.py deleted file mode 100644 index c601475..0000000 --- a/pywrapper/setup.py +++ /dev/null @@ -1,44 +0,0 @@ -r"""setup""" -import platform -from setuptools import setup, Extension - -libraries = None -library_dirs = None -runtime_library_dirs = None -extra_objects = None - -if platform.system() == "Linux": - libraries = ["ecx"] - library_dirs = ["./src/pyecx"] - runtime_library_dirs = ["$ORIGIN"] -if platform.system() == "Windows": - extra_objects = ["./src/pyecx/libecx.dll.a"] -if platform.system() == "Darwin": - libraries = ["ecx"] - library_dirs = ["./src/pyecx"] - runtime_library_dirs = ["@loader_path"] - - -if __name__ == "__main__": - - mod_version = Extension(name="pyecx.version", - sources=["./src/pyecx/cpy_version.c"], - libraries=libraries, - library_dirs=library_dirs, - runtime_library_dirs=runtime_library_dirs, - extra_objects=extra_objects) - mod_eis = Extension(name="pyecx.eis", - sources=["./src/pyecx/cpy_eis.c", "./src/pyecx/cpy_common.c"], - libraries=libraries, - library_dirs=library_dirs, - runtime_library_dirs=runtime_library_dirs, - extra_objects=extra_objects) - mod_core = Extension(name="pyecx.core", - sources=["./src/pyecx/cpy_core.c", "./src/pyecx/cpy_common.c"], - libraries=libraries, - library_dirs=library_dirs, - runtime_library_dirs=runtime_library_dirs, - extra_objects=extra_objects) - - setup(ext_modules=[mod_version, mod_core, mod_eis]) - diff --git a/src/capi.f90 b/src/capi.f90 new file mode 100644 index 0000000..dc95524 --- /dev/null +++ b/src/capi.f90 @@ -0,0 +1,5 @@ +module capi + !! Main module for ECX library: C API. + use capi__version + +end module diff --git a/src/cecx_version.f90 b/src/capi_version.f90 similarity index 80% rename from src/cecx_version.f90 rename to src/capi_version.f90 index 51a5c3e..77beba2 100644 --- a/src/cecx_version.f90 +++ b/src/capi_version.f90 @@ -1,4 +1,4 @@ -module cecx__version +module capi__version !! version use iso_c_binding, only: c_loc, c_ptr, c_null_char use ecx__version, only: get_version @@ -7,11 +7,11 @@ module cecx__version character(len=:), allocatable, target :: version_c - public :: cecx_get_version + public :: capi_get_version contains -function cecx_get_version()bind(c)result(cptr) +function capi_get_version()bind(c, name="ecx_get_version")result(cptr) !! Get the version. implicit none @@ -31,4 +31,4 @@ function cecx_get_version()bind(c)result(cptr) cptr = c_loc(fptr) end function -end module cecx__version +end module capi__version diff --git a/src/cecx.f90 b/src/cecx.f90 deleted file mode 100644 index 6804ac8..0000000 --- a/src/cecx.f90 +++ /dev/null @@ -1,5 +0,0 @@ -module cecx - !! Main module for ECX library - use cecx__version - -end module diff --git a/src/ecx.f90 b/src/ecx.f90 index 0602a66..959a9ef 100644 --- a/src/ecx.f90 +++ b/src/ecx.f90 @@ -5,6 +5,6 @@ module ecx use ecx__eis use ecx__pec use ecx__version - use cecx + use capi end module diff --git a/srcgen/version/generator.exe b/srcgen/version/generator.exe new file mode 100644 index 0000000..5c96966 Binary files /dev/null and b/srcgen/version/generator.exe differ