Merge branch 'master' into patch-v220

.github/workflows/actions.yml

@@ -52,10 +52,10 @@ jobs:
           ./configure --enable-silent-rules
 
       - name: compile TREXIO
-        run: make -j 2
+        run: make -j2
 
       - name: check TREXIO
-        run: make check
+        run: make -j2 check
 
       - name: create virtual environment
         run: |
@@ -82,8 +82,22 @@ jobs:
           name: pytrexio-source
           path: ./trexio-*.tar.gz
 
-      - name: clean
-        run: make clean
+      - name: maintainer clean
+        run: make maintainer-clean
+
+      - name: reconfigure with clang and AddressSanitizer
+        run: |
+          ./autogen.sh
+          ./configure CC=clang-11 CFLAGS="-O2 -fsanitize=address -fno-omit-frame-pointer" LDFLAGS="-fsanitize=address" --enable-silent-rules
+
+      - name: recompile TREXIO
+        run: make -j2
+
+      - name: recheck TREXIO for memory leaks
+        run: make -j2 check
+
+      - name: maintainer clean
+        run: make maintainer-clean
 
   trexio_macos:
 

.github/workflows/build-wheels.yml

@@ -222,7 +222,7 @@ jobs:
 
       #- name: Publish distribution 📦 to Test PyPI
       #  uses: pypa/gh-action-pypi-publish@master
-      # with:
+      #  with:
       #    password: ${{ secrets.TEST_PYPI_API_TOKEN }}
       #    repository_url: https://test.pypi.org/legacy/
           #verbose: true

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
 
 # Initialize the CMake project.
 project(Trexio
-	VERSION 2.2.1
+	VERSION 2.3.0
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)

ChangeLog

@@ -1,6 +1,17 @@
 CHANGES
 =======
 
+2.3
+---
+
+- Added trexio_to_bitfield_list functionality
+- Added `trexio_has_group` functionality
+- Added OCaml binding
+- Added spin and energy in MOs
+- Added CSF group
+- Added `trexio_flush` functionality
+- Optional compilation `--without-fortran`
+
 2.2
 ---
 

Makefile.am

@@ -34,7 +34,11 @@
 
 ACLOCAL_AMFLAGS = -I m4
 CLEANFILES = trexio.mod
+if HAVE_FORTRAN
 BUILT_SOURCES = trexio.mod
+else
+BUILT_SOURCES = 
+endif
 EXTRA_DIST = .git_hash
 
 PACKAGE_VERSION = @PACKAGE_VERSION@
@@ -45,18 +49,20 @@ pkgconfig_DATA = pkgconfig/trexio.pc
 
 # =============== BUILD =============== #
 
-trexio_h = $(srcdir)/include/trexio.h
-trexio_f = $(srcdir)/include/trexio_f.f90
+trexio_h = include/trexio.h
+include_HEADERS = $(trexio_h)
 
-include_HEADERS = $(trexio_h) $(trexio_f)
+if HAVE_FORTRAN
+trexio_f = include/trexio_f.f90
+include_HEADERS += $(trexio_f)
+endif
 
 AM_CPPFLAGS = -I$(srcdir)/src -I$(srcdir)/include
 
 lib_LTLIBRARIES = src/libtrexio.la
 
 
 SOURCES = \
-  $(trexio_h) \
   src/trexio.c \
   src/trexio_private.h \
   src/trexio_s.h \
@@ -75,7 +81,7 @@ ORG_FILES = \
   trex.org
 
 
-src_libtrexio_la_SOURCES = $(SOURCES)
+src_libtrexio_la_SOURCES = $(trexio_h) $(SOURCES)
 
 # Include CMake-related files in the distribution.
 EXTRA_DIST += CMakeLists.txt \
@@ -117,28 +123,37 @@ TESTS_C += \
   tests/overwrite_all_hdf5
 endif
 
-TESTS_F = \
-  tests/test_f
+TESTS = $(TESTS_C)
+
+if HAVE_FORTRAN
+TESTS_F = tests/test_f
+TESTS += $(TESTS_F)
+endif
 
-TESTS = $(TESTS_C) $(TESTS_F)
 check_PROGRAMS = $(TESTS)
 
 # specify common LDADD options for all tests
 LDADD = src/libtrexio.la
 
-test_trexio_f = $(srcdir)/tests/trexio_f.f90
-CLEANFILES += $(test_trexio_f)
+if HAVE_FORTRAN
+test_trexio_f = tests/trexio_f.f90
 
 $(test_trexio_f): $(trexio_f)
 	cp $(trexio_f) $(test_trexio_f)
 
 trexio.mod: tests/trexio_f.o
 
 tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
+endif
 
 clean-local:
 	-rm -rf -- *.dir/ *.h5 __pycache__/
 
+# =============== GUIX MANIFEST =============== #
+
+trexio_scm = $(srcdir)/tools/trexio.scm
+EXTRA_DIST += $(trexio_scm)
+
 # =============== DOCUMENTATION =============== #
 
 HTML_TANGLED = docs/index.html            \
@@ -176,9 +191,15 @@ HDF5_CPPFLAGS = @HDF5_CPPFLAGS@
 
 if TREXIO_DEVEL
 
-CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h) $(HTML_TANGLED) $(htmlizer) .git_hash
+CLEANFILES += $(SOURCES) $(trexio_h) $(HTML_TANGLED) $(htmlizer) .git_hash
 
-BUILT_SOURCES += $(SOURCES) $(trexio_f) $(test_trexio_f)
+BUILT_SOURCES += $(SOURCES) $(trexio_h)
+
+if HAVE_FORTRAN
+CLEANFILES += $(trexio_f)
+BUILT_SOURCES += $(trexio_f) $(test_trexio_f)
+$(trexio_f): $(trexio_h)
+endif
 
 .git_hash: FORCE
 	git log | head -1 | cut -d ' ' -f 2 > .git_hash
@@ -188,10 +209,10 @@ all: .git_hash
 GENERATOR_FILES = $(srcdir)/tools/generator.py \
 		  $(srcdir)/tools/generator_tools.py
 
-$(SOURCES): $(trexio_f)
+$(SOURCES): $(trexio_h)
 src/trexio.c: $(trexio_h)
 
-$(trexio_f): $(ORG_FILES) $(GENERATOR_FILES)
+$(trexio_h): $(ORG_FILES) $(GENERATOR_FILES)
 	cd $(srcdir)/tools && ./build_trexio.sh
 
 $(htmlizer): $(ORG_FILES) $(srcdir)/src/README.org
@@ -208,6 +229,22 @@ cppcheck.out: $(trexio_h)
 	  --language=c --std=c99 -rp --platform=unix64  \
 	  -I../include *.c *.h 2>../$@
 
+#################
+# OCaml binding #
+#################
+
+ocaml/trexio/_build/default/lib/trexio.cma:
+	$(MAKE) -C ocaml/trexio
+
+ocaml: ocaml/trexio/_build/default/lib/trexio.cma
+
+ocaml-install: ocaml/trexio/_build/default/lib/trexio.cma
+	opam install ocaml/trexio
+
+##################
+# Python binding #
+##################
+
 setup_py      = $(srcdir)/python/setup.py
 setup_cfg     = $(srcdir)/python/setup.cfg
 pytrexio_py   = $(srcdir)/python/pytrexio/pytrexio.py
@@ -277,6 +314,6 @@ CLEANFILES += $(pytrexio_c) \
               python/src/*.c \
               python/src/*.h
 
-.PHONY: cppcheck python-test python-install python-sdist check-numpy FORCE
+.PHONY: cppcheck python-test python-install python-sdist check-numpy FORCE ocaml
 
 endif

README.md

@@ -1,5 +1,6 @@
 
 # TREXIO
+<img src="https://trex-coe.eu/sites/default/files/styles/responsive_no_crop/public/2022-01/TREXIO%20Code.png" width=200>
 
 [![build](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml/badge.svg)](https://github.com/TREX-CoE/trexio/actions/workflows/actions.yml)
 ![GitHub release (latest by date)](https://img.shields.io/github/v/release/TREX-CoE/trexio)
@@ -9,10 +10,10 @@ TREX library for efficient I/O.
 
 ## Minimal requirements (for users):
 
-- Autotools             (autoconf >= 2.69, automake >= 1.11, libtool >= 2.2)	or	CMake (>= 3.16)
+- Autotools             (autoconf >= 2.69, automake >= 1.11, libtool >= 2.2) or CMake (>= 3.16)
 - C compiler            (gcc/icc/clang)
 - Fortran compiler      (gfortran/ifort)
-- HDF5 library          (>= 1.8)	[optional, recommended for high performance]
+- HDF5 library          (>= 1.8) [optional, recommended for high performance]
 
 
 ## Installation procedure from the tarball (for users):
@@ -63,6 +64,9 @@ The aforementioned instructions rely on [Autotools](https://www.gnu.org/software
 
 ## Installation procedure for conda users
 
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/trexio/badges/version.svg)](https://anaconda.org/conda-forge/trexio)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/trexio/badges/platforms.svg)](https://anaconda.org/conda-forge/trexio)
+
 The official releases of TREXIO `>2.0.0` are also available via the `conda-forge` channel.
 The pre-compiled stable binaries of `trexio` can be installed as follows:
 
@@ -73,6 +77,33 @@ conda install trexio -c conda-forge
 More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
 Note that both parallel (see `mpi_openmpi` prefix) and serial (`nompi`) variants are provided.
 
+## Installation procedure for Guix users
+
+The official releases of TREXIO `>=2.0.0` can be installed using the
+[GNU Guix](https://guix.gnu.org) functional package manager.
+The [trexio.scm](https://github.com/TREX-CoE/trexio/blob/master/tools/trexio.scm)
+Schema file contains the manifest specification for the `trexio` package.
+It can be installed within the selected `$GUIX_PROFILE` as follows:
+
+```
+guix package \
+	--profile=$GUIX_PROFILE \
+	--cores=<n_cores> \
+	--install-from-file=trexio.scm
+```
+
+## Installation procedure for Spack users
+
+The official releases `>=2.0.0` and the development version of TREXIO can be installed using the
+[Spack](https://spack.io/) package manager.
+The [trexio/package.py](https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/trexio/package.py)
+file contains the Spack specifications required to build different variants of `trexio` library.
+It can be installed as follows
+
+```
+spack install --jobs <n_cores> trexio
+```
+
 ## Compilation without the HDF5 library
 
 By default, the configuration step proceeds to search for the [HDF5 library](https://portal.hdfgroup.org/display/HDF5/HDF5).

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio],[2.2.1],[https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio],[2.3.0],[https://github.com/TREX-CoE/trexio/issues])
 
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])
@@ -50,12 +50,18 @@ AS_IF([test "$ac_cv_prog_cc_c99" = "no"],
       [AC_MSG_ERROR([The compiler does not support C99])])
 AC_PROG_CC_C_O
 
-# Fortran
-AC_PROG_FC
-AC_FC_FREEFORM
-AC_FC_SRCEXT([f90])
-AC_PROG_FC_C_O
-AC_FC_LIBRARY_LDFLAGS
+
+# Fortran API [default: --with-fortran], do not disable in the dev mode
+AC_ARG_WITH(fortran, [AS_HELP_STRING([--without-fortran],[do not test and install the Fortran API])], ok=$withval, ok=yes)
+if test "$ok" = "yes"; then
+        AC_PROG_FC
+        AC_FC_FREEFORM
+        AC_FC_SRCEXT([f90])
+        AC_PROG_FC_C_O
+        AC_FC_LIBRARY_LDFLAGS
+fi
+
+AM_CONDITIONAL([HAVE_FORTRAN],[test "$ok" = "yes"])
 
 # pkg-config
 PKG_PROG_PKG_CONFIG()
@@ -66,6 +72,31 @@ AC_PROG_INSTALL
 AC_PROG_LN_S
 AC_PROG_GREP
 
+# Specific options required with some compilers
+case $FC in
+ *gfortran*)
+      FCFLAGS="$FCFLAGS -fPIC"
+      ;;
+ *flang*)
+      FCFLAGS="$FCFLAGS -fPIC"
+      ;;
+ *ifort*)
+      FCFLAGS="$FCFLAGS -fPIC"
+      ;;
+esac
+
+case $CC in
+  *gcc*)
+        CFLAGS="$CFLAGS -fPIC"
+        ;;
+  *clang*)
+        CFLAGS="$CFLAGS -fPIC"
+        ;;
+  *icc*)
+        CFLAGS="$CFLAGS -fPIC"
+        ;;
+esac
+
 
 ## ---------
 ## Libraries
@@ -138,7 +169,7 @@ AC_TYPE_UINT32_T
 AC_TYPE_UINT64_T
 
 # Checks for library functions.
-AC_FUNC_MALLOC
+# AC_FUNC_MALLOC
 AC_CHECK_FUNCS([memset mkdir strerror])
 
 if test "x$enable_maintainer_mode" == "xyes"; then