Merge pull request #129 from TREX-CoE/rust

Rust interface

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
 
 # Initialize the CMake project.
 project(Trexio
-	VERSION 2.4.0
+	VERSION 2.4.2
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)

ChangeLog

@@ -6,6 +6,9 @@ CHANGES
 
 - Added state/energy
 - Made state/id an index instead of an int
+- Added JSON configuration data as a C variable in trexio.h
+- Added JSON configuration file in tar.gz release
+- Added Rust interface
 
 2.3
 ---

Makefile.am

@@ -34,10 +34,9 @@
 
 ACLOCAL_AMFLAGS = -I m4
 CLEANFILES = trexio.mod
+BUILT_SOURCES = trex.json
 if HAVE_FORTRAN
-BUILT_SOURCES = trexio.mod
-else
-BUILT_SOURCES =
+BUILT_SOURCES += trexio.mod
 endif
 EXTRA_DIST = .git_hash
 
@@ -87,14 +86,63 @@ src_libtrexio_la_SOURCES = $(trexio_h) $(SOURCES)
 
 # Include CMake-related files in the distribution.
 EXTRA_DIST += CMakeLists.txt \
+              trex.json \
               src/CMakeLists.txt \
               tests/CMakeLists.txt \
+              tests/test_macros.h  \
               cmake/cmake_uninstall.cmake.in \
               cmake/FindTREXIO.cmake
 
 
 # =============== TESTS =============== #
 
+TEST_FILES = \
+    tests/delete_group.c \
+    tests/delete_group_hdf5.c \
+    tests/delete_group_text.c \
+    tests/io_all.c \
+    tests/io_determinant.c \
+    tests/io_determinant_hdf5.c \
+    tests/io_determinant_text.c \
+    tests/io_dset_float.c \
+    tests/io_dset_float_hdf5.c \
+    tests/io_dset_float_text.c \
+    tests/io_dset_int.c \
+    tests/io_dset_int_hdf5.c \
+    tests/io_dset_int_text.c \
+    tests/io_dset_sparse.c \
+    tests/io_dset_sparse_hdf5.c \
+    tests/io_dset_sparse_text.c \
+    tests/io_dset_str.c \
+    tests/io_dset_str_hdf5.c \
+    tests/io_dset_str_text.c \
+    tests/io_jastrow.c \
+    tests/io_jastrow_hdf5.c \
+    tests/io_jastrow_text.c \
+    tests/io_num.c \
+    tests/io_num_hdf5.c \
+    tests/io_num_text.c \
+    tests/io_safe_dset_float.c \
+    tests/io_safe_dset_float_hdf5.c \
+    tests/io_safe_dset_float_text.c \
+    tests/io_str.c \
+    tests/io_str_hdf5.c \
+    tests/io_str_text.c \
+    tests/open.c \
+    tests/open_hdf5.c \
+    tests/open_text.c \
+    tests/overwrite_all.c \
+    tests/overwrite_all_hdf5.c \
+    tests/overwrite_all_text.c \
+    tests/pre_close.c \
+    tests/template_hdf5.c \
+    tests/template_text.c \
+    tests/test_f.f90 \
+    tests/test_macros.h \
+    tests/trexio_f.f90
+
+EXTRA_DIST += $(TEST_FILES)
+
 TESTS_C = \
   tests/open_text \
   tests/io_num_text \
@@ -221,6 +269,8 @@ src/trexio.c: $(trexio_h)
 $(trexio_h): $(ORG_FILES) $(GENERATOR_FILES)
 	cd $(srcdir)/tools && ./build_trexio.sh
 
+trex.json: $(trexio_h)
+
 $(htmlizer): $(ORG_FILES) $(srcdir)/src/README.org
 	touch $(htmlizer)
 	cd $(srcdir)/tools && ./build_doc.sh

README.md

@@ -5,7 +5,7 @@
 [![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)
 
-TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and exchanging wave function parameters and matrix elements, making it an important tool for researchers in the field of quantum chemistry. In this work, we present an overview of the TREXIO file format and library. The library consists of a front-end implemented in the C programming language and two different back-ends: a text back-end and a binary back-end utilizing the HDF5 library which enables fast read and write operations. It is compatible with a variety of platforms and has interfaces for the Fortran, Python, and OCaml programming languages. In addition, a suite of tools has been developed to facilitate the use of the TREXIO format and library, including converters for popular quantum chemistry codes and utilities for validating and manipulating data stored in TREXIO files. The simplicity, versatility, and ease of use of TREXIO make it a valuable resource for researchers working with quantum chemistry data.
+TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and exchanging wave function parameters and matrix elements. The library consists of a front-end implemented in the C programming language and two different back-ends: a text back-end and a binary back-end utilizing the HDF5 library which enables fast read and write operations. It is compatible with a variety of platforms and has interfaces for the Fortran, Python, OCaml and Rust programming languages.
 
 ## Minimal requirements (for users):
 
@@ -191,6 +191,34 @@ make python-test
 We highly recommend to use virtual environments to avoid compatibility issues and to improve reproducibility.
 
 
+## Rust API
+
+The Rust API is available on Crates.io, so you can simply run 
+```
+cargo add trexio
+```
+to your Rust project.
+
+If you prefer to install the Rust API provided with this repository:
+```
+cargo add --path /path/to/trexio/rust/trexio
+```
+
+## OCaml API
+
+The TREXIO OCaml API is available in OPAM:
+```
+opam install trexio
+```
+
+If you prefer to install it from this repository,
+
+```
+cd ocaml/trexio
+make
+opam install .
+```
+
 ## Tutorial
 
 TREXIO tutorials in Jupyter notebook format can be found in the

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio],[2.4.0],[https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio],[2.4.2],[https://github.com/TREX-CoE/trexio/issues])
 
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])

ocaml/trexio/Makefile

@@ -10,6 +10,7 @@ lib/trexio.h:
 sources: lib/trexio.ml lib/trexio.h
 
 clean:
+	rm lib/trexio.h lib/trexio.ml lib/trexio.mli lib/trexio_stubs.c
 	dune clean
 
 .PHONY: sources default

ocaml/trexio/dune-project

@@ -1,7 +1,7 @@
 (lang dune 3.1)
 
 (name trexio)
-(version 2.3.2)
+(version 2.4.2)
 
 (generate_opam_files false)
 

ocaml/trexio/read_json.py

@@ -7,6 +7,21 @@
 ml_file   = "trexio.ml"
 mli_file  = ml_file+"i"
 
+def check_version():
+   with open('trexio.opam','r') as f:
+      for line in f:
+         if line.startswith("version"):
+            ocaml_version = line.split(':')[1].strip()[1:-1]
+            break
+   with open('../../configure.ac','r') as f:
+      for line in f:
+         if line.startswith("AC_INIT"):
+            trexio_version = line.split(',')[1].strip()[1:-1]
+            break
+   if ocaml_version != trexio_version:
+      print(f"Inconsistent versions:\nTREXIO:{trexio_version}\nOCaml: {ocaml_version}\n")
+      raise
+
 def write_stubs(data):
 
     with open("src/"+stubs_file,'r') as f:
@@ -643,10 +658,12 @@ def write_ml(data):
 
 def main():
 
+    check_version()
     with open(json_file,'r') as f:
         data = json.load(f)
         for group in data:
           for element in data[group]:
+             print(f"{group}_{element}")
              if data[group][element][0] == "str":
                   data[group][element][0] = "string"
 

ocaml/trexio/trexio.opam

@@ -1,6 +1,6 @@
 # This file is generated by dune, edit dune-project instead
 opam-version: "2.0"
-version: "2.3.2"
+version: "2.4.2"
 synopsis: "Binding for the TREXIO Input/Output library"
 description:
   "TREXIO is a file format and library for storing wave functions and integrals for quantum chemistry."

python/pytrexio/_version.py

@@ -1 +1 @@
-__version__ = "2.4.0"
+__version__ = "2.4.2"

rust/trexio/.gitignore

@@ -0,0 +1,5 @@
+Cargo.lock
+src/generated.rs
+target/
+wrapper.h
+

rust/trexio/Cargo.toml

@@ -0,0 +1,26 @@
+[package]
+name = "trexio"
+version = "2.4.2"
+edition = "2021"
+license = "BSD-3-Clause"
+authors = ["Anthony Scemama <[email protected]>", "Evgeny Posenitskiy"]
+description = "TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and exchanging wave function parameters and matrix elements."
+repository = "https://github.com/trex-coe/trexio"
+keywords = ["quantum",  "chemistry"]
+readme = "README.md"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[build-dependencies]
+bindgen = "0.65.1"
+serde_json = "1.0"
+serde = { version = "1.0", features = ["derive"] }
+reqwest = { version = "0.11", features = ["blocking", "rustls-tls"] }
+tar = "0.4"
+flate2 = "1.0"
+
+[lib]
+doctest = false
+
+[dependencies]
+hdf5 = "0.8.1"

rust/trexio/Makefile

@@ -0,0 +1,10 @@
+default: src/generated.rs
+	cargo build
+	cargo test
+
+src/generated.rs: build.py
+	python3 build.py
+
+test: default
+	- cargo test -- --show-output
+

rust/trexio/README.md

@@ -0,0 +1,42 @@
+# TREXIO
+<img src="https://trex-coe.eu/sites/default/files/styles/responsive_no_crop/public/2022-01/TREXIO%20Code.png" width=200>
+
+TREXIO is an open-source file format and library developed for the storage and
+manipulation of data produced by quantum chemistry calculations. It is designed
+with the goal of providing a reliable and efficient method of storing and
+exchanging wave function parameters and matrix elements.
+
+This crate is the Rust binding for the TREXIO C library:
+![GitHub release (latest by date)](https://img.shields.io/github/v/release/TREX-CoE/trexio)
+
+
+## Documentation
+
+[TREXIO Documentation.](https://trex-coe.github.io/trexio/)
+
+
+## Citation
+
+The journal article reference describing TREXIO can be cited as follows:
+
+```
+@article{10.1063/5.0148161,
+    author = {Posenitskiy, Evgeny and Chilkuri, Vijay Gopal and Ammar, Abdallah and Hapka, Michał and Pernal, Katarzyna and Shinde, Ravindra and Landinez Borda, Edgar Josué and Filippi, Claudia and Nakano, Kosuke and Kohulák, Otto and Sorella, Sandro and de Oliveira Castro, Pablo and Jalby, William and Ríos, Pablo López and Alavi, Ali and Scemama, Anthony},
+    title = "{TREXIO: A file format and library for quantum chemistry}",
+    journal = {The Journal of Chemical Physics},
+    volume = {158},
+    number = {17},
+    year = {2023},
+    month = {05},
+    issn = {0021-9606},
+    doi = {10.1063/5.0148161},
+    url = {https://doi.org/10.1063/5.0148161},
+    note = {174801},
+    eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0148161/17355866/174801\_1\_5.0148161.pdf},
+}
+```
+
+Journal paper: [![doi](https://img.shields.io/badge/doi-10.1063/5.0148161-5077AB.svg)](https://doi.org/10.1063/5.0148161)
+
+ArXiv paper: [![arXiv](https://img.shields.io/badge/arXiv-2302.14793-b31b1b.svg)](https://arxiv.org/abs/2302.14793)
+