Merge branch 'master' of github.com:TREX-CoE/trexio

.github/workflows/actions.yml

@@ -20,7 +20,7 @@ jobs:
       message: ${{ steps.commit_message.outputs.message }}
     steps:
       - name: Checkout the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
         # Gets the correct commit message for pull request
         with:
           ref: ${{ github.event.pull_request.head.sha }}
@@ -31,15 +31,13 @@ jobs:
           COMMIT_MSG=$(git log --no-merges -1 --oneline)
           echo "::set-output name=message::$COMMIT_MSG"
 
-
   trexio_ubuntu:
-
-    runs-on: ubuntu-20.04
     name: x86 Ubuntu 20.04
+    runs-on: ubuntu-20.04
     needs: get_commit_message
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
 
       - name: install dependencies
         run: |
@@ -84,7 +82,7 @@ jobs:
         if: >-
           contains(needs.get_commit_message.outputs.message, '[wheel build]') ||
           github.event_name == 'release'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2
         with:
           name: pytrexio-source
           path: ./trexio-*.tar.gz
@@ -114,12 +112,11 @@ jobs:
         run: make maintainer-clean
 
   trexio_macos:
-
-    runs-on: macos-11
     name: x86 MacOS 11
+    runs-on: macos-11
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791
 
       - name: install dependencies
         run: |
@@ -133,10 +130,10 @@ jobs:
           ./configure FC=gfortran-10 --enable-silent-rules
 
       - name: compile TREXIO
-        run: make -j 2
+        run: make -j3
 
       - name: check TREXIO
-        run: make check
+        run: make -j3 check
 
       - name: Archive test log file
         if: failure()

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.16)
 
 # Initialize the CMake project.
 project(Trexio
-	VERSION 2.3.0
+	VERSION 2.4.0
 	DESCRIPTION "TREX I/O library"
 	LANGUAGES C Fortran
 	)

README.md

@@ -22,8 +22,8 @@ TREX library for efficient I/O.
 2. `gzip -cd trexio-<version>.tar.gz | tar xvf -`
 3. `cd trexio-<version>`
 4. `./configure`
-5. `make`
+5. ```make -j`getconf _NPROCESSORS_ONLN` ```
-6. `make check`
+6. ```make -j`getconf _NPROCESSORS_ONLN` check```
 7. `sudo make install`
 
 
@@ -45,8 +45,8 @@ TREX library for efficient I/O.
 2. `cd trexio`
 3. `./autogen.sh`
 4. `./configure`
-5. `make`
+5. ```make -j`getconf _NPROCESSORS_ONLN` ```
-6. `make check`
+6. ```make -j`getconf _NPROCESSORS_ONLN` check```
 7. `sudo make install`
 
 ## Installation procedure for CMake users (from the tarball or GitHub repo clone):
@@ -56,8 +56,8 @@ The aforementioned instructions rely on [Autotools](https://www.gnu.org/software
 
 1. `cmake -S. -Bbuild`
 2. `cd build`
-3. `make`
+3. ```make -j`getconf _NPROCESSORS_ONLN` ```
-4. `ctest` (or `make test`)
+4. ```ctest -j`getconf _NPROCESSORS_ONLN` ```
 5. `sudo make install`
 
 **Note: on systems with no `sudo` access, one can add `-DCMAKE_INSTALL_PREFIX=build` as an argument to the `cmake` command so that `make install/uninstall` can be run without `sudo` privileges.**
@@ -73,7 +73,7 @@ The official releases of TREXIO `>2.0.0` are also available via the `conda-forge
 The pre-compiled stable binaries of `trexio` can be installed as follows:
 
 ```
-conda install trexio -c conda-forge
+conda install -c conda-forge trexio
 ```
 
 More details can be found in the corresponding [trexio-feedstock](https://github.com/conda-forge/trexio-feedstock).
@@ -88,7 +88,7 @@ Schema file contains the manifest specification for the `trexio` package.
 It can be installed as follows:
 
 ```
-guix package --cores=<n_cores> --install-from-file=trexio.scm
+guix package --cores=`getconf _NPROCESSORS_ONLN` --install-from-file=trexio.scm
 ```
 
 ## Installation procedure for Spack users
@@ -100,7 +100,7 @@ file contains the Spack specifications required to build different variants of `
 It can be installed as follows
 
 ```
-spack install --jobs <n_cores> trexio
+spack install --jobs `getconf _NPROCESSORS_ONLN` trexio
 ```
 
 ## Installation procedure for Debian/Ubuntu users
@@ -127,14 +127,14 @@ To build TREXIO without HDF5 back end, append `--without-hdf5` option to `config
 ## Linking to your program
 
 The `make install` command takes care of installing the TREXIO shared library on the user machine.
-Once installed, add `-ltrexio` to the list of compiler options.
+After installation, append `-ltrexio` to the list of compiler  (`$LIBS`) options.
 
-In some cases (e.g. when using custom `prefix` during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LIBRARY_PATH`.
+In some cases (e.g. when using custom installation prefix during configuration), the TREXIO library might end up installed in a directory, which is absent in the default `$LD_LIBRARY_PATH`.
-In order to link the program against TREXIO, the search paths can be modified as follows:
+In order to link the program against TREXIO, the search path can be modified as follows:
 
-`export LIBRARY_PATH=$LIBRARY_PATH:<path_to_trexio>/lib`
+`export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_trexio>/lib`
 
-(same holds for `$LD_LIBRARY_PATH`). The `<path_to_trexio>` has to be replaced by the prefix used during the installation.
+where the `<path_to_trexio>` has to be replaced by the prefix used during the installation.
 
 If your project relies on CMake build system, feel free to use the
 [FindTREXIO.cmake](https://github.com/TREX-CoE/trexio/blob/master/cmake/FindTREXIO.cmake)

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio],[2.3.0],[https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio],[2.4.0],[https://github.com/TREX-CoE/trexio/issues])
 
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])

python/pytrexio/_version.py

@@ -1 +1 @@
-__version__ = "1.3.0"
+__version__ = "1.4.0"

src/CMakeLists.txt

@@ -66,7 +66,7 @@ option(ENABLE_HDF5 "Enable HDF5 support" ON)
 
 if(ENABLE_HDF5)
   # Try to detect HDF5 installation using built-in FindHDF5.cmake macro.
-  find_package(HDF5 REQUIRED COMPONENTS C HL)
+  find_package(HDF5 REQUIRED COMPONENTS C)
 
   if(HDF5_FOUND)
     message(STATUS "HDF5 version     :: ${HDF5_VERSION}")
@@ -87,9 +87,7 @@ if(ENABLE_HDF5)
   # - include directories with HDF5 header files
   target_include_directories(trexio PRIVATE ${HDF5_C_INCLUDE_DIRS})
   # - link to HDF5 C libraries
-  target_link_libraries(trexio PRIVATE
+  target_link_libraries(trexio PRIVATE ${HDF5_C_LIBRARIES})
-         ${HDF5_C_HL_LIBRARIES}
-         ${HDF5_C_LIBRARIES})
 endif()
 
 # Private headers have to be listed as sources, otherwise they are installed

tools/trexio.scm

@@ -60,8 +60,22 @@
 		"1n9n1gbk5hgvg73am991xrv7ap002rz719a3nvh8m8ff9x10qd76"
                 ))))))
 
+(define-public trexio-2.3
+  (package/inherit trexio-2.0
+    (version "2.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/TREX-CoE/trexio/releases/download/v" version
+				  "/trexio-" version
+                                  ".tar.gz"))
+              (sha256
+               (base32
+		;; the hash below is produced by guix download <url>
+		"183wljg1avsia2pf2wb59s2i2qw6y19qfw164ffy1g024b6362ii"
+                ))))))
+
 (define-public trexio
   ;; Default version of TREXIO.
-  trexio-2.2)
+  trexio-2.3)
 
 trexio