Merge pull request #173 from tschoonj/4.1.0

Get ready for 4.1.0

.github/workflows/ci.yml

@@ -354,11 +354,6 @@ jobs:
             buildsystem: meson
           - image: centos:8
             buildsystem: meson
-          - image: fedora:latest
-            buildsystem: meson
-          # autoconf doesnt like the rawhide shell
-          - image: fedora:rawhide
-            buildsystem: autotools
         include:
           # at least some versions of clang cannot compile php bindings
           - cython: cython
@@ -393,6 +388,11 @@ jobs:
             perl: disable
             python: disable
             clang_cflags: -Qunused-arguments
+          - cc: clang
+            image: fedora:rawhide
+            perl: disable
+            python: disable
+            clang_cflags: -Qunused-arguments
           - image: ubuntu:bionic
             lua: /usr/bin/lua5.3
           - image: ubuntu:focal
@@ -505,7 +505,7 @@ jobs:
         # disable java for now
         ./configure --disable-python --disable-python-numpy --${PERL_ENABLE}-perl --enable-lua --${FPC_ENABLE}-pascal --disable-java --${PHP_ENABLE}-php --enable-ruby --${FORTRAN_ENABLE}-fortran2003 || (cat config.log && exit 1)
         make
-        make check || (cat ruby/tests/test-suite.log && exit 1)
+        make check || (cat example/xrlexample12.sh.log && exit 1)
         make distclean
         ./configure --disable-all-bindings CFLAGS="-std=c89 -pedantic $CFLAGS"
         make

Changelog

@@ -1,3 +1,14 @@
+Version 4.1.0 Tom Schoonjans
+
+- Add meson as alternative buildsystem
+- Add API to calculate XRF cross sections for whole shells, instead of
+individual lines (suggested by Oleg Shirokobrod)
+- Lightweight C++ wrappers through a header-only library (contributed by Marius Schollmeier and myself)
+- Add Google Analytics tracking to Python bindings and Java implementation
+- Update L values of CosKronTransProb and FluorYield for W, Re, Sn and Sb,
+using work from Ayri, Kaur, Kumar, Czyzycki, Karydas and Puri
+
+
 Version 4.0.0 Tom Schoonjans
 
 Major changes:

INSTALL

@@ -13,7 +13,7 @@ required in addition to the C compiler.
 After unpacking the distribution, if the "configure" file is missing, this file
 is generated using the command:
 
-	autoreconf -i
+  autoreconf -i
 
 If errors are generated, make sure you have a relatively up-to-date version of autoconf.
 Makefiles can be prepared using the configure command:
@@ -42,100 +42,44 @@ configure. Consult the "Further information" section below for
 instructions on installing the library in another location or changing
 other default compilation options.
 
+Alternatively, you can also use the meson buildsystem to compile the core C library, Python and Fortran bindings:
 
+  mkdir build
+  meson ..
+  ninja
+  ninja test
+  ninja install
+
+This works particularly well on Windows, and comes with support for the Visual Studio compilers.
 
     -----------------------------------------------
 
 
 Platforms known to compile and run xraylib
 ==========================================
 
-  Linux (32-bit/64-bit)
-  Solaris 10 (32-bit/64-bit)
-  Mac OS X (32-bit/64-bit)
-  Windows (native and Cygwin)
-  FreeBSD (64-bit)
+  Linux (64-bit)
+  macOS (64-bit)
+  Windows (MSYS2 and Visual Studio)
+
+32-bit builds should still work, but are no longer routinely tested.
 
 Not all bindings have been tested on each of these platforms. The
 following table summarizes the current status.
 
-         | Linux | Mac OS X | Solaris | Cygwin | FreeBSD | MinGW |
-------------------------------------------------------------------
- Fortran |   x   |     x    |    x    |    x   |    x    |   x   |
-  Perl   |   x   |     x    |    x    |    x   |    x    |       |
- Python  |   x   |     x    |         |    x   |         |   x   |
-   IDL   |   x   |     x    |         |        |         |       |
-  Java   |   x   |     x    |    ?    |    ?   |         |       |
-   Lua   |   x   |     x    |         |        |         |       |
+         | Linux |   macOS  |  MSYS2  |   VS   |
+------------------------------------------------
+ Fortran |   x   |     x    |    x    |    x   |
+  Perl   |   x   |     x    |    x    |    x   |
+ Python  |   x   |     x    |    x    |    x   |
+  Java   |   x   |     x    |    ?    |    ?   |
+   Lua   |   x   |     x    |    ?    |        |
+  Ruby   |   x   |     x    |    ?    |        |
 
 
     -----------------------------------------------
 
 
-
-
-Platform Specific Compilation Notes
-===================================
-
-This section documents any known issues with installing xraylib on
-specific platforms.
-  * Mac OS X
-  * Solaris
-  * mingw32
-
-Hints for Mac OS X
-==================
-
-Standard Mac OS X installations do not come with a C compiler. You can
-install this essential compiler by installing the XCode package which
-can be found on the Mac OS X cd or can be downloaded from the Apple
-Developer Connection website.  A free Fortran compiler can be
-downloaded from macports.org.
-
-When compiling the IDL bindings on Snow Leopard, make sure that you
-are using IDL 7.1. Older IDL versions do not have the necessary 64-bit
-libraries
-
-
-Hints for Solaris
-=================
-
-The Sun compiler tools are stored in non-standard directories -- make
-sure that all the compiler and linker tools (cc, ar, ranlib, ld) are
-on the PATH.  A typical PATH should include the directories
-/opt/SUNWspro/bin:/usr/ccs/bin:/usr/ucb in that order.
-
-For example,
-
-  $ PATH=/opt/SUNWspro/bin:/usr/ccs/bin:/usr/ucb:$PATH
-  $ ./configure CC=cc 
-
-Use gmake instead of make. To do this, invoke:
-
-  $ ./configure MAKE=gmake
-
-gmake is not installed by default on Solaris 10, it can be downloaded
-from blastwave.org
-
-We have noticed that the compilation of the xrayglob_inline.c file
-(using the Sun Studio C compiler) produces many warnings. These can be
-ignored safely.
-
-Also, the fortran compiler of the Sun Studio package requires the -M
-command line option or the MODDIR environment variable to search for
-.mod files. Since not all fortran compilers support this option, we
-did not include this in the Makefile of the examples, causing the
-fortran test to fail. This can however be circumvented by setting the
-MODDIR variable pointing to the src directory.
-
-The IDL bindings currently do not work on Solaris. The main reason
-would be that none of the developers currently have access to an IDL
-software package on this platform. If you do, and can test the
-bindings, please contact the developers.
-
-
-                    ------------------------------
-
 Further information on the standard GNU installation procedure
 ==============================================================
 

README

@@ -14,10 +14,8 @@ The current stable version of xraylib is always available from http://github.com
 Installation
 ============
 
-xraylib follows the standard GNU installation procedure. Please consult the INSTALL file in this distribution for more detailed instructions. 
-An installer for Windows including a 32-bit dll and the xraylib headers is also available from the Download section of the github repository. 
-
-For information about specific platforms and compilers see the "Compilation Notes" section in the INSTALL file.
+xraylib can be compiled using GNU Autotools or meson. Please consult the INSTALL file in this distribution for more detailed instructions. 
+An installer for Windows including a 64-bit dll and the xraylib headers is also available. 
 
 More information about xraylib
 ==============================
@@ -32,7 +30,7 @@ This paper was recently superseded by a new publication, covering all aspects of
 
 If you would publish scientific results that were obtained using xraylib, please refer to this paper.
 
-We recently started a mailinglist. Subscription is possible at https://lists.ugent.be/wws/info/xraylib
+Subscription to our mailing list is possible at https://lists.ugent.be/wws/info/xraylib
 
 Reporting bugs
 ==============

example/xrlexample12.php

@@ -204,15 +204,15 @@
 printf ("  Name: %s\n", $cdn["name"]);
 printf ("  Density: %f g/cm3\n", $cdn["density"]);
 for ($i = 0 ; $i < $cdn["nElements"] ; $i++) {
-	printf("  Element %i: %f %%\n",$cdn["Elements"][$i],$cdn["massFractions"][$i]*100.0);
+	printf("  Element %d: %f %%\n",$cdn["Elements"][$i],$cdn["massFractions"][$i]*100.0);
 }
 
 $cdn = GetCompoundDataNISTByIndex(NIST_COMPOUND_BRAIN_ICRP);
 printf ("NIST_COMPOUND_BRAIN_ICRP\n");
 printf ("  Name: %s\n", $cdn["name"]);
 printf ("  Density: %f g/cm3\n", $cdn["density"]);
 for ($i = 0 ; $i < $cdn["nElements"] ; $i++) {
-	printf("  Element %i: %f %%\n",$cdn["Elements"][$i],$cdn["massFractions"][$i]*100.0);
+	printf("  Element %d: %f %%\n",$cdn["Elements"][$i],$cdn["massFractions"][$i]*100.0);
 }
 
 $nistCompounds = GetCompoundDataNISTList();

windows/Makefile.am

@@ -48,11 +48,13 @@ common:
 	unix2dos -n ${top_srcdir}/include/xraylib-error.h xraylib-error.h
 	unix2dos -n ${top_srcdir}/include/xraylib-nist-compounds.h xraylib-nist-compounds.h
 	unix2dos -n ${top_srcdir}/include/xraylib-radionuclides.h xraylib-radionuclides.h
+	unix2dos -n ${top_srcdir}/include/xraylib-aux.h xraylib-aux.h
 	unix2dos -n ${top_srcdir}/pascal/xraylib.pas xraylib.pas
 	unix2dos -n ${top_srcdir}/pascal/xraylib_const.pas xraylib_const.pas
 	unix2dos -n ${top_srcdir}/pascal/xraylib_iface.pas xraylib_iface.pas
 	unix2dos -n ${top_srcdir}/pascal/xraylib_impl.pas xraylib_impl.pas
 	unix2dos -n ${top_srcdir}/example/xrlexample14.pas xrlexample14.pas
+	unix2dos -n ${top_srcdir}/cplusplus/xraylib++.h xraylib++.h