Merge branch 'main' of github.com:MatteoLacki/IsoSpec

michalsta · michalsta · commit 9fd4e998ad82 · 2025-11-11T20:05:05.000+01:00
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -15,7 +15,7 @@ cmake_minimum_required(VERSION 3.12)
 ############################################################
 # Basic information about project
 
-project(IsoSpec VERSION 2.3.0
+project(IsoSpec VERSION 2.3.2
     DESCRIPTION "A program to calculate isotopic clusters"
     HOMEPAGE_URL "https://github.com/MatteoLacki/IsoSpec")
 
@@ -177,8 +177,8 @@ message(STATUS "${BoldYellow}CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}.${Col
 
 # message(STATUS CMAKE_MODULE_PATH: ${CMAKE_MODULE_PATH})
 
-# Now actually deal with the C++ source code.
-add_subdirectory(IsoSpec++)
+# Now actually deal with the source code.
+add_subdirectory(src)
 
 # if (UNIX AND NOT APPLE)
 #   add_subdirectory(skbuild)
diff --git a/CMakeStuff/doxyfile.in b/CMakeStuff/doxyfile.in
@@ -791,7 +791,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @CMAKE_SOURCE_DIR@/IsoSpec++
+INPUT                  = @CMAKE_SOURCE_DIR@/src/IsoSpec++
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
diff --git a/CMakeStuff/isospec_logo2_high.svg.in b/CMakeStuff/isospec_logo2_high.svg.in
@@ -33994,6 +33994,6 @@
          id="tspan21336"
          x="19.724558"
          y="174.68359"
-         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'EB Garamond SC';-inkscape-font-specification:'EB Garamond SC';fill:#00fff3;fill-opacity:1;stroke-width:0.26458332px">IsoSpec2 v @VERSION@</tspan></text>
+         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'EB Garamond SC';-inkscape-font-specification:'EB Garamond SC';fill:#00fff3;fill-opacity:1;stroke-width:0.26458332px">IsoSpec2 v @PROJECT_VERSION@</tspan></text>
   </g>
 </svg>
diff --git a/CMakeStuff/isospec_logo2_long.svg.in b/CMakeStuff/isospec_logo2_long.svg.in
@@ -34006,6 +34006,6 @@
          id="tspan21336"
          x="33.963207"
          y="46.170403"
-         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'EB Garamond SC';-inkscape-font-specification:'EB Garamond SC';fill:#00fff3;fill-opacity:1;stroke-width:0.26458332px">IsoSpec2 v @VERSION@</tspan></text>
+         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'EB Garamond SC';-inkscape-font-specification:'EB Garamond SC';fill:#00fff3;fill-opacity:1;stroke-width:0.26458332px">IsoSpec2 v @PROJECT_VERSION@</tspan></text>
   </g>
 </svg>
diff --git a/debian/changelog b/debian/changelog
@@ -1,12 +1,30 @@
-isospec (2.3.0-1) unstable; urgency=medium
+isospec (2.3.2-1) unstable; urgency=medium
 
-  * New upstream release with source configuration worked alongside
-    upstream.
+  * Steer away from graphicsmagick and replace by librsvg2-bin for
+    conversion of svg to png.
+
+  * libisospec++-dev: Drop Multi-Arch: same (Janitor pull request).
+
+ -- Filippo Rusconi <lopippo@debian.org>  Tue, 04 Nov 2025 19:05:21 +0100
+
+isospec (2.3.1-2) unstable; urgency=medium
+
+  * Fix missing dh_quilt_patch at configure target. Odd because in my
+    chroot the package builds fine.
+
+  * libisospec++-dev: Drop Multi-Arch: same (Janitor pull request).
+
+ -- Filippo Rusconi <lopippo@debian.org>  Wed, 29 Oct 2025 12:32:42 +0100
+
+isospec (2.3.1-1) unstable; urgency=medium
+
+  * New upstream release with source configuration and Debian packaging
+    worked alongside upstream (thank you michalsta !).
 
   * Disabled production of the refman.pdf file due to bug in Doxygen
-    (Closes: #1114157) and synchronize the git repos.
+    (Closes: #1114157).
 
- -- Filippo Rusconi <lopippo@debian.org> Wed, 22 Oct 2025 21:06:59 +0200
+ -- Filippo Rusconi <lopippo@debian.org>  Wed, 22 Oct 2025 21:06:59 +0200
 
 isospec (2.2.3+cleaned2-1) UNRELEASED; urgency=medium
 
diff --git a/debian/control b/debian/control
@@ -6,7 +6,8 @@ Uploaders: Filippo Rusconi <lopippo@debian.org>
 Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
  quilt,
  dh-exec,
- graphicsmagick-imagemagick-compat,
+# To export from svg to png
+ librsvg2-bin,
  cmake,
  d-shlibs,
  dh-python,
@@ -33,7 +34,6 @@ Vcs-Git: https://salsa.debian.org/debichem-team/isospec.git
 Package: libisospec++-dev
 Section: libdevel
 Architecture: any
-Multi-Arch: same
 Depends: libisospec++2t64 (= ${binary:Version}),
          ${misc:Depends}
 Recommends: libisospec++-doc
diff --git a/debian/copyright b/debian/copyright
@@ -1,25 +1,25 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: libisospec
 Source: https://github.com/MatteoLacki/IsoSpec
-Comment: The upstream source tarball contains Windows dll files and 
+Comment: The upstream source tarball contains Windows dll files and
     other documentation files that are regenerated using doxygen.
-    All these files are thereby not useful or appropriate for use as 
+    All these files are thereby not useful or appropriate for use as
     source files. This violates DFSG §2.
 
 Files: *
-Copyright: 2015-2018 Micha Startek
+Copyright: 2015-2018 Michal Startek
            2015-2018 Mateusz Lacki
 License: BSD-2-Clause
  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions are met:
- . 
+ .
  1. Redistributions of source code must retain the above copyright notice, this
  list of conditions and the following disclaimer.
- . 
+ .
  2. Redistributions in binary form must reproduce the above copyright notice,
  this list of conditions and the following disclaimer in the documentation and/or
  other materials provided with the distribution.
- . 
+ .
  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
@@ -33,7 +33,7 @@ License: BSD-2-Clause
 
 
 Files: debian/*
-Copyright: 2018 Filippo Rusconi <lopippo@debian.org>
+Copyright: 2018-2025 Filippo Rusconi <lopippo@debian.org>
 License: GPL-3+
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
diff --git a/debian/libisospec++-dev.install b/debian/libisospec++-dev.install
@@ -1,4 +1,4 @@
-IsoSpec++/*.h usr/include/IsoSpec++ 
+usr/include/IsoSpec++
 
 usr/lib/*/libIsoSpec++.a
 
diff --git a/debian/libisospec++-doc.doc-base b/debian/libisospec++-doc.doc-base
@@ -8,8 +8,3 @@ Section: Science/Chemistry
 Format: HTML
 Index: /usr/share/doc/isospec/html/index.html
 Files: /usr/share/doc/isospec/html/*.html
-
-# As of 20251016, pdflatex refman.tex fails.
-# Format: PDF
-# Files: /usr/share/doc/isospec/pdf/refman.pdf.gz
-
diff --git a/debian/patches/disable-pdf-refman-generation.patch b/debian/patches/disable-pdf-refman-generation.patch
@@ -1,30 +1,17 @@
 diff --git a/man/CMakeLists.txt b/man/CMakeLists.txt
-index 79c91a1..ef07d8f 100644
+index 7511860..ef07d8f 100644
 --- a/man/CMakeLists.txt
 +++ b/man/CMakeLists.txt
-@@ -54,13 +54,18 @@ install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/images
+@@ -54,8 +54,10 @@ install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/images
  install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html
  	DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec)
  
 -install(FILES ${CMAKE_CURRENT_BINARY_DIR}/latex/refman.pdf
--	DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec/pdf)
--
--file(GLOB man3_pages "${CMAKE_CURRENT_BINARY_DIR}/man/man3/*")
--
--install(FILES ${man3_pages}
--	DESTINATION ${CMAKE_INSTALL_FULL_MANDIR}/man3)
+-  DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec/pdf)
 +# As of 20251020 the Doxygen-based generation of the pdf
 +# man page via pdflatex fails.
 +# install(FILES ${CMAKE_CURRENT_BINARY_DIR}/latex/refman.pdf
 +# 	DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec/pdf)
-+
-+# Install the man pages
-+install(
-+    DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/man/man3
-+    DESTINATION ${CMAKE_INSTALL_FULL_MANDIR}/
-+    FILES_MATCHING
-+    PATTERN "*.3"
-+)
  
- message("")
- message(STATUS "${BoldGreen}Finished configuration of the doc material.${ColourReset}")
+ # Install the man pages
+ install(
diff --git a/debian/patches/library-version.patch b/debian/patches/library-version.patch
@@ -5,9 +5,9 @@ index d839ba8..3fa336b 100644
 @@ -15,7 +15,7 @@ cmake_minimum_required(VERSION 3.12)
  ############################################################
  # Basic information about project
- 
--project(IsoSpec VERSION 2.3.0
-+project(IsoSpec VERSION 2.3.0
+
+-project(IsoSpec VERSION 2.3.2
++project(IsoSpec VERSION 2.3.2
      DESCRIPTION "A program to calculate isotopic clusters"
      HOMEPAGE_URL "https://github.com/MatteoLacki/IsoSpec")
- 
+
diff --git a/debian/patches/mtune-march-flags-in-python-setup.patch b/debian/patches/mtune-march-flags-in-python-setup.patch
diff --git a/debian/replace-mathjax-cloudflare-url-local-file.sh b/debian/replace-mathjax-cloudflare-url-local-file.sh
@@ -1,13 +1,13 @@
 #!/bin/sh
 
-cd man/html
+cd obj-$(dpkg-architecture -qDEB_HOST_MULTIARCH)/man/html
 
 for file in *.html
 do
 	grep -i "src=\"https://cdnjs.cloudflare.com/ajax/libs/mathjax/[0-9].[0-9].[0-9]/MathJax.js\"" ${file}
 
 	if [ "$?" = "0" ]
 	then
-		sed -i 's|src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/\([0-9].[0-9].[0-9]\)/MathJax.js\"|src="file:///usr/share/javascript/mathjax/MathJax.js"|' ${file} 
+		sed -i 's|src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/\([0-9].[0-9].[0-9]\)/MathJax.js\"|src="file:///usr/share/javascript/mathjax/MathJax.js"|' ${file}
 	fi
 done
diff --git a/debian/rules b/debian/rules
@@ -45,19 +45,20 @@ override_dh_clean:
 	dh_clean
 
 configure_cpp_library:
-	dh_auto_configure -O--buildsystem=cmake -- \
+	dh_auto_configure -O--buildsystem=cmake  --sourcedirectory=./src/IsoSpec++ -- \
 		-DCMAKE_INSTALL_PREFIX=/usr \
 		-DISOSPEC_LIB_VERSION=$(ISOSPEC_LIB_VERSION) -DISOSPEC_LIB_SOVERSION=$(ISOSPEC_LIB_SOVERSION)
 
 configure_python_module:
-	dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=./IsoSpecPy
+	dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=./src/IsoSpecPy
 
 configure_cpp_library_doc:
 	dh_auto_configure -O--buildsystem=cmake -- \
 		-DCMAKE_INSTALL_PREFIX=/usr \
 		-DISOSPEC_LIB_VERSION=$(ISOSPEC_LIB_VERSION) -DISOSPEC_LIB_SOVERSION=$(ISOSPEC_LIB_SOVERSION)
 
 override_dh_auto_configure:
+	dh_quilt_patch
 	dh_auto_configure -O--buildsystem=cmake -- \
 		-DCMAKE_INSTALL_PREFIX=/usr \
 		-DISOSPEC_LIB_VERSION=$(ISOSPEC_LIB_VERSION) -DISOSPEC_LIB_SOVERSION=$(ISOSPEC_LIB_SOVERSION)
diff --git a/man/CMakeLists.txt b/man/CMakeLists.txt
@@ -18,13 +18,13 @@ configure_file(${CMAKE_SOURCE_DIR}/CMakeStuff/isospec_logo2_long.svg.in
 
 if(UNIX AND NOT APPLE)
 
-	execute_process(COMMAND gm convert -geometry 200x
-		${CMAKE_CURRENT_BINARY_DIR}/images/isospec_logo2_high_versioned.svg
-		${CMAKE_CURRENT_BINARY_DIR}/images/isospec_logo2_high_versioned.png)
+  execute_process(COMMAND rsvg-convert -w 200 -f png -o
+    ${CMAKE_CURRENT_BINARY_DIR}/images/isospec_logo2_high_versioned.png
+    ${CMAKE_CURRENT_BINARY_DIR}/images/isospec_logo2_high_versioned.svg)
 
-		execute_process(COMMAND gm convert -geometry 200x
-		${CMAKE_CURRENT_BINARY_DIR}/images/isospec_logo2_long_versioned.svg
-		${CMAKE_CURRENT_BINARY_DIR}/images/isospec_logo2_long_versioned.png)
+		execute_process(COMMAND rsvg-convert -w 200 -f png -o
+		${CMAKE_CURRENT_BINARY_DIR}/images/isospec_logo2_long_versioned.png
+		${CMAKE_CURRENT_BINARY_DIR}/images/isospec_logo2_long_versioned.svg)
 
 endif()
 
@@ -55,12 +55,15 @@ install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html
 	DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec)
 
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/latex/refman.pdf
-	DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec/pdf)
-
-file(GLOB man3_pages "${CMAKE_CURRENT_BINARY_DIR}/man/man3/*")
-
-install(FILES ${man3_pages}
-	DESTINATION ${CMAKE_INSTALL_FULL_MANDIR}/man3)
+  DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec/pdf)
+
+# Install the man pages
+install(
+    DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/man/man3
+    DESTINATION ${CMAKE_INSTALL_FULL_MANDIR}/
+    FILES_MATCHING
+    PATTERN "*.3"
+)
 
 message("")
 message(STATUS "${BoldGreen}Finished configuration of the doc material.${ColourReset}")
diff --git a/pyproject.toml b/pyproject.toml
@@ -9,7 +9,7 @@ cmake.source-dir = "skbuild"
 name = "IsoSpecPy"
 dependencies = ["cffi"]
 description = "IsoSpecPy is a Python library for computing isotopic distributions of molecules."
-version = "2.3.0"
+version = "2.3.2"
 license = "BSD-2-Clause"
 license-files = ["LICENCE"]
 authors = [{name = "Michał Startek"}, {name = "Mateusz Łącki"}]
diff --git a/reinstall.sh b/reinstall.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+pip uninstall -y IsoSpecPy
+VERBOSE=1 pip install -v .
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(IsoSpec++)
diff --git a/src/IsoSpec++/CMakeLists.txt b/src/IsoSpec++/CMakeLists.txt
@@ -46,8 +46,7 @@ install(TARGETS IsoSpec++-shared IsoSpec++-static
 	)
 
 # Install the header files
-install(
-    DIRECTORY IsoSpec++
+install(DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
     DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
     FILES_MATCHING
     PATTERN "*.h"
diff --git a/src/IsoSpec++/marginalTrek++.cpp b/src/IsoSpec++/marginalTrek++.cpp
@@ -265,17 +265,23 @@ double Marginal::getHeaviestConfMass() const
     return ret_mass*atomCnt;
 }
 
-double Marginal::getMonoisotopicConfMass() const
+size_t Marginal::getMonoisotopicAtomIndex() const
 {
     double found_prob = -std::numeric_limits<double>::infinity();
-    double found_mass = 0.0;  // to avoid uninitialized var warning
+    size_t found_idx = 0;
     for(unsigned int ii = 0; ii < isotopeNo; ii++)
         if( found_prob < atom_lProbs[ii] )
         {
             found_prob = atom_lProbs[ii];
-            found_mass = atom_masses[ii];
+            found_idx = ii;
         }
-    return found_mass*atomCnt;
+    return found_idx;
+}
+
+double Marginal::getMonoisotopicConfMass() const
+{
+    size_t idx = getMonoisotopicAtomIndex();
+    return atom_masses[idx]*atomCnt;
 }
 
 double Marginal::getAtomAverageMass() const
diff --git a/src/IsoSpec++/marginalTrek++.h b/src/IsoSpec++/marginalTrek++.h
@@ -109,10 +109,17 @@ class Marginal
     */
     double getMonoisotopicConfMass() const;
 
+    //! Get the index of the monoisotopic (most probable) atom.
+    /*!
+        \return The index of the most probable isotope of the element.
+    */
+    size_t getMonoisotopicAtomIndex() const;
+
     //! The the mass of the mode subisotopologue.
     /*!
         \return The mass of one of the most probable subisotopologues.
     */
+
     inline double getModeMass() { ensureModeConf(); return calc_mass(mode_conf, atom_masses, isotopeNo); }
 
     //! Get the log-probability of the mode subisotopologue.
diff --git a/tests/Python/test_iface.py b/tests/Python/test_iface.py

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-IsoSpec++/*.h usr/include/IsoSpec++`
	`1`	`+usr/include/IsoSpec++`
`2`	`2`
`3`	`3`	`usr/lib/*/libIsoSpec++.a`
`4`	`4`