Merge branch 'master' into multichrom

MesserLab · Nov 12, 2024 · 08651e2 · 08651e2
2 parents 519d459 + 6e77cf4
commit 08651e2
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -13,6 +13,7 @@ jobs:
       - name: Cancel previous runs
         uses: styfle/[email protected]
   tests-Unix-CLI:
+    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
     strategy:
       fail-fast: false
       matrix:
@@ -22,22 +23,20 @@ jobs:
           - {os: ubuntu-20.04, gcc: 7, python: 3.8}
           - {os: ubuntu-20.04, gcc: 11, python: 3.9}
           # macOS, oldest supported version
-          # (macos-10.15 and macos-11 were removed by GitHub)
-          - {os: macos-12, python: 3.8}
-          # macOS, newest supported version (haven't tried macos-14 yet)
+          # (macos-10.15, macos-11, and macos-12 were removed by GitHub)
           - {os: macos-13, python: 3.9}
+          # macOS, newest supported version
+          - {os: macos-15, python: 3.9}
 
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repository code
         uses: actions/checkout@v4
-      - name: Setup Mambaforge
+      - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           activate-environment: anaconda-client-env
-          use-mamba: true
           python-version: ${{ matrix.python }}
       - name: Get Date
         id: get-date
@@ -58,7 +57,7 @@ jobs:
         id: cache
       - name: Update environment
         run:
-          mamba env update -n anaconda-client-env -f treerec/tests/environment.yml
+          conda env update -n anaconda-client-env -f treerec/tests/environment.yml
         if: steps.cache.outputs.cache-hit != 'true'
       - name: Workaround for gcc-11
         if: startsWith(matrix.os, 'ubuntu') && matrix.gcc == 11
@@ -93,6 +92,7 @@ jobs:
             cd treerec/tests && python -m pytest -xv
   
   tests-Windows-CLI:
+    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
     runs-on: windows-latest
     strategy:
       fail-fast: false
@@ -117,13 +117,11 @@ jobs:
             msys2-devel
             mingw-w64-${{matrix.env}}-toolchain
             mingw-w64-${{matrix.env}}-cmake
-      - name: Setup Mambaforge
+      - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           activate-environment: anaconda-client-env
-          use-mamba: true
           auto-update-conda: true
           python-version: ${{ matrix.python }}
       - name: Get Date
@@ -132,21 +130,27 @@ jobs:
         shell: bash
       - name: Cache Conda env
         uses: actions/cache@v3
+        env:
+          # Increase this value to reset cache if treerec/tests/environment.yml has not changed
+          CACHE_NUMBER: 0
         with:
-          path: ${{ env.CONDA }}/envs
+          # Use faster GNU tar
+          enableCrossOsArchive: true
+          path: D:\conda_pkgs_dir
           key:
             conda-${{ runner.os }}--python-${{ matrix.python }}--${{ runner.arch }}--${{
             steps.get-date.outputs.today }}-${{
             hashFiles('treerec/tests/environment.yml') }}-${{ env.CACHE_NUMBER}}
-        env:
-          # Increase this value to reset cache if
-          # treerec/tests/environment.yml has not changed
-          CACHE_NUMBER: 0
         id: cache
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: anaconda-client-env
+          environment-file: treerec/tests/environment.yml
+          pkgs-dirs: D:\conda_pkgs_dir
       - name: Update environment
         shell: bash -el {0}
         run:
-          mamba env update -n anaconda-client-env -f treerec/tests/environment.yml
+          conda env update -n anaconda-client-env -f treerec/tests/environment.yml
         if: steps.cache.outputs.cache-hit != 'true'
       - name: Build and test (Debug)
         run: |
@@ -175,6 +179,7 @@ jobs:
             cd treerec/tests && python -m pytest -xv
   
   tests-Unix-GUI:
+    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
     strategy:
       fail-fast: false
       matrix:
@@ -227,6 +232,7 @@ jobs:
           make -j 2 && make test
   
   tests-Windows-GUI:
+    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
     strategy:
       fail-fast: false
       matrix:
@@ -264,6 +270,7 @@ jobs:
           make -j 2 && make test
 
   tests-windows-latest-pacman:
+    if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
     runs-on: windows-latest
     strategy:
       fail-fast: false

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -87,8 +87,8 @@ if(NOT CMAKE_BUILD_TYPE)
 endif(NOT CMAKE_BUILD_TYPE)
 
 # Add "-D BUILD_SLIMGUI=ON" to the CMake command to build SLiMgui
-# This requires that Qt 5, a widget framework, is installed
-option(BUILD_SLIMGUI "Build the Qt5-based GUI for SLiM" OFF)
+# This requires that Qt, a widget framework, is installed
+option(BUILD_SLIMGUI "Build the Qt-based GUI for SLiM" OFF)
 
 # Add "-D PARALLEL=ON" to the CMake command to make a parallel (multi-threaded) build
 # This is supported only for the command-line tools, not for SLiMgui; do not set BUILD_SLIMGUI

diff --git a/SLiM.spec b/SLiM.spec
@@ -1,9 +1,27 @@
 # Cross-distribution SLiM RPM spec.
-# Defines:
 %if %{defined suse_version}
-%define qt5 libqt5
+%if 0%{?suse_version} < 1600
+%global qtNameAndVersion libqt5
 %else
-%define qt5 qt5
+%global qtNameAndVersion qt6
+%endif
+%endif
+
+%if %{defined fedora}
+%if 0%{?fedora} >= 39
+%global qtNameAndVersion qt6
+%else
+%global qtNameAndVersion qt5
+%endif
+%endif
+
+%if %{defined rhel}
+%if 0%{?epel} >= 9
+# qt6 is only available through EPEL on RHEL 9 and higher
+%global qtNameAndVersion qt6
+%else
+%global qtNameAndVersion qt5
+%endif
 %endif
 
 Name:           SLiM
@@ -22,21 +40,29 @@ Conflicts:      slim
 BuildRequires:  cmake
 # openSUSE Build Requires
 %if %{defined suse_version}
-%if 0%{?suse_version} >= 1500
 BuildRequires:  glew-devel
 BuildRequires:  Mesa-libGL-devel
 BuildRequires:  gcc-c++
-BuildRequires:  libqt5-qtbase-devel
 BuildRequires:  appstream-glib-devel
+%if 0%{?suse_version} < 1600
+BuildRequires:  %{qtNameAndVersion}-qtbase-devel
+%else
+# only Tumbleweed officially supports Qt6; further, it's "base" not "qtbase" in Tumbleweed. :(
+BuildRequires:  %{qtNameAndVersion}-base-devel
 %endif
 %else
-BuildRequires:  qt5-qtbase-devel
+# if not on openSUSE
+BuildRequires:  %{qtNameAndVersion}-qtbase-devel
 BuildRequires:  libappstream-glib
 %endif
 ExclusiveArch:  x86_64
 
 # RHEL 8 has the oldest point release of 5.15, and is the oldest RHEL supported.
-Requires: %{qt5}-qtbase >= 5.15.1
+%if 0%{?rhel} == 8
+Requires: qt5-qtbase >= 5.15.1
+%else
+Requires: %{qtNameAndVersion}-qtbase
+%endif
 
 %description
 SLiM is an evolutionary simulation framework that combines a powerful engine for
@@ -53,11 +79,32 @@ visualization of simulation output.
 %setup -q
 
 %build
+%if 0%{?rhel} == 8
+%if "%_vpath_builddir" != "%_vpath_srcdir"
+echo "current directory: %(pwd)"
+echo "source directory: %_vpath_srcdir"
+echo "build directory: %_vpath_builddir"
+mkdir -p %_vpath_builddir
+%else
+%{warn "The build directory is the same as the source directory on RHEL 8!"}
+%endif
+
+## Tell CMake where the source directory and the build directory are, directly.
+%cmake -S %_vpath_srcdir -B %_vpath_builddir -DBUILD_SLIMGUI=ON
+cd %_vpath_builddir
+%else
+# rpmbuild is not running on RHEL 8
 %cmake -DBUILD_SLIMGUI=ON
+%endif
+
 %cmake_build
 
 %install
+%if 0%{?rhel} == 8
+cmake --install %_vpath_builddir --prefix %{buildroot}/usr
+%else
 %cmake_install
+%endif
 
 %files
 %{_bindir}/eidos
@@ -72,6 +119,16 @@ visualization of simulation output.
 %{_datadir}/mime/packages/org.messerlab.slimgui-mime.xml
 
 %changelog
+* Sun Sep 15 2024 Bryce Carson <[email protected]> - 4.3-2
+- Significant work has been invested into debugging the build of RHEL 8 on COPR. For whatever reason, since 4.0.1-1, we were unable to build on RHEL 8 (or perhaps it was EPEL 8?). Regardless, the ability to build on RHEL 8 and EPEL 8 has been achieved or restored, using conditionals which check what distribution the build is occuring on. These conditionals check the distribution using the defined RPM macros, a reliable system that the operating systems try not to step on each others toes; it'd be nicer if CentOS didn't call itself RHEL, though, but CentOS purposefully tries to be "bug-compatible" (if I recall) with RHEL, yet be slightly upstream of it with RHEL. The buildroot (which is the installation prefix within the CHROOT) and the source and build directories must be manually specified when building on RHEL 8 or EPEL 8 systems (which is RHEL 8 + EPEL [the extra packages for enterprise linux repository] for RHEL 8). I don't know what changed amongst the macros, if anything ever did change, but with 4.0.1-1 we were able to build for EPEL 8 two years ago, and then we weren't when I tried however long ago that issue four-hundred and forty cropped up. This has been resolved with the use of conditionals in the RPM preprocessor (do recall that "if" is not actually a macro) and RPM macros.
+- Conditionals and macros are used to decide whether to use Qt 6 or Qt 5.
+
+* Mon Sep 02 2024 Bryce Carson <[email protected]> - 4.3-1
+- Changes to the package have occurred. See the following points.
+- Further version checks for various distributions are introduced to allow cross-distribution packaging and building against Qt5 or Qt6, appropriate to the platform.
+- An attempt to fix issue 440 is made
+- See the SLiM release notes on GitHub for information about changes to the packaged software.
+
 * Tue Apr 30 2024 Ben Haller <[email protected]> - 4.2.2-1
 - No changes to the package have been made since the last release.
 - Ship the fix for the 4.2.1-2 crashing bug as a separate release.
@@ -85,7 +142,7 @@ visualization of simulation output.
 - No changes to the package have been made since the last release.
 - Fix for a crashing bug under certain conditions.
 
-* Thu Mar 20 2024 Bryce Carson <[email protected]> - 4.2-1
+* Wed Mar 20 2024 Bryce Carson <[email protected]> - 4.2-1
 - No changes to the package have been made since the last release. See the SLiM release notes on GitHub for information about changes to the packaged software.
 
 * Mon Dec 4 2023 Bryce Carson <[email protected]> - 4.1-1

diff --git a/VERSIONS b/VERSIONS
@@ -6,6 +6,7 @@ Note that not every commit will be logged here; that is what the Github commit h
 
 
 development head (in the master branch):
+	fix the wiring for calcPi() and calcTajimasD() to call the correct code; they were broken in SLiM 4.3
 	multi-chromosome transition:
 		API changes:
 		x	class Genome -> class Haplosome

diff --git a/core/slim_functions.cpp b/core/slim_functions.cpp
@@ -42,6 +42,8 @@ extern const char *gSLiMSourceCode_calcPairHeterozygosity;
 extern const char *gSLiMSourceCode_calcHeterozygosity;
 extern const char *gSLiMSourceCode_calcWattersonsTheta;
 extern const char *gSLiMSourceCode_calcInbreedingLoad;
+extern const char *gSLiMSourceCode_calcPi;
+extern const char *gSLiMSourceCode_calcTajimasD;
 
 
 const std::vector<EidosFunctionSignature_CSP> *Community::SLiMFunctionSignatures(void)
@@ -71,8 +73,8 @@ const std::vector<EidosFunctionSignature_CSP> *Community::SLiMFunctionSignatures
 		sim_func_signatures_.emplace_back((EidosFunctionSignature *)(new EidosFunctionSignature("calcHeterozygosity", gSLiMSourceCode_calcHeterozygosity, kEidosValueMaskFloat | kEidosValueMaskSingleton, "SLiM"))->AddObject("haplosomes", gSLiM_Haplosome_Class)->AddObject_ON("muts", gSLiM_Mutation_Class, gStaticEidosValueNULL)->AddInt_OSN("start", gStaticEidosValueNULL)->AddInt_OSN("end", gStaticEidosValueNULL));
 		sim_func_signatures_.emplace_back((EidosFunctionSignature *)(new EidosFunctionSignature("calcWattersonsTheta", gSLiMSourceCode_calcWattersonsTheta, kEidosValueMaskFloat | kEidosValueMaskSingleton, "SLiM"))->AddObject("haplosomes", gSLiM_Haplosome_Class)->AddObject_ON("muts", gSLiM_Mutation_Class, gStaticEidosValueNULL)->AddInt_OSN("start", gStaticEidosValueNULL)->AddInt_OSN("end", gStaticEidosValueNULL));
 		sim_func_signatures_.emplace_back((EidosFunctionSignature *)(new EidosFunctionSignature("calcInbreedingLoad", gSLiMSourceCode_calcInbreedingLoad, kEidosValueMaskFloat | kEidosValueMaskSingleton, "SLiM"))->AddObject("haplosomes", gSLiM_Haplosome_Class)->AddObject_OSN("mutType", gSLiM_MutationType_Class, gStaticEidosValueNULL));
-		sim_func_signatures_.emplace_back((EidosFunctionSignature *)(new EidosFunctionSignature("calcPi", gSLiMSourceCode_calcWattersonsTheta, kEidosValueMaskFloat | kEidosValueMaskSingleton, "SLiM"))->AddObject("haplosomes", gSLiM_Haplosome_Class)->AddObject_ON("muts", gSLiM_Mutation_Class, gStaticEidosValueNULL)->AddInt_OSN("start", gStaticEidosValueNULL)->AddInt_OSN("end", gStaticEidosValueNULL));
-		sim_func_signatures_.emplace_back((EidosFunctionSignature *)(new EidosFunctionSignature("calcTajimasD", gSLiMSourceCode_calcWattersonsTheta, kEidosValueMaskFloat | kEidosValueMaskSingleton, "SLiM"))->AddObject("haplosomes", gSLiM_Haplosome_Class)->AddObject_ON("muts", gSLiM_Mutation_Class, gStaticEidosValueNULL)->AddInt_OSN("start", gStaticEidosValueNULL)->AddInt_OSN("end", gStaticEidosValueNULL));
+		sim_func_signatures_.emplace_back((EidosFunctionSignature *)(new EidosFunctionSignature("calcPi", gSLiMSourceCode_calcPi, kEidosValueMaskFloat | kEidosValueMaskSingleton, "SLiM"))->AddObject("haplosomes", gSLiM_Haplosome_Class)->AddObject_ON("muts", gSLiM_Mutation_Class, gStaticEidosValueNULL)->AddInt_OSN("start", gStaticEidosValueNULL)->AddInt_OSN("end", gStaticEidosValueNULL));
+		sim_func_signatures_.emplace_back((EidosFunctionSignature *)(new EidosFunctionSignature("calcTajimasD", gSLiMSourceCode_calcTajimasD, kEidosValueMaskFloat | kEidosValueMaskSingleton, "SLiM"))->AddObject("haplosomes", gSLiM_Haplosome_Class)->AddObject_ON("muts", gSLiM_Mutation_Class, gStaticEidosValueNULL)->AddInt_OSN("start", gStaticEidosValueNULL)->AddInt_OSN("end", gStaticEidosValueNULL));
 
 		// Other built-in SLiM functions
 		sim_func_signatures_.emplace_back((EidosFunctionSignature *)(new EidosFunctionSignature("summarizeIndividuals", SLiM_ExecuteFunction_summarizeIndividuals, kEidosValueMaskFloat, "SLiM"))->AddObject("individuals", gSLiM_Individual_Class)->AddInt("dim")->AddNumeric("spatialBounds")->AddString_S("operation")->AddLogicalEquiv_OSN("empty", gStaticEidosValue_Float0)->AddLogical_OS("perUnitArea", gStaticEidosValue_LogicalF)->AddString_OSN("spatiality", gStaticEidosValueNULL));

diff --git a/treerec/tests/environment.yml b/treerec/tests/environment.yml
@@ -1,6 +1,6 @@
 channels:
   - conda-forge
-  - defaults
+  - nodefaults
 dependencies:
   - tskit >= 0.4.1
   - msprime >= 1.2.0