switch to using meson

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "libdeflate"]
+	path = libdeflate
+	url = https://github.com/ebiggers/libdeflate
+[submodule "wrapper"]
+	path = wrapper
+	url = https://github.com/wtsi-hpag/SIMDExtensionWrapper

.travis.yml

@@ -5,40 +5,48 @@ jobs:
   - os: osx
 language: c
 install:
-- if [ "$TRAVIS_OS_NAME" = "osx" ]; then export conda_url=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh;
-  fi
-- if [ "$TRAVIS_OS_NAME" = "linux" ]; then export conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh;
-  fi
+- if [ "$TRAVIS_OS_NAME" = "osx" ]; then export conda_url=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh; fi
+- if [ "$TRAVIS_OS_NAME" = "linux" ]; then export conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh; fi
 - wget $conda_url -O miniconda.sh
 - bash miniconda.sh -b -p $HOME/miniconda
 - source "$HOME/miniconda/etc/profile.d/conda.sh"
 - hash -r
 - conda config --set always_yes yes --set changeps1 no
 - conda update -q conda
 - conda info -a
+- conda install -c conda-forge mamba
 - if [ "$TRAVIS_OS_NAME" = "osx" ]; then export toolchain=clangxx_osx-64; fi
 - if [ "$TRAVIS_OS_NAME" = "linux" ]; then export toolchain=gxx_linux-64; fi
-- conda create -q -n test-environment -c conda-forge -c bioconda -y python=3.8 clang=10
-  $toolchain make pytest
+- mamba create -q -n test-environment -c conda-forge -c bioconda -y meson clang $toolchain samtools
 - conda activate test-environment
-- "./install"
+- if [ "$TRAVIS_OS_NAME" = "linux" ]; then env CC=clang CXX=clang meson setup --buildtype=release --unity on builddir; fi
+- if [ "$TRAVIS_OS_NAME" = "osx" ]; then meson setup --buildtype=release --unity on builddir; fi
+- cd builddir
+- meson compile
+- meson test
 script:
-- pytest -v
+- echo "done"
 before_deploy:
 - echo "Auto release generated by Travis CI on "$(date +'%Y:%m:%d at %H:%M:%S') >
   release_notes
 - export release_name="PretextGraph-"$(git describe --tags)
+- mkdir $release_name
+- cp -r $TRAVIS_BUILD_DIR/*.{cpp,h} $TRAVIS_BUILD_DIR/meson.build $TRAVIS_BUILD_DIR/wrapper $TRAVIS_BUILD_DIR/libdeflate $TRAVIS_BUILD_DIR/LICENSE $TRAVIS_BUILD_DIR/README.md $release_name/
+- tar -czf Source_with_Submodules.tar.gz $release_name
 deploy:
   edge: true
   provider: releases
   token: "$GITHUB_TOKEN"
-  file: release_notes
+  file: 
+  - release_notes
+  - Source_with_Submodules.tar.gz
   name: "$release_name"
   body: Auto-generated release by Travis CI
+  skip_cleanup: true
   prerelease: true
   on:
     tags: true
-    condition: "$TRAVIS_OS_NAME = linux"
+    condition: $TRAVIS_OS_NAME = linux
 env:
   global:
     secure: 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

PretextGraph.cpp

@@ -22,7 +22,7 @@ SOFTWARE.
 
 #include "Header.h"
 
-#define PretextGraph_Version "PretextGraph Version 0.0.4"
+#define PretextGraph_Version "PretextGraph Version 0.0.5"
 
 global_variable
 u08

README.md

@@ -36,36 +36,19 @@ Important: only non-negative integer data is supported.
 # Viewing graphs
 [PretextView](https://github.com/wtsi-hpag/PretextView) version 0.1.2 or later.
 
-# Mac and Linux builds
-Prebuilt binaries for Mac and Linux are available<br/>
-The Mac binary was build on MacOS 10.13.6<br/>
-The Linux binary was build on kernel 3.13<br/>
-Prebuilt binaries now come in 4-different varieties: AVX2, AVX, SSE4.2 and SSE4.1 along with a wrapper program. Just keep all the binaries on the same path and run the wrapper (PretextGraph); the correct binary for your architecture will be executed.
-
 # Third-Party acknowledgements
 PretextGraph uses the following third-party libraries:<br/>
-    libdeflate (https://github.com/ebiggers/libdeflate)<br/>
-    stb_sprintf.h (https://github.com/nothings/stb/blob/master/stb_sprintf.h)
-
-# Requirments, building via script (Mac and Linux)
-make<br/>
-python (2 or 3) to run the installation script<br/>
-clang or gcc to compile<br/>
-
-Tested on Ubuntu linux kernel 3.13 with clang-10, gcc-5.5<br/>
-Tested on MacOS 10.13.6 with clang-10<br/>
-
-PretextGraph requires libdeflate (https://github.com/ebiggers/libdeflate). By default the install script will clone and build the libdeflate.a static library for compilation with PretextGraph. You can specify your own version to the install script if you wish (you'll have to specify appropriate linking flags as well if you specify a shared library).
-
-run ./install to build (run ./install -h to see options)
-
-# Requirments, building on Windows
-Only recomended you know how to compile executables for Windows.<br/>
-
-Tested on Windows 10 using the Visual Studio 2019 toolchain<br/>
-Tested with clang-9<br/>
-Requires at least SSE4.1 support. 
-
-Requires libdeflate (https://github.com/ebiggers/libdeflate)<br/>
-
-Compile PretextGraph.cpp and link against libdeflate<br/>
+* [libdeflate](https://github.com/ebiggers/libdeflate)<br/>
+* [stb_sprintf.h](https://github.com/nothings/stb/blob/master/stb_sprintf.h)
+
+# Installation
+Requires:
+* clang >= 11.0.0
+* meson >= 0.57.1
+```bash
+git submodule update --init --recursive
+env CXX=clang meson setup --buildtype=release --unity on --prefix=<installation prefix> builddir
+cd builddir
+meson compile
+meson test
+meson install