[WIP] v2.0.0 release

.github/workflows/build.yml

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+on:
+  push:
+    paths:
+      - '.github/workflows/build.yml'
+      - 'CMakeLists.txt'
+      - 'dataset/**'
+      - 'include/**'
+      - 'source/**'
+      - 'scripts/**'
+      - 'tests/**'
+  pull_request:
+    paths:
+      - '.github/workflows/build.yml'
+      - 'CMakeLists.txt'
+      - 'dataset/**'
+      - 'include/**'
+      - 'scripts/**'
+      - 'source/**'
+      - 'tests/**'
+name: Build 
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        arch: [x86, x86_64, armv7, aarch64]
+        cpu_instr: [non-SIMD, SSE2, auto-selected]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+            submodules: true
+      - name: Setup Alpine Linux for x86
+        if: matrix.arch == 'x86'
+        uses: jirutka/setup-alpine@v1
+        with:
+          arch: x86
+          packages: >
+            cmake
+            file
+            g++
+            make
+          shell-name: alpine-x86.sh
+
+      - name: Build trimal for Linux x86
+        if: matrix.arch == 'x86' && matrix.cpu_instr == 'non-SIMD'
+        run: cmake . -DDISABLE_SSE2=1 -DDISABLE_AVX2=1 && make && file bin/trimal && file bin/readal &&
+          ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh 
+        shell: alpine-x86.sh {0}
+      - name: Build trimal for Linux x86 and SSE2
+        if: matrix.arch == 'x86' && matrix.cpu_instr == 'SSE2'
+        run: cmake . -DDISABLE_AVX2=1 && make && file bin/trimal && file bin/readal &&
+          ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh 
+        shell: alpine-x86.sh {0}
+      - name: Build trimal for Linux x86 and auto-selected SIMD (AVX2 if available)
+        if: matrix.arch == 'x86' && matrix.cpu_instr == 'auto-selected'
+        run: cmake . && make && file bin/trimal && file bin/readal &&
+          ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh 
+        shell: alpine-x86.sh {0}
+
+      - name: Build trimal for Linux x86_64
+        if: matrix.arch == 'x86_64' && matrix.cpu_instr == 'non-SIMD'
+        run: cmake . -DDISABLE_SSE2=1 -DDISABLE_AVX2=1 && make && file bin/trimal && file bin/readal &&
+          ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh
+      - name: Build trimal for Linux x86_64 and SSE2
+        if: matrix.arch == 'x86_64' && matrix.cpu_instr == 'SSE2'
+        run: cmake . -DDISABLE_AVX2=1 && make && file bin/trimal && file bin/readal &&
+          ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh
+      - name: Build trimal for Linux x86_64 and auto-selected SIMD (AVX2 if available)
+        if: matrix.arch == 'x86_64' && matrix.cpu_instr == 'auto-selected'
+        run: cmake . && make && file bin/trimal && file bin/readal &&
+          ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh
+
+      - name: Setup Alpine Linux for armv7
+        if: matrix.arch == 'armv7'
+        uses: jirutka/setup-alpine@v1
+        with:
+          arch: armv7
+          packages: >
+            cmake
+            file
+            g++
+            make
+          shell-name: alpine-armv7.sh
+
+      - name: Build trimal for Linux armv7
+        if: matrix.arch == 'armv7' && matrix.cpu_instr == 'non-SIMD'
+        run: cmake . -DDISABLE_NEON=1 && make && file bin/trimal && file bin/readal &&
+          ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh 
+        shell: alpine-armv7.sh {0}
+      - name: Build trimal for Linux armv7 and auto-selected SIMD (NEON)
+        if: matrix.arch == 'armv7' && matrix.cpu_instr == 'auto-selected'
+        run: cmake . && make && file bin/trimal && file bin/readal &&
+          ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh 
+        shell: alpine-armv7.sh {0}
+
+      - name: Build trimal for Linux aarch64
+        if: matrix.arch == 'aarch64' && matrix.cpu_instr == 'non-SIMD'
+        uses: uraimo/run-on-arch-action@v2
+        # Emulate ARM architecture since it's not natively supported by GitHub. 
+        # Warning about image and host platforms not matching may be ignored (https://github.com/uraimo/run-on-arch-action/issues/127#issuecomment-1605691328)
+        with:
+          arch: ${{ matrix.arch }}
+          distro: ubuntu20.04
+          githubToken: ${{ github.token }}
+          dockerRunArgs: |
+            --volume "${PWD}:/trimal" 
+          install: |
+            apt-get update -q -y
+            apt-get install -q -y cmake make g++ file
+          run: |
+            cmake . -DDISABLE_NEON=1 && make && file bin/trimal && file bin/readal &&
+            ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh
+      - name: Build trimal for Linux aarch64 and auto-selected SIMD (NEON)
+        if: matrix.arch == 'aarch64' && matrix.cpu_instr == 'auto-selected'
+        uses: uraimo/run-on-arch-action@v2
+        # Emulate ARM architecture since it's not natively supported by GitHub. 
+        # Warning about image and host platforms not matching may be ignored (https://github.com/uraimo/run-on-arch-action/issues/127#issuecomment-1605691328)
+        with:
+          arch: ${{ matrix.arch }}
+          distro: ubuntu20.04
+          githubToken: ${{ github.token }}
+          dockerRunArgs: |
+            --volume "${PWD}:/trimal" 
+          install: |
+            apt-get update -q -y
+            apt-get install -q -y cmake make g++ file
+          run: |
+            cmake . && make && file bin/trimal && file bin/readal &&
+            ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh

.gitignore

@@ -0,0 +1,27 @@
+#.gitignore
+*.svg 
+*.pdf
+*.zip
+*.save
+*.user
+*.cbp
+*kdev*
+*.json
+*.css
+*.tcl
+.idea*
+
+*Makefile*
+*Cache*
+
+bin
+build
+CMakeFiles
+Testing
+dev_files
+test_msas
+
+CTestTestfile.cmake
+cmake_install.cmake
+
+source/Catch/test_generated_alignment.cpp

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "vendor/cpu_features"]
+	path = vendor/cpu_features
+	url = https://github.com/google/cpu_features

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt

AUTHORS

@@ -1,16 +1,30 @@
-** Authors **
+* Authors*
+Victor Fernandez Rodriguez.
+ INB Hub. Life Sciences Department.
+ Barcelona Supercomputing Center (BSC). Barcelona, Spain.
+ e-mail: victor.fernandez _at_ bsc.es
 
 Salvador Capella-Gutierrez.
-  Comparative Genomics Group. Bioinformatics and Genomics Department.
-  Centre for Genomic Regulation. Barcelona, Spain.
-  e-mail: scapella _at_ crg.es
+ INB Hub. Life Sciences Department.
+ Barcelona Supercomputing Center (BSC). Barcelona, Spain.
+ e-mail: salvador.capella _at_ bsc.es
 
 Toni Gabaldón.
-  Comparative Genomics Group. Bioinformatics and Genomics Department.
-  Centre for Genomic Regulation. Barcelona, Spain.
-  e-mail: tgabaldon _at_ crg.es
+ Comparative Genomics Group. Life Sciences Department.
+ Barcelona Supercomputing Center (BSC). Barcelona, Spain.
+ e-mail: toni.gabaldon _at_ bsc.es
 
-** Authors (until trimAl v1.1) **
+** Up to trimAl v1.4 **
+Salvador Capella-Gutierrez.
+ Comparative Genomics Group. Bioinformatics and Genomics Department.
+ Centre for Genomic Regulation. Barcelona, Spain.
+ e-mail: scapella _at_ crg.es
+
+Toni Gabaldón.
+ Comparative Genomics Group. Bioinformatics and Genomics Department.
+ Centre for Genomic Regulation. Barcelona, Spain.
+ e-mail: tgabaldon _at_ crg.es
 
+** Up to trimAl v1.1 **
 Jose Ma. Silla-Martínez.
-  e-mail: josilma1 _at_ gmail.com
+ e-mail: josilma1 _at_ gmail.com

CMakeLists.txt

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+cmake_minimum_required(VERSION 3.13.3)
+project(trimAl)
+
+# Make project C++ 11
+set(CMAKE_CXX_STANDARD 11)
+
+# Specify bin folder to output the compiled programs
+set (CMAKE_RUNTIME_OUTPUT_DIRECTORY bin)
+
+# Set common files for all executables
+set(TRIMAL_OBJECTS
+    $<TARGET_OBJECTS:CoreOBJLib>
+    $<TARGET_OBJECTS:FormatsOBJLib>
+    $<TARGET_OBJECTS:FormatHandlerOBJLib>
+    $<TARGET_OBJECTS:ReportSystemOBJLib>
+    $<TARGET_OBJECTS:StatisticOBJLib>
+    $<TARGET_OBJECTS:UtilsOBJLib>
+    $<TARGET_OBJECTS:InternalBenchmarkOBJLib>)
+
+# Scripts to detect various SIMD support for the current compiler
+if (NOT DISABLE_AVX2)
+    include("./scripts/CMake/FindAVX2.cmake")
+endif()
+if (NOT DISABLE_NEON)
+    include("./scripts/CMake/FindNEON.cmake")
+endif()
+if (NOT DISABLE_SSE2)
+    include("./scripts/CMake/FindSSE2.cmake")
+endif()
+
+# Add SIMD code if compiler supports it
+if (HAVE_SSE2)
+    list(APPEND TRIMAL_OBJECTS $<TARGET_OBJECTS:SSE2OBJLib>)
+endif()
+if (HAVE_AVX2)
+    list(APPEND TRIMAL_OBJECTS $<TARGET_OBJECTS:AVX2OBJLib>)
+endif()
+if (HAVE_NEON)
+    list(APPEND TRIMAL_OBJECTS $<TARGET_OBJECTS:NEONOBJLib>)
+endif()
+
+# Add the executables to the project.
+add_executable(trimal
+        source/trimAlMain.cpp               # Main
+        source/trimalManager.cpp            # trimAl Manager
+
+        source/VCFHandler.cpp               # VCF only present on trimAl
+        ${TRIMAL_OBJECTS})
+
+add_executable(readal
+        source/FormatHandling/readAlMain.cpp        # Main
+
+       ${TRIMAL_OBJECTS})
+
+# Add the executables to the project.
+add_executable(test
+        tests/testMain.cpp
+        tests/catch.hpp
+        source/trimalManager.cpp            # trimAl Manager
+
+        source/VCFHandler.cpp               # VCF only present on trimAl
+        ${TRIMAL_OBJECTS})
+SET_TARGET_PROPERTIES(test PROPERTIES EXCLUDE_FROM_ALL True)
+
+# Add `cpu_features` for detecting supported SIMD at compile time
+add_subdirectory(vendor/cpu_features)
+include_directories(vendor/cpu_features/include)
+target_link_libraries(trimal cpu_features)
+target_link_libraries(readal cpu_features)
+
+# Link the mathematical library to the targets
+target_link_libraries(trimal m)
+target_link_libraries(readal m)
+
+target_link_libraries(test stdc++fs)
+
+# Script that sets Release type to default and prints information on configuration
+include("./scripts/CMake/BuildTypeWrapper.cmake")
+
+# Script to handle static and dynamic compilation.
+#   Static compilation is useful if compiling for containers without SO
+include("./scripts/CMake/staticCompilationWrapper.cmake")
+
+# Script to create intermediate OBJLib objects to include in targets
+include("./scripts/CMake/OBJ-LIB-creator.cmake")
+
+# Script to configure the overwrite policy of the format manager:
+#   - Overwrite and warn.
+#   - Dont overwrite unless needed. If needed, overwrite original.
+#   - Dont overwrite unless needed. If needed, overwrite last available.
+include("./scripts/CMake/FormatHandlerOverwritePolicy.cmake")
+
+# Script to create the Format Handler constructor, which incorporates
+#   all found stats to the internal pool of the handler
+include("./scripts/CMake/FormatHandlerHeaderCreator.cmake")
+

DockerFolder/Dockerfile.readAl

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+FROM scratch
+
+#COPY bin/new_trimal /trimal 
+COPY bin/readalMS /readal 
+#COPY bin/statal /statal
+#COPY bin/launcher /main 
+
+ENTRYPOINT ["/readal"]

DockerFolder/Dockerfile.statAl

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+FROM scratch
+
+#COPY bin/new_trimal /trimal 
+#COPY bin/readalMS /readal 
+COPY bin/statal /statal
+#COPY bin/launcher /main 
+
+ENTRYPOINT ["/statal"]

DockerFolder/Dockerfile.trimAl

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+FROM scratch
+
+COPY bin/new_trimal /trimal 
+#COPY bin/readalMS /readal 
+#COPY bin/statal /statal
+#COPY bin/launcher /main 
+
+ENTRYPOINT ["/trimal"]