Merge pull request #291 from nickjcroucher/master

Upgrade to version 3.0

.github/workflows/push.yml

@@ -0,0 +1,49 @@
+on:
+    push:
+        branches:
+        - master
+
+name: Push test
+
+jobs:
+
+    test-osx:
+      runs-on: macos-latest
+
+      steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install dependencies with conda
+        run: |
+            sudo chown -R $UID $CONDA && source $CONDA/etc/profile.d/conda.sh && conda env update --file environment.yml
+      - name: Install subunit from source
+        run: |
+            source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" && export CFLAGS="-I${CONDA_PREFIX}/include/" && export CPPUNIT_CFLAGS="-I${CONDA_PREFIX}/include/" && export CPPUNIT_LIBS="-L${CONDA_PREFIX}/lib/" && git clone https://github.com/testing-cabal/subunit.git && cd subunit && autoreconf -vi && CXXFLAGS="${CXXFLAGS} -I${CONDA_PREFIX}/include/" LDFLAGS="${LDFLAGS} -L${CONDA_PREFIX}/lib/ -lcppunit" ./configure --prefix=$CONDA_PREFIX && sudo make install && cd ..
+      - name: Run C++ and python tests
+        run: |
+            source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export PATH=$PATH:/lib/python3.9/site-packages/ && conda install pytest-cov && autoreconf -i &&  ./configure  --prefix=$CONDA_PREFIX --exec_prefix $CONDA_PREFIX --enable-maintainer-mode CFLAGS="-O0 --coverage -I${CONDA_PREFIX}/include/" LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" --host=x86_64-apple-darwin --build=x86_64-apple-darwin && make && sudo make install && make check
+
+    test-linux:
+      runs-on: ubuntu-latest
+
+      steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install dependencies with conda
+        run: |
+            $CONDA/bin/conda env update --file environment.yml && conda init
+      - name: Install subunit from source
+        run: |
+            source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" && export CFLAGS="-I${CONDA_PREFIX}/include/" && export CPPUNIT_CFLAGS="-I${CONDA_PREFIX}/include/" && export CPPUNIT_LIBS="-L${CONDA_PREFIX}/lib/" && git clone https://github.com/testing-cabal/subunit.git && cd subunit && autoreconf -vi && CXXFLAGS="${CXXFLAGS} -I${CONDA_PREFIX}/include/" LDFLAGS="${LDFLAGS} -L${CONDA_PREFIX}/lib/ -lcppunit" ./configure --prefix=$CONDA_PREFIX && sudo make install && cd ..
+      - name: Run C++ and python tests
+        run: |
+            source $CONDA/etc/profile.d/conda.sh && conda activate gubbins_env && export PATH=$PATH:/lib/python3.9/site-packages/ && conda install pytest-cov && autoreconf -i &&  ./configure --prefix=$CONDA_PREFIX --exec_prefix $CONDA_PREFIX --enable-maintainer-mode CFLAGS="-O0 --coverage -I${CONDA_PREFIX}/include/" LDFLAGS="-L${CONDA_PREFIX}/lib/ -Wl,-rpath,${CONDA_PREFIX}/lib/" --host=x86_64-linux-gnu --build=x86_64-linux-gnu && make && sudo make install && make check
+      - name: Upload python code coverage analysis
+        run: |
+          bash <(curl -s https://codecov.io/bash)

Dockerfile

@@ -31,10 +31,18 @@ RUN pip3 install certifi \
   && pip3 install nose \
   && pip3 install pillow \
   && pip3 install dendropy \
-  && pip3 install biopython
-
-# Install RAxML
+  && pip3 install biopython \
+  && pip3 install functools \
+  && pip3 install multiprocess
+
+# Get tree builder versions
 ARG raxml_version='8.2.12'
+ARG fasttree_version='2.1.11'
+ARG iqtree_version='2.0.3'
+ARG raxmlng_version='1.0.1'
+ARG rapidnj_version='2.3.2'
+
+# Install RAxML
 RUN curl -L https://github.com/stamatak/standard-RAxML/archive/v${raxml_version}.tar.gz -o standard-RAxML-${raxml_version}.tar.gz \
   && tar xzf standard-RAxML-${raxml_version}.tar.gz \
   && cd standard-RAxML-${raxml_version} \
@@ -46,19 +54,31 @@ RUN curl -L https://github.com/stamatak/standard-RAxML/archive/v${raxml_version}
   && rm -rf standard-RAxML-${raxml_version}
 
 # Install FastTree
-ARG fasttree_version='2.1.10'
 RUN curl http://www.microbesonline.org/fasttree/FastTree-${fasttree_version}.c -o FastTree.c \
   && gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm \
   && mv FastTree /usr/local/bin/ \
   && rm FastTree.c
 
 # Install IQTree
-ARG iqtree_version='1.6.6'
 RUN curl -L https://github.com/Cibiv/IQ-TREE/releases/download/v${iqtree_version}/iqtree-${iqtree_version}-Linux.tar.gz -o iqtree-${iqtree_version}-Linux.tar.gz \
   && tar xzf iqtree-${iqtree_version}-Linux.tar.gz \
   && cp iqtree-${iqtree_version}-Linux/bin/iqtree /usr/local/bin \
   && rm -rf iqtree-${iqtree_version}-Linux
 
+# Install RAxML-NG
+RUN curl https://github.com/amkozlov/raxml-ng/releases/download/${raxmlng_version}/raxml-ng_v${raxmlng_version}_linux_x86_64.zip \
+  && unzip raxml-ng_v${raxmlng_version}_linux_x86_64.zip \
+  && cp raxml-ng /usr/local/bin
+
+# Install RapidNJ
+RUN curl https://github.com/johnlees/rapidnj/archive/${rapidnj_version}.zip \
+  && unzip ${rapidnj_version}.zip \
+  && cd rapidnj-${rapidnj_version} \
+  && make \
+  && cp bin/rapidnj /usr/local/bin \
+  && cd .. \
+  && rm -rf rapidnj-${rapidnj_version}
+
 # Install Gubbins
 ENV BUILD_DIR /opt/gubbins
 RUN mkdir -p ${BUILD_DIR}
@@ -71,3 +91,6 @@ RUN cd ${BUILD_DIR} \
   && make install \
   && cd python \
   && python3 setup.py install
+
+# Remove downloaded files
+RUN rm standard-RAxML-${raxml_version}.tar.gz iqtree-${iqtree_version}-Linux.tar.gz iqtree-${iqtree_version}-Linux.tar.gz raxml-ng_v${raxmlng_version}_linux_x86_64.zip ${rapidnj_version}.zip

VERSION

@@ -1 +1 @@
-2.4.1
+3.0.0

configure.ac

@@ -29,7 +29,7 @@ PKG_CHECK_MODULES([zlib], [zlib])
 AC_CHECK_HEADERS([zlib.h math.h])
 
 # Check for Python
-AM_PATH_PYTHON([3.0],
+AM_PATH_PYTHON([3.8],
                [],
                [AC_MSG_WARN([Python not found. Python is required to build presage python binding. Python can be obtained from http://www.python.org])])
 

environment.yml

@@ -0,0 +1,32 @@
+name: gubbins_env
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - r
+dependencies:
+# python
+  - python>=3.8
+# installation
+  - autoconf
+  - automake
+  - pytest
+  - check
+  - libtool
+  - cppunit
+  - pkg-config
+  - wheel
+  - nose
+  - pillow
+# algorithm
+  - scipy
+  - dendropy
+  - biopython
+  - multiprocess
+  - numpy
+# phylogenetics
+  - raxml=8.2.12
+  - iqtree=2.0.3
+  - rapidnj
+  - raxml-ng=1.0.1
+  - fasttree=2.1.10

install_dependencies.sh

@@ -5,22 +5,57 @@ set -e
 
 start_dir=$(pwd)
 
+# Determine OS type
+OS="Linux"
+if [[ $OSTYPE == "darwin"* ]]; then
+    OS="OSX"
+fi
+
+# Alias wget on OSX
+if [[ $OS == "OSX" ]]; then
+    function _wget() { curl "${1}" -o $(basename "${1}") ; };
+    alias wget='_wget'
+fi
+
+# Get tree builder options
 RAXML_VERSION="8.2.12"
-FASTTREE_VERSION="2.1.10"
-IQTREE_VERSION="1.6.6"
+FASTTREE_VERSION="2.1.11"
+IQTREE_VERSION="2.0.3"
+RAXMLNG_VERSION="1.0.1"
+RAPIDNJ_VERSION="2.3.2"
 
 RAXML_DIR="standard-RAxML-$RAXML_VERSION"
 RAXML_ZIP_FILE="$RAXML_DIR.tar.gz"
 
-IQTREE_DIR="iqtree-$IQTREE_VERSION-Linux"
-IQTREE_ZIP_FILE="$IQTREE_DIR.tar.gz"
+IQTREE_DIR=""
+IQTREE_ZIP_FILE=""
+if [[ $OS == "Linux" ]]; then
+    IQTREE_DIR="iqtree-$IQTREE_VERSION-Linux"
+    IQTREE_ZIP_FILE="$IQTREE_DIR.tar.gz"
+elif [[ $OS == "OSX" ]]; then
+    IQTREE_DIR="iqtree-$IQTREE_VERSION-MacOSX"
+    IQTREE_ZIP_FILE="$IQTREE_DIR.zip"
+fi
 
 FASTTREE_DIR="FastTree-$FASTTREE_VERSION"
 FASTTREE_SOURCE="$FASTTREE_DIR.c"
 
+RAXMLNG_DIR="raxmlng_dir"
+RAXMLNG_ZIP_FILE=""
+if [[ $OS == "Linux" ]]; then
+    RAXMLNG_ZIP_FILE="raxml-ng_v${RAXMLNG_VERSION}_linux_x86_64.zip"
+elif [[ $OS == "OSX" ]]; then
+    RAXMLNG_ZIP_FILE="raxml-ng_v${RAXMLNG_VERSION}_macos_x86_64.zip"
+fi
+
+RAPIDNJ_DIR="rapidnj-$RAPIDNJ_VERSION"
+RAPIDNJ_ZIP_FILE="$RAPIDNJ_VERSION.zip"
+
 RAXML_DOWNLOAD_URL="https://github.com/stamatak/standard-RAxML/archive/v$RAXML_VERSION.tar.gz"
 FASTTREE_DOWNLOAD_URL="http://www.microbesonline.org/fasttree/$FASTTREE_SOURCE"
 IQTREE_DOWNLOAD_URL="https://github.com/Cibiv/IQ-TREE/releases/download/v$IQTREE_VERSION/$IQTREE_ZIP_FILE"
+RAXMLNG_DOWNLOAD_URL="https://github.com/amkozlov/raxml-ng/releases/download/$RAXMLNG_VERSION/$RAXMLNG_ZIP_FILE"
+RAPIDNJ_DOWNLOAD_URL="https://github.com/johnlees/rapidnj/archive/$RAPIDNJ_ZIP_FILE"
 
 # Make an install location
 if [ ! -d 'build' ]; then
@@ -45,11 +80,11 @@ download () {
 download $RAXML_DOWNLOAD_URL $RAXML_ZIP_FILE
 download $FASTTREE_DOWNLOAD_URL $FASTTREE_SOURCE
 download $IQTREE_DOWNLOAD_URL $IQTREE_ZIP_FILE
+download $RAXMLNG_DOWNLOAD_URL $RAXMLNG_ZIP_FILE
+download $RAPIDNJ_DOWNLOAD_URL $RAPIDNJ_ZIP_FILE
 
 # Update dependencies
-if [ "$TRAVIS" = 'true' ]; then
-  echo "Using Travis's apt plugin"
-else
+if [[ "$OS" == 'Linux' ]]; then
   sudo apt-get update -q
   sudo apt-get install -y -q autoconf \
                              check \
@@ -94,13 +129,36 @@ fi
 ## IQTree
 cd $build_dir
 if [ ! -d $IQTREE_DIR ]; then
-  tar xzf $IQTREE_ZIP_FILE
+   if [[ $OS == "Linux" ]]; then
+      tar xzf $IQTREE_ZIP_FILE
+   elif [[ $OS == "OSX" ]]; then
+      unzip $IQTREE_ZIP_FILE
+   fi
 fi
 cd $IQTREE_DIR
 if [ -e "bin/iqtree" ]; then
   cp bin/iqtree iqtree
 fi
 
+## RAxML-NG
+cd $build_dir
+if [ ! -d $RAXMLNG_DIR ]; then
+  mkdir $RAXMLNG_DIR
+fi
+unzip $RAXMLNG_ZIP_FILE
+mv raxml-ng $RAXMLNG_DIR
+
+## RapidNJ
+cd $build_dir
+if [ ! -d $RAPIDNJ_DIR ]; then
+  unzip $RAPIDNJ_ZIP_FILE
+fi
+cd $RAPIDNJ_DIR
+make
+if [ -e "bin/rapidnj" ]; then
+  cp bin/rapidnj rapidnj
+fi
+
 # Setup environment variables
 update_path () {
   new_dir=$1
@@ -112,6 +170,8 @@ update_path () {
 update_path $build_dir/$RAXML_DIR
 update_path $build_dir/$FASTTREE_DIR
 update_path $build_dir/$IQTREE_DIR
+update_path $build_dir/$RAXMLNG_DIR
+update_path $build_dir/$RAPIDNJ_DIR
 
 cd $start_dir
 

python/Makefile.am

@@ -1,4 +1,4 @@
-EXTRA_DIST=gubbins/* setup.py scripts/*
+EXTRA_DIST=gubbins/*
 
 all-local:
 	${PYTHON} setup.py build
@@ -14,4 +14,4 @@ clean-local:
 	$(PYTHON) setup.py clean --all
 
 check-local:
-	$(PYTHON) setup.py test
+	pytest --cov=gubbins gubbins/tests/

python/VERSION

@@ -0,0 +1 @@
+../VERSION

python/gubbins/ValidateFastaAlignment.py

@@ -41,9 +41,6 @@ def does_each_sequence_have_a_name_and_genomic_data(self):
                 if re.search('[^ACGTNacgtn-]', str(record.seq))  != None:
                   print("Error with the input FASTA file: One of the sequences contains odd characters, only ACGTNacgtn- are permitted")
                   return False
-        if number_of_sequences <= 3:
-          print("Error with input FASTA file: you need more than 3 sequences to build a meaningful tree")
-          return False
         input_handle.close()
       return True
 
@@ -79,4 +76,4 @@ def are_sequence_names_unique(self):
           return False
         input_handle.close()
       return True
-
+

python/gubbins/__init__.py

@@ -8,6 +8,7 @@
 
 import sys
 import os
+import pkg_resources
 
 ###############################################################################
 ## Populate the 'gubbins' namespace
@@ -18,7 +19,6 @@
 ## PACKAGE METADATA
 
 __project__ = "Gubbins"
-__version__ = "0.1"
 
 try:
     try:
@@ -32,8 +32,8 @@
 except:
     __homedir__ = None
 
-__author__ = "Andrew J. Page, Nicholas Croucher, Aidan Delaney and Simon Harris"
-__copyright__ = "Copyright 2013 Wellcome Trust Sanger Institutue"
+__author__ = "Andrew Page, Nicholas Croucher, Aidan Delaney, Christoph Puethe and Simon Harris"
+__copyright__ = "Copyright 2020 Wellcome Trust Sanger Institute and Imperial College London"
 __license__ = """
 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License
@@ -49,14 +49,20 @@
 along with this program; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 """
-PACKAGE_VERSION = __version__
+
+def version():
+    os.environ["PATH"] = os.environ["PATH"] + ":/usr/lib/gubbins/"
+    program_version = ""
+    try:
+        program_version = str(pkg_resources.get_distribution(__project__).version)
+    except pkg_resources.RequirementParseError:
+        pass
+    return "%s" % program_version
+
+__version__ = version()
 
 def description():
-    if __revision__.is_available:
-        revision_text = " (%s)" % str(__revision__)
-    else:
-        revision_text = ""
-    return "%s %s%s" % (__project__, __version__, revision_text)
+    return "%s %s" % (__project__, version())
 
 if __name__ == "__main__":
     sys.stdout.write("%s\n" % description())