Merge branch 'percolator:master' into master

statisticalbiotechnology · Mar 11, 2024 · fa3328a · fa3328a
2 parents 88903ed + f56e1ed
commit fa3328a
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -38,7 +38,7 @@ jobs:
       run: cd ../my_build/percolator-test && make install && make test-install
 
   build-osx:
-    runs-on: macos-11
+    runs-on: macos-12
     steps:
     - uses: actions/checkout@v2
     - name: create_dirs

diff --git a/.github/workflows/triggered_build.yml b/.github/workflows/triggered_build.yml
@@ -16,7 +16,7 @@ jobs:
     - name: test
       run: cd ../my_build/percolator && sudo make install && make test ARGS="-V"
     - name: zip raw binary
-      run: zip -j ../my_rel/percolator-noxml.zip ../my_build/percolator-noxml/src/percolator
+      run: zip -j ../my_rel/percolator-noxml-ubuntu-portable.zip ../my_build/percolator-noxml/src/percolator
     - name: Upload packages
       uses: actions/upload-artifact@v1
       with:
@@ -35,15 +35,15 @@ jobs:
     - name: test
       run: cd ../my_build/percolator && make install && make test ARGS="-V"
     - name: zip raw binary
-      run: zip -j ../my_rel/percolator-noxml.zip ../my_build/percolator-noxml/src/percolator
+      run: zip -j ../my_rel/percolator-noxml-linux-portable.zip ../my_build/percolator-noxml/src/percolator
     - name: Upload packages
       uses: actions/upload-artifact@v1
       with:
         name: centos-packages
         path: ../my_rel
 
   build-osx:
-    runs-on: macos-11
+    runs-on: macos-12
     steps:
     - uses: actions/checkout@v2
     - name: create_dirs
@@ -53,7 +53,7 @@ jobs:
     - name: test
       run: cd ../my_build/percolator && sudo make install && make test ARGS="-V"
     - name: zip raw binary
-      run: zip ../my_rel/percolator-noxml.zip ../my_build/percolator-noxml/src/percolator
+      run: zip ../my_rel/percolator-noxml-osx-portable.zip ../my_build/percolator-noxml/src/percolator
     - name: Upload packages
       uses: actions/upload-artifact@v1
       with:
@@ -77,7 +77,8 @@ jobs:
         ECHO %base_dir%
         CALL percolator\admin\builders\nativew64_build.bat -s %base_dir% -r %homedrive%%homepath%\my_rel -b %homedrive%%homepath%\my_build
     - name: zip raw binary
-      run: TAR -czvf %homedrive%%homepath%\my_rel\percolator-noxml.tgz %homedrive%%homepath%\my_build\percolator-noxml\src\Release\percolator.exe
+      shell: pwsh
+      run: Compress-Archive -Path ${env:homedrive}${env:homepath}\my_build\percolator-noxml\src\Release\*.exe -Destination ${env:homedrive}${env:homepath}\my_rel\percolator-noxml-windows-portable.zip
     - name: Upload packages
       uses: actions/upload-artifact@v3
       with:

diff --git a/CommonCMake.txt b/CommonCMake.txt
@@ -51,7 +51,7 @@ set(CMAKE_MODULE_PATH ${PERCOLATOR_SOURCE_DIR}/cmake)
 # VERSION AND NAMESPACES
 set(CPACK_PACKAGE_VERSION_MAJOR "3")
 set(CPACK_PACKAGE_VERSION_MINOR "06")
-set(CPACK_PACKAGE_VERSION_PATCH "1")
+set(CPACK_PACKAGE_VERSION_PATCH "5")
 set(PIN_VERSION_MAJOR "1")
 set(PIN_VERSION_MINOR "3")
 set(POUT_VERSION_MAJOR "1")

diff --git a/ReadMe.md b/ReadMe.md
@@ -1,5 +1,5 @@
 ## Percolator
-[![https://github.com/percolator/percolator/actions?query=workflow%3A%22Build+and+release%22](https://github.com/percolator/percolator/workflows/Build%20and%20release/badge.svg)](https://github.com/percolator/percolator/actions?query=workflow%3A%22Build+and+release%22) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](code_of_conduct.md)
+[![Build status](https://github.com/percolator/percolator/actions/workflows/build.yml/badge.svg)](https://github.com/percolator/percolator/actions/workflows/build.yml) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](code_of_conduct.md)
 
 This repository holds the source code for percolator and format
 converters software packages; a software for postprocessing of shotgun

diff --git a/admin/builders/ubuntu64_build.sh b/admin/builders/ubuntu64_build.sh
@@ -2,32 +2,38 @@
 # managing input arguments
 
 while getopts “s:b:r:t:” OPTION; do
-  case $OPTION in
-    s) src_dir=${OPTARG};;
-    t) branch=${OPTARG};;
-    r) release_dir=${OPTARG};;
-    b) build_dir=${OPTARG};;
-    \?) echo "Invalid option: -${OPTARG}" >&2;;
-  esac
+    case $OPTION in
+        s) src_dir=${OPTARG};;
+        t) branch=${OPTARG};;
+        r) release_dir=${OPTARG};;
+        b) build_dir=${OPTARG};;
+        \?) echo "Invalid option: -${OPTARG}" >&2;;
+    esac
 done
 
+sudo apt-get -y install gawk;
+if [[ ! -z `echo -e "$(lsb_release -r)" | gawk '($2>="22.04"){print
+    $2}'` ]]; then
+    sudo apt-get -y install libcurl4-openssl-dev;
+fi
+
 if [[ -z ${build_dir} ]]; then
-  build_dir="$(mktemp -d --tmpdir ubuntu_build_XXXX)";
+    build_dir="$(mktemp -d --tmpdir ubuntu_build_XXXX)";
 fi
 if [[ -z ${src_dir} ]]; then
-  if [[ -n  ${branch} ]]; then
-    sudo apt-get install git;
-    src_dir="$(mktemp -d --tmpdir ubuntu_build_XXXX)";
-    git clone --branch "$1" https://github.com/percolator/percolator.git "${src_dir}/percolator";
-  else
-    src_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"/../../../
-  fi
+    if [[ -n  ${branch} ]]; then
+        sudo apt-get install git;
+        src_dir="$(mktemp -d --tmpdir ubuntu_build_XXXX)";
+        git clone --branch "$1" https://github.com/percolator/percolator.git "${src_dir}/percolator";
+    else
+        src_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"/../../../
+    fi
 fi
 if [[ -z ${release_dir} ]]; then
-  release_dir=${HOME}/release
-  if [ ! -d "${release_dir}" ]; then
-    mkdir ${release_dir}
-  fi
+    release_dir=${HOME}/release
+    if [ ! -d "${release_dir}" ]; then
+        mkdir ${release_dir}
+    fi
 fi
 
 echo "The Builder $0 is building the Percolator packages with src=${src_dir} an\
@@ -41,9 +47,9 @@ echo "Checking necessary packages for building percolator...";
 # Do not apt-upgrade if this is a travis-ci job
 sudo apt-get update;
 if [ -z "$TRAVIS" ] && [ -z "$CI" ]; then
-  # trap 'echo "EXIT (rc: $?)" && exit 1' ERR
-  sudo apt-get upgrade;
-  sudo apt-get -y install g++ make cmake rpm fakeroot;
+    # trap 'echo "EXIT (rc: $?)" && exit 1' ERR
+    sudo apt-get upgrade;
+    sudo apt-get -y install g++ make cmake rpm fakeroot;
 fi
 
 cd ${src_dir}
@@ -56,32 +62,32 @@ cd ${build_dir}
 
 # download and patch xsd
 if [[ $(lsb_release -a) == *"14.04"* ]]; then
-  if [ ! -d ${ubuntu_xsd} ]; then
-    echo "Installing XSD"
-    wget --quiet ${ubuntu_xsd_url}
-    tar xjf ${ubuntu_xsd}.tar.bz2
-    sed -i 's/setg/this->setg/g' ${ubuntu_xsd}/libxsd/xsd/cxx/zc-istream.txx
-    sed -i 's/ push_back/ this->push_back/g' ${ubuntu_xsd}/libxsd/xsd/cxx/tree/parsing.txx
-    sed -i 's/ push_back/ this->push_back/g' ${ubuntu_xsd}/libxsd/xsd/cxx/tree/stream-extraction.hxx
-  fi
+    if [ ! -d ${ubuntu_xsd} ]; then
+        echo "Installing XSD"
+        wget --quiet ${ubuntu_xsd_url}
+        tar xjf ${ubuntu_xsd}.tar.bz2
+        sed -i 's/setg/this->setg/g' ${ubuntu_xsd}/libxsd/xsd/cxx/zc-istream.txx
+        sed -i 's/ push_back/ this->push_back/g' ${ubuntu_xsd}/libxsd/xsd/cxx/tree/parsing.txx
+        sed -i 's/ push_back/ this->push_back/g' ${ubuntu_xsd}/libxsd/xsd/cxx/tree/stream-extraction.hxx
+    fi
 else
-  sudo apt-get -y install xsdcxx;
+    sudo apt-get -y install xsdcxx;
 fi
 
 # issue with XercesC in Ubuntu 16.04: https://github.com/percolator/percolator/issues/188
 if [[ ! -z `echo -e "$(lsb_release -r)" | gawk '($2>="18.04"){print $2}'` ]]; then
-  if [[ ! -d ${ubuntu_xerces}/lib ]]; then
-    echo "Installing XercesC"
-    # download, compile and link xerces
-    wget --no-check-certificate --quiet ${ubuntu_xerces_url}
-    tar xzf ${ubuntu_xerces}.tar.gz
-    cd ${ubuntu_xerces}/
-    ./configure --prefix=${build_dir}/${ubuntu_xerces} --disable-netaccessor-curl --disable-transcoder-icu > ../xercesc_config.log 2>&1
-    make -j 4 > ../xercesc_make.log 2>&1
-    make install > ../xercesc_install.log 2>&1
-  fi
+    if [[ ! -d ${ubuntu_xerces}/lib ]]; then
+        echo "Installing XercesC"
+        # download, compile and link xerces
+        wget --no-check-certificate --quiet ${ubuntu_xerces_url}
+        tar xzf ${ubuntu_xerces}.tar.gz
+        cd ${ubuntu_xerces}/
+        ./configure --prefix=${build_dir}/${ubuntu_xerces} --disable-netaccessor-curl --disable-transcoder-icu > ../xercesc_config.log 2>&1
+        make -j 4 > ../xercesc_make.log 2>&1
+        make install > ../xercesc_install.log 2>&1
+    fi
 else
-  sudo apt-get -y install libxerces-c-dev
+    sudo apt-get -y install libxerces-c-dev
 fi
 
 # end of section to remove
@@ -95,8 +101,8 @@ mkdir -p $build_dir/percolator-noxml $build_dir/percolator $build_dir/converters
 #-----cmake-----
 cd $build_dir/percolator-noxml;
 echo "cmake percolator-noxml.....";
-(set -x; 
-cmake -DTARGET_ARCH=amd64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DXML_SUPPORT=OFF $src_dir/percolator;
+(set -x;
+    cmake -DTARGET_ARCH=amd64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DXML_SUPPORT=OFF $src_dir/percolator;
 )
 #-----make------
 echo "make percolator (this will take few minutes).....";
@@ -106,8 +112,8 @@ make -j 4 package;
 #-----cmake-----
 cd $build_dir/percolator;
 echo "cmake percolator.....";
-(set -x; 
-cmake -DTARGET_ARCH=amd64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DGOOGLE_TEST=1 -DCMAKE_PREFIX_PATH="${build_dir}/${ubuntu_xerces}/;${build_dir}/${ubuntu_xsd}/" -DXML_SUPPORT=ON $src_dir/percolator;
+(set -x;
+    cmake -DTARGET_ARCH=amd64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DGOOGLE_TEST=1 -DCMAKE_PREFIX_PATH="${build_dir}/${ubuntu_xerces}/;${build_dir}/${ubuntu_xsd}/" -DXML_SUPPORT=ON $src_dir/percolator;
 )
 #-----make------
 echo "make percolator (this will take few minutes).....";
@@ -118,8 +124,8 @@ make -j 4 package;
 cd $build_dir/converters
 #-----cmake-----
 echo "cmake converters.....";
-(set -x; 
-cmake -DTARGET_ARCH=amd64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="${build_dir}/${ubuntu_xerces}/;${build_dir}/${ubuntu_xsd}/" -DSERIALIZE="TokyoCabinet" $src_dir/percolator/src/converters;
+(set -x;
+    cmake -DTARGET_ARCH=amd64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="${build_dir}/${ubuntu_xerces}/;${build_dir}/${ubuntu_xsd}/" -DSERIALIZE="TokyoCabinet" $src_dir/percolator/src/converters;
 )
 #-----make------
 echo "make converters (this will take few minutes).....";

diff --git a/docs/ReleaseChecklist.md b/docs/ReleaseChecklist.md
@@ -1,8 +1,8 @@
 # Creating a new release version
 
 1. change version number in CommonCMake.txt
-2. create binaries for all platforms with vagrant and fix build bugs
-3. verify that all system tests pass
+2. create binaries for all platforms with GitHub Actions and fix build bugs
+3. verify that all system (from the build directory: `make test-install`) and unit tests (`make CTEST_OUTPUT_ON_FAILURE=1 test`) pass
 4. verify that crux-toolkit cucumber tests pass
 5. add information to changelog on master
 6. commit and push to master on github

diff --git a/src/BaseSpline.cpp b/src/BaseSpline.cpp
@@ -225,6 +225,8 @@ double BaseSpline::alphaLinearSearchBA(double min_p,
 }
 
 void BaseSpline::initiateQR() {
+  // NOTE: at least 4 data points are needed to construct a quadratic spline!
+  assert(x.size() >= 4);
   int n = static_cast<int>(x.size());
   dx.resize(n-1);
   for (std::size_t ix = 0; static_cast<int>(ix) < n - 1; ix++) {

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -114,13 +114,13 @@ if(XML_SUPPORT)
   add_library(perclibrary STATIC ${xsdfiles_in} ${xsdfiles_out} parser.cxx serializer.cxx BaseSpline.cpp MassHandler.cpp
                   PSMDescription.cpp ResultHolder.cpp
 								  XMLInterface.cpp SetHandler.cpp StdvNormalizer.cpp svm.cpp Caller.cpp CrossValidation.cpp Enzyme.cpp Globals.cpp NoNormalizer.cpp Normalizer.cpp
-								  SanityCheck.cpp UniNormalizer.cpp DataSet.cpp FeatureNames.cpp LogisticRegression.cpp Option.cpp PosteriorEstimator.cpp
+								  SanityCheck.cpp UniNormalizer.cpp DataSet.cpp TabFileValidator.cpp FeatureNames.cpp LogisticRegression.cpp Option.cpp PosteriorEstimator.cpp
 								  ProteinProbEstimator.cpp ProteinFDRestimator.cpp Scores.cpp PseudoRandom.cpp SqtSanityCheck.cpp ssl.cpp PackedVector.cpp
 								  PackedMatrix.cpp Matrix.cpp Logger.cpp MyException.cpp FidoInterface.cpp ProteinScoreHolder.cpp PickedProteinInterface.cpp FeatureMemoryPool.cpp GoogleAnalytics.cpp Timer.cpp TmpDir.cpp ValidateTabFile.cpp)
 else(XML_SUPPORT)
   add_library(perclibrary STATIC BaseSpline.cpp MassHandler.cpp ResultHolder.cpp PSMDescription.cpp
 								  XMLInterface.cpp SetHandler.cpp StdvNormalizer.cpp svm.cpp Caller.cpp CrossValidation.cpp Enzyme.cpp Globals.cpp NoNormalizer.cpp Normalizer.cpp
-								  SanityCheck.cpp UniNormalizer.cpp DataSet.cpp FeatureNames.cpp LogisticRegression.cpp Option.cpp PosteriorEstimator.cpp
+								  SanityCheck.cpp UniNormalizer.cpp DataSet.cpp TabFileValidator.cpp FeatureNames.cpp LogisticRegression.cpp Option.cpp PosteriorEstimator.cpp
 								  ProteinProbEstimator.cpp ProteinFDRestimator.cpp Scores.cpp PseudoRandom.cpp SqtSanityCheck.cpp ssl.cpp PackedVector.cpp
 								  PackedMatrix.cpp Matrix.cpp Logger.cpp MyException.cpp FidoInterface.cpp ProteinScoreHolder.cpp PickedProteinInterface.cpp FeatureMemoryPool.cpp GoogleAnalytics.cpp Timer.cpp TmpDir.cpp ValidateTabFile.cpp)
 endif(XML_SUPPORT)