Merge pull request #749 from kjsanger/feature/perl5.34

Add Perl 5.34 to CI matrix

.github/workflows/perlbrew.sha256

@@ -0,0 +1 @@
+c3996e4fae37a0ae01839cdd73752fb7b17e81bac2a8b39712463a7d518c4945  perlbrew.sh

.github/workflows/run-tests.yml

@@ -0,0 +1,127 @@
+name: "Unit tests"
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l -e -o pipefail {0}
+
+    env:
+      PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
+      NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
+      WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
+      WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF}
+
+
+    strategy:
+      matrix:
+        perl: ["5.26.3", "5.34.1"]
+
+    services:
+       mysql:
+         image: mysql:8.0
+         ports:
+           - 3306:3306
+         env:
+           MYSQL_ALLOW_EMPTY_PASSWORD: yes
+           MYSQL_ROOT_PASSWORD: null
+           MYSQL_DATABASE: npgt
+         options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=10s --health-retries=5 
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Change dbhost to 127.0.0.1
+        run: |
+            sed -i s/localhost/127.0.0.1/ ${GITHUB_WORKSPACE}/data/config.ini
+
+      - name: set timezone
+        run: |
+            sudo timedatectl set-timezone Europe/London 
+
+      - name: "Install OS dependencies"
+        run: |
+          sudo apt-get update
+          # https://github.com/actions/runner-images/issues/2139
+          sudo apt-get remove -y nginx libgd3
+          sudo apt-get install -y libgd-dev uuid-dev libgd-text-perl
+
+      - name: "Cache Perl"
+        id: cache-perl
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.PERL_CACHE }}
+          key: ${{ runner.os }}-${{ matrix.perl }}-perl
+
+      - name: "Install Perlbrew"
+        if: steps.cache-perl.outputs.cache-hit != 'true'
+        run: |
+          curl -sSL https://install.perlbrew.pl -o perlbrew.sh
+          sha256sum -c .github/workflows/perlbrew.sha256
+          export PERLBREW_ROOT=${{ env.PERL_CACHE }}
+          sh perlbrew.sh
+            
+          source ${{ env.PERL_CACHE }}/etc/bashrc
+          perlbrew available
+          perlbrew install --notest perl-${{ matrix.perl }}
+          perlbrew use perl-${{ matrix.perl }}
+          perlbrew install-cpanm
+
+      - name: "Initialize Perlbrew"
+        run: |
+          echo "source ${{ env.PERL_CACHE }}/etc/bashrc" >> "$HOME/.bash_profile"
+
+      - name: "Install Perl dependencies"
+        run: |
+          cpanm --local-lib=${{ env.PERL_CACHE }} local::lib
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
+          
+          cpanm --quiet --notest Module::Build
+          cpanm --quiet --notest Alien::Tidyp
+          
+          ./scripts/install_wsi_dependencies.sh "$NPG_LIB" \
+             perl-dnap-utilities \
+             ml_warehouse
+
+          cpanm --installdeps --notest .
+
+      - name: "Log install failure"
+        if: ${{ failure() }}
+        run: |
+          find ~/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;
+
+      - name: "Archive CPAN logs on failure"
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: cpan_log
+          path: ~/.cpanm/work/*/build.log
+          retention-days: 5
+
+      - name: "Run tests"
+        run: |
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          
+          export TEST_AUTHOR=1
+          perl Build.PL
+          ./Build test --verbose
+          ./Build install
+
+      - name: "Build distribution"
+        run: |
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          export TEST_AUTHOR=1
+          
+          ./Build dist
+          export DIST_FILE=$(ls npg-tracking-*.tar.gz)
+          export MD5_FILE=$DIST_FILE.md5
+          md5sum $DIST_FILE > $MD5_FILE
+          export SHA256_FILE=$DIST_FILE.sha256
+          shasum -a 256 $DIST_FILE > $SHA256_FILE

MANIFEST

@@ -1,4 +1,3 @@
-.github/workflows/testing_and_building_repos.yml
 bin/event_notifications
 bin/illumina_instruments_uptime
 bin/npg_daemon_control
@@ -1468,6 +1467,5 @@ t/useragent.pm
 t/util.pm
 wtsi_local/httpd.conf
 wtsi_local/httpd_sfweb.conf
-
 META.yml
 META.json

scripts/install_wsi_dependencies.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+set -e -u -x
+
+WSI_NPG_GITHUB_URL=${WSI_NPG_GITHUB_URL:=https://github.com/wtsi-npg}
+WSI_NPG_BUILD_BRANCH=${WSI_NPG_BUILD_BRANCH:=devel}
+
+# The first argument is the install base for NPG modules, enabling them to be
+# installed independently of CPAN dependencies. E.g. for cases where we want
+# different caching behaviour.
+NPG_ROOT="$1"
+shift
+
+repos=""
+for repo in "$@" ; do
+    cd /tmp
+
+    # Clone deeper than depth 1 to get the tag even if something has been already
+    # committed over the tag
+    git clone --branch master --depth 3 "$WSI_NPG_GITHUB_URL/${repo}.git" "${repo}.git"
+    cd "/tmp/${repo}.git"
+
+    # Shift off master to appropriate branch (if possible)
+    git ls-remote --heads --exit-code origin "$WSI_NPG_BUILD_BRANCH" && \
+	    git pull origin "$WSI_NPG_BUILD_BRANCH" && \
+	    echo "Switched to branch $WSI_NPG_BUILD_BRANCH"
+    repos="$repos /tmp/${repo}.git"
+done
+
+# Install CPAN dependencies. The src libs are on PERL5LIB because of
+# circular dependencies. The blibs are on PERL5LIB because the package
+# version, which cpanm requires, is inserted at build time. They must
+# be before the libs for cpanm to pick them up in preference.
+for repo in $repos
+do
+    export PERL5LIB="$PERL5LIB:$repo/blib/lib:$repo/lib"
+done
+
+for repo in $repos
+do
+    cd "$repo"
+    cpanm --quiet --notest --installdeps .
+    perl Build.PL
+    ./Build
+done
+
+# Finally, bring any common dependencies up to the latest version and
+# install
+for repo in $repos
+do
+    cd "$repo"
+    cpanm --quiet --notest --installdeps .
+    ./Build install --install-base "$NPG_ROOT"
+done