Add shellcheck ci

.github/workflows/perl-code-tidy.yml

@@ -15,24 +15,19 @@ on:
 jobs:
   tidy-critic-check:
     runs-on: ubuntu-latest
-    steps:
-    - name: Set up Perl environment
-      uses: shogo82148/actions-setup-perl@v1
-      with:
-        perl-version: '5.34'
-
-    - name: Install Dependencies
-      run: |
-        cpanm --quiet Code::TidyAll Perl::Critic
+    container:
+      image: perldocker/perl-tester:latest
 
-    - name: Check out code
-      uses: actions/checkout@v4
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
 
-    - name: Run tidyall with Perl::Critic
-      run: |
-        cd perl
-        tidyall -a
-        if [[ $? != 0 ]]; then
-          echo "Perl code is not tidy or has critic violations!"
-          exit 1
-        fi
+      - name: Run tidyall
+        shell: bash
+        run: |
+          cd perl
+          tidyall -a
+          if [[ $? != 0 ]]; then
+            echo "Perl code is not tidy or has critic violations"
+            exit 1
+          fi

.github/workflows/perl-package-build.yml

@@ -5,40 +5,38 @@ on: [push, pull_request]
 jobs:
   test-perl-package:
     runs-on: ubuntu-latest
+    container:
+      image: perldocker/perl-tester:latest
 
     steps:
-      - name: Setup perl
-        uses: shogo82148/actions-setup-perl@v1
-        with:
-          perl-version: ${{ inputs.perl-version }}
-
-      - name: Install Dist::Zilla
-        shell: bash
-        run: |
-          cpanm --quiet Dist::Zilla Archive::Tar::Wrapper
+      - name: Perl version
+        run: perl -V
 
       - name: Install system dependencies
         shell: bash
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y lz4
+        run: apt-get install --no-install-recommends -y lz4
 
       - name: Install one-off Bystro dependencies
         shell: bash
         run: |
-          cpanm --quiet https://github.com/bystrogenomics/msgpack-perl.git
-          cpanm --quiet --notest MouseX::Getopt
-          cpanm --quiet DBD::mysql@4.051
+          cpm install -g https://github.com/bystrogenomics/msgpack-perl.git
+          cpm install -g --no-test MouseX::Getopt
+          cpm install -g DBD::mysql@4.051
           git clone --depth 1 --recurse-submodules https://github.com/salortiz/LMDB_File.git \
             && cd LMDB_File \
             && cpanm --quiet .
 
       - name: Checkout code
         uses: actions/checkout@v4
 
-      - name: Test Bystro perl codebase
+      - name: Install Bystro dependencies
         run: |
           cd perl
-          dzil authordeps --missing | cpanm --quiet
-          dzil listdeps --missing | cpanm --quiet
-          dzil test
+          cpm install -g --show-build-log-on-failure $(dzil authordeps --missing)
+          cpm install -g --show-build-log-on-failure $(dzil listdeps --missing)
+
+      - name: Test Bystro
+        run: cd perl && dzil test --all
+
+      - name: Build Bystro tarball
+        run: cd perl && dzil build

.github/workflows/shellcheck.yml

@@ -0,0 +1,21 @@
+---
+on:
+  push:
+    paths:
+    - '**.sh'
+    - '**.bash'
+  pull_request:
+    paths:
+    - '**.sh'
+    - '**.bash'
+
+name: shellcheck
+
+jobs:
+  shellcheck:
+    name: Shellcheck
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Run ShellCheck
+        uses: ludeeus/action-shellcheck@master

perl/Dockerfile

@@ -25,7 +25,6 @@ ENV PATH="/app/bin:${PATH}"
 # Note: installing libmariadb-dev rather than libmysql-dev since the latter was removed
 RUN apt-get update \
   && apt-get install -y \
-  awscli \
   build-essential \
   bzip2 \
   git \
@@ -34,8 +33,6 @@ RUN apt-get update \
   libmariadb-dev \
   libssl-dev \
   lz4 \
-  nodejs \
-  npm \
   openssl \
   patch \
   pigz \
@@ -45,9 +42,6 @@ RUN apt-get update \
   && apt-get clean \
   && rm -rf /var/lib/apt/lists/*
 
-# Install pm2
-RUN npm install -g pm2
-
 WORKDIR /app/liftOver
 
 # Install liftOver into a common system directory, /usr/local/bin
@@ -60,18 +54,21 @@ RUN rm -rf /app/liftOver
 # Change working directory to perl-deps
 WORKDIR /app/perl-deps
 
+# install cpm for faster installation of perl packages
+RUN curl -fsSL https://raw.githubusercontent.com/skaji/cpm/main/cpm | perl - install -g App::cpm
+
 # Install Dist::Zilla
-RUN cpanm --quiet Dist::Zilla Archive::Tar::Wrapper
+RUN cpm install -g Dist::Zilla Archive::Tar::Wrapper
 
 # Install one-off Bystro dependencies that require special installation
-RUN cpanm --quiet https://github.com/bystrogenomics/msgpack-perl.git
-RUN cpanm --quiet --notest MouseX::Getopt
+RUN cpm install -g https://github.com/bystrogenomics/msgpack-perl.git
+RUN cpm install -g --no-test MouseX::Getopt
 RUN git clone --depth 1 --recurse-submodules https://github.com/salortiz/LMDB_File.git \
   && cd LMDB_File \
   && cpanm --quiet .
 
 # Install workaround because default DBD::mysql, i.e. version >5.x, will not automatically install on ubuntu
-RUN cpanm --quiet DBD::mysql@4.051
+RUN cpm install -g DBD::mysql@4.051
 
 # Remove perl-deps directory
 RUN rm -rf /app/perl-deps
@@ -83,12 +80,12 @@ WORKDIR /app/bystro-perl
 COPY . /app/bystro-perl/
 
 # Install build dependencies
-RUN dzil authordeps --missing | cpanm --quiet
+RUN cpm install -g --show-build-log-on-failure $(dzil authordeps --missing)
 
 # install Bystro package dependencies
-RUN dzil listdeps --missing | cpanm --quiet
+RUN cpm install -g --show-build-log-on-failure $(dzil listdeps --missing)
 
-# Build Bystro package and
+# Test and Install Bystro
 RUN dzil install
 
 RUN rm -rf /app/perl-deps

perl/cpanfile

@@ -46,6 +46,7 @@ requires "Types::Path::Tiny" => "0";
 requires "Types::Standard" => "0";
 requires "YAML::XS" => "0";
 requires "namespace::autoclean" => "0";
+requires "perl" => "v5.16.0";
 requires "strict" => "0";
 requires "warnings" => "0";
 
@@ -64,6 +65,10 @@ on 'configure' => sub {
 };
 
 on 'develop' => sub {
-  requires "Test::More" => "0";
-  requires "Test::Version" => "1";
+  requires "Test::CPAN::Meta" => "0";
+  requires "Test::EOF" => "0";
+  requires "Test::EOL" => "0";
+  requires "Test::MinimumVersion" => "0";
+  requires "Test::More" => "0.88";
+  requires "Test::NoTabs" => "0";
 };

perl/dist.ini

@@ -23,38 +23,43 @@ match = .*\.gz$
 [ExecDir]
 dir = bin
 
-[PruneCruft]
+[ShareDir]
 
-[ManifestSkip]
+[PruneCruft]
 
-[MetaYAML]
+[MakeMaker]
 
-[CPANFile]
+[Manifest]
 
-[CopyFilesFromBuild::Filtered]
-copy = cpanfile
+[ManifestSkip]
 
 [License]
 
 [Readme]
 
-[MakeMaker]
+[MetaYAML]
 
-[ShareDir]
+[CPANFile]
 
-[Manifest]
+[ConfirmRelease]
 
-[TestRelease]
+[AutoPrereqs]
 
-[ConfirmRelease]
+; Tests
+[MetaTests]
 
 [Test::ReportPrereqs]
+verify_prereqs = 1
 
-[Test::Version]
+[Test::NoTabs]
 
-[AutoPrereqs]
+[Test::EOL]
 
-[RemovePrereqs]
-remove = perl
-remove = Sys::Info
-remove = Sys::Info::Constants
+[Test::EOF]
+
+[Test::MinimumVersion]
+
+[TestRelease]
+
+[CopyFilesFromBuild::Filtered]
+copy = cpanfile

perl/t/lib/TestUtils.pm

@@ -0,0 +1,32 @@
+package TestUtils;
+
+use 5.10.0;
+use strict;
+use warnings;
+
+use Exporter 'import';
+use Path::Tiny;
+use YAML::XS qw/LoadFile/;
+
+use Type::Params          qw(compile);
+use Types::Standard       qw(HashRef);
+use Types::Common::String qw(NonEmptySimpleStr);
+
+our @EXPORT_OK = qw/ UpdateConfigAttrs /;
+
+sub UpdateConfigAttrs {
+  state $check = compile( NonEmptySimpleStr, HashRef );
+  my ( $file, $href ) = $check->(@_);
+
+  # load config yaml
+  my $config = LoadFile($file);
+
+  # update directory keys with new location
+  for my $key ( keys %{$href} ) {
+    $config->{$key} = $href->{$key};
+  }
+
+  return $config;
+}
+
+1;

perl/t/tracks/base/01-convert.t

@@ -1,11 +1,11 @@
-#!/usr/bin/env perl
 use 5.10.0;
 use strict;
 use warnings;
+
 use Test::More;
 use Mouse 2;
+
 use Seq::Tracks::Base::Types;
-use DDP;
 use Scalar::Util qw/looks_like_number/;
 
 my $converter = Seq::Tracks::Base::Types->new();

perl/t/tracks/base/02-convert-pack.t

@@ -3,7 +3,6 @@ use strict;
 use warnings;
 
 use Test::More;
-use DDP;
 
 use Data::MessagePack;
 use Seq::Tracks::Base::Types;

perl/t/tracks/base/normalizeWantedChr.t

@@ -3,20 +3,22 @@ use strict;
 use warnings;
 
 use Test::More;
+use Path::Tiny;
+
 use Seq::Tracks::Base;
 use Seq::DBManager;
 use Seq::Output::Delimiters;
-use DDP;
-# use Path::Tiny qw/path/;
+
+# use DDP;
 # use Scalar::Util qw/looks_like_number/;
 # use YAML::XS qw/LoadFile/;
-# use DDP;
 # use Seq::Tracks::Gene::Site::SiteTypeMap;
 # use Seq::Tracks::Reference::MapBases;
 
 # my $baseMapper = Seq::Tracks::Reference::MapBases->new();
 # my $siteTypes = Seq::Tracks::Gene::Site::SiteTypeMap->new();
-Seq::DBManager::initialize( { databaseDir => './t/tracks/base/db/index', } );
+
+Seq::DBManager::initialize( { databaseDir => Path::Tiny->tempdir() } );
 
 my $seq = Seq::Tracks::Base->new(
   {

perl/t/tracks/base/types.t

@@ -2,9 +2,10 @@ use 5.10.0;
 use strict;
 use warnings;
 
-use Seq::Tracks::Base::Types;
 use Test::More;
 
+use Seq::Tracks::Base::Types;
+
 my $rounder = Seq::Tracks::Base::Types->new();
 
 my $rounded = $rounder->convert( "2.032", "number(2)" );

perl/t/tracks/build/02-local-files.t

@@ -2,9 +2,10 @@ use 5.10.0;
 use strict;
 use warnings;
 
-use Seq::Tracks::Build::LocalFilesPaths;
-use Path::Tiny;
 use Test::More;
+use Path::Tiny;
+
+use Seq::Tracks::Build::LocalFilesPaths;
 
 my $localPaths = Seq::Tracks::Build::LocalFilesPaths->new();