Unit testing (#77)

* trying unit testing with github finally

* perl_ci.yml: update OS; only one perl version

* apt before cpanm

* perl_ci.yml: apt-get update

* perl_ci.yml: force a perl cache

* trying to cache again

* perl_ci.yml: --no-test --force

* perl_ci.yml: remove bio::kmer from cache

* perl_ci.yml: typo

* perl_ci.yml: add in more apt-get

* perl_ci.yml: enable-modules-cache:true

* perl_ci.yml: cpanm installdeps

* perl_ci.yml: modules and versions checking

* perl_ci.yml: make test

* perl_ci.yml: add in libdb-dev

* perl_ci.yml: force notest cpanm

* perl_ci.yml: force notest cpanm

* perl_ci.yml: force notest cpanm, second try

* use shogo82148/actions-setup-perl directly for testing cache

* update cache.yml

* update cache.yml

* update cache.yml

* cache.yml: added JSON

* install bio::perl natively in the github actions

* added threading; more modules

* multithreading for perl_ci

* simplify the apt/cpanm portions

* v1.3.1

.github/workflows/cache.yml

@@ -0,0 +1,33 @@
+name: force-cache
+on: [push]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-22.04']
+        perl: [ '5.34' ]
+    name: Perl ${{ matrix.perl }} on ${{ matrix.os }}
+    steps:
+      - name: apt-get to prepare for cached perl packages
+        run:  |
+          sudo apt-get update -y
+          sudo apt-get install -y libdb-dev sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl
+      - uses: actions/checkout@v3
+      - uses: shogo82148/actions-setup-perl@v1
+        with:
+          perl-version: '5.34'
+          install-modules-with: cpanm
+          install-modules-args: --with-develop --with-configure
+          multi-thread: true
+          install-modules: |
+            JSON
+            Bio::Perl
+            Bio::Kmer
+            Bio::Tree::Statistics
+            Bio::Matrix::IO
+            Bio::Tree::DistanceFactory
+      - run: |
+          echo "hello world!"
+          # prove -lv t

.github/workflows/perl_ci.yml

@@ -0,0 +1,49 @@
+# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions
+# https://docs.github.com/en/actions/guides/publishing-docker-images
+# https://github.com/docker/build-push-action/blob/master/docs/advanced/share-image-jobs.md
+name: unit-testing
+on: [push]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-22.04']
+        perl: [ '5.34' ]
+        #perl: [ '5.34', '5.32', '5.16.3' ]
+    name: Perl ${{ matrix.perl }} on ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up perl
+        uses: shogo82148/actions-setup-perl@v1
+        with:
+          perl-version: ${{ matrix.perl }}
+          install-modules-with: cpanm
+          install-modules-args: --with-develop --with-configure --force --no-test
+          enable-modules-cache: true
+          multi-thread: true
+          install-modules: |
+            JSON
+            Bio::Perl
+            Bio::Kmer
+            Bio::Tree::Statistics
+            Bio::Matrix::IO
+            Bio::Tree::DistanceFactory
+      - name: apt-get to prepare for cached perl packages
+        run:  |
+          sudo apt-get update -y
+          sudo apt-get install -y libdb-dev sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl quicktree mash
+      - name: cpanm installdeps --no-test --force
+        run: cpanm --installdeps . --no-test --force
+      - name: versions
+        run:  |
+          mash --version
+          quicktree -v
+          sqlite3 --version
+      - run: perl -V
+      - name: perl modules checks
+        run: |
+          for i in Bio::Tree::Statistics threads Bio::Matrix::IO Bio::Tree::DistanceFactory; do perl -M$i -e 'print "checking module $i";'; done
+      - name: make test
+        run: perl Makefile.PL && make && make test

.gitignore

@@ -33,3 +33,13 @@ inc/
 /MANIFEST.bak
 /pm_to_blib
 /*.zip
+
+# temp testing files
+t/lambda/lambda.fofn
+t/lambda/lambda/
+t/lambda/list.lst
+t/lambda/mashtree2.tmp/
+t/lambda/sketches/
+t/lambda/tmp.dnd
+t/lambda/tmp/
+

lib/Mashtree.pm

@@ -26,7 +26,7 @@ local $0=basename $0;
 ######
 # CONSTANTS
 
-our $VERSION = "1.3.0";
+our $VERSION = "1.3.1";
 our $MASHTREE_VERSION=$VERSION;
 our @fastqExt=qw(.fastq.gz .fastq .fq .fq.gz);
 our @fastaExt=qw(.fasta .fna .faa .mfa .fas .fsa .fa);

t/10_sqlite.t

@@ -7,6 +7,10 @@ use File::Basename qw/dirname/;
 use File::Temp qw/tempdir/;
 use Data::Dumper;
 
+use FindBin qw/$RealBin/;
+use lib "$RealBin/../lib/perl5";
+use lib "$RealBin/../lib/perl5/x86_64-linux-thread-multi/";
+
 use Test::More tests => 5;
 
 use_ok 'Mashtree';