From 8ffc1bfc58e6ba2fbfc42d9d6518827c77314bf7 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 10:12:15 -0400 Subject: [PATCH 01/28] trying unit testing with github finally --- .github/workflows/perl_ci.yml | 36 +++++++++++++++++++++++++++++++++++ .gitignore | 10 ++++++++++ t/10_sqlite.t | 4 ++++ 3 files changed, 50 insertions(+) create mode 100644 .github/workflows/perl_ci.yml diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml new file mode 100644 index 0000000..9a438d4 --- /dev/null +++ b/.github/workflows/perl_ci.yml @@ -0,0 +1,36 @@ +# 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-20.04'] + 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: ${{ matrix.perl }} + - name: cpanm installations + run: cpanm --installdeps . + - name: apt-get + run: | + sudo apt-get install -y quicktree bioperl mash sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl + - name: versions + run: | + mash --version + quicktree -v + sqlite3 --version + - run: perl -V + - name: perl modules checks + run: | + for i in Bio::Tree::Statistics threads Bio::Matrix::IO Bio::Tree::DistanceFactory; do perl -M$i -e 'print "checking module $i";'; done + - name: make test + run: perl Makefile.PL && make && make test diff --git a/.gitignore b/.gitignore index fb8b193..39c3ac3 100644 --- a/.gitignore +++ b/.gitignore @@ -33,3 +33,13 @@ inc/ /MANIFEST.bak /pm_to_blib /*.zip + +# temp testing files +t/lambda/lambda.fofn +t/lambda/lambda/ +t/lambda/list.lst +t/lambda/mashtree2.tmp/ +t/lambda/sketches/ +t/lambda/tmp.dnd +t/lambda/tmp/ + diff --git a/t/10_sqlite.t b/t/10_sqlite.t index dd69d02..3d182c2 100644 --- a/t/10_sqlite.t +++ b/t/10_sqlite.t @@ -7,6 +7,10 @@ use File::Basename qw/dirname/; use File::Temp qw/tempdir/; use Data::Dumper; +use FindBin qw/$RealBin/; +use lib "$RealBin/../lib/perl5"; +use lib "$RealBin/../lib/perl5/x86_64-linux-thread-multi/"; + use Test::More tests => 5; use_ok 'Mashtree'; From 37819704e4cbe3651fb830ce408569af5f6dd920 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 10:13:49 -0400 Subject: [PATCH 02/28] perl_ci.yml: update OS; only one perl version --- .github/workflows/perl_ci.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 9a438d4..87df65e 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -9,8 +9,9 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - os: ['ubuntu-20.04'] - perl: [ '5.34', '5.32', '5.16.3' ] + 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 From f5dd76458a28c87f359276730a204da63f6ab91d Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 10:22:33 -0400 Subject: [PATCH 03/28] apt before cpanm --- .github/workflows/perl_ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 87df65e..59b99ef 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -19,11 +19,11 @@ jobs: uses: shogo82148/actions-setup-perl@v1 with: perl-version: ${{ matrix.perl }} - - name: cpanm installations - run: cpanm --installdeps . - name: apt-get run: | sudo apt-get install -y quicktree bioperl mash sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl + - name: cpanm installations + run: cpanm --installdeps . - name: versions run: | mash --version From ea90fd1fe4be4cfc30ef981aeb4cb5d4aa042590 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 10:29:18 -0400 Subject: [PATCH 04/28] perl_ci.yml: apt-get update --- .github/workflows/perl_ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 59b99ef..6629316 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -21,6 +21,7 @@ jobs: perl-version: ${{ matrix.perl }} - name: apt-get run: | + sudo apt-get update -y sudo apt-get install -y quicktree bioperl mash sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl - name: cpanm installations run: cpanm --installdeps . From e6173949d787eeb3a11d0a035c144e80e5c40084 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 10:42:14 -0400 Subject: [PATCH 05/28] perl_ci.yml: force a perl cache --- .github/workflows/perl_ci.yml | 20 ++++---------------- 1 file changed, 4 insertions(+), 16 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 6629316..babfad6 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -19,20 +19,8 @@ jobs: uses: shogo82148/actions-setup-perl@v1 with: perl-version: ${{ matrix.perl }} - - name: apt-get - run: | - sudo apt-get update -y - sudo apt-get install -y quicktree bioperl mash sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl + install-modules-with: cpanm + install-modules-args: --with-develop --with-configure --force - name: cpanm installations - run: cpanm --installdeps . - - name: versions - run: | - mash --version - quicktree -v - sqlite3 --version - - run: perl -V - - name: perl modules checks - run: | - for i in Bio::Tree::Statistics threads Bio::Matrix::IO Bio::Tree::DistanceFactory; do perl -M$i -e 'print "checking module $i";'; done - - name: make test - run: perl Makefile.PL && make && make test + run: cpanm DBI DBI::SQLite Bio::Kmer JSON + From 8e69083f71b34b11f4b2f49485b32d464c866138 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 10:55:20 -0400 Subject: [PATCH 06/28] trying to cache again --- .github/workflows/perl_ci.yml | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index babfad6..99bd015 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -21,6 +21,27 @@ jobs: perl-version: ${{ matrix.perl }} install-modules-with: cpanm install-modules-args: --with-develop --with-configure --force - - name: cpanm installations + - name: apt-get + run: | + sudo apt-get update -y + sudo apt-get install -y sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl + - name: cpanm installations hopefully cached run: cpanm DBI DBI::SQLite Bio::Kmer JSON +# - name: apt-get +# run: | +# sudo apt-get update -y +# sudo apt-get install -y quicktree bioperl mash sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl +# - name: cpanm installations +# run: cpanm --installdeps . +# - name: versions +# run: | +# mash --version +# quicktree -v +# sqlite3 --version +# - run: perl -V +# - name: perl modules checks +# run: | +# for i in Bio::Tree::Statistics threads Bio::Matrix::IO Bio::Tree::DistanceFactory; do perl -M$i -e 'print "checking module $i";'; done +# - name: make test +# run: perl Makefile.PL && make && make test From 443fe9894f6b5aa431df3caa85322ad871b2349d Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 10:56:42 -0400 Subject: [PATCH 07/28] perl_ci.yml: --no-test --force --- .github/workflows/perl_ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 99bd015..6d8e9d5 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -20,8 +20,8 @@ jobs: with: perl-version: ${{ matrix.perl }} install-modules-with: cpanm - install-modules-args: --with-develop --with-configure --force - - name: apt-get + install-modules-args: --with-develop --with-configure --force --no-test + - name: apt-get to prepare for cached perl packages run: | sudo apt-get update -y sudo apt-get install -y sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl @@ -31,7 +31,7 @@ jobs: # - name: apt-get # run: | # sudo apt-get update -y -# sudo apt-get install -y quicktree bioperl mash sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl +# sudo apt-get install -y quicktree bioperl mash # - name: cpanm installations # run: cpanm --installdeps . # - name: versions From 96ef25cec977b33e53e67f02b46c866cc1b79413 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:07:52 -0400 Subject: [PATCH 08/28] perl_ci.yml: remove bio::kmer from cache --- .github/workflows/perl_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 6d8e9d5..d9643ea 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -26,7 +26,7 @@ jobs: sudo apt-get update -y sudo apt-get install -y sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl - name: cpanm installations hopefully cached - run: cpanm DBI DBI::SQLite Bio::Kmer JSON + run: cpanm DBI DBI::SQLite JSON # - name: apt-get # run: | From 2f0945673113c5e02d8c69ff5f73e5b3e6ee1204 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:11:01 -0400 Subject: [PATCH 09/28] perl_ci.yml: typo --- .github/workflows/perl_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index d9643ea..0a0184c 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -26,7 +26,7 @@ jobs: sudo apt-get update -y sudo apt-get install -y sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl - name: cpanm installations hopefully cached - run: cpanm DBI DBI::SQLite JSON + run: cpanm DBI DBD::SQLite JSON # - name: apt-get # run: | From 8654d64a308bacb2e1baf1d15e8ec6e8361ca734 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:17:19 -0400 Subject: [PATCH 10/28] perl_ci.yml: add in more apt-get --- .github/workflows/perl_ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 0a0184c..e826a6a 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -28,10 +28,10 @@ jobs: - name: cpanm installations hopefully cached run: cpanm DBI DBD::SQLite JSON -# - name: apt-get -# run: | -# sudo apt-get update -y -# sudo apt-get install -y quicktree bioperl mash + - name: apt-get + run: | + sudo apt-get update -y + sudo apt-get install -y quicktree bioperl mash # - name: cpanm installations # run: cpanm --installdeps . # - name: versions From 644c15cd6356688d9da85685fb64a8283d213262 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:19:03 -0400 Subject: [PATCH 11/28] perl_ci.yml: enable-modules-cache:true --- .github/workflows/perl_ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index e826a6a..a925746 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -21,6 +21,7 @@ jobs: perl-version: ${{ matrix.perl }} install-modules-with: cpanm install-modules-args: --with-develop --with-configure --force --no-test + enable-modules-cache: true - name: apt-get to prepare for cached perl packages run: | sudo apt-get update -y From d972bbe1eddec9aafe689ca65f4ddbcc8acb2d87 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:21:35 -0400 Subject: [PATCH 12/28] perl_ci.yml: cpanm installdeps --- .github/workflows/perl_ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index a925746..dd5dcef 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -33,8 +33,8 @@ jobs: run: | sudo apt-get update -y sudo apt-get install -y quicktree bioperl mash -# - name: cpanm installations -# run: cpanm --installdeps . + - name: cpanm installdeps + run: cpanm --installdeps . # - name: versions # run: | # mash --version From 05adc9ad757cc90332b281346113bf0f0bbe3e0d Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:27:42 -0400 Subject: [PATCH 13/28] perl_ci.yml: modules and versions checking --- .github/workflows/perl_ci.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index dd5dcef..5184c44 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -35,14 +35,14 @@ jobs: sudo apt-get install -y quicktree bioperl mash - name: cpanm installdeps run: cpanm --installdeps . -# - name: versions -# run: | -# mash --version -# quicktree -v -# sqlite3 --version -# - run: perl -V -# - name: perl modules checks -# run: | -# for i in Bio::Tree::Statistics threads Bio::Matrix::IO Bio::Tree::DistanceFactory; do perl -M$i -e 'print "checking module $i";'; done + - name: versions + run: | + mash --version + quicktree -v + sqlite3 --version + - run: perl -V + - name: perl modules checks + run: | + for i in Bio::Tree::Statistics threads Bio::Matrix::IO Bio::Tree::DistanceFactory; do perl -M$i -e 'print "checking module $i";'; done # - name: make test # run: perl Makefile.PL && make && make test From 49972088298f93c2de891ed68852e4b0e064d299 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:32:52 -0400 Subject: [PATCH 14/28] perl_ci.yml: make test --- .github/workflows/perl_ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 5184c44..bda3a53 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -44,5 +44,5 @@ jobs: - name: perl modules checks run: | for i in Bio::Tree::Statistics threads Bio::Matrix::IO Bio::Tree::DistanceFactory; do perl -M$i -e 'print "checking module $i";'; done -# - name: make test -# run: perl Makefile.PL && make && make test + - name: make test + run: perl Makefile.PL && make && make test From fa80d237198e222e60362ec2c23e4034727ec929 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:34:42 -0400 Subject: [PATCH 15/28] perl_ci.yml: add in libdb-dev --- .github/workflows/perl_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index bda3a53..bc8a5ad 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -25,7 +25,7 @@ jobs: - name: apt-get to prepare for cached perl packages run: | sudo apt-get update -y - sudo apt-get install -y sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl + sudo apt-get install -y libdb-dev sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl - name: cpanm installations hopefully cached run: cpanm DBI DBD::SQLite JSON From e8f714eb578f6afd0668b411fd93c1f1b7050400 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 11:59:21 -0400 Subject: [PATCH 16/28] perl_ci.yml: force notest cpanm --- .github/workflows/perl_ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index bc8a5ad..8c5da93 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -32,8 +32,8 @@ jobs: - name: apt-get run: | sudo apt-get update -y - sudo apt-get install -y quicktree bioperl mash - - name: cpanm installdeps + sudo apt-get install -y quicktree bioperl bioperl-run mash + - name: cpanm installdeps --no-test --force run: cpanm --installdeps . - name: versions run: | From 16deb8fd1824a1af11692405938a977a67e3e860 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 12:00:11 -0400 Subject: [PATCH 17/28] perl_ci.yml: force notest cpanm --- .github/workflows/perl_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 8c5da93..2e17484 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -27,7 +27,7 @@ jobs: sudo apt-get update -y sudo apt-get install -y libdb-dev sqlite3 libgd-dev libsqlite3-dev libberkeleydb-perl libcdb-file-perl - name: cpanm installations hopefully cached - run: cpanm DBI DBD::SQLite JSON + run: cpanm DBI DBD::SQLite JSON --no-test --force - name: apt-get run: | From 703ae70acc14f9ab490b07eb09c5015103950d3e Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:02:08 -0400 Subject: [PATCH 18/28] perl_ci.yml: force notest cpanm, second try --- .github/workflows/perl_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 2e17484..aa235d1 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -34,7 +34,7 @@ jobs: sudo apt-get update -y sudo apt-get install -y quicktree bioperl bioperl-run mash - name: cpanm installdeps --no-test --force - run: cpanm --installdeps . + run: cpanm --installdeps . --no-test --force - name: versions run: | mash --version From 80d92bf8cc57790ec1408d306569cd28ac63da9e Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:11:53 -0400 Subject: [PATCH 19/28] use shogo82148/actions-setup-perl directly for testing cache --- .github/workflows/cache.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 .github/workflows/cache.yml diff --git a/.github/workflows/cache.yml b/.github/workflows/cache.yml new file mode 100644 index 0000000..0ff799c --- /dev/null +++ b/.github/workflows/cache.yml @@ -0,0 +1,10 @@ +steps: +- 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 +- run: | + echo "hello world!" + # prove -lv t From 1717af9189435389670c70b9ddc60d2974f897f5 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:14:08 -0400 Subject: [PATCH 20/28] update cache.yml --- .github/workflows/cache.yml | 30 ++++++++++++++++++++---------- 1 file changed, 20 insertions(+), 10 deletions(-) diff --git a/.github/workflows/cache.yml b/.github/workflows/cache.yml index 0ff799c..f44f4c0 100644 --- a/.github/workflows/cache.yml +++ b/.github/workflows/cache.yml @@ -1,10 +1,20 @@ -steps: -- 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 -- run: | - echo "hello world!" - # prove -lv t +name: force-cache +on: [push] + +jobs: + build: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: ['ubuntu-22.04'] + perl: [ '5.34' ] + steps: + - 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 + - run: | + echo "hello world!" + # prove -lv t From 8e54c98d90eb782680d99ad54737339eddbcc50a Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:14:58 -0400 Subject: [PATCH 21/28] update cache.yml --- .github/workflows/cache.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/cache.yml b/.github/workflows/cache.yml index f44f4c0..e8af23c 100644 --- a/.github/workflows/cache.yml +++ b/.github/workflows/cache.yml @@ -9,12 +9,12 @@ jobs: os: ['ubuntu-22.04'] perl: [ '5.34' ] steps: - - 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 - - run: | - echo "hello world!" - # prove -lv t + - 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 + - run: | + echo "hello world!" + # prove -lv t From d9a05d2de3bb79eb09b7f066cfc2bdcf5d3bb227 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:16:17 -0400 Subject: [PATCH 22/28] update cache.yml --- .github/workflows/cache.yml | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/.github/workflows/cache.yml b/.github/workflows/cache.yml index e8af23c..3f20688 100644 --- a/.github/workflows/cache.yml +++ b/.github/workflows/cache.yml @@ -8,13 +8,14 @@ jobs: matrix: os: ['ubuntu-22.04'] perl: [ '5.34' ] - steps: - - 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 - - run: | - echo "hello world!" - # prove -lv t + name: Perl ${{ matrix.perl }} on ${{ matrix.os }} + steps: + - 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 + - run: | + echo "hello world!" + # prove -lv t From 9dadf03dabe90ad62724e938089c16cd0bd4be63 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:17:58 -0400 Subject: [PATCH 23/28] cache.yml: added JSON --- .github/workflows/cache.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/cache.yml b/.github/workflows/cache.yml index 3f20688..ee23d02 100644 --- a/.github/workflows/cache.yml +++ b/.github/workflows/cache.yml @@ -16,6 +16,8 @@ jobs: perl-version: '5.34' install-modules-with: cpanm install-modules-args: --with-develop --with-configure + install-modules: | + JSON - run: | echo "hello world!" # prove -lv t From 6c9a684daa544de8d3f05d3f033713335cde3ff8 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:22:25 -0400 Subject: [PATCH 24/28] install bio::perl natively in the github actions --- .github/workflows/cache.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/cache.yml b/.github/workflows/cache.yml index ee23d02..b875d09 100644 --- a/.github/workflows/cache.yml +++ b/.github/workflows/cache.yml @@ -10,6 +10,10 @@ jobs: 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: @@ -18,6 +22,7 @@ jobs: install-modules-args: --with-develop --with-configure install-modules: | JSON + Bio::Perl - run: | echo "hello world!" # prove -lv t From 726c8d6d3247b96d3034314fea6d46af8d57ec6f Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:32:33 -0400 Subject: [PATCH 25/28] added threading; more modules --- .github/workflows/cache.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/cache.yml b/.github/workflows/cache.yml index b875d09..e9bc02b 100644 --- a/.github/workflows/cache.yml +++ b/.github/workflows/cache.yml @@ -20,9 +20,14 @@ jobs: 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 From f35b4cbcde94236e54660799d0ed3303f6cae607 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:51:38 -0400 Subject: [PATCH 26/28] multithreading for perl_ci --- .github/workflows/perl_ci.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index aa235d1..49e23b5 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -22,6 +22,14 @@ jobs: 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 @@ -32,7 +40,7 @@ jobs: - name: apt-get run: | sudo apt-get update -y - sudo apt-get install -y quicktree bioperl bioperl-run mash + sudo apt-get install -y quicktree mash - name: cpanm installdeps --no-test --force run: cpanm --installdeps . --no-test --force - name: versions From 44362f7bb9c8b7cb69e5335990f7d19ca5a410d8 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 14:57:29 -0400 Subject: [PATCH 27/28] simplify the apt/cpanm portions --- .github/workflows/perl_ci.yml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/workflows/perl_ci.yml b/.github/workflows/perl_ci.yml index 49e23b5..2e8624c 100644 --- a/.github/workflows/perl_ci.yml +++ b/.github/workflows/perl_ci.yml @@ -33,14 +33,7 @@ jobs: - 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 - - name: cpanm installations hopefully cached - run: cpanm DBI DBD::SQLite JSON --no-test --force - - - name: apt-get - run: | - sudo apt-get update -y - sudo apt-get install -y quicktree mash + 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 From e1400ff25aa09508a08ac3f6eb7abc8883336db2 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 3 Aug 2023 15:14:38 -0400 Subject: [PATCH 28/28] v1.3.1 --- lib/Mashtree.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/Mashtree.pm b/lib/Mashtree.pm index 168aae6..8019d4f 100644 --- a/lib/Mashtree.pm +++ b/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);