From 6e6ab806abdd879c76b07f97d5f949e4858eca81 Mon Sep 17 00:00:00 2001 From: Jorge Alvarez Jarreta Date: Thu, 31 Oct 2024 13:42:43 +0000 Subject: [PATCH 1/3] move Travis to GitHub Actions --- .github/workflows/ci.yml | 54 ++++++++++++++++++++++++++++++++++++ .github/workflows/notice.yml | 37 ++++++++++++++++++++++++ .travis.yml | 30 -------------------- 3 files changed, 91 insertions(+), 30 deletions(-) create mode 100644 .github/workflows/ci.yml create mode 100644 .github/workflows/notice.yml delete mode 100644 .travis.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 000000000..9c736da85 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,54 @@ +# See the NOTICE file distributed with this work for additional information +# regarding copyright ownership. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +name: "CI" + +on: + push: + branches: + - master + pull_request: + +defaults: + run: + working-directory: ./ + +jobs: + tests: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - uses: shogo82148/actions-setup-perl@v1 + with: + perl-version: "5.28" + + - name: Install dependencies + run: | + sudo apt-get install -y wget python3 python3-pip python3-setuptools mysql-client libmysqlclient-dev libdb-dev g++-10 bedtools r-base + make install_REST + make install_ensembl + make install_repeats + make install_pangenes + PERL5LIB=$PWD/lib:$PERL5LIB + export PERL5LIB + shell: bash + + - name: Run tests + run: | + make test_travis + make test_repeats_travis + make test_pangenes diff --git a/.github/workflows/notice.yml b/.github/workflows/notice.yml new file mode 100644 index 000000000..f963334f2 --- /dev/null +++ b/.github/workflows/notice.yml @@ -0,0 +1,37 @@ +# See the NOTICE file distributed with this work for additional information +# regarding copyright ownership. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +name: "Update NOTICE copyright year at the start of every year" + +on: + schedule: + - cron: '15 15 1 1 *' + +jobs: + notice_update: + name: Update NOTICE copyright year + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Update NOTICE file + run: | + sed -i "s/$(date +%Y --date='1 year ago')/$(date +%Y)/" NOTICE + + - uses: EndBug/add-and-commit@v9 + with: + add: 'NOTICE' + message: 'Update NOTICE copyright year' diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index acd4200d1..000000000 --- a/.travis.yml +++ /dev/null @@ -1,30 +0,0 @@ -# removed as test_demo depends on too many dependencies -os: linux -dist: focal -language: perl -perl: - - "5.28" - -before_install: - #- "sudo apt-get update" - - "sudo apt-get install -y wget python3 python3-pip python3-setuptools mysql-client libmysqlclient-dev libdb-dev g++-10 bedtools r-base" - -# https://travis-ci.community/t/accessing-old-versions-of-perl-in-a-c-language-build/10948/5 -install: skip - -before_script: - - "make install_REST" - - "make install_ensembl" - - "make install_repeats" - - "make install_pangenes" - - PERL5LIB=$PWD/lib:$PERL5LIB - - export PERL5LIB - -script: - - "make test_travis" - - "make test_repeats_travis" - - "make test_pangenes" - -notifications: - email: - on_failure: always From 134750601c36dd678a75605395bc17fcbd24115f Mon Sep 17 00:00:00 2001 From: Jorge Alvarez Jarreta Date: Thu, 31 Oct 2024 13:43:12 +0000 Subject: [PATCH 2/3] update license and add notice file --- LICENSE | 8 +++----- NOTICE | 7 +++++++ 2 files changed, 10 insertions(+), 5 deletions(-) create mode 100644 NOTICE diff --git a/LICENSE b/LICENSE index c8a008191..261eeb9e9 100644 --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,4 @@ - Apache License + Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ @@ -178,7 +178,7 @@ APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following - boilerplate notice, with the fields enclosed by brackets "{}" + boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a @@ -186,8 +186,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute - Copyright [2016-2020] EMBL-European Bioinformatics Institute + Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -200,4 +199,3 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. - diff --git a/NOTICE b/NOTICE new file mode 100644 index 000000000..1836a03c6 --- /dev/null +++ b/NOTICE @@ -0,0 +1,7 @@ +Ensembl +Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute +Copyright [2016-2024] EMBL-European Bioinformatics Institute + +This product includes software developed at: +- EMBL-European Bioinformatics Institute +- Wellcome Trust Sanger Institute From f00ffc26a301eda4e62b846da7ec0de175ee614c Mon Sep 17 00:00:00 2001 From: Jorge Alvarez Jarreta Date: Thu, 31 Oct 2024 14:15:29 +0000 Subject: [PATCH 3/3] update README badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b4df215fd..ac0d59411 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ from your own scripts and for masking & annotating [repeats](#repeat-masking-and-annotation) and [calling pangenes](#pangenes) in plant genomes. -[![Build Status](https://travis-ci.com/Ensembl/plant-scripts.svg?branch=master)](https://app.travis-ci.com/Ensembl/plant-scripts) +[![Build Status](https://github.com/Ensembl/plant-scripts/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/Ensembl/plant-scripts/actions/workflows/ci.yml) - [List of recipes](#list-of-recipes) - [Dependencies of recipes](#dependencies)