Move CI pipeline from Travis to GitHub Actions

.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

.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'

LICENSE

@@ -1,4 +1,4 @@
-                                Apache License
+                                 Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/
 
@@ -178,16 +178,15 @@
    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
       file or class name and description of purpose be included on the
       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.
-

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

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)