From 8e88914fb6ebfd75504a6273bae7dbe85a53c0ed Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 6 Nov 2023 15:40:28 +0100
Subject: [PATCH] Replace Travis-CI with GitHub Actions for running CI/CD

---
 .github/workflows/package.yml | 89 +++++++++++++++++++++++++++++++++++
 .github/workflows/test.yml    | 48 +++++++++++++++++++
 .travis.yml                   | 41 ----------------
 3 files changed, 137 insertions(+), 41 deletions(-)
 create mode 100644 .github/workflows/package.yml
 create mode 100644 .github/workflows/test.yml
 delete mode 100644 .travis.yml

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
new file mode 100644
index 0000000..4acdb68
--- /dev/null
+++ b/.github/workflows/package.yml
@@ -0,0 +1,89 @@
+name: Package
+
+on:
+  push:
+    tags:
+      - v*.*.*
+
+jobs:
+
+  wheel:
+    runs-on: ubuntu-latest
+    name: Build universal wheel
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        submodules: true
+    - name: Setup Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install build requirements
+      run: python -m pip install -r ci/requirements.txt
+    - name: Build wheel
+      run: python setup.py bdist_wheel
+    - name: Store built wheels
+      uses: actions/upload-artifact@v2
+      with:
+        name: dist
+        path: dist/*
+
+  sdist:
+    runs-on: ubuntu-latest
+    name: Build source distribution
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        submodules: true
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install build requirements
+      run: python -m pip install -r ci/requirements.txt
+    - name: Build wheel distribution
+      run: python setup.py sdist
+    - name: Store built wheels
+      uses: actions/upload-artifact@v2
+      with:
+        name: dist
+        path: dist/*
+
+  upload:
+    environment: PyPI
+    runs-on: ubuntu-latest
+    name: Upload
+    needs:
+    - sdist
+    - wheel
+    steps:
+    - name: Download built distributions
+      uses: actions/download-artifact@v2
+      with:
+          name: dist
+          path: dist
+    - name: Publish distributions to PyPI
+      if: startsWith(github.ref, 'refs/tags/v')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+        skip_existing: false
+
+  release:
+    environment: GitHub Releases
+    runs-on: ubuntu-latest
+    if: "startsWith(github.ref, 'refs/tags/v')"
+    name: Release
+    needs: upload
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v1
+      with:
+        submodules: true
+    - name: Release a Changelog
+      uses: rasmus-saks/release-a-changelog-action@v1.0.1
+      with:
+        github-token: '${{ secrets.GITHUB_TOKEN }}'
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..414efd1
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,48 @@
+name: Test
+
+on:
+  - push
+  - pull_request
+
+jobs:
+
+  test-linux:
+    name: Test (Linux)
+    runs-on: ubuntu-latest
+    env:
+      OS: Linux
+    strategy:
+      matrix:
+        python-version:
+          - '3.7'
+          - '3.8'
+          - '3.9'
+          # - '3.10'
+          # - '3.11'
+          # - '3.12'
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        submodules: true
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Update pip
+      run: python -m pip install -U pip wheel setuptools
+    - name: Install library
+      run: python -m pip install .
+    - name: Install test requirements
+      run: python -m pip install -r tests/requirements.txt --prefer-binary
+    - name: Install coverage
+      run: python -m pip install coverage --prefer-binary
+    - name: Test with coverage
+      run: python -m coverage run -m unittest discover -vv
+    - name: Upload to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        flags: ${{ matrix.python-version }}
+        name: test-python-${{ matrix.python-version }}
+        fail_ci_if_error: true
+        token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index a4e829a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,41 +0,0 @@
-sudo: false
-language: python
-python:
-- '3.6'
-- '3.5'
-- '3.4'
-- '2.7'
-
-cache:
-  pip: true
-  directories:
-  - $HOME/nmrML
-  - $HOME/MetaboLightsConfig
-  - $HOME/MetaboLightsStudies
-
-before_install:
-- pip install -U pip setuptools wheel
-- pip install -r tests/requirements.txt
-
-install:
-- pip install -r requirements.txt
-- pip install .
-
-script:
-- python -m unittest discover -v
-
-notifications:
-  email:
-  - althonosdev@gmail.com
-
-deploy:
-- provider: pypi
-  user: althonos
-  skip_cleanup: true
-  distributions: sdist bdist_wheel
-  password:
-    secure: 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
-  on:
-    python: '3.5'
-    tags: true
-    repo: ISA-tools/nmrml2isa