From 0fd1a775d4bd0904d16edad9c098ca96fc10a581 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 ----------------
tests/requirements.txt | 1 +
4 files changed, 138 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
diff --git a/tests/requirements.txt b/tests/requirements.txt
index b553814..ddcc8ba 100644
--- a/tests/requirements.txt
+++ b/tests/requirements.txt
@@ -1 +1,2 @@
isatools
+markupsafe==2.0.1