Merge branch 'trs/dev/stop-using-mambaforge' #1513
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name: CI | |
on: | |
push: | |
branches: | |
- master | |
tags: | |
# Version tags. | |
# | |
# Tags matching this pattern will cause the "release" job below to run, | |
# so edit it carefully! It should not match arbitrary tags. | |
- "[0-9]+.[0-9]+.[0-9]+*" | |
pull_request: | |
workflow_dispatch: | |
# Routinely check that we continue to work in the face of external changes. | |
schedule: | |
# Every day at 17:42 UTC / 9:42 Seattle (winter) / 10:42 Seattle (summer) | |
- cron: "42 17 * * *" | |
jobs: | |
lint: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: nextstrain/.github/actions/shellcheck@master | |
test-source: | |
name: test-source (python=${{ matrix.python }} os=${{ matrix.os }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
os: | |
- ubuntu-latest | |
- macos-latest | |
- windows-latest | |
python: | |
- '3.8' | |
- '3.9' | |
- '3.10' | |
- '3.11' | |
- '3.12' | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python }} | |
- name: Install Nextstrain CLI | |
run: python3 -m pip install --upgrade '.[dev]' | |
- run: ./devel/pytest -v | |
build-dist: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
# Install up-to-date packaging toolchain. | |
- run: python3 -m pip install --upgrade pip setuptools wheel | |
- run: python3 -m pip install --upgrade build | |
# Update version to include local git rev if we're not building a release tag. | |
- if: github.ref_type != 'tag' | |
run: | | |
version="$(./devel/read-version)" | |
git_rev="$(git rev-parse --short @)" | |
./devel/update-version "${version%%+*}+git.${git_rev}" | |
# Build dists. | |
- run: python3 -m build | |
# Upload dists as workflow artifacts. | |
- uses: actions/upload-artifact@v4 | |
with: | |
name: dist | |
path: dist/ | |
build-standalone: | |
needs: build-dist | |
strategy: | |
fail-fast: false | |
matrix: | |
# Generally we want to build on the oldest supported OS to maximize the | |
# final binary's compatibility. See pyoxidizer's docs for more | |
# considerations affecting the choice of build machine OS¹ and future | |
# plans for robust, turnkey build environments². | |
# | |
# On Linux, we build inside a container to avoid portability issues, so | |
# the container's host OS version here doesn't have an impact (other | |
# than CI stability). | |
# | |
# ¹ https://pyoxidizer.readthedocs.io/en/stable/pyoxidizer_distributing_binary_portability.html | |
# ² https://pyoxidizer.readthedocs.io/en/stable/pyoxidizer_status.html#an-official-build-environment | |
include: | |
- os: ubuntu-22.04 | |
target: x86_64-unknown-linux-gnu | |
exe: nextstrain | |
- os: macos-12 | |
target: x86_64-apple-darwin | |
exe: nextstrain | |
- os: macos-14 | |
target: aarch64-apple-darwin | |
exe: nextstrain | |
- os: windows-2019 | |
target: x86_64-pc-windows-msvc | |
exe: nextstrain.exe | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash | |
steps: | |
# Note that this Python version doesn't impact the actual build. | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
# Build the executable + necessary external files from the dists. | |
- uses: actions/checkout@v4 | |
- uses: actions/download-artifact@v4 | |
with: | |
name: dist | |
path: dist/ | |
- name: Set DIST, DIST_VERSION, and INSTALLATION_ARCHIVE_STEM | |
run: | | |
# shellcheck disable=SC2034 | |
DISTS=(dist/nextstrain_cli-*-py3-none-any.whl) | |
DIST="${DISTS[0]}" | |
DIST_VERSION="$DIST" | |
DIST_VERSION="${DIST_VERSION#dist/nextstrain_cli-}" | |
DIST_VERSION="${DIST_VERSION%-py3-none-any.whl}" | |
INSTALLATION_ARCHIVE_STEM="nextstrain-cli-${DIST_VERSION}-standalone-${{ matrix.target }}" | |
for var in DIST DIST_VERSION INSTALLATION_ARCHIVE_STEM; do | |
echo "${var}=${!var}" | tee -a "$GITHUB_ENV" | |
done | |
- run: | | |
./devel/pyoxidizer build \ | |
--release \ | |
--target-triple ${{ matrix.target }} \ | |
--var NEXTSTRAIN_CLI_DIST "$DIST" | |
# Analyze the executable for potential portability issues. | |
# | |
# This is for informational purposes only in build logs, so we don't care | |
# if it fails. Currently it only works on Linux, though it's supposed to | |
# eventually work on all platforms supported by pyoxidizer. | |
- if: runner.os == 'Linux' | |
run: ./devel/pyoxidizer analyze build/${{ matrix.target }}/release/installation/${{ matrix.exe }} | |
continue-on-error: true | |
# XXX TODO: Review and report on licensing of all the stuff built into | |
# the binary, as bundling things statically can trigger different license | |
# terms than "normal" installs (e.g. via pip). See also pyoxidizer's | |
# docs about this and the tooling it includes to support license review.¹ | |
# -trs, 1 June 2022 | |
# | |
# ¹ https://pyoxidizer.readthedocs.io/en/stable/pyoxidizer_packaging_licensing.html#licensing-considerations | |
# Create installation archive. | |
# | |
# Use tar on Unix to preserve file modes (e.g. the executable bit), thus | |
# avoiding having to restore them manually after archive extraction. Use | |
# zip on Windows because it's a native format which requires no extra | |
# tooling. | |
- if: runner.os != 'Windows' | |
run: tar czvpf "$INSTALLATION_ARCHIVE_STEM.tar.gz" -C build/${{ matrix.target }}/release/installation/ . | |
- if: runner.os == 'Windows' | |
run: Compress-Archive -DestinationPath "$Env:INSTALLATION_ARCHIVE_STEM.zip" -Path build/${{ matrix.target }}/release/installation/* | |
shell: pwsh | |
# Upload installation archive as a workflow artifact. | |
# | |
# At least one path needs to match, or this errors. | |
- uses: actions/upload-artifact@v4 | |
with: | |
name: standalone-${{ matrix.target }} | |
path: | | |
${{ env.INSTALLATION_ARCHIVE_STEM }}.tar.gz | |
${{ env.INSTALLATION_ARCHIVE_STEM }}.zip | |
if-no-files-found: error | |
# Quick smoke test that the executable at least runs! Useful before | |
# launching the more extensive tests below. | |
- run: ./build/${{ matrix.target }}/release/installation/${{ matrix.exe }} --help | |
write-install-commands: | |
needs: build-standalone | |
runs-on: ubuntu-latest | |
steps: | |
- name: Write installation commands to job summary | |
run: | | |
cat >"$GITHUB_STEP_SUMMARY" <<'~~' | |
Build complete. Commands to install locally: | |
Linux: | |
```bash | |
curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/linux | bash -s ci-build/${{ github.run_id }} | |
``` | |
macOS: | |
```bash | |
curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/mac | bash -s ci-build/${{ github.run_id }} | |
``` | |
Windows: | |
```powershell | |
Invoke-Expression "& { $(Invoke-RestMethod https://nextstrain.org/cli/installer/windows) } ci-build/${{ github.run_id }}" | |
``` | |
~~ | |
test-dist: | |
needs: build-dist | |
name: test-dist (python=${{ matrix.python }} os=${{ matrix.os }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
os: | |
- ubuntu-latest | |
- macos-latest | |
- windows-latest | |
python: | |
- '3.8' | |
- '3.9' | |
- '3.10' | |
# XXX TODO: Add 3.11 here once supported by bioconda: https://github.com/nextstrain/augur/issues/1334 | |
# XXX TODO: Add 3.12 here once supported by bioconda: https://github.com/nextstrain/augur/issues/1334 | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
# Add -l for setup-integration-tests → setup-miniconda → automatic | |
# activation of "test" environment. | |
shell: bash -l -eo pipefail {0} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
path: src/ | |
- uses: ./src/.github/actions/setup-integration-tests | |
with: | |
python-version: ${{ matrix.python }} | |
- uses: actions/download-artifact@v4 | |
with: | |
name: dist | |
path: dist/ | |
- name: Install Nextstrain CLI | |
run: python3 -m pip install --upgrade dist/nextstrain_cli-*-py3-none-any.whl | |
- uses: ./src/.github/actions/run-integration-tests | |
test-standalone: | |
needs: build-standalone | |
name: test-standalone (os=${{ matrix.os}}, target=${{ matrix.target }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
# Test on all the platforms available via GitHub Actions. | |
# | |
# Ideally we'd test on machines with ~fresh OS installs. The kitchen | |
# sink of development/build software pre-installed into GitHub Action's | |
# virtual-environments has a decent risk of making this CI blind to | |
# end-user runtime issues with our binaries (e.g. missing DLLs). Such | |
# fresh CI machines are not readily available, however, since | |
# pre-installation is convenient for builds. | |
include: | |
- { os: ubuntu-20.04, target: x86_64-unknown-linux-gnu } | |
- { os: ubuntu-22.04, target: x86_64-unknown-linux-gnu } | |
- { os: macos-12, target: x86_64-apple-darwin } | |
- { os: macos-14, target: aarch64-apple-darwin } | |
- { os: windows-2019, target: x86_64-pc-windows-msvc } | |
- { os: windows-2022, target: x86_64-pc-windows-msvc } | |
runs-on: ${{matrix.os}} | |
defaults: | |
run: | |
# Add -l for setup-integration-tests → setup-miniconda → automatic | |
# activation of "test" environment. | |
shell: bash -l -eo pipefail {0} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
path: src/ | |
- uses: ./src/.github/actions/setup-integration-tests | |
with: | |
python-version: '3.9' | |
# Download and extract the installation archive. | |
- uses: actions/download-artifact@v4 | |
with: | |
name: standalone-${{ matrix.target }} | |
- if: runner.os != 'Windows' | |
run: tar xzvpf nextstrain-cli-*-standalone-${{ matrix.target }}.tar.gz | |
- if: runner.os == 'Windows' | |
run: Expand-Archive -Path nextstrain-cli-*-standalone-${{ matrix.target }}.zip -DestinationPath . | |
shell: pwsh | |
- run: echo "$PWD" >> "$GITHUB_PATH" | |
- uses: ./src/.github/actions/run-integration-tests | |
doc: | |
uses: nextstrain/.github/.github/workflows/docs-ci.yaml@master | |
with: | |
docs-directory: doc/ | |
pip-install-target: .[dev] | |
make-target: dirhtml | |
release: | |
# Restricted to version tags by the "on: push: tags: …" config at the top. | |
if: |2 | |
github.event_name == 'push' | |
&& github.ref_type == 'tag' | |
needs: | |
- build-dist | |
- build-standalone | |
- test-source | |
- test-dist | |
- test-standalone | |
- lint | |
- doc | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
# In actions/checkout@v4 above, annotated tags are intentionally | |
# **overwritten** and converted to a lightweight tag. Forcibly restore | |
# the annotated tag object from the remote so we can verify/use it later. | |
- run: git fetch --force origin tag "$GITHUB_REF_NAME" | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
- run: python3 -m pip install --upgrade twine | |
- uses: actions/download-artifact@v4 | |
with: | |
name: dist | |
path: dist/ | |
- uses: actions/download-artifact@v4 | |
with: | |
name: standalone-x86_64-unknown-linux-gnu | |
- uses: actions/download-artifact@v4 | |
with: | |
name: standalone-x86_64-apple-darwin | |
- uses: actions/download-artifact@v4 | |
with: | |
name: standalone-aarch64-apple-darwin | |
- uses: actions/download-artifact@v4 | |
with: | |
name: standalone-x86_64-pc-windows-msvc | |
- run: twine upload dist/* | |
env: | |
TWINE_USERNAME: __token__ | |
TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} | |
TWINE_REPOSITORY_URL: https://upload.pypi.org/legacy/ | |
- run: ./devel/create-github-release "${{github.ref_name}}" dist/* nextstrain-cli-*-standalone-* | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |