modified: csubst_commands.sh #3

	name: csubst ci

	on:
	push:
	branches: [ "**" ]
	pull_request:
	workflow_dispatch:

	concurrency:
	group: smoke-csubst-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	smoke:
	runs-on: ${{ matrix.os }}
	timeout-minutes: 30
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest, macos-latest]
	python: ['3.10']
	install: [source] # bioconda は後で復活可

	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Set up micromamba
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-name: csubst-smoke
	create-args: >-
	python=${{ matrix.python }}
	pip
	condarc: \|
	channels:
	- conda-forge
	- bioconda
	channel_priority: strict
	cache-environment: true
	cache-downloads: true

	- name: Install runtime deps
	shell: bash -l {0}
	run: \|
	micromamba install -y \
	numpy=1.26.* cython=0.29.* iqtree \
	conda-forge::biopython conda-forge::requests

	- name: Install csubst (from source)
	if: matrix.install == 'source'
	shell: bash -l {0}
	run: \|
	python -m pip install --upgrade pip
	pip install --no-build-isolation .

	# --- Smoke ---
	- name: Run smoke test
	shell: bash -l {0}
	run: bash ci/csubst_smoke.sh

	# --- CLI tests ---
	- name: Run CLI tests
	shell: bash -l {0}
	run: bash ci/csubst_cli.sh

	- name: Upload artifacts (always)
	if: always()
	uses: actions/upload-artifact@v4
	with:
	name: smoke-and-cli-${{ matrix.os }}-${{ matrix.install }}
	path: \|
	$RUNNER_TEMP/csubst_smoke/_artifacts*
	if-no-files-found: ignore
	retention-days: 7

	- name: Run command tests
	shell: bash -l {0}
	env:
	MPLBACKEND: Agg
	run: bash ci/csubst_commands.sh

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