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fix(ci): use --no-sync in no-pysam job to prevent re-installing pysam
uv run without --no-sync re-syncs the environment with default groups, which includes the pysam group. Add --no-sync to all uv run commands in the Tests-without-pysam job so the environment stays as uv sync set it up. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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.github/workflows/tests.yml

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@@ -71,11 +71,11 @@ jobs:
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- name: Verify pysam is not installed
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run: |
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uv run python -c "import pysam" 2>&1 && exit 1 || echo "pysam correctly not installed"
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uv run --no-sync python -c "import pysam" 2>&1 && exit 1 || echo "pysam correctly not installed"
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- name: Run pysam-independent tests
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run: |
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uv run pytest \
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uv run --no-sync pytest \
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tests/fgpyo/test_read_structure.py \
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tests/fgpyo/test_sequence.py \
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tests/fgpyo/test_requirements.py \
@@ -90,4 +90,4 @@ jobs:
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- name: Verify pysam-dependent modules are importable
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run: |
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uv run python -c "from fgpyo.sam import Cigar; print('fgpyo.sam importable without pysam')"
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uv run --no-sync python -c "from fgpyo.sam import Cigar; print('fgpyo.sam importable without pysam')"

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