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Fix pixi resolver: pytantan from PyPI, bump buscolite, drop Dockerfile source rebuild #57

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Merged
nextgenusfs merged 3 commits into from
Apr 22, 2026
Merged

Fix pixi resolver: pytantan from PyPI, bump buscolite, drop Dockerfile source rebuild #57

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c673f55
fix(docker): move pytantan to PyPI, bump buscolite, drop source rebuild
Apr 22, 2026
1cc8fe2
fix: bump buscolite floor to >=26.4.22 (typo was >=26.2.22)
Apr 22, 2026
b75fc6c
fix: rebuild pytantan 0.1.4 from source in Docker + CI
Apr 22, 2026
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9 changes: 7 additions & 2 deletions .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ jobs:
run: |
if [[ "$RUNNER_OS" == "Linux" ]]; then
sudo apt-get update
sudo apt-get install -y build-essential zlib1g-dev
sudo apt-get install -y build-essential cmake zlib1g-dev
fi

- name: Setup conda (macOS only)
Expand All @@ -51,10 +51,15 @@ jobs:
python-version: ${{ matrix.python-version }}

- name: Install dependencies
env:
# Force pytantan to build from sdist so all Python versions get the
# same AVX2-off baseline. The published cp3x wheels have caused
# import-time failures on 3.9/3.10/3.11 in this matrix.
PIP_NO_BINARY: pytantan
run: |
if [[ "${{ matrix.use_conda }}" == "true" ]]; then
# Use conda for macOS to avoid mappy build issues
conda install -c conda-forge -c bioconda mappy numpy pytest pytest-cov -y
conda install -c conda-forge -c bioconda mappy numpy pytest pytest-cov cmake -y
# Install funannotate2 in editable mode - this will install all dependencies from pyproject.toml
pip install -e .
else
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -4,7 +4,7 @@

ARG PIXI_VERSION=0.67.0
ARG UBUNTU_VERSION=22.04
ARG PYTANTAN_VERSION=0.1.3
ARG PYTANTAN_VERSION=0.1.4

# ---------------------------------------------------------------------------
# Stage 1: build — resolve + install the pixi environment from pixi.lock
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87 changes: 33 additions & 54 deletions pixi.lock
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5 changes: 3 additions & 2 deletions pixi.toml
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Expand Up @@ -23,11 +23,10 @@ table2asn = "*"
# funannotate2 python deps available via bioconda / conda-forge
gfftk = ">=26.2.12"
gapmm2 = ">=25.8.12"
buscolite = ">=26.1.26"
buscolite = ">=26.4.22"
pyhmmer = ">=0.12.0"
pyfastx = ">=2.0.0"
gb-io = ">=0.3.2"
pytantan = "*"
mappy = "*"

# general python + scientific libs from conda-forge
Expand All @@ -50,4 +49,6 @@ funannotate2 = { path = ".", editable = false }
"funannotate2-addons" = "*"
helixerlite = "*"
annorefine = ">=2026.2.9"
# pytantan: bioconda lags at 0.1.3; pull 0.1.4+ from PyPI
pytantan = ">=0.1.4"

2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -16,7 +16,7 @@ dependencies = [
"numpy",
"mappy",
"gfftk>=26.2.12",
"buscolite>=26.2.22",
"buscolite>=26.4.22",
"gapmm2>=25.8.12",
"pyhmmer>=0.12.0",
"pyfastx>=2.0.0",
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