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update

update #235

Workflow file for this run

name: Testing Python
on:
workflow_call:
pull_request:
push:
jobs:
test:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.8, 3.9, "3.10", 3.11, 3.12]
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install ./taxoniumtools
- name: Download files
run: |
wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.meta.tsv.gz
wget https://raw.githubusercontent.com/theosanderson/taxonium/master/taxoniumtools/test_data/hu1.gb
wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.pb
wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/test_config.json
wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/test.nwk
- name: Basic test
run: |
usher_to_taxonium --input tfci.pb --output tfci-taxonium.jsonl.gz --metadata tfci.meta.tsv.gz --genbank hu1.gb --columns genbank_accession,country,date,pangolin_lineage --clade_types nextstrain,pango
- uses: actions/upload-artifact@v3
with:
name: tfci-taxonium
path: tfci-taxonium.jsonl.gz
- name: Test with chronumental
run: |
pip install chronumental
usher_to_taxonium --input tfci.pb --output tfci-taxonium-chron.jsonl.gz --metadata tfci.meta.tsv.gz --genbank hu1.gb --columns genbank_accession,country,date,pangolin_lineage --chronumental --chronumental_steps 300 --clade_types nextstrain,pango
- uses: actions/upload-artifact@v3
with:
name: tfci-taxonium-chron
path: tfci-taxonium-chron.jsonl.gz
- name: Test with config
run: |
usher_to_taxonium --input tfci.pb --output tfci-taxonium-config.jsonl.gz --metadata tfci.meta.tsv.gz --genbank hu1.gb --columns genbank_accession,country,date,pangolin_lineage --config_json test_config.json --name_internal_nodes
- uses: actions/upload-artifact@v3
with:
name: tfci-taxonium-config
path: tfci-taxonium-config.jsonl.gz
- name: Test no genbank, no metadata
run: |
usher_to_taxonium --input tfci.pb --output tfci-bare.jsonl.gz
- name: Test only varaible sites
run: |
usher_to_taxonium --input tfci.pb --output tfci-var.jsonl.gz --only_variable_sites --metadata tfci.meta.tsv.gz --genbank hu1.gb --columns genbank_accession,country,date,pangolin_lineage
- uses: actions/upload-artifact@v3
with:
name: tfci-var
path: tfci-var.jsonl.gz
- name: Basic test, nwk
run: |
newick_to_taxonium --input test.nwk --output nwk.jsonl.gz
- uses: LouisBrunner/[email protected]
if: always()
with:
token: ${{ secrets.GITHUB_TOKEN }}
name: Python tests
conclusion: ${{ job.status }}