Pin numpy to 1.22.3 in environment_BSF.yml and environment_Windows.yml #203
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name: CI | |
# specify trigger events for ci workflow | |
on: | |
push: | |
branches: [main] | |
pull_request: | |
types: [opened, edited, reopened, synchronize, review_requested] | |
jobs: | |
# apply formating and linting | |
Format: | |
runs-on: ubuntu-20.04 | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Apply snakefmt | |
uses: github/super-linter@v4 | |
env: | |
VALIDATE_ALL_CODEBASE: false | |
DEFAULT_BRANCH: main | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
LINTER_RULES_PATH: snekmer/rules/ | |
VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
# run all tests | |
Test: | |
runs-on: ubuntu-20.04 | |
needs: | |
- Format | |
permissions: | |
contents: 'read' | |
id-token: 'write' | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Build test environment | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
mamba-version: "*" | |
channels: anaconda,conda-forge,bioconda,numba | |
auto-activate-base: false | |
activate-environment: snekmer | |
environment-file: .test/test-env.yml | |
- shell: bash -l {0} | |
run: | | |
conda info | |
conda list | |
conda config --show | |
- shell: bash -l {0} | |
run: mamba install -y -c conda-forge snakemake==7.0 tabulate==0.8.10 | |
- shell: bash -l {0} | |
run: pip install -e git+https://github.com/PNNL-CompBio/Snekmer@kmer-association#egg=snekmer | |
#test clustering step | |
- name: Snekmer Cluster | |
run: | | |
export PATH="/usr/share/miniconda/bin:$PATH" | |
conda info --envs | |
source activate snekmer | |
conda config --get channel_priority --json | |
snekmer cluster --configfile .test/config.yaml -d .test | |
rm -rf .test/output | |
# --use-conda --conda-cleanup-pkgs cache --show-failed-logs --conda-frontend mamba | |
# run modeling step and move output files for search | |
- name: Snekmer Model | |
run: | | |
export PATH="/usr/share/miniconda/bin:$PATH" | |
source activate snekmer | |
snekmer model --configfile .test/config.yaml -d .test --cores 1 | |
mkdir .test/output/example-model | |
mv .test/output/model/*.model .test/output/example-model/ | |
mv .test/output/kmerize/*.kmers .test/output/example-model/ | |
mv .test/output/scoring/*.scorer .test/output/example-model/ | |
# search against previously generated model files | |
- name: Snekmer Search | |
run: | | |
export PATH="/usr/share/miniconda/bin:$PATH" | |
source activate snekmer | |
ls .test | |
pwd | |
snekmer search --configfile .test/config.yaml -d .test --cores 1 | |
rm -rf .test/output | |
# run Snekmer Learn kmer counts and confidence creation | |
- name: Snekmer Learn | |
run: | | |
export PATH="/usr/share/miniconda/bin:$PATH" | |
source activate snekmer | |
snekmer learn --configfile .test/config_learnapp.yaml -d .test --cores 1 | |
mkdir .test/counts .test/confidence | |
mv .test/output/learn/kmer-counts-total.csv .test/counts/kmer-counts-total.csv | |
mv .test/output/eval_conf/global-confidence-scores.csv .test/confidence/global-confidence-scores.csv | |
rm -rf .test/output | |
# run Snekmer Learn against previously generated counts files | |
- name: Snekmer Apply | |
run: | | |
export PATH="/usr/share/miniconda/bin:$PATH" | |
source activate snekmer | |
snekmer apply --configfile .test/config_learnapp.yaml -d .test --cores 1 | |
rm -rf .test/output |