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first attempt to change from csv to parquet #221

first attempt to change from csv to parquet

first attempt to change from csv to parquet #221

Workflow file for this run

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Python application
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install flake8 pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Test with pytest
run: |
python setup.py install
python tests/test_proteomicslfq.py
- name: Test LFQ dataset
run: |
wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/lfq/lfq.zip
unzip -d ./lfq lfq.zip
python setup.py install
multiqc -f ./lfq --config ./lfq/multiqc_config.yml -o ./results_lfq
- uses: actions/upload-artifact@v1
if: always()
name: Upload results
with:
name: results_lfq
path: ./results_lfq
- name: Test TMT dataset
run: |
wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/tmt-replicates/tmt-replicates.zip
unzip -d ./tmt tmt-replicates.zip
python setup.py install
multiqc -f ./tmt --config ./tmt/multiqc_config.yml -o ./results_tmt
- uses: actions/upload-artifact@v1
if: always()
name: Upload results
with:
name: results_tmt
path: ./results_tmt
- name: Test DIA dataset
run: |
wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/dia/dia.zip
unzip -d ./dia dia.zip
python setup.py install
multiqc -f ./dia --config ./dia/multiqc_config.yml -o ./results_dia
- uses: actions/upload-artifact@v1
if: always()
name: Upload results
with:
name: results_dia
path: ./results_dia