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fix CI #5

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merged 3 commits into from
Mar 10, 2025
Merged

fix CI #5

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2b50f26
fix CI
antgonza Mar 10, 2025
88611ad
update python and postgres version
antgonza Mar 10, 2025
2fc1563
update qiita conda install
antgonza Mar 10, 2025
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46 changes: 22 additions & 24 deletions .github/workflows/qiita-plugin-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

on:
push:
branches: [ dev ]
branches: [dev]
pull_request:

jobs:
Expand All @@ -13,7 +13,7 @@ jobs:
services:
postgres:
# Docker Hub image
image: postgres:9.5
image: postgres:13.4
env:
POSTGRES_DB: postgres
POSTGRES_USER: postgres
Expand All @@ -39,7 +39,7 @@ jobs:
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: 3.6
python-version: 3.9

- name: Basic dependencies install
env:
Expand All @@ -62,10 +62,8 @@ jobs:

# Setting up main qiita conda environment
conda config --add channels conda-forge
conda create -q --yes -n qiita python=3.6 pip==9.0.3 libgfortran numpy nginx cython redis
conda create -q --yes -n qiita python=3.9 libgfortran numpy nginx cython redis
conda activate qiita
pip install --upgrade pip
pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click

- name: Qiita install
shell: bash -l {0}
Expand All @@ -80,13 +78,13 @@ jobs:
conda create -q --yes -n qtp-job-output-folder python=3.6 pip==9.0.3
conda activate qtp-job-output-folder

export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
pip --quiet install -U pip
pip --quiet install .
pip --quiet install coveralls

configure_qtp_job_output_folder --env-script "source /home/runner/.profile; conda activate qtp-job-output-folder" --server-cert $QIITA_SERVER_CERT
configure_qtp_job_output_folder --env-script "source /home/runner/.profile; conda activate qtp-job-output-folder" --ca-cert $QIITA_ROOTCA_CERT

echo "Available Qiita plugins"
ls ~/.qiita_plugins/
Expand All @@ -95,7 +93,7 @@ jobs:
shell: bash -l {0}
run: |
conda activate qiita
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}

Expand Down Expand Up @@ -127,7 +125,7 @@ jobs:
COVER_PACKAGE: ${{ matrix.cover_package }}
run: |
conda activate qtp-job-output-folder
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg

export PYTHONWARNINGS="ignore:Certificate for localhost has no \`subjectAltName\`"
Expand All @@ -136,21 +134,21 @@ jobs:

- uses: codecov/codecov-action@v1
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: codecov.yml
token: ${{ secrets.CODECOV_TOKEN }}
file: codecov.yml

lint:
runs-on: ubuntu-latest
steps:
- name: flake8
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: install dependencies
run: python -m pip install --upgrade pip
- name: Check out repository code
uses: actions/checkout@v2
- name: lint
run: |
pip install -q flake8
flake8 qtp_job_output_folder setup.py scripts/*
- name: flake8
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: install dependencies
run: python -m pip install --upgrade pip
- name: Check out repository code
uses: actions/checkout@v2
- name: lint
run: |
pip install -q flake8
flake8 qtp_job_output_folder setup.py scripts/*
11 changes: 5 additions & 6 deletions scripts/configure_qtp_job_output_folder
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Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,12 @@ from qtp_job_output_folder import plugin
@click.command()
@click.option('--env-script', prompt='Environment script',
default='conda activate qtp-job-output-folder')
@click.option('--server-cert', prompt='Server certificate', default='None')
def config(env_script, server_cert):
@click.option('--ca-cert', prompt='Server certificate', default='None')
def config(env_script, ca_cert):
"""Generates the Qiita configuration files"""
if server_cert == 'None':
server_cert = None
plugin.generate_config(env_script, 'start_qtp_job_output_folder',
server_cert=server_cert)
if ca_cert == 'None':
ca_cert = None
plugin.generate_config(env_script, 'start_qtp_job_output_folder', ca_cert)


if __name__ == '__main__':
Expand Down