diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 2f875b2..7e6c620 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -2,7 +2,7 @@ on: push: - branches: [ dev ] + branches: [dev] pull_request: jobs: @@ -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 @@ -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: @@ -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} @@ -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 $QIITA_ROOTCA_CERT echo "Available Qiita plugins" ls ~/.qiita_plugins/ @@ -95,7 +93,7 @@ jobs: shell: bash -l {0} run: | conda activate qiita - export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt + export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP} @@ -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\`" @@ -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/* diff --git a/scripts/configure_qtp_job_output_folder b/scripts/configure_qtp_job_output_folder index bf91765..815b728 100755 --- a/scripts/configure_qtp_job_output_folder +++ b/scripts/configure_qtp_job_output_folder @@ -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__':