From 94c5c2cb96af9d5c68544c07e4f4448114bfbd07 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Wed, 1 Oct 2025 07:29:26 -0600 Subject: [PATCH 1/4] minor change to test actions --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 169b086..deb2b7a 100644 --- a/README.rst +++ b/README.rst @@ -5,7 +5,7 @@ Target Gene Qiita Plugin Qiita (canonically pronounced *cheetah*) is an analysis environment for microbiome (and other "comparative -omics") datasets. -This package includes the target gene plugin for Qiita. This makes the functionality to analyze target gene data available in the Qiita installation. +This package includes the target gene, currently based on QIIME 1, plugin for Qiita. This makes the functionality to analyze target gene data available in the Qiita installation. .. |Build Status| image:: https://github.com/qiita-spots/qp-target-gene/actions/workflows/qiita-plugin-ci.yml/badge.svg :target: https://github.com/qiita-spots/qp-target-gene/actions/workflows/qiita-plugin-ci.yml From 381471809942ca97b152186804e34e519b4bab9f Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Wed, 1 Oct 2025 07:46:28 -0600 Subject: [PATCH 2/4] update Qiita install --- .github/workflows/qiita-plugin-ci.yml | 40 +++++++++++++-------------- 1 file changed, 19 insertions(+), 21 deletions(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index c183404..ef9ae9d 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: @@ -62,16 +62,14 @@ jobs: # Setting up main qiita conda environment conda config --add channels conda-forge - conda create -q --yes -n qiita python=3.6 pip libgfortran numpy nginx cython redis + conda create -q --yes -n qiita python=3.9 libgfortran numpy nginx cython redis conda activate qiita - pip install 'setuptools<=58.0.1' - pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click - name: Qiita install shell: bash -l {0} run: | conda activate qiita - pip install qiita-dev/ --no-binary redbiom + pip --quiet install qiita-dev/ --no-binary redbiom mkdir ~/.qiita_plugins - name: Install Qiita plugins @@ -137,21 +135,21 @@ 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 qp_target_gene setup.py scripts qp_target_gene/support_files/patches/*.py + - 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 qp_target_gene setup.py scripts qp_target_gene/support_files/patches/*.py From 7d36eaed9f77162b18f32d30820b29ac139da84c Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Wed, 1 Oct 2025 08:01:29 -0600 Subject: [PATCH 3/4] update configure_target_gene --- .github/workflows/qiita-plugin-ci.yml | 6 +++--- scripts/configure_target_gene | 11 +++++------ 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index ef9ae9d..d7be773 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -75,18 +75,18 @@ jobs: - name: Install Qiita plugins shell: bash -l {0} run: | + conda config --add channels bioconda conda create --override-channels -c defaults --quiet --yes -n qp-target-gene python=2.7 conda activate qp-target-gene conda install --yes -c bioconda -c biocore SortMeRNA==2.0 numpy==1.13.1 pigz - 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_target_gene --env-script "source /home/runner/.profile; conda activate qp-target-gene" --server-cert $QIITA_SERVER_CERT - + configure_target_gene --env-script "source /home/runner/.profile; conda activate qp-target-gene" --ca-cert $QIITA_ROOTCA_CERT echo "Available Qiita plugins" ls ~/.qiita_plugins/ diff --git a/scripts/configure_target_gene b/scripts/configure_target_gene index ac187b6..dd68880 100755 --- a/scripts/configure_target_gene +++ b/scripts/configure_target_gene @@ -16,13 +16,12 @@ from qp_target_gene import plugin @click.command() @click.option('--env-script', prompt='Environment script', default='source activate qp-target-gene') -@click.option('--server-cert', prompt='Server certificate', default='None') -def config(env_script, server_cert): +@click.option('--ca-cert', prompt='Server certificate', default='None') +def config(env_script, ca_cert): """Generates the Qiita configuration files""" - if server_cert == 'None': - server_cert = None - plugin.generate_config(env_script, 'start_target_gene', - server_cert=server_cert) + if ca_cert == 'None': + ca_cert = None + plugin.generate_config(env_script, 'start_target_gene', ca_cert) if __name__ == '__main__': config() From 66ab7e6e1829027b88e50687e2bace58dade13ef Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Wed, 1 Oct 2025 08:14:45 -0600 Subject: [PATCH 4/4] QIITA_SERVER_CERT -> QIITA_ROOTCA_CERT --- .github/workflows/qiita-plugin-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index d7be773..0db8def 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -94,7 +94,7 @@ jobs: shell: bash -l {0} run: | conda activate qiita - export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt + export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP} @@ -126,7 +126,7 @@ jobs: COVER_PACKAGE: ${{ matrix.cover_package }} run: | conda activate qp-target-gene - 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\`"