minor change to test actions

.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:
@@ -62,41 +62,39 @@ 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
         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/
 
       - name: Starting Main Services
         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}
 
@@ -128,7 +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\`"
@@ -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

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

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()