CI: Add CI

.github/workflows/ci.yml

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+name: CI
+on:
+  pull_request:
+    branches: ["main"]
+  push:
+    branches: ["main"]
+
+jobs:
+  ci:
+    uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev
+    with:
+      distro: metagenome
+      additional-reports-path: ./coverage.xml
+      additional-reports-name: coverage
+
+  coverage:
+    needs: [ci]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v3
+        name: 'Fetch coverage from builds'
+        with:
+          name: ${{ needs.ci.outputs.additional-reports-name }}
+          path: ${{ needs.ci.outputs.additional-reports-path }}
+
+      - uses: codecov/codecov-action@v4
+        name: 'Upload coverage'
+        with:
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-merge-conflict
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        files: ^(.+)(?<!\_version)\.py$
+        args: ["--profile", "black"]
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args:
+          - --safe
+          - --quiet
+        files: ^(.+)(?<!\_version)\.py$
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        additional_dependencies:
+          - pycodestyle==2.8.0
+          - pyflakes==2.4.0
+          - pydocstyle==6.1.1
+          - flake8-comprehensions==3.8.0
+          - flake8-noqa==1.2.1
+          - mccabe==0.6.1
+        files: ^(.+)(?<!\_version)\.py$
+  - repo: local
+    hooks:
+      - id: q2lint
+        name: q2lint
+        language: python
+        pass_filenames: false
+        entry: q2lint
+        stages: [ commit ]
+        additional_dependencies:
+          - https://github.com/qiime2/q2lint/archive/master.zip

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Christos Matzoros.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ci/recipe/meta.yaml

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+{% set data = load_setup_py_data() %}
+{% set version = data.get('version') or 'placehold' %}
+
+package:
+  name: q2-viromics
+  version: {{ version }}
+
+source:
+  path: ../..
+
+build:
+  script: make install
+
+requirements:
+  host:
+    - python {{ python }}
+    - setuptools
+
+  run:
+    - python {{ python }}
+    - qiime2 {{ qiime2_epoch }}.*
+    - q2-types {{ qiime2_epoch }}.*
+    - checkv
+    - pyhmmer
+
+test:
+  requires:
+    - coverage
+    - pytest-cov
+  imports:
+    - q2_viromics
+    - qiime2.plugins.viromics
+  commands:
+    - pytest --cov q2_viromics --cov-report xml:coverage.xml --pyargs q2_viromics
+
+about:
+  home: https://github.com/bokulich-lab/q2-viromics
+  license: BSD-3-Clause
+  license_family: BSD