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Moved requirments and setup to pyproject and simplified requirments (#163)
* Cleaned up requirments. Seeing how CICD handles it. * Got sick of travis. Trying out github actions * Opened it up so it CICD will actually run * Added back utils * Trying gitlab * Moved setup to pyproject.toml * fixed regex * Added travis back in :( * Added mysqlclient to dependencies * Added mysqlclient to dependencies * updated versions * Cleaned up requirments. Seeing how CICD handles it. * Got sick of travis. Trying out github actions * Opened it up so it CICD will actually run * Added back utils * Moved setup to pyproject.toml * fixed regex * Added travis back in :( * Added mysqlclient to dependencies * Added mysqlclient to dependencies * updated versions
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‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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pull_request:
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jobs:
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test:
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runs-on: ubuntu-20.04 # Equivalent to Travis 'focal'
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strategy:
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matrix:
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python-version: [ "3.10", "3.11" ]
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services:
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mysql:
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image: mysql:8.0
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env:
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MYSQL_ALLOW_EMPTY_PASSWORD: yes
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MYSQL_DATABASE: test_db
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ports:
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- 3306:3306
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options: >-
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--health-cmd="mysqladmin ping"
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--health-interval=10s
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--health-timeout=5s
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--health-retries=3
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache pip dependencies
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Configure MySQL
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run: |
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# Enable local_infile (equivalent to Travis before_script)
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mysql -h127.0.0.1 -P3306 -uroot -e "SET GLOBAL local_infile=1;"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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# Install with test dependencies using new pyproject.toml structure
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pip install .[test]
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- name: Run tests
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run: |
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echo "DB_HOST $METADATA_URI $TAXONOMY_URI"
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coverage run -m pytest -c pyproject.toml --server mysql://[email protected]:3306
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- name: Upload coverage reports
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uses: codecov/codecov-action@v3
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with:
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fail_ci_if_error: false

‎.gitlab-ci.yml‎

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coverage_format: cobertura
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path: coverage.xml
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expire_in: 1 week
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‎.travis.yml‎

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# In MySQL 8, local_infile is disabled by default for security reasons.
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# By adding SET GLOBAL local_infile=1;, we enable this feature at runtime.
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- mysql -e "SET GLOBAL local_infile=1;"
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- pip install -r requirements-test.txt
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- pip install .
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- pip install .[test]
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script:
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- echo "DB_HOST $METADATA_URI $TAXONOMY_URI"
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- coverage run -m pytest -c pyproject.toml --server mysql://[email protected]:3306
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- coverage run -m pytest -c pyproject.toml --server mysql://[email protected]:3306

‎pyproject.toml‎

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# See the License for the specific language governing permissions and
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# limitations under the License.
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[build-system]
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build-backend = "setuptools.build_meta"
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requires = [
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"setuptools",
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"wheel",
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]
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[project]
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name = "ensembl-metadata-api"
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description = "# Ensembl Metadata API / GRPC API, SQLAlchemy ORM for the Ensembl Metadata database."
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description = "Ensembl Metadata API"
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requires-python = ">= 3.10"
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version="3.0.0"
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readme = "README.md"
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version = "3.0.0"
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dynamic = ["readme"]
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authors = [
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{name = "Ensembl", email = "[email protected]"},
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{ name = "Alisha Aneja", email = "[email protected]" },
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{ name = "Bilal El Houdaigui", email = "[email protected]" },
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{ name = "Daniel Poppleton", email = "[email protected]" },
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{ name = "Marc Chakiachvili", email = "[email protected]" },
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{ name = "Sanjay Boddu", email = "[email protected]" },
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{ name = "Vinay Kaikala", email = "[email protected]" },
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]
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license = {text = "Apache License 2.0"}
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keywords = [
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"grpc"
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]
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classifiers = [
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"Development Status :: 5 - Production/Stable",
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"Environment :: Console",
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: POSIX",
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"Operating System :: Unix",
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"Natural Language :: English",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3 :: Only",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Topic :: Utilities",
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"Topic :: System :: Distributed Computing",
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]
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dependencies = [
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"ensembl-utils >= 0.8.0",
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"ensembl-py >= 3.0.0",
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"grpcio",
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"protobuf",
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"grpcio-tools",
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"grpcio-reflection",
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"sqlalchemy >= 2.0",
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"duckdb >= 1.2.0",
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"duckdb-engine >= 0.17.0",
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"pymysql",
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"mysqlclient",
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]
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[project.urls]
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Homepage = "https://www.ensembl.org"
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Repository = "https://github.com/Ensembl/ensembl-metadata-api"
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"Download" = "https://github.com/Ensembl/ensembl-metadata-api"
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Issues = "https://github.com/Ensembl/ensembl-metadata-api/issues"
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[project.optional-dependencies]
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test = [
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"pylint",
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"mypy",
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"coverage[toml]",
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"pytest-grpc",
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"yagrc == 1.1.2",
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]
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dev = [
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"ensembl-metadata-api[test]", # Include test dependencies
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"black",
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]
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[project.scripts]
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ensembl-release = "scripts.release:main"
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[tool.setuptools]
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package-dir = {"" = "src"}
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include-package-data = true
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[tool.setuptools.packages.find]
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where = ["src"]
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[build-system]
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build-backend = "setuptools.build_meta"
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requires = [
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"setuptools",
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"setuptools-scm",
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"wheel",
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]
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[tool.setuptools.dynamic]
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readme = { file = ["README.md"] }
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[tool.black]
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line-length = 110
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"unspecified-encoding",
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"wildcard-import",
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]
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[tool.mypy]
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mypy_path = "src/ensembl"
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explicit_package_bases = true
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]
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norecursedirs = ["docs", "*.egg_info"]
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[tool.coverage.report]
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exclude_also = [
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# Do not complain about missing debug-only code

‎requirements-dev.txt‎

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‎requirements-test.txt‎

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‎requirements.in‎

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‎requirements.txt‎

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‎setup.py‎

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