diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index c045e76..226233f 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -1,21 +1,6 @@ --- name: build -# ----------------- -# Control variables (GitHub Secrets) -# ----------------- -# -# At the GitHub 'organisation' or 'project' level you must have the following -# GitHub 'Repository Secrets' defined (i.e. via 'Settings -> Secrets'): - -# -# (none) -# -# ----------- -# Environment (GitHub Environments) -# ----------- -# -# Environment (none) - on: push: branches: @@ -32,30 +17,23 @@ jobs: strategy: matrix: python-version: - - '3.10' + - '3.11' + - '3.12' + - '3.13' + - '3.14' steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} - name: Install requirements - run: | - python -m pip install --upgrade pip - python -m pip install --upgrade build - pip install -r requirements.txt - pip install -r build-requirements.txt + run: pip install uv - name: Static Analysis run: | - pre-commit run --all-files - pyroma . + uv run pre-commit run --all-files - name: Build - run: | - python -m build --sdist --wheel --outdir dist/ + run: uv build - name: Compile Documentation - run: | - pip install -r docs-requirements.txt - sphinx-build -b html docs _readthedocs/html/ - env: - PYTHONPATH: ./src + run: uv run sphinx-build -b html docs _readthedocs/html/ diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml index d6467fc..5ed2bf8 100644 --- a/.github/workflows/publish.yaml +++ b/.github/workflows/publish.yaml @@ -1,19 +1,7 @@ --- -name: publish - -# Actions for any tag. -# ----------------- -# Control variables (GitHub Secrets) -# ----------------- -# -# None -# -# ----------- -# Environment (GitHub Environments) -# ----------- -# -# Environment (none) +# Publish the application to PyPI +name: publish on: push: @@ -21,25 +9,44 @@ on: - '**' jobs: - build-and-publish: + build: runs-on: ubuntu-latest - permissions: - id-token: write # IMPORTANT: this permission is mandatory for trusted publishing steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Inject slug/short variables - uses: rlespinasse/github-slug-action@v4 + uses: rlespinasse/github-slug-action@v5 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: - python-version: '3.10' - - name: Install dependencies - run: | - python -m pip install --upgrade pip - python -m pip install --upgrade build + python-version: '3.14' + - name: Install build dependencies + run: pip install uv - name: Build run: | - python -m build --sdist --wheel --outdir dist/ + uv version $GITHUB_REF_SLUG + uv build + - name: Store the distribution + uses: actions/upload-artifact@v5 + with: + name: python-package-distribution + path: dist/ + + publish: + name: Publish to PyPI + needs: + - build + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/im-squonk2-client + permissions: + id-token: write + steps: + - name: Download distribution + uses: actions/download-artifact@v6 + with: + name: python-package-distribution + path: dist/ - name: Publish uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.mypy.ini b/.mypy.ini deleted file mode 100644 index 976ba02..0000000 --- a/.mypy.ini +++ /dev/null @@ -1,2 +0,0 @@ -[mypy] -ignore_missing_imports = True diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8f5a284..fc3257b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ --- -minimum_pre_commit_version: 2.20.0 +minimum_pre_commit_version: 4.5.1 exclude: ^(docs|tests) repos: @@ -9,7 +9,7 @@ repos: # Conventional Commit message checker (commitizen) - repo: https://github.com/commitizen-tools/commitizen - rev: v2.28.1 + rev: v4.13.9 hooks: - id: commitizen stages: @@ -20,7 +20,7 @@ repos: # Standard pre-commit rules - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + rev: v6.0.0 hooks: - id: check-case-conflict - id: check-executables-have-shebangs @@ -30,39 +30,28 @@ repos: - id: trailing-whitespace args: - --markdown-linebreak-ext=md -# Black (uncompromising) Python code formatter -- repo: https://github.com/psf/black - rev: 24.2.0 + +# Checking packaging +- repo: https://github.com/regebro/pyroma + rev: 5.0.1 hooks: - - id: black - args: - - --target-version - - py310 -# MyPy -- repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.8.0 + - id: pyroma + +# Ruff +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.15.6 hooks: - - id: mypy - files: ^src + - id: ruff-check args: - - --ignore-missing-imports - additional_dependencies: - - types-protobuf - - types-PyYAML - - types-python-dateutil - - types-pytz - - types-requests -# Pylint -# To check import errors we need to install every package -# used by the DM. This is often impractical on the client, -# and so we disable import errors on pre-commit and rely -# on this category of test in the CI stage. Consequently, -# pylint may pass on pre-commit but fail in CI - but at least -# the user has done 90% of the lint checks before the code -# hits the server. -- repo: https://github.com/pycqa/pylint - rev: v3.1.0 + - --fix + - id: ruff-format + +# Ty (Experimental) +- repo: local hooks: - - id: pylint - args: - - --disable=import-error + - id: ty + name: ty check + entry: ty check . + language: system + pass_filenames: false + always_run: true diff --git a/.pylintrc b/.pylintrc deleted file mode 100644 index c2c4e48..0000000 --- a/.pylintrc +++ /dev/null @@ -1,12 +0,0 @@ -[messages control] -disable = bare-except, - duplicate-code, - broad-exception-raised, - too-few-public-methods, - too-many-arguments, - too-many-branches, - too-many-instance-attributes, - too-many-lines, - too-many-locals, - too-many-public-methods, - too-many-statements diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 92fa9be..6c80814 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,7 +7,7 @@ version: 2 build: os: ubuntu-20.04 tools: - python: "3.10" + python: "3.11" commands: - pip install --upgrade pip - pip install -r requirements.txt diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 22421dd..e251c34 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -4,7 +4,8 @@ The project uses: - - [pre-commit] to enforce linting of files prior to committing them to the repository - [Commitizen] to enforce a [Convention Commit] commit message format -- [Black] as a code formatter +- [ruff] as a code linter and formatter +- [uv] for project management You **MUST** comply with these choices in order to contribute to the project. @@ -12,31 +13,31 @@ To get started review the pre-commit utility and the conventional commit style and then set-up your local clone by following the **Installation** and **Quick Start** sections: - - pip install --upgrade pip - pip install -r build-requirements.txt - pre-commit install -t commit-msg -t pre-commit + uv venv + uv sync --group dev + uv run pre-commit install -t commit-msg -t pre-commit Now the project's rules will run on every commit, and you can check the current health of your clone with: - - pre-commit run --all-files + uv run pre-commit run --all-files ## Local Development You can build and install the package locally using the same process used by the GitHib Actions: - - pip install build - rm -rf /dist/* - python -m build --sdist --wheel --outdir dist/ - pip install dist/im-squonk2-client-*.tar.gz + rm -rf dist/* + uv build + pip install dist/im_squonk2_client-*.tar.gz And then uninstall using pip: - - pip uninstall -y im-squonk2-client + pip uninstall im-squonk2-client -y --- -[black]: https://black.readthedocs.io/en/stable +[ruff]: https://docs.astral.sh/ruff [commitizen]: https://commitizen-tools.github.io/commitizen/ [conventional commit]: https://www.conventionalcommits.org/en/v1.0.0/ [pre-commit]: https://pre-commit.com +[uv]: https://docs.astral.sh/uv/ diff --git a/build-requirements.txt b/build-requirements.txt deleted file mode 100644 index 16e9358..0000000 --- a/build-requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -black == 23.7.0 -pre-commit == 2.20.0 -pylint == 2.17.4 -pyroma == 4.2 diff --git a/docs-requirements.txt b/docs-requirements.txt deleted file mode 100644 index a5585c8..0000000 --- a/docs-requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -sphinx == 5.0.2 -sphinx-rtd-theme == 1.0.0 -sphinx-toolbox == 3.1.2 diff --git a/docs/conf.py b/docs/conf.py index 05ba83f..822b067 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -12,19 +12,18 @@ # import os import sys -sys.path.insert(0, os.path.abspath('..')) -sys.path.append(os.path.abspath( - os.path.join(os.path.dirname(__file__), "../src") -)) + +sys.path.insert(0, os.path.abspath("..")) +sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "../src"))) # -- Project information ----------------------------------------------------- -project = 'Squonk2 Python Client' -copyright = '2022, Alan Christie' -author = 'Alan Christie' +project = "Squonk2 Python Client" +copyright = "2022, Alan Christie" +author = "Alan Christie" # The full version, including alpha/beta/rc tags -release = '1.0' +release = "1.0" # -- General configuration --------------------------------------------------- @@ -32,11 +31,12 @@ # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = ['sphinx.ext.autodoc', +extensions = [ + "sphinx.ext.autodoc", ] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. @@ -49,9 +49,9 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'sphinx_rtd_theme' +html_theme = "sphinx_rtd_theme" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] \ No newline at end of file +html_static_path = ["_static"] diff --git a/examples/calc_rdkit_props.py b/examples/calc_rdkit_props.py index 6572474..3c3f56f 100755 --- a/examples/calc_rdkit_props.py +++ b/examples/calc_rdkit_props.py @@ -7,6 +7,7 @@ 'https://data-manager.xchem-dev.diamond.ac.uk/data-manager-api' or set the API URL programmatically with a call to DmApi.set_api_url(). """ + import os import sys import time @@ -89,7 +90,7 @@ # We can now use the 'task_id' to query the state of the running Job # (an instance). When we receive 'done' the Job's finished. -ITERATIONS = 0 +ITERATIONS = 0 # pylint: disable=invalid-name while True: if ITERATIONS > 10: print("TIMEOUT") diff --git a/examples/get_token.py b/examples/get_token.py index 55a8007..dc33a54 100755 --- a/examples/get_token.py +++ b/examples/get_token.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -"""Get and print a Squonk2 access token. -""" +"""Get and print a Squonk2 access token.""" + import argparse import os diff --git a/examples/units_products_and_projects.py b/examples/units_products_and_projects.py index c8a65ea..3103236 100755 --- a/examples/units_products_and_projects.py +++ b/examples/units_products_and_projects.py @@ -10,6 +10,7 @@ KEYCLOAK_TOKEN_AS ORG_ID """ + import os import sys diff --git a/pyproject.toml b/pyproject.toml index 7badb6e..70543a7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,61 @@ [build-system] -requires = ["setuptools>=60"] +requires = ["setuptools>=82"] build-backend = "setuptools.build_meta" + +[project] +name = "im-squonk2-client" +version = "0.0.0" +description = "Squonk2 Python Client" +readme = "README.rst" +keywords = ["api"] +license = "MIT" +license-files = ["LICENSE"] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Environment :: Console", + "Intended Audience :: Developers", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Topic :: System :: Installation/Setup", + "Operating System :: POSIX :: Linux", +] +authors = [ + {name = "Alan Christie", email = "achristie@informaticsmatters.com"}, +] +maintainers = [ + {name = "Alan Christie", email = "achristie@informaticsmatters.com"}, +] +requires-python = ">=3.11" +dependencies = [ + "authlib>=1.0.1,<2.0", + "munch>=4.0.0,<5.0", + "pyyaml>=5.2,<7.0", + "requests>=2.22.0", + "wrapt>=1.14.1,< 2.0", +] + +[project.urls] +Repository = "https://github.com/InformaticsMatters/squonk2-python-client.git" + +[dependency-groups] +dev = [ + "pre-commit>=4.5.1", + "pyroma>=5.0.1", + "ruff>=0.15.6", + "sphinx>=9.0.4", + "sphinx-rtd-theme>=3.1.0", + "sphinx-toolbox>=4.1.2", + "ty>=0.0.23", +] + +[tool.ruff] +exclude = [ + "examples", +] + +[tool.ty.src] +exclude = [ + "examples", +] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 4b8a869..0000000 --- a/requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -authlib >= 1.0.1, < 2.0 -munch >= 4.0.0, < 5.0 -pyyaml >= 5.2, < 7.0 -requests >= 2.22.0 -wrapt >= 1.14.1, < 2.0 diff --git a/setup.py b/setup.py deleted file mode 100755 index 5765bbc..0000000 --- a/setup.py +++ /dev/null @@ -1,48 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -"""Setup module for the Squonk2 Python Client module. -""" - -# July 2022 - -import os -import setuptools - -# Pull in the essential run-time requirements -with open("requirements.txt", "r", encoding="utf-8") as fh: - requirements = fh.read().splitlines() - -# Use the README.rst as the long description. -with open("README.rst", "r", encoding="utf-8") as fh: - long_description = fh.read() - -setuptools.setup( - name="im-squonk2-client", - version=os.environ.get("GITHUB_REF_SLUG", "1.0.0"), - author="Alan Christie", - author_email="achristie@informaticsmatters.com", - url="https://github.com/informaticsmatters/squonk2-python-client", - license="MIT", - description="Squonk2 Python Client", - long_description=long_description, - keywords="api", - platforms=["any"], - # Our modules to package - package_dir={"": "src"}, - packages=setuptools.find_packages(where="src"), - include_package_data=True, - # Project classification: - # https://pypi.python.org/pypi?%3Aaction=list_classifiers - classifiers=[ - "Development Status :: 5 - Production/Stable", - "Environment :: Other Environment", - "Intended Audience :: Developers", - "License :: OSI Approved :: MIT License", - "Programming Language :: Python :: 3.10", - "Topic :: Software Development :: Libraries :: Python Modules", - "Operating System :: POSIX :: Linux", - ], - install_requires=requirements, - python_requires=">=3", - zip_safe=False, -) diff --git a/src/squonk2/api.py b/src/squonk2/api.py index 1ce674a..2bef71d 100644 --- a/src/squonk2/api.py +++ b/src/squonk2/api.py @@ -1,5 +1,4 @@ -"""Python utilities common to UI, DM and AS. -""" +"""Python utilities common to UI, DM and AS.""" import copy from dataclasses import dataclass diff --git a/src/squonk2/auth.py b/src/squonk2/auth.py index 5a5fbb4..17aac7e 100644 --- a/src/squonk2/auth.py +++ b/src/squonk2/auth.py @@ -6,7 +6,7 @@ import json import logging from typing import Any, Dict, Optional -import urllib +from urllib import request from authlib.jose import jwt from wrapt import synchronized @@ -79,7 +79,7 @@ def get_access_token( if prior_token and Auth.__access_token_realm_url != realm_url: # New realm URL, remember and get the public key Auth.__access_token_realm_url = realm_url - with urllib.request.urlopen(realm_url) as realm_stream: + with request.urlopen(realm_url) as realm_stream: response = realm_stream.read() public_key = json.loads(response)["public_key"] assert public_key diff --git a/src/squonk2/dm_api.py b/src/squonk2/dm_api.py index 0180597..fbef06a 100644 --- a/src/squonk2/dm_api.py +++ b/src/squonk2/dm_api.py @@ -23,7 +23,6 @@ from .api import ApiRv - TEST_PRODUCT_ID: str = "product-11111111-1111-1111-1111-111111111111" """A test Account Server (AS) Product ID. This ID does not actually exist in the AS but is accepted as valid by the Data Manager for Administrative users and used for @@ -651,7 +650,8 @@ def put_unmanaged_project_files( return ret_val assert resp is not None - http_status_code = resp.status_code + assert resp.status_code + http_status_code = int(resp.status_code) if resp.status_code in [200]: existing_path_files.extend( item["file_name"] for item in resp.json()["files"] diff --git a/src/squonk2/environment.py b/src/squonk2/environment.py index 7614bef..070f8f2 100644 --- a/src/squonk2/environment.py +++ b/src/squonk2/environment.py @@ -162,7 +162,7 @@ def __init__(self, environment: Optional[str] = None): # User has named an environment, # use it self.__environment: str = environment - if not environment in Environment.__environment_names: + if environment not in Environment.__environment_names: raise Exception( f"{Environment.__environments_file} '{environment}'" " environment does not exist" diff --git a/src/squonk2/examples/data_manager/job_chain.py b/src/squonk2/examples/data_manager/job_chain.py index 1483a14..d43dc4e 100755 --- a/src/squonk2/examples/data_manager/job_chain.py +++ b/src/squonk2/examples/data_manager/job_chain.py @@ -52,6 +52,7 @@ -d https://data-manager.example.com/data-manager-api """ + import argparse from pathlib import Path import time diff --git a/src/squonk2/ui_api.py b/src/squonk2/ui_api.py index 67f0bd2..d822071 100644 --- a/src/squonk2/ui_api.py +++ b/src/squonk2/ui_api.py @@ -1,5 +1,4 @@ -"""Python utilities to simplify calls to some parts of the Data Manager UI. -""" +"""Python utilities to simplify calls to some parts of the Data Manager UI.""" import contextlib import logging @@ -14,7 +13,6 @@ from .api import ApiRv - # A common read timeout _READ_TIMEOUT_S: int = 4 diff --git a/test.py b/test.py index 9ee74f6..1295f63 100755 --- a/test.py +++ b/test.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -"""A simple developer-centric test script. -""" +"""A simple developer-centric test script.""" + import argparse import os import sys @@ -74,7 +74,7 @@ def main(): ) if not first_token: fail(f"Failed to get token from {KEYCLOAK_URL} for '{KEYCLOAK_USER}'") - sys.exit(1) + print(f"DM-API authorised as '{KEYCLOAK_USER}' ({DMAPI_URL})") # Get another token using the existing token. @@ -260,5 +260,4 @@ def main(): if __name__ == "__main__": - main() diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..ecbe07b --- /dev/null +++ b/uv.lock @@ -0,0 +1,1399 @@ +version = 1 +revision = 3 +requires-python = ">=3.11" +resolution-markers = [ + "python_full_version >= '3.13'", + "python_full_version == '3.12.*'", + "python_full_version < '3.12'", +] + +[[package]] +name = "alabaster" +version = "1.0.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/a6/f8/d9c74d0daf3f742840fd818d69cfae176fa332022fd44e3469487d5a9420/alabaster-1.0.0.tar.gz", hash = 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