From ee09c97eef8e4c2948f912dbd03eec264bfc885b Mon Sep 17 00:00:00 2001 From: Marcelo Lotif <lotif@users.noreply.github.com> Date: Thu, 29 Feb 2024 15:36:40 -0500 Subject: [PATCH] Applying latest changes on aieng-template (#6) Applying latest changes from aieng-template, which includes Ruff for python checks, pip-audit and documentation. --- .flake8 | 3 - .github/workflows/docs_build.yml | 45 + .github/workflows/docs_deploy.yml | 55 + .github/workflows/integration_tests.yaml | 61 + .github/workflows/publish.yml | 27 + .github/workflows/static_code_checks.yaml | 60 +- .github/workflows/tests.yaml | 42 - .github/workflows/unit_tests.yaml | 61 + .gitignore | 2 + .pre-commit-config.yaml | 67 +- CODE_OF_CONDUCT.md | 128 ++ CONTRIBUTING.md | 15 +- LICENSE | 21 - LICENSE.md | 201 +++ docs/Makefile | 20 + docs/make.bat | 35 + docs/source/_templates/page.html | 211 +++ docs/source/api.rst | 8 + docs/source/conf.py | 120 ++ docs/source/index.md | 68 + docs/source/reference/api/florist.bar.rst | 7 + docs/source/reference/api/florist.foo.rst | 7 + docs/source/reference/api/florist.rst | 15 + docs/source/user_guide.md | 62 + florist/__init__.py | 1 + florist/api/__init__.py | 1 + florist/api/client.py | 4 +- florist/api/index.py | 7 + florist/api/launchers/launch.py | 65 +- florist/tests/unit/api/test_client.py | 2 + florist/tests/utils/api/fl4health_utils.py | 4 +- florist/tests/utils/api/models.py | 2 +- mypy.ini | 11 - poetry.lock | 1349 +++++++++++++++++--- pyproject.toml | 150 ++- 35 files changed, 2576 insertions(+), 361 deletions(-) delete mode 100644 .flake8 create mode 100644 .github/workflows/docs_build.yml create mode 100644 .github/workflows/docs_deploy.yml create mode 100644 .github/workflows/integration_tests.yaml create mode 100644 .github/workflows/publish.yml delete mode 100644 .github/workflows/tests.yaml create mode 100644 .github/workflows/unit_tests.yaml create mode 100644 CODE_OF_CONDUCT.md delete mode 100644 LICENSE create mode 100644 LICENSE.md create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/_templates/page.html create mode 100644 docs/source/api.rst create mode 100644 docs/source/conf.py create mode 100644 docs/source/index.md create mode 100644 docs/source/reference/api/florist.bar.rst create mode 100644 docs/source/reference/api/florist.foo.rst create mode 100644 docs/source/reference/api/florist.rst create mode 100644 docs/source/user_guide.md delete mode 100644 mypy.ini diff --git a/.flake8 b/.flake8 deleted file mode 100644 index 06945f4..0000000 --- a/.flake8 +++ /dev/null @@ -1,3 +0,0 @@ -[flake8] -max-line-length = 119 -ignore = E203, W503 diff --git a/.github/workflows/docs_build.yml b/.github/workflows/docs_build.yml new file mode 100644 index 0000000..86f56c1 --- /dev/null +++ b/.github/workflows/docs_build.yml @@ -0,0 +1,45 @@ +name: docs (build) + +on: + pull_request: + branches: + - main + paths: + - .pre-commit-config.yaml + - .github/workflows/docs_build.yml + - '**.py' + - '**.ipynb' + - poetry.lock + - pyproject.toml + - '**.rst' + - '**.md' + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + - name: Install dependencies, build docs and coverage report + run: python3 -m pip install --upgrade pip && python3 -m pip install poetry + - uses: actions/setup-python@v5.0.0 + with: + python-version: '3.9' + cache: 'poetry' + - run: | + python3 -m pip install --upgrade pip && python3 -m pip install poetry + poetry env use '3.9' + source $(poetry env info --path)/bin/activate + poetry install --with docs,test + cd docs && rm -rf source/reference/api/_autosummary && make html + cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m +# - name: Upload coverage to Codecov +# uses: Wandalen/wretry.action@v1.4.4 +# with: +# action: codecov/codecov-action@v4.0.1 +# with: | +# token: ${{ secrets.CODECOV_TOKEN }} +# file: ./coverage.xml +# name: codecov-umbrella +# fail_ci_if_error: true +# attempt_limit: 5 +# attempt_delay: 30000 diff --git a/.github/workflows/docs_deploy.yml b/.github/workflows/docs_deploy.yml new file mode 100644 index 0000000..37eabc9 --- /dev/null +++ b/.github/workflows/docs_deploy.yml @@ -0,0 +1,55 @@ +name: docs + +on: + push: + branches: + - main + paths: + - .pre-commit-config.yaml + - .github/workflows/static_code_checks.yml + - .github/workflows/docs_build.yml + - .github/workflows/docs_deploy.yml + - .github/workflows/tests.yml + - '**.py' + - '**.ipynb' + - poetry.lock + - pyproject.toml + - '**.rst' + - '**.md' + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + with: + submodules: 'true' + - name: Install dependencies, build docs and coverage report + run: python3 -m pip install --upgrade pip && python3 -m pip install poetry + - uses: actions/setup-python@v5.0.0 + with: + python-version: '3.9' + cache: 'poetry' + - run: | + python3 -m pip install --upgrade pip && python3 -m pip install poetry + poetry env use '3.9' + source $(poetry env info --path)/bin/activate + poetry install --with docs,test + cd docs && rm -rf source/reference/api/_autosummary && make html + cd .. && coverage run -m pytest -m "not integration_test" && coverage xml && coverage report -m +# - name: Upload coverage to Codecov +# uses: Wandalen/wretry.action@v1.4.4 +# with: +# action: codecov/codecov-action@v4.0.1 +# with: | +# token: ${{ secrets.CODECOV_TOKEN }} +# file: ./coverage.xml +# name: codecov-umbrella +# fail_ci_if_error: true +# attempt_limit: 5 +# attempt_delay: 30000 + - name: Deploy to Github pages + uses: JamesIves/github-pages-deploy-action@v4.5.0 + with: + branch: github_pages + folder: docs/build/html diff --git a/.github/workflows/integration_tests.yaml b/.github/workflows/integration_tests.yaml new file mode 100644 index 0000000..7421d82 --- /dev/null +++ b/.github/workflows/integration_tests.yaml @@ -0,0 +1,61 @@ +name: tests + +on: + push: + branches: + - main + paths: + - .pre-commit-config.yaml + - .github/workflows/static_code_checks.yml + - .github/workflows/docs_build.yml + - .github/workflows/docs_deploy.yml + - .github/workflows/tests.yml + - '**.py' + - '**.ipynb' + - poetry.lock + - pyproject.toml + - '**.rst' + - '**.md' + pull_request: + branches: + - main + paths: + - .pre-commit-config.yaml + - .github/workflows/static_code_checks.yml + - .github/workflows/docs_build.yml + - .github/workflows/docs_deploy.yml + - .github/workflows/tests.yml + - '**.py' + - '**.ipynb' + - poetry.lock + - pyproject.toml + - '**.rst' + - '**.md' + +jobs: + python-tests: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + - name: Install poetry + run: python3 -m pip install --upgrade pip && python3 -m pip install poetry + - uses: actions/setup-python@v5.0.0 + with: + python-version: '3.9' + - name: Install dependencies and check code + run: | + poetry env use '3.9' + source $(poetry env info --path)/bin/activate + poetry install --with docs,test + coverage run -m pytest florist/tests/integration && coverage xml && coverage report -m +# - name: Upload coverage to Codecov +# uses: Wandalen/wretry.action@v1.4.4 +# with: +# action: codecov/codecov-action@v4.0.1 +# with: | +# token: ${{ secrets.CODECOV_TOKEN }} +# file: ./coverage.xml +# name: codecov-umbrella +# fail_ci_if_error: true +# attempt_limit: 5 +# attempt_delay: 30000 diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..da22deb --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,27 @@ +name: publish package + +on: + release: + types: [published] + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - name: Install apt dependencies + run: | + sudo apt-get update + sudo apt-get install libcurl4-openssl-dev libssl-dev + - uses: actions/checkout@v4.1.1 + - name: Install poetry + run: python3 -m pip install --upgrade pip && python3 -m pip install poetry + - uses: actions/setup-python@v5.0.0 + with: + python-version: '3.9' + - name: Build package + run: poetry build + - name: Publish package + uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 + with: + user: __token__ + password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/static_code_checks.yaml b/.github/workflows/static_code_checks.yaml index 4ce815c..abcbdaa 100644 --- a/.github/workflows/static_code_checks.yaml +++ b/.github/workflows/static_code_checks.yaml @@ -1,26 +1,58 @@ -# only has to pass for python 3.9 -name: Static code checks +name: code checks on: push: branches: - main + - main + paths: + - .pre-commit-config.yaml + - .github/workflows/code_checks.yml + - '**.py' + - poetry.lock + - pyproject.toml + - '**.ipynb' pull_request: branches: - main + - main + paths: + - .pre-commit-config.yaml + - .github/workflows/code_checks.yml + - '**.py' + - poetry.lock + - pyproject.toml + - '**.ipynb' jobs: run-code-check: runs-on: ubuntu-latest steps: - - - name: Checkout code - uses: actions/checkout@v3 - - - name: Set up Python 3.9 - uses: actions/setup-python@v3 + - uses: actions/checkout@v4.1.1 + - name: Install and configure Poetry + uses: snok/install-poetry@v1 with: - python-version: 3.9 - - - name: precommit checker - uses: pre-commit/action@v3.0.1 + virtualenvs-create: true + virtualenvs-in-project: true + - uses: actions/setup-python@v5.0.0 + with: + python-version: '3.9' + cache: 'poetry' + - name: Install dependencies and check code + run: | + poetry env use '3.9' + source .venv/bin/activate + poetry install --with test --all-extras + pre-commit run --all-files + - name: pip-audit (gh-action-pip-audit) + uses: pypa/gh-action-pip-audit@v1.0.8 + with: + virtual-environment: .venv/ + # Ignoring security vulnerabilities in Pillow because pycyclops cannot update it to the + # version that fixes them (>10.0.1). + # Remove those when the issue below is fixed and pycyclops changes its requirements: + # https://github.com/SeldonIO/alibi/issues/991 + ignore-vulns: | + PYSEC-2023-175 + PYSEC-2023-227 + GHSA-j7hp-h8jx-5ppr + GHSA-56pw-mpj4-fxww + GHSA-3f63-hfp8-52jq diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml deleted file mode 100644 index 442c8b6..0000000 --- a/.github/workflows/tests.yaml +++ /dev/null @@ -1,42 +0,0 @@ -# only has to pass for python 3.9 -name: PyTest Unit Tests - -on: - push: - branches: - main - pull_request: - branches: - main - -jobs: - test: - runs-on: ubuntu-latest - steps: - - name: Checkout code - uses: actions/checkout@v3 - - name: Set up Python 3.9 - uses: actions/setup-python@v3 - with: - python-version: 3.9 - # Display the Python version being used - - name: Display Python version - run: python -c "import sys; print(sys.version)" - - name: Install and configure Poetry - uses: snok/install-poetry@v1 - with: - virtualenvs-create: true - virtualenvs-in-project: true - - name: Set up cache - uses: actions/cache@v2 - id: cached-poetry-dependencies - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }} - - name: Install dependencies - run: poetry install --with "dev, test" - if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' - - name: Run Tests - run: | - source .venv/bin/activate - pytest florist/tests/* diff --git a/.github/workflows/unit_tests.yaml b/.github/workflows/unit_tests.yaml new file mode 100644 index 0000000..411861e --- /dev/null +++ b/.github/workflows/unit_tests.yaml @@ -0,0 +1,61 @@ +name: tests + +on: + push: + branches: + - main + paths: + - .pre-commit-config.yaml + - .github/workflows/static_code_checks.yml + - .github/workflows/docs_build.yml + - .github/workflows/docs_deploy.yml + - .github/workflows/tests.yml + - '**.py' + - '**.ipynb' + - poetry.lock + - pyproject.toml + - '**.rst' + - '**.md' + pull_request: + branches: + - main + paths: + - .pre-commit-config.yaml + - .github/workflows/static_code_checks.yml + - .github/workflows/docs_build.yml + - .github/workflows/docs_deploy.yml + - .github/workflows/tests.yml + - '**.py' + - '**.ipynb' + - poetry.lock + - pyproject.toml + - '**.rst' + - '**.md' + +jobs: + python-tests: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4.1.1 + - name: Install poetry + run: python3 -m pip install --upgrade pip && python3 -m pip install poetry + - uses: actions/setup-python@v5.0.0 + with: + python-version: '3.9' + - name: Install dependencies and check code + run: | + poetry env use '3.9' + source $(poetry env info --path)/bin/activate + poetry install --with docs,test + coverage run -m pytest florist/tests/unit && coverage xml && coverage report -m +# - name: Upload coverage to Codecov +# uses: Wandalen/wretry.action@v1.4.4 +# with: +# action: codecov/codecov-action@v4.0.1 +# with: | +# token: ${{ secrets.CODECOV_TOKEN }} +# file: ./coverage.xml +# name: codecov-umbrella +# fail_ci_if_error: true +# attempt_limit: 5 +# attempt_delay: 30000 diff --git a/.gitignore b/.gitignore index a56e7ee..8ae2206 100644 --- a/.gitignore +++ b/.gitignore @@ -166,3 +166,5 @@ yarn-error.log* *.tsbuildinfo next-env.d.ts /florist/tsconfig.json + +/metrics/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 88d095c..c577a37 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,45 +1,48 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 # Use the ref you want to point at + rev: v4.4.0 # Use the ref you want to point at hooks: - - id: trailing-whitespace - - id: check-ast - - id: check-builtin-literals - - id: check-docstring-first - - id: check-executables-have-shebangs - - id: debug-statements - - id: end-of-file-fixer - - id: mixed-line-ending - args: [--fix=lf] - - id: requirements-txt-fixer - - id: trailing-whitespace - - id: check-yaml + - id: trailing-whitespace + - id: check-ast + - id: check-builtin-literals + - id: check-docstring-first + - id: check-executables-have-shebangs + - id: debug-statements + - id: end-of-file-fixer + - id: mixed-line-ending + args: [--fix=lf] + - id: requirements-txt-fixer + - id: check-yaml + - id: check-toml - - repo: https://github.com/PyCQA/flake8 - rev: 7.0.0 + - repo: https://github.com/charliermarsh/ruff-pre-commit + rev: 'v0.2.2' hooks: - - id: flake8 - - - repo: https://github.com/psf/black - rev: 24.1.1 - hooks: - - id: black - - - repo: https://github.com/PyCQA/isort - rev: 5.13.2 - hooks: - - id: isort + - id: ruff + args: [--fix, --exit-non-zero-on-fix] + types_or: [python, jupyter] + - id: ruff-format + types_or: [python, jupyter] - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.8.0 hooks: - - id: mypy + - id: mypy + entry: python3 -m mypy --config-file pyproject.toml + language: system + types: [python] + exclude: "florist/tests/" - repo: https://github.com/nbQA-dev/nbQA rev: 1.7.1 hooks: - - id: nbqa-black - - id: nbqa-isort - - id: nbqa-check-ast - - id: nbqa-flake8 - - id: nbqa-mypy + - id: nbqa-ruff + args: [--fix, --exit-non-zero-on-fix] + + - repo: local + hooks: + - id: doctest + name: doctest + entry: python3 -m doctest -o NORMALIZE_WHITESPACE + files: "(^florist/api/|florist/tests/api/)" + language: system diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..4f79bf3 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +cyclops@vectorinstitute.ai. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7418b47..600941c 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -27,7 +27,7 @@ We use [Poetry](https://python-poetry.org/) to manage back-end dependencies: ```shell pip install --upgrade pip poetry -poetry install --with dev +poetry install --with test ``` We use [Yarn](https://yarnpkg.com/) to manage front-end dependencies. Install it on MacOS @@ -44,17 +44,12 @@ yarn ## Coding guidelines -For code style, we recommend the [google style guide](https://google.github.io/styleguide/pyguide.html). - -Pre-commit hooks apply the [black](https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html) -code formatting. +For code style, we recommend the [PEP 8 style guide](https://peps.python.org/pep-0008/). For docstrings we use [numpy format](https://numpydoc.readthedocs.io/en/latest/format.html). -We also use [flake8](https://flake8.pycqa.org/en/latest/) and [pylint](https://pylint.pycqa.org/en/stable/) -for further static code analysis. The pre-commit hooks show errors which you need -to fix before submitting a PR. +We use [ruff](https://docs.astral.sh/ruff/) for code formatting and static code +analysis. Ruff checks various rules including [flake8](https://docs.astral.sh/ruff/faq/#how-does-ruff-compare-to-flake8). The pre-commit hooks show errors which you need to fix before submitting a PR. Last but not the least, we use type hints in our code which is then checked using -[mypy](https://mypy.readthedocs.io/en/stable/). Currently, mypy checks are not -strict, but will be enforced more as the API code becomes more stable. +[mypy](https://mypy.readthedocs.io/en/stable/). diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 9aea952..0000000 --- a/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2022 Vector Institute - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..766ba2e --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/_templates/page.html b/docs/source/_templates/page.html new file mode 100644 index 0000000..b908ccd --- /dev/null +++ b/docs/source/_templates/page.html @@ -0,0 +1,211 @@ +{% extends "base.html" %} + +{% block body -%} +{{ super() }} +{% include "partials/icons.html" %} + +<input type="checkbox" class="sidebar-toggle" name="__navigation" id="__navigation"> +<input type="checkbox" class="sidebar-toggle" name="__toc" id="__toc"> +<label class="overlay sidebar-overlay" for="__navigation"> + <div class="visually-hidden">Hide navigation sidebar</div> +</label> +<label class="overlay toc-overlay" for="__toc"> + <div class="visually-hidden">Hide table of contents sidebar</div> +</label> + +{% if theme_announcement -%} +<div class="announcement"> + <aside class="announcement-content"> + {% block announcement %} {{ theme_announcement }} {% endblock announcement %} + </aside> +</div> +{%- endif %} + +<div class="page"> + <header class="mobile-header"> + <div class="header-left"> + <label class="nav-overlay-icon" for="__navigation"> + <div class="visually-hidden">Toggle site navigation sidebar</div> + <i class="icon"><svg><use href="#svg-menu"></use></svg></i> + </label> + </div> + <div class="header-center"> + <a href="{{ pathto(master_doc) }}"><div class="brand">{{ docstitle if docstitle else project }}</div></a> + </div> + <div class="header-right"> + <div class="theme-toggle-container theme-toggle-header"> + <button class="theme-toggle"> + <div class="visually-hidden">Toggle Light / Dark / Auto color theme</div> + <svg class="theme-icon-when-auto"><use href="#svg-sun-half"></use></svg> + <svg class="theme-icon-when-dark"><use href="#svg-moon"></use></svg> + <svg class="theme-icon-when-light"><use href="#svg-sun"></use></svg> + </button> + </div> + <label class="toc-overlay-icon toc-header-icon{% if furo_hide_toc %} no-toc{% endif %}" for="__toc"> + <div class="visually-hidden">Toggle table of contents sidebar</div> + <i class="icon"><svg><use href="#svg-toc"></use></svg></i> + </label> + </div> + </header> + <aside class="sidebar-drawer"> + <div class="sidebar-container"> + {% block left_sidebar %} + <div class="sidebar-sticky"> + {%- for sidebar_section in sidebars %} + {%- include sidebar_section %} + {%- endfor %} + </div> + {% endblock left_sidebar %} + </div> + </aside> + <div class="main"> + <div class="content"> + <div class="article-container"> + <a href="#" class="back-to-top muted-link"> + <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"> + <path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8v12z"></path> + </svg> + <span>{% trans %}Back to top{% endtrans %}</span> + </a> + <div class="content-icon-container"> + {% if theme_top_of_page_button == "edit" -%} + {%- include "components/edit-this-page.html" with context -%} + {%- elif theme_top_of_page_button != None -%} + {{ warning("Got an unsupported value for 'top_of_page_button'") }} + {%- endif -%} + {#- Theme toggle -#} + <div class="theme-toggle-container theme-toggle-content"> + <button class="theme-toggle"> + <div class="visually-hidden">Toggle Light / Dark / Auto color theme</div> + <svg class="theme-icon-when-auto"><use href="#svg-sun-half"></use></svg> + <svg class="theme-icon-when-dark"><use href="#svg-moon"></use></svg> + <svg class="theme-icon-when-light"><use href="#svg-sun"></use></svg> + </button> + </div> + <label class="toc-overlay-icon toc-content-icon{% if furo_hide_toc %} no-toc{% endif %}" for="__toc"> + <div class="visually-hidden">Toggle table of contents sidebar</div> + <i class="icon"><svg><use href="#svg-toc"></use></svg></i> + </label> + </div> + <article role="main"> + {% block content %}{{ body }}{% endblock %} + </article> + </div> + <footer> + {% block footer %} + <div class="related-pages"> + {% if next -%} + <a class="next-page" href="{{ next.link }}"> + <div class="page-info"> + <div class="context"> + <span>{{ _("Next") }}</span> + </div> + <div class="title">{{ next.title }}</div> + </div> + <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg> + </a> + {%- endif %} + {% if prev -%} + <a class="prev-page" href="{{ prev.link }}"> + <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg> + <div class="page-info"> + <div class="context"> + <span>{{ _("Previous") }}</span> + </div> + {% if prev.link == pathto(master_doc) %} + <div class="title">{{ _("Home") }}</div> + {% else %} + <div class="title">{{ prev.title }}</div> + {% endif %} + </div> + </a> + {%- endif %} + </div> + <div class="bottom-of-page"> + <div class="left-details"> + {%- if show_copyright %} + <div class="copyright"> + {%- if hasdoc('copyright') %} + {% trans path=pathto('copyright'), copyright=copyright|e -%} + <a href="{{ path }}">Copyright</a> © {{ copyright }} + {%- endtrans %} + {%- else %} + {% trans copyright=copyright|e -%} + Copyright © {{ copyright }} + {%- endtrans %} + {%- endif %} + </div> + {%- endif %} + <!-- + {% trans %}Made with {% endtrans -%} + {%- if show_sphinx -%} + {% trans %}<a href="https://www.sphinx-doc.org/">Sphinx</a> and {% endtrans -%} + <a class="muted-link" href="https://pradyunsg.me">@pradyunsg</a>'s + {% endif -%} + {% trans %} + <a href="https://github.com/pradyunsg/furo">Furo</a> + {% endtrans %} + --> + {%- if last_updated -%} + <div class="last-updated"> + {% trans last_updated=last_updated|e -%} + Last updated on {{ last_updated }} + {%- endtrans -%} + </div> + {%- endif %} + </div> + <div class="right-details"> + {% if theme_footer_icons or READTHEDOCS -%} + <div class="icons"> + {% if theme_footer_icons -%} + {% for icon_dict in theme_footer_icons -%} + <a class="muted-link {{ icon_dict.class }}" href="{{ icon_dict.url }}" aria-label="{{ icon_dict.name }}"> + {{- icon_dict.html -}} + </a> + {% endfor %} + {%- else -%} + {#- Show Read the Docs project -#} + {%- if READTHEDOCS and slug -%} + <a class="muted-link" href="https://readthedocs.org/projects/{{ slug }}" aria-label="On Read the Docs"> + <svg x="0px" y="0px" viewBox="-125 217 360 360" xml:space="preserve"> + <path fill="currentColor" d="M39.2,391.3c-4.2,0.6-7.1,4.4-6.5,8.5c0.4,3,2.6,5.5,5.5,6.3 c0,0,18.5,6.1,50,8.7c25.3,2.1,54-1.8,54-1.8c4.2-0.1,7.5-3.6,7.4-7.8c-0.1-4.2-3.6-7.5-7.8-7.4c-0.5,0-1,0.1-1.5,0.2 c0,0-28.1,3.5-50.9,1.6c-30.1-2.4-46.5-7.9-46.5-7.9C41.7,391.3,40.4,391.1,39.2,391.3z M39.2,353.6c-4.2,0.6-7.1,4.4-6.5,8.5 c0.4,3,2.6,5.5,5.5,6.3c0,0,18.5,6.1,50,8.7c25.3,2.1,54-1.8,54-1.8c4.2-0.1,7.5-3.6,7.4-7.8c-0.1-4.2-3.6-7.5-7.8-7.4 c-0.5,0-1,0.1-1.5,0.2c0,0-28.1,3.5-50.9,1.6c-30.1-2.4-46.5-7.9-46.5-7.9C41.7,353.6,40.4,353.4,39.2,353.6z M39.2,315.9 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class="toc-tree"> + {{ toc }} + </div> + </div> + </div> + {% endif %} + {% endblock right_sidebar %} + </aside> + </div> +</div> +{%- endblock %} diff --git a/docs/source/api.rst b/docs/source/api.rst new file mode 100644 index 0000000..f40c0ed --- /dev/null +++ b/docs/source/api.rst @@ -0,0 +1,8 @@ +API Reference +============= + +.. toctree:: + :maxdepth: 1 + :glob: + + reference/api/florist.rst diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..ce76fe7 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,120 @@ +"""Configuration file for the Sphinx documentation builder.""" +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import os +import sys +from typing import List + + +sys.path.insert(0, os.path.abspath("../../florist")) + + +# -- Project information ----------------------------------------------------- + +project = "FLorist" +copyright = "2024, Vector AI Engineering" # noqa: A001 +author = "Vector AI Engineering" + + +# -- General configuration --------------------------------------------------- + +# 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", + "sphinx.ext.coverage", + "sphinx.ext.doctest", + "sphinx.ext.napoleon", + "sphinx.ext.autosummary", + "sphinx_autodoc_typehints", + "sphinx.ext.intersphinx", + "numpydoc", + "sphinx.ext.viewcode", + "sphinxcontrib.apidoc", + "sphinx.ext.autosectionlabel", + "myst_parser", + "sphinx_design", + "sphinx_copybutton", +] +numpydoc_show_inherited_class_members = False +numpydoc_show_class_members = False +napoleon_google_docstring = False +napoleon_numpy_docstring = True +napoleon_include_init_with_doc = True +add_module_names = False +autosectionlabel_prefix_document = True +copybutton_prompt_text = r">>> |\.\.\. " +copybutton_prompt_is_regexp = True + +apidoc_module_dir = "../../florist" +apidoc_excluded_paths = ["florist/tests"] +apidoc_output_dir = "reference/api" +apidoc_separate_modules = True +apidoc_extra_args = ["-f", "-M", "-T", "--implicit-namespaces"] + +intersphinx_mapping = { + "python": ("https://docs.python.org/3.9/", None), +} + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns: List[str] = [] + +# -- Options for Markdown files ---------------------------------------------- +# + +myst_enable_extensions = [ + "colon_fence", + "deflist", +] +myst_heading_anchors = 2 + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "furo" +html_title = "Vector AI Engineering template repository" +html_theme_options = { + "dark_css_variables": { + "color-brand-primary": "#faad1a", + "color-brand-content": "#eb088a", + "color-foreground-secondary": "#52c7de", + }, + "footer_icons": [ + { + "name": "GitHub", + "url": "https://github.com/VectorInstitute/FLorist", + "html": """ + <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16"> + <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path> + </svg> + """, + "class": "", + }, + ], +} + + +# 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". +templates_path = ["_templates"] +html_static_path = ["_static"] +html_additional_pages = {"page": "page.html"} diff --git a/docs/source/index.md b/docs/source/index.md new file mode 100644 index 0000000..65e0c55 --- /dev/null +++ b/docs/source/index.md @@ -0,0 +1,68 @@ +--- +hide-toc: true +--- + +# FLorist + +```{toctree} +:hidden: + +user_guide +api + +``` + +# TODO: modify this when working on updating documentation + +This template repository can be used to bootstrap AI Engineering project repositories +on Github! The template is meant for python codebases since Python is the most commonly +used language by our team. + +The template includes: + +- [pyproject.toml](https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/) +file to specify repository information and manage dependencies using +[Poetry](https://python-poetry.org/). + +- [README.md](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-readmes) which should have basic information on why the project is +useful, installation instructions and other information on how users can get started. + +- [.pre-commit-config.yaml](https://pre-commit.com/) for running pre-commit hooks that +check for code-style, apply formatting, check for type hints and run tests. + +- [.github/pull_request_template.md](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/creating-a-pull-request-template-for-your-repository) for PRs. + +- [.github/ISSUE_TEMPLATE](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository) for bug reports and issues that can be raised on the repository. + +- [.github/workflows](https://docs.github.com/en/actions/using-workflows) for running CI +workflows using Github actions. The template includes CI workflows for code checks, +documentation building and releasing python packages to PyPI. + +- [LICENSE.md](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/licensing-a-repository) for adding a license to the project repository. +By default, this is the [Apache-2.0 license](http://www.apache.org/licenses/). Please +change according to your project! + +- [docs](https://pradyunsg.me/furo/) for adding project documentation. Typically +projects should have API reference documentation, user guides and tutorials. + +- [CONTRIBUTING.md](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors) with basic guidelines on how others can +contribute to the repository. + +- [CODE_OF_CONDUCT.md](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-code-of-conduct-to-your-project) with standards on how the community engages in +a healthy and constructive manner. + +- [.gitignore](https://docs.github.com/en/get-started/getting-started-with-git/ignoring-files) +with some standard file extensions to be ignored by git. Please add/modify as necessary. + +- [codecov.yml](https://docs.codecov.com/docs/codecov-yaml) for using codecov.io to +generate code coverage information for your repository. You would need to add codecov.io +app as an [integration to your repository](https://docs.codecov.com/docs/how-to-create-a-github-app-for-codecov-enterprise). + + +If you are starting a new project, you can navigate to the [Use this template](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template) button +on the top right corner of the [template repository home page](https://github.com/VectorInstitute/FLorist) +which will allow you to bootstrap your project repo using this template. + +Please check out the user guide page for more detailed information on using the +template features. For exisiting projects, the [user guide](user_guide.md) +can be followed to migrate to following the template more closely. diff --git a/docs/source/reference/api/florist.bar.rst b/docs/source/reference/api/florist.bar.rst new file mode 100644 index 0000000..0c4f012 --- /dev/null +++ b/docs/source/reference/api/florist.bar.rst @@ -0,0 +1,7 @@ +florist.bar module +========================== + +.. automodule:: florist.bar + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/reference/api/florist.foo.rst b/docs/source/reference/api/florist.foo.rst new file mode 100644 index 0000000..1cb0de4 --- /dev/null +++ b/docs/source/reference/api/florist.foo.rst @@ -0,0 +1,7 @@ +florist.foo module +========================== + +.. automodule:: florist.foo + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/reference/api/florist.rst b/docs/source/reference/api/florist.rst new file mode 100644 index 0000000..4f8f068 --- /dev/null +++ b/docs/source/reference/api/florist.rst @@ -0,0 +1,15 @@ +florist package +=============== + +.. automodule:: florist + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + florist.api diff --git a/docs/source/user_guide.md b/docs/source/user_guide.md new file mode 100644 index 0000000..bcee30e --- /dev/null +++ b/docs/source/user_guide.md @@ -0,0 +1,62 @@ +(user_guide)= + +# User Guide + +# TODO: modify this when working on updating documentation + +## pyproject.toml file and dependency management + +If your project doesn't have a pyproject.toml file, simply copy the one from the +template and update file according to your project. + +For managing dependencies, [Poetry](https://python-poetry.org/) is the recommended tool +for our team. Hence, install Poetry to setup the development virtual environment. Poetry +supports [optional dependency groups](https://python-poetry.org/docs/managing-dependencies/#optional-groups) +which help manage dependencies for different parts of development such as `documentation`, +`testing`, etc. The core dependencies are installed using the command: + +```bash +python3 -m poetry install +``` + +Additional dependency groups can be installed using the `--with` flag. For example: + +```bash +python3 -m poetry install --with docs,test +``` + +## documentation + +If your project doesn't have documentation, copy the directory named `docs` to the root +directory of your repository. The provided source files use [Furo](https://pradyunsg.me/furo/), +a clean and customisable Sphinx documentation theme. + +In order to build the documentation, install the documentation dependencies as mentioned +in the previous section, navigate to the `docs` folder and run the command: + +```bash +make html +``` + +You can configure the documentation by updating the `docs/source/conf.py`. The markdown +files in `docs/source` can be updated to reflect the project's documentation. + + +## github actions + +The template consists of some github action continuous integration workflows that you +can add to your repository. + +The available workflows are: + +- [code checks](https://github.com/VectorInstitute/FLorist/blob/main/.github/workflows/code_checks.yml): Static code analysis, code formatting and unit tests +- [documentation](https://github.com/VectorInstitute/FLorist/blob/main/.github/workflows/docs_deploy.yml): Project documentation including example API reference +- [integration tests](https://github.com/VectorInstitute/FLorist/blob/main/.github/workflows/integration_tests.yml): Integration tests +- [publish](https://github.com/VectorInstitute/FLorist/blob/main/.github/workflows/publish.yml): +Publishing python package to PyPI. Create a `PYPI_API_TOKEN` and add it to the +repository's actions [secret variables](https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions) +in order to publish PyPI packages when new software releases are created on Github. + +The test workflows also compute coverage and upload code coverage metrics to +[codecov.io](https://app.codecov.io/gh/VectorInstitute/FLorist). Create a +`CODECOV_TOKEN` and add it to the repository's actions [secret variables](https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions). diff --git a/florist/__init__.py b/florist/__init__.py index e69de29..982131f 100644 --- a/florist/__init__.py +++ b/florist/__init__.py @@ -0,0 +1 @@ +"""Root folder for FLorist source code.""" diff --git a/florist/api/__init__.py b/florist/api/__init__.py index e69de29..115aa9f 100644 --- a/florist/api/__init__.py +++ b/florist/api/__init__.py @@ -0,0 +1 @@ +"""Root folder for FLorist backend API.""" diff --git a/florist/api/client.py b/florist/api/client.py index 56d0183..6973b36 100644 --- a/florist/api/client.py +++ b/florist/api/client.py @@ -1,13 +1,15 @@ +"""FLorist client FastAPI endpoints.""" from fastapi import FastAPI from fastapi.responses import JSONResponse + app = FastAPI() @app.get("/api/client/connect") def connect() -> JSONResponse: """ - Confirms the client is up and ready to accept instructions. + Confirm the client is up and ready to accept instructions. :return: JSON `{"status": "ok"}` """ diff --git a/florist/api/index.py b/florist/api/index.py index e7ca917..656ad2f 100644 --- a/florist/api/index.py +++ b/florist/api/index.py @@ -1,8 +1,15 @@ +"""Initial sample FastAPI endpoints file.""" from fastapi import FastAPI + app = FastAPI() @app.get("/api/python") def hello_world() -> str: + """ + Provide a simple hello world endpoint. + + :return: the string `hello world` + """ return "hello world" diff --git a/florist/api/launchers/launch.py b/florist/api/launchers/launch.py index 0501882..04e8e81 100644 --- a/florist/api/launchers/launch.py +++ b/florist/api/launchers/launch.py @@ -1,3 +1,4 @@ +"""Launcher functions for clients and servers.""" import logging import sys import time @@ -13,12 +14,11 @@ def redirect_logging_from_console_to_file(log_file_path: str) -> None: """ - Function that redirects loggers outputing to console to specified file. + Redirect loggers outputting to console to specified file. Args: log_file_path (str): The path to the file to log to. """ - # Define file handler to log to and set format fh = logging.FileHandler(log_file_path) fh.setFormatter(DEFAULT_FORMATTER) @@ -27,7 +27,7 @@ def redirect_logging_from_console_to_file(log_file_path: str) -> None: # If they do, remove them (to prevent logging to the console) and add filehandler for name in logging.root.manager.loggerDict: logger = logging.getLogger(name) - if not all([isinstance(h, logging.StreamHandler) is False for h in logger.handlers]): + if not all([isinstance(h, logging.StreamHandler) is False for h in logger.handlers]): # noqa: C419 logger.handlers = [h for h in logger.handlers if not isinstance(h, logging.StreamHandler)] logger.addHandler(fh) @@ -39,7 +39,7 @@ def start_server( server_log_file_name: str, ) -> None: """ - Function to start server. Redirects logging to console, stdout and stderr to file. + Start server. Redirects logging to console, stdout and stderr to file. Args: server_constructor (Callable[FlServer]): Callable that constructs FL server. @@ -48,24 +48,23 @@ def start_server( server_log_file_name (str): The name of the server log file. """ redirect_logging_from_console_to_file(server_log_file_name) - log_file = open(server_log_file_name, "a") - # Send remaining ouput (ie print) from stdout and stderr to file - sys.stdout = log_file - sys.stderr = log_file - server = server_constructor() - fl.server.start_server( - server=server, - server_address=server_address, - config=ServerConfig(num_rounds=n_server_rounds), - ) - server.shutdown() - server.metrics_reporter.dump() - log_file.close() + with open(server_log_file_name, "a") as log_file: + # Send remaining ouput (ie print) from stdout and stderr to file + sys.stdout = log_file + sys.stderr = log_file + server = server_constructor() + fl.server.start_server( + server=server, + server_address=server_address, + config=ServerConfig(num_rounds=n_server_rounds), + ) + server.shutdown() + server.metrics_reporter.dump() def start_client(client: BasicClient, server_address: str, client_log_file_name: str) -> None: """ - Function to start client. Redirects logging to console, stdout and stderr to file. + Start client. Redirects logging to console, stdout and stderr to file. Args: client (BasicClient): BasicClient instance to launch. @@ -73,14 +72,13 @@ def start_client(client: BasicClient, server_address: str, client_log_file_name: client_log_file_name (str): The name of the client log file. """ redirect_logging_from_console_to_file(client_log_file_name) - log_file = open(client_log_file_name, "a") - # Send remaining ouput (ie print) from stdout and stderr to file - sys.stdout = log_file - sys.stderr = log_file - fl.client.start_numpy_client(server_address=server_address, client=client) - client.shutdown() - client.metrics_reporter.dump() - log_file.close() + with open(client_log_file_name, "a") as log_file: + # Send remaining ouput (ie print) from stdout and stderr to file + sys.stdout = log_file + sys.stderr = log_file + fl.client.start_numpy_client(server_address=server_address, client=client) + client.shutdown() + client.metrics_reporter.dump() def launch_server( @@ -91,7 +89,7 @@ def launch_server( seconds_to_sleep: int = 10, ) -> Process: """ - Function that spawns a process that starts FL server. + Spawn a process that starts FL server. Args: server_constructor (Callable[FlServer]): Callable that constructs FL server. @@ -100,7 +98,8 @@ def launch_server( server_log_file_name (str): The name of the log file for the server. seconds_to_sleep (int): The number of seconds to sleep before launching server. - Returns: + Returns + ------- Process: The process running the FL server. """ server_process = Process( @@ -119,7 +118,7 @@ def launch_server( def launch_client(client: BasicClient, server_address: str, client_log_file_name: str) -> None: """ - Function that spawns a process that starts FL client. + Spawn a process that starts FL client. Args: client (BasicClient): BasicClient instance to launch. @@ -139,9 +138,11 @@ def launch( client_base_log_file_name: str = "client", ) -> None: """ - Function to launch FL experiment. First launches server than subsequently clients. - Joins server process after clients are launched to block until FL is complete. - (Server is last to finish executing) + Launch an FL experiment. + + First launches server than subsequently clients. Joins server + process after clients are launched to block until FL is complete. + (Server is last to finish executing). Args: server_constructor (Callable[FlServer]): Callable that constructs FL server. diff --git a/florist/tests/unit/api/test_client.py b/florist/tests/unit/api/test_client.py index 7f7a5ea..5b0c3cc 100644 --- a/florist/tests/unit/api/test_client.py +++ b/florist/tests/unit/api/test_client.py @@ -1,9 +1,11 @@ +"""Tests for FLorist's client FastAPI endpoints.""" import json from florist.api import client def test_connect() -> None: + """Tests the client's connect endpoint.""" response = client.connect() assert response.status_code == 200 diff --git a/florist/tests/utils/api/fl4health_utils.py b/florist/tests/utils/api/fl4health_utils.py index 1fce3ed..fac9cc9 100644 --- a/florist/tests/utils/api/fl4health_utils.py +++ b/florist/tests/utils/api/fl4health_utils.py @@ -1,7 +1,6 @@ from typing import Callable, List, Tuple import torch -import torch.nn as nn from fl4health.client_managers.base_sampling_manager import SimpleClientManager from fl4health.clients.basic_client import BasicClient from fl4health.server.base_server import FlServer @@ -9,6 +8,7 @@ from flwr.common.parameter import ndarrays_to_parameters from flwr.common.typing import Config, Metrics, Parameters from flwr.server.strategy import FedAvg +from torch import nn from torch.nn.modules.loss import _Loss from torch.optim import Optimizer from torch.utils.data import DataLoader @@ -60,7 +60,7 @@ def normalize_metrics(total_examples: int, aggregated_metrics: Metrics) -> Metri # Normalize all metric values by the total count of examples seen. normalized_metrics: Metrics = {} for metric_name, metric_value in aggregated_metrics.items(): - if isinstance(metric_value, float) or isinstance(metric_value, int): + if isinstance(metric_value, (float, int)): normalized_metrics[metric_name] = metric_value / total_examples return normalized_metrics diff --git a/florist/tests/utils/api/models.py b/florist/tests/utils/api/models.py index 0f31e26..7627489 100644 --- a/florist/tests/utils/api/models.py +++ b/florist/tests/utils/api/models.py @@ -1,6 +1,6 @@ import torch -import torch.nn as nn import torch.nn.functional as F +from torch import nn class MnistNet(nn.Module): diff --git a/mypy.ini b/mypy.ini deleted file mode 100644 index 11e5fa7..0000000 --- a/mypy.ini +++ /dev/null @@ -1,11 +0,0 @@ -[mypy] -mypy_path=. -follow_imports = normal -ignore_missing_imports = True -install_types = True -pretty = True -non_interactive = True -disallow_untyped_defs = True -no_implicit_optional = True -check_untyped_defs = True -exclude = venv diff --git a/poetry.lock b/poetry.lock index 4fb786d..7d5e456 100644 --- a/poetry.lock +++ b/poetry.lock @@ -142,6 +142,17 @@ files = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] +[[package]] +name = "anyascii" +version = "0.3.2" +description = "Unicode to ASCII transliteration" +optional = false +python-versions = ">=3.3" +files = [ + {file = "anyascii-0.3.2-py3-none-any.whl", hash = "sha256:3b3beef6fc43d9036d3b0529050b0c48bfad8bc960e9e562d7223cfb94fe45d4"}, + {file = "anyascii-0.3.2.tar.gz", hash = "sha256:9d5d32ef844fe225b8bc7cba7f950534fae4da27a9bf3a6bea2cb0ea46ce4730"}, +] + [[package]] name = "anyio" version = "4.2.0" @@ -175,6 +186,17 @@ files = [ {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, ] +[[package]] +name = "appnope" +version = "0.1.4" +description = "Disable App Nap on macOS >= 10.9" +optional = false +python-versions = ">=3.6" +files = [ + {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"}, + {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"}, +] + [[package]] name = "array-api-compat" version = "1.4.1" @@ -190,6 +212,38 @@ files = [ cupy = ["cupy"] numpy = ["numpy"] +[[package]] +name = "astroid" 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[tool.poetry.dependencies] python = ">=3.9.0,<3.11" -fastapi = "0.100.1" -uvicorn = {version = "0.23.2", extras = ["standard"]} +fastapi = "^0.109.1" +uvicorn = {version = "^0.23.2", extras = ["standard"]} fl4health = "^0.1.11" wandb = "^0.16.3" torchvision = "0.14.1" -[tool.poetry.group.dev.dependencies] -black = "^24.1.1" -flake8 = "^7.0.0" -isort = "^5.13.2" -mypy = "^1.8.0" -pre-commit = "^3.6.0" -toml = "^0.10.2" -types-requests = "^2.31.0.20240125" -types-setuptools = "^69.0.0.20240125" - +[tool.poetry.group.test] +optional = true [tool.poetry.group.test.dependencies] -pytest = "^8.0.0" -pytest-cov = "^4.1.0" +pytest = "^7.1.1" +pre-commit = "^2.17.0" +pytest-cov = "^3.0.0" +codecov = "^2.1.13" +mypy = "^1.7.0" +ruff = "^0.2.0" +pip-audit = "^2.7.1" +nbqa = {extras = ["toolchain"], version = "^1.7.1"} -[build-system] -requires = ["setuptools", "wheel"] -build-backend = "setuptools.build_meta" +[tool.poetry.group.docs] +optional = true -[tool.isort] -multi_line_output = 10 -skip_gitignore = true -use_parentheses = true -profile = "black" - -[tool.black] -line-length = 119 +[tool.poetry.group.docs.dependencies] +numpydoc = "^1.2" +sphinx = "^7.2.5" +sphinxcontrib-apidoc = "^0.4.0" +sphinx-autodoc-typehints = "^1.24.0" +myst-parser = "^2.0.0" +sphinx-design = "^0.5.0" +sphinx-copybutton = "^0.5.0" +sphinx-autoapi = "^2.0.0" +nbsphinx = "^0.9.3" +ipython = "^8.8.0" +ipykernel = "^6.23.0" +furo = "^2024.01.29" [tool.mypy] ignore_missing_imports = true install_types = true pretty = true +namespace_packages = true +explicit_package_bases = true non_interactive = true +warn_unused_configs = true +allow_any_generics = false +allow_subclassing_any = false +allow_untyped_calls = false +allow_untyped_defs = false +allow_incomplete_defs = false +check_untyped_defs = true +allow_untyped_decorators = false +warn_redundant_casts = true +warn_unused_ignores = true +warn_return_any = true +implicit_reexport = false +strict_equality = true +extra_checks = true +disallow_untyped_defs = true +no_implicit_optional = true +exclude = "venv" +mypy_path = "." +follow_imports = "normal" + +[tool.ruff] +include = ["*.py", "pyproject.toml", "*.ipynb"] +exclude = ["florist/tests"] +line-length = 119 + +[tool.ruff.format] +quote-style = "double" +indent-style = "space" +docstring-code-format = true + +[tool.ruff.lint] +select = [ + "A", # flake8-builtins + "B", # flake8-bugbear + "COM", # flake8-commas + "C4", # flake8-comprehensions + "RET", # flake8-return + "SIM", # flake8-simplify + "ICN", # flake8-import-conventions + "Q", # flake8-quotes + "RSE", # flake8-raise + "D", # pydocstyle + "E", # pycodestyle + "F", # pyflakes + "I", # isort + "W", # pycodestyle + "N", # pep8-naming + "ERA", # eradicate + "PL", # pylint +] +fixable = ["A", "B", "COM", "C4", "RET", "SIM", "ICN", "Q", "RSE", "D", "E", "F", "I", "W", "N", "ERA", "PL"] +ignore = [ + "B905", # `zip()` without an explicit `strict=` parameter + "E501", # line too long + "D203", # 1 blank line required before class docstring + "D213", # Multi-line docstring summary should start at the second line + "PLR2004", # Replace magic number with named constant + "PLR0913", # Too many arguments + "COM812", # Missing trailing comma +] + +# Ignore import violations in all `__init__.py` files. +[tool.ruff.lint.per-file-ignores] +"__init__.py" = ["E402", "F401", "F403", "F811"] + +[tool.ruff.lint.pep8-naming] +ignore-names = ["X*", "setUp"] + +[tool.ruff.lint.isort] +lines-after-imports = 2 + +[tool.ruff.lint.pydocstyle] +convention = "numpy" + +[tool.ruff.lint.pycodestyle] +max-doc-length = 119 + +[tool.pytest.ini_options] +markers = [ + "integration_test: marks tests as integration tests", +] + +[tool.coverage] + [tool.coverage.run] + source=["florist"] + omit=["florist/tests/*", "*__init__.py"] + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api"