diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 00000000..f40ac81c --- /dev/null +++ b/.dockerignore @@ -0,0 +1,39 @@ +# Git +.git +.gitignore +.github + +# Docker +.dockerignore + +# IDE +.idea +.vscode + +# Byte-compiled / optimized / DLL files +__pycache__/ +**/__pycache__/ +*.pyc +*.pyo +*.pyd +.Python +*.py[cod] +*$py.class +.pytest_cache/ +..mypy_cache/ + +# poetry +.venv +venv + +# C extensions +*.so + +# Virtual environment +.venv +venv + +.DS_Store +.AppleDouble +.LSOverride +._* diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 00000000..7f578f15 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,24 @@ +# Check http://editorconfig.org for more information +# This is the main config file for this project: +root = true + +[*] +charset = utf-8 +end_of_line = lf +insert_final_newline = true +indent_style = space +indent_size = 2 +trim_trailing_whitespace = true + +[*.{py, pyi}] +indent_style = space +indent_size = 4 + +[Makefile] +indent_style = tab + +[*.md] +trim_trailing_whitespace = false + +[*.{diff,patch}] +trim_trailing_whitespace = false diff --git a/.github/.stale.yml b/.github/.stale.yml new file mode 100644 index 00000000..dc90e5a1 --- /dev/null +++ b/.github/.stale.yml @@ -0,0 +1,17 @@ +# Number of days of inactivity before an issue becomes stale +daysUntilStale: 60 +# Number of days of inactivity before a stale issue is closed +daysUntilClose: 7 +# Issues with these labels will never be considered stale +exemptLabels: + - pinned + - security +# Label to use when marking an issue as stale +staleLabel: wontfix +# Comment to post when marking an issue as stale. Set to `false` to disable +markComment: > + This issue has been automatically marked as stale because it has not had + recent activity. It will be closed if no further activity occurs. Thank you + for your contributions. +# Comment to post when closing a stale issue. Set to `false` to disable +closeComment: false diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md deleted file mode 100644 index a07ba11e..00000000 --- a/.github/ISSUE_TEMPLATE.md +++ /dev/null @@ -1,26 +0,0 @@ -## Description - -Please provide a clear and concise description of the issue. - -## Steps to Reproduce - -1. Go to '...' -2. Click on '....' -3. Scroll down to '....' -4. See error - -## Expected Outcome - -A clear and concise description of what you expected to happen. - -## Actual Outcome - -A clear and concise description of what actually happened. - -## Screenshots - -If applicable, add screenshots to help explain your problem. - -## Additional Information - -Please add any other additional information that might be useful diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 00000000..bdd76779 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,42 @@ +--- +name: πŸ› Bug report +about: If something isn't working πŸ”§ +title: '' +labels: bug +assignees: +--- + +## πŸ› Bug Report + + + +## πŸ”¬ How To Reproduce + +Steps to reproduce the behavior: + +1. ... + +### Code sample + + + +### Environment + +* OS: [e.g. Linux / Windows / macOS] +* Python version, get it with: + +```bash +python --version +``` + +### Screenshots + + + +## πŸ“ˆ Expected behavior + + + +## πŸ“Ž Additional context + + diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 00000000..8f2da548 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,3 @@ +# Configuration: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository + +blank_issues_enabled: false diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 00000000..c387120f --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,23 @@ +--- +name: πŸš€ Feature request +about: Suggest an idea for this project πŸ– +title: '' +labels: enhancement +assignees: +--- + +## πŸš€ Feature Request + + + +## πŸ”ˆ Motivation + + + +## πŸ›° Alternatives + + + +## πŸ“Ž Additional context + + diff --git a/.github/ISSUE_TEMPLATE/question.md b/.github/ISSUE_TEMPLATE/question.md new file mode 100644 index 00000000..13f746bd --- /dev/null +++ b/.github/ISSUE_TEMPLATE/question.md @@ -0,0 +1,25 @@ +--- +name: ❓ Question +about: Ask a question about this project πŸŽ“ +title: '' +labels: question +assignees: +--- + +## Checklist + + + +- [ ] I've searched the project's [`issues`](https://github.com/lighter/lighter/issues?q=is%3Aissue). + +## ❓ Question + + + +How can I [...]? + +Is it possible to [...]? + +## πŸ“Ž Additional context + + diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 00000000..cb61c3db --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,28 @@ +## Description + + + +## Related Issue + + + +## Type of Change + + + +- [ ] πŸ“š Examples / docs / tutorials / dependencies update +- [ ] πŸ”§ Bug fix (non-breaking change which fixes an issue) +- [ ] πŸ₯‚ Improvement (non-breaking change which improves an existing feature) +- [ ] πŸš€ New feature (non-breaking change which adds functionality) +- [ ] πŸ’₯ Breaking change (fix or feature that would cause existing functionality to change) +- [ ] πŸ” Security fix + +## Checklist + + + +- [ ] I've read the [`CODE_OF_CONDUCT.md`](https://github.com/lighter/lighter/blob/master/CODE_OF_CONDUCT.md) document. +- [ ] I've read the [`CONTRIBUTING.md`](https://github.com/lighter/lighter/blob/master/CONTRIBUTING.md) guide. +- [ ] I've updated the code style using `make codestyle`. +- [ ] I've written tests for all new methods and classes that I created. +- [ ] I've written the docstring in Google format for all the methods and classes that I used. diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..f6c346e1 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,35 @@ +# Configuration: https://dependabot.com/docs/config-file/ +# Docs: https://docs.github.com/en/github/administering-a-repository/keeping-your-dependencies-updated-automatically + +version: 2 + +updates: + - package-ecosystem: "pip" + directory: "/" + schedule: + interval: "daily" + allow: + - dependency-type: "all" + commit-message: + prefix: ":arrow_up:" + open-pull-requests-limit: 50 + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "daily" + allow: + - dependency-type: "all" + commit-message: + prefix: ":arrow_up:" + open-pull-requests-limit: 50 + + - package-ecosystem: "docker" + directory: "/docker" + schedule: + interval: "weekly" + allow: + - dependency-type: "all" + commit-message: + prefix: ":arrow_up:" + open-pull-requests-limit: 50 diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml new file mode 100644 index 00000000..0ce0984f --- /dev/null +++ b/.github/release-drafter.yml @@ -0,0 +1,28 @@ +# Release drafter configuration https://github.com/release-drafter/release-drafter#configuration +# Emojis were chosen to match the https://gitmoji.carloscuesta.me/ + +name-template: "v$NEXT_PATCH_VERSION" +tag-template: "v$NEXT_PATCH_VERSION" + +categories: + - title: ":rocket: Features" + labels: [enhancement, feature] + - title: ":wrench: Fixes & Refactoring" + labels: [bug, refactoring, bugfix, fix] + - title: ":package: Build System & CI/CD" + labels: [build, ci, testing] + - title: ":boom: Breaking Changes" + labels: [breaking] + - title: ":pencil: Documentation" + labels: [documentation] + - title: ":arrow_up: Dependencies updates" + labels: [dependencies] + +template: | + ## What’s Changed + + $CHANGES + + ## :busts_in_silhouette: List of contributors + + $CONTRIBUTORS diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 00000000..daca0619 --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,42 @@ +name: Lighter CI + +on: [push, pull_request] + +jobs: + build: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.8", "3.9", "3.10"] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2.2.2 + with: + python-version: ${{ matrix.python-version }} + + - name: Install poetry + run: make poetry-download + + - name: Set up cache + uses: actions/cache@v2.1.6 + with: + path: .venv + key: venv-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }} + - name: Install dependencies + run: | + poetry config virtualenvs.in-project true + poetry install + + - name: Run style checks + run: | + make check-codestyle + + - name: Run tests + run: | + make test + + - name: Run safety checks + run: | + make check-safety diff --git a/.github/workflows/greetings.yml b/.github/workflows/greetings.yml new file mode 100644 index 00000000..955d5c30 --- /dev/null +++ b/.github/workflows/greetings.yml @@ -0,0 +1,16 @@ +name: Greetings + +on: [pull_request, issues] + +jobs: + greeting: + runs-on: ubuntu-latest + steps: + - uses: actions/first-interaction@v1 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + pr-message: 'Hello @${{ github.actor }}, thank you for submitting a PR! We will respond as soon as possible.' + issue-message: | + Hello @${{ github.actor }}, thank you for your interest in our work! + + If this is a bug report, please provide screenshots and **minimum viable code to reproduce your issue** diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml new file mode 100644 index 00000000..f55b27f1 --- /dev/null +++ b/.github/workflows/release-drafter.yml @@ -0,0 +1,16 @@ +name: Release Drafter + +on: + push: + # branches to consider in the event; optional, defaults to all + branches: + - master + +jobs: + update_release_draft: + runs-on: ubuntu-latest + steps: + # Drafts your next Release notes as Pull Requests are merged into "master" + - uses: release-drafter/release-drafter@v5.15.0 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..a7745cee --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,33 @@ +default_stages: [commit, push] + +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v2.5.0 + hooks: + - id: check-yaml + - id: end-of-file-fixer + exclude: LICENSE + + - repo: local + hooks: + - id: pyupgrade + name: pyupgrade + entry: poetry run pyupgrade + types: [python] + language: system + + - repo: local + hooks: + - id: isort + name: isort + entry: poetry run isort --settings-path pyproject.toml + types: [python] + language: system + + - repo: local + hooks: + - id: black + name: black + entry: poetry run black --config pyproject.toml + types: [python] + language: system diff --git a/.safety-policy.yml b/.safety-policy.yml new file mode 100644 index 00000000..facc5cc3 --- /dev/null +++ b/.safety-policy.yml @@ -0,0 +1,81 @@ +# Safety Security and License Configuration file +# We recommend checking this file into your source control in the root of your Python project +# If this file is named .safety-policy.yml and is in the same directory where you run `safety check` it will be used by default. +# Otherwise, you can use the flag `safety check --policy-file ` to specify a custom location and name for the file. +# To validate and review your policy file, run the validate command: `safety validate policy_file --path ` +security: # configuration for the `safety check` command + ignore-cvss-severity-below: 4 # A severity number between 0 and 10. Some helpful reference points: 9=ignore all vulnerabilities except CRITICAL severity. 7=ignore all vulnerabilities except CRITICAL & HIGH severity. 4=ignore all vulnerabilities except CRITICAL, HIGH & MEDIUM severity. + ignore-cvss-unknown-severity: False # True or False. We recommend you set this to False. + ignore-vulnerabilities: # Here you can list multiple specific vulnerabilities you want to ignore (optionally for a time period) + # We recommend making use of the optional `reason` and `expires` keys for each vulnerability that you ignore. + 51457: # Example vulnerability ID + reason: 'This is a dependency of pytest-htnk, look here for more info:https://github.com/pytest-dev/pytest-html/issues/350' # optional, for internal note purposes to communicate with your team. This reason will be reported in the Safety reports + expires: '2023-12-31' # datetime string - date this ignore will expire, best practice to use this variable + continue-on-vulnerability-error: False # Suppress non-zero exit codes when vulnerabilities are found. Enable this in pipelines and CI/CD processes if you want to pass builds that have vulnerabilities. We recommend you set this to False. +alert: # configuration for the `safety alert` command + security: + # Configuration specific to Safety's GitHub Issue alerting + github-issue: + # Same as for security - these allow controlling if this alert will fire based + # on severity information. + # default: not set + # ignore-cvss-severity-below: 6 + # ignore-cvss-unknown-severity: False + + # Add a label to pull requests with the cvss severity, if available + # default: true + # label-severity: True + + # Add a label to pull requests, default is 'security' + # requires private repo permissions, even on public repos + # default: security + # labels: + # - security + + # Assign users to pull requests, default is not set + # requires private repo permissions, even on public repos + # default: empty + # assignees: + # - example-user + + # Prefix to give issues when creating them. Note that changing + # this might cause duplicate issues to be created. + # default: "[PyUp] " + # issue-prefix: "[PyUp] " + + # Configuration specific to Safety's GitHub PR alerting + github-pr: + # Same as for security - these allow controlling if this alert will fire based + # on severity information. + # default: not set + # ignore-cvss-severity-below: 6 + # ignore-cvss-unknown-severity: False + + # Set the default branch (ie, main, master) + # default: empty, the default branch on GitHub + branch: '' + + # Add a label to pull requests with the cvss severity, if available + # default: true + # label-severity: True + + # Add a label to pull requests, default is 'security' + # requires private repo permissions, even on public repos + # default: security + # labels: + # - security + + # Assign users to pull requests, default is not set + # requires private repo permissions, even on public repos + # default: empty + # assignees: + # - example-user + + # Configure the branch prefix for PRs created by this alert. + # NB: Changing this will likely cause duplicate PRs. + # default: pyup/ + branch-prefix: pyup/ + + # Set a global prefix for PRs + # default: "[PyUp] " + pr-prefix: "[PyUp] " diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..5598af04 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,76 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, 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. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or + advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers 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, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an appointed +representative at an online or offline event. Representation of a project may be +further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at ibrahimhadzic45@gmail.com. All +complaints will be reviewed and investigated and will result in a response that +is deemed necessary and appropriate to the circumstances. The project team is +obligated to maintain confidentiality with regard to the reporter of an incident. +Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, +available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see +https://www.contributor-covenant.org/faq diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..a2325bfe --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,47 @@ +# How to contribute + +## Dependencies + +We use `poetry` to manage the [dependencies](https://github.com/python-poetry/poetry). +If you dont have `poetry`, you should install with `make poetry-download`. + +To install dependencies and prepare [`pre-commit`](https://pre-commit.com/) hooks you would need to run `install` command: + +```bash +make install +make pre-commit-install +``` + +To activate your `virtualenv` run `poetry shell`. + +## Codestyle + +After installation you may execute code formatting. + +```bash +make codestyle +``` + +### Checks + +Many checks are configured for this project. Command `make check-codestyle` will check black and isort. +The `make check-safety` command will look at the security of your code. + +Comand `make lint` applies all checks. + +### Before submitting + +Before submitting your code please do the following steps: + +1. Add any changes you want +1. Add tests for the new changes +1. Edit documentation if you have changed something significant +1. Run `make codestyle` to format your changes. +1. Run `make lint` to ensure that types, security and docstrings are okay. + +## Other help + +You can contribute by spreading a word about this library. +It would also be a huge contribution to write +a short article on how you are using this project. +You can also share your best practices with us. diff --git a/LICENSE b/LICENSE index 74b8aba3..d9ee9431 100644 --- a/LICENSE +++ b/LICENSE @@ -1,29 +1,20 @@ -BSD 3-Clause License +The MIT License (MIT) +Copyright (c) 2023 project-lighter -Copyright (c) 2021, Ibrahim Hadzic -All rights reserved. +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: -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. -1. Redistributions of source code must retain the above copyright notice, this - list of conditions and the following disclaimer. - -2. Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - -3. Neither the name of the copyright holder nor the names of its - contributors may be used to endorse or promote products derived from - this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +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. \ No newline at end of file diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..7e252fe3 --- /dev/null +++ b/Makefile @@ -0,0 +1,123 @@ +#* Variables +SHELL := /usr/bin/env bash +PYTHON := python +PYTHONPATH := `pwd` +#* Docker variables +IMAGE := lighter +VERSION := latest + + +#* Poetry + +#* Fix for issue with poetry +.PHONY: setup +setup: poetry-download + @echo export PYTHON_KEYRING_BACKEND=keyring.backends.null.Keyring >> ~/.bashrc + @echo export PYTHON_KEYRING_BACKEND=keyring.backends.null.Keyring >> ~/.profile + source ~/.bashrc + source ~/.profile + poetry self add poetry-bumpversion + + +.PHONY: poetry-download +poetry-download: + curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) - + +.PHONY: poetry-remove +poetry-remove: + curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) - --uninstall + +#* Installation +.PHONY: install +install: + export + poetry install -n + +.PHONY: pre-commit-install +pre-commit-install: + poetry run pre-commit install + +#* Formatters +.PHONY: codestyle +codestyle: + poetry run pyupgrade --exit-zero-even-if-changed --py37-plus **/*.py + poetry run isort --settings-path pyproject.toml ./ + poetry run black --config pyproject.toml ./ + +.PHONY: formatting +formatting: codestyle + +#* Linting +.PHONY: test +test: + PYTHONPATH=$(PYTHONPATH) poetry run pytest -c pyproject.toml --cov-report=html --cov=lighter tests/ + poetry run coverage-badge -o assets/images/coverage.svg -f + +.PHONY: check-codestyle +check-codestyle: + poetry run isort --diff --check-only --settings-path pyproject.toml ./ + poetry run black --diff --check --config pyproject.toml ./ + poetry run pylint lighter + +.PHONY: mypy +mypy: + poetry run mypy --config-file pyproject.toml ./ + +.PHONY: check-safety +check-safety: + poetry check + poetry run safety check --full-report + poetry run bandit -ll --recursive lighter tests + +.PHONY: lint +lint: test check-codestyle mypy check-safety + +.PHONY: update-dev-deps +update-dev-deps: + poetry add -G dev bandit@latest "isort[colors]@latest" mypy@latest pre-commit@latest pydocstyle@latest pylint@latest pytest@latest pyupgrade@latest safety@latest coverage@latest coverage-badge@latest pytest-html@latest pytest-cov@latest + poetry add -G dev --allow-prereleases black@latest + +#* Docker +# Example: make docker-build VERSION=latest +# Example: make docker-build IMAGE=some_name VERSION=0.0.1 +.PHONY: docker-build +docker-build: + @echo Building docker $(IMAGE):$(VERSION) ... + docker build \ + -t $(IMAGE):$(VERSION) . \ + -f ./docker/Dockerfile --no-cache + +# Example: make docker-remove VERSION=latest +# Example: make docker-remove IMAGE=some_name VERSION=0.0.1 +.PHONY: docker-remove +docker-remove: + @echo Removing docker $(IMAGE):$(VERSION) ... + docker rmi -f $(IMAGE):$(VERSION) + +#* Cleaning +.PHONY: pycache-remove +pycache-remove: + find . | grep -E "(__pycache__|\.pyc|\.pyo$$)" | xargs rm -rf + +.PHONY: dsstore-remove +dsstore-remove: + find . | grep -E ".DS_Store" | xargs rm -rf + +.PHONY: mypycache-remove +mypycache-remove: + find . | grep -E ".mypy_cache" | xargs rm -rf + +.PHONY: ipynbcheckpoints-remove +ipynbcheckpoints-remove: + find . | grep -E ".ipynb_checkpoints" | xargs rm -rf + +.PHONY: pytestcache-remove +pytestcache-remove: + find . | grep -E ".pytest_cache" | xargs rm -rf + +.PHONY: build-remove +build-remove: + rm -rf build/ + +.PHONY: cleanup +cleanup: pycache-remove dsstore-remove mypycache-remove ipynbcheckpoints-remove pytestcache-remove diff --git a/README.md b/README.md index 9e5e2ba0..d62edb1c 100644 --- a/README.md +++ b/README.md @@ -1 +1,17 @@ # Lighter +[![build](https://github.com/project-lighter/lighter/actions/workflows/build.yml/badge.svg?branch=main)](https://github.com/project-lighter/lighter/actions/workflows/build.yml) ![Coverage](./assets/images/coverage.svg) + + +## Setup + +Run the following commands to develop with the repository and add the package in develop mode to your environment + +```` +make setup +make install +```` + +To setup the pre-commit hook to format code before commit, +```` +make pre-commit-install +```` diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 00000000..0db2edd0 --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,27 @@ +# Security + +## πŸ” Reporting Security Issues + +> Do not open issues that might have security implications! +> It is critical that security related issues are reported privately so we have time to address them before they become public knowledge. + +Vulnerabilities can be reported by emailing core members: + +- project-lighter [ibrahimhadzic45@gmail.com](mailto:ibrahimhadzic45@gmail.com), [surajballambat@gmail.com](mailto:surajballambat@gmail.com) + +Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue: + +- Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.) +- Full paths of source file(s) related to the manifestation of the issue +- The location of the affected source code (tag/branch/commit or direct URL) +- Any special configuration required to reproduce the issue +- Environment (e.g. Linux / Windows / macOS) +- Step-by-step instructions to reproduce the issue +- Proof-of-concept or exploit code (if possible) +- Impact of the issue, including how an attacker might exploit the issue + +This information will help us triage your report more quickly. + +## Preferred Languages + +We prefer all communications to be in English. diff --git a/assets/images/coverage.svg b/assets/images/coverage.svg new file mode 100644 index 00000000..a9d4cc45 --- /dev/null +++ b/assets/images/coverage.svg @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + coverage + coverage + 32% + 32% + + diff --git a/docker/Dockerfile b/docker/Dockerfile new file mode 100644 index 00000000..05746468 --- /dev/null +++ b/docker/Dockerfile @@ -0,0 +1,25 @@ +FROM python:3.8-slim-buster + +ENV LANG=C.UTF-8 \ + LC_ALL=C.UTF-8 \ + PATH="${PATH}:/root/.poetry/bin" + +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + curl \ + && rm -rf /var/lib/apt/lists/* + +COPY pyproject.toml ./ + +# Install Poetry +RUN curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | POETRY_HOME=/opt/poetry python && \ + cd /usr/local/bin && \ + ln -s /opt/poetry/bin/poetry && \ + poetry config virtualenvs.create false + +# Allow installing dev dependencies to run tests +ARG INSTALL_DEV=false +RUN bash -c "if [ $INSTALL_DEV == 'true' ] ; then poetry install --no-root ; else poetry install --no-root --no-dev ; fi" + +CMD mkdir -p /workspace +WORKDIR /workspace diff --git a/docker/README.md b/docker/README.md new file mode 100644 index 00000000..dab70c6e --- /dev/null +++ b/docker/README.md @@ -0,0 +1,47 @@ +# Docker for lighter + +## Installation + +To create Docker you need to run: + +```bash +make docker-build +``` + +which is equivalent to: + +```bash +make docker-build VERSION=latest +``` + +You may provide name and version for the image. +Default name is `IMAGE := lighter`. +Default version is `VERSION := latest`. + +```bash +make docker-build IMAGE=some_name VERSION=0.0.1 +``` + +## Usage + +```bash +docker run -it --rm \ + -v $(pwd):/workspace \ + lighter bash +``` + +## How to clean up + +To uninstall docker image run `make docker-remove` with `VERSION`: + +```bash +make docker-remove VERSION=0.0.1 +``` + +you may also choose the image name + +```bash +make docker-remove IMAGE=some_name VERSION=latest +``` + +If you want to clean all, including `build` and `pycache` run `make cleanup` diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index 9e132142..00000000 --- a/docs/index.md +++ /dev/null @@ -1 +0,0 @@ -# lighter \ No newline at end of file diff --git a/docs/installation.md b/docs/installation.md deleted file mode 100644 index dd8a0145..00000000 --- a/docs/installation.md +++ /dev/null @@ -1,7 +0,0 @@ -# Installation - -``` -git clone https://github.com/ibro45/lighter -cd lighter -pip install -e . # flag -e (editable) -``` \ No newline at end of file diff --git a/lighter/__init__.py b/lighter/__init__.py index 1878c8bd..ea91c118 100644 --- a/lighter/__init__.py +++ b/lighter/__init__.py @@ -1 +1,2 @@ -from .system import LighterSystem +__version__ = "0.0.1" +from .system import LighterSystem diff --git a/lighter/callbacks/logger.py b/lighter/callbacks/logger.py index dc4240db..7d1e4718 100644 --- a/lighter/callbacks/logger.py +++ b/lighter/callbacks/logger.py @@ -1,8 +1,9 @@ +from typing import Any, Dict, List, Optional, Tuple, Union + import re import sys from datetime import datetime from pathlib import Path -from typing import Any, Dict, List, Tuple, Union, Optional import torch import torch.distributed as dist @@ -18,11 +19,19 @@ LIGHTNING_TO_LIGHTER_STAGE = {"train": "train", "validate": "val", "test": "test"} OPTIONAL_IMPORTS = {} -class LighterLogger(Callback): - - def __init__(self, project, log_dir, tensorboard=False, wandb=False, - input_type=None, target_type=None, pred_type=None, max_samples=None) -> None: +class LighterLogger(Callback): + def __init__( + self, + project, + log_dir, + tensorboard=False, + wandb=False, + input_type=None, + target_type=None, + pred_type=None, + max_samples=None, + ) -> None: self.project = project # Only used on rank 0, the dir is created in setup(). self.log_dir = Path(log_dir) / project / datetime.now().strftime("%Y%m%d_%H%M%S") @@ -142,7 +151,7 @@ def _log(self, outputs: dict, mode: str, global_step: int, is_epoch=False) -> No name = name if identifier is None else f"{name}_{identifier}" # Slice to `max_samples` only if it less than the batch size. if self.max_samples is not None and self.max_samples < image.shape[0]: - image = image[:self.max_samples] + image = image[: self.max_samples] # Preprocess a batch of images into a single, loggable, image. image = preprocess_image(image) self._log_image(name, image, global_step) @@ -231,7 +240,7 @@ def _on_epoch_end(self, trainer: Trainer, pl_module: LighterSystem) -> None: # Divide the accumulated loss by the number of steps in the epoch. loss /= self.epoch_step_counter[mode] outputs["loss"] = loss - + # Metrics # Get the torchmetrics. metrics = getattr(pl_module, f"{mode}_metrics") @@ -258,7 +267,7 @@ def _get_global_step(self, trainer: Trainer) -> int: """ mode = LIGHTNING_TO_LIGHTER_STAGE[trainer.state.stage] # When validating in Trainer.fit(), return the train steps instead of the - # val steps to correctly + # val steps to correctly if mode == "val" and trainer.state.fn == "fit": return self.global_step_counter["train"] return self.global_step_counter[mode] @@ -273,16 +282,17 @@ def on_validation_epoch_start(self, trainer: Trainer, pl_module: LighterSystem) self.loss["val"] = 0 self.epoch_step_counter["val"] = 0 - def on_train_batch_end(self, trainer: Trainer, pl_module: LighterSystem, outputs: Any, - batch: Any, batch_idx: int) -> None: + def on_train_batch_end(self, trainer: Trainer, pl_module: LighterSystem, outputs: Any, batch: Any, batch_idx: int) -> None: self._on_batch_end(outputs, trainer) - def on_validation_batch_end(self, trainer: Trainer, pl_module: LighterSystem, outputs: Any, - batch: Any, batch_idx: int, dataloader_idx: int) -> None: + def on_validation_batch_end( + self, trainer: Trainer, pl_module: LighterSystem, outputs: Any, batch: Any, batch_idx: int, dataloader_idx: int + ) -> None: self._on_batch_end(outputs, trainer) - def on_test_batch_end(self, trainer: Trainer, pl_module: LighterSystem, outputs: Any, - batch: Any, batch_idx: int, dataloader_idx: int) -> None: + def on_test_batch_end( + self, trainer: Trainer, pl_module: LighterSystem, outputs: Any, batch: Any, batch_idx: int, dataloader_idx: int + ) -> None: self._on_batch_end(outputs, trainer) def on_train_epoch_end(self, trainer: Trainer, pl_module: LighterSystem) -> None: @@ -330,7 +340,7 @@ def check_image_data_type(data: Any, name: str) -> None: Args: data (Any): image data to check - name (str): name of the image data, for logging purposes. + name (str): name of the image data, for logging purposes. """ if isinstance(data, dict): is_valid = all(check_image_data_type(elem) for elem in data.values()) @@ -340,15 +350,19 @@ def check_image_data_type(data: Any, name: str) -> None: is_valid = True else: is_valid = False - + if not is_valid: - logger.error(f"`{name}` has to be a Tensor, List[Tensors], Dict[str, Tensor]" - f", or Dict[str, List[Tensor]]. `{type(data)}` is not supported.") + logger.error( + f"`{name}` has to be a Tensor, List[Tensors], Dict[str, Tensor]" + f", or Dict[str, List[Tensor]]. `{type(data)}` is not supported." + ) sys.exit() -def parse_image_data(data: Union[Dict[str, torch.Tensor], Dict[str, List[torch.Tensor]], List[torch.Tensor], torch.Tensor]) -> List[Tuple[Optional[str], torch.Tensor]]: - """Given input data, this function will parse it and return a list of tuples where +def parse_image_data( + data: Union[Dict[str, torch.Tensor], Dict[str, List[torch.Tensor]], List[torch.Tensor], torch.Tensor] +) -> List[Tuple[Optional[str], torch.Tensor]]: + """Given input data, this function will parse it and return a list of tuples where each tuple contains an identifier and a tensor. Args: diff --git a/lighter/system.py b/lighter/system.py index 413a5292..e5109d26 100644 --- a/lighter/system.py +++ b/lighter/system.py @@ -1,6 +1,7 @@ +from typing import Any, Callable, Dict, List, Optional, Tuple, Union + import sys from functools import partial -from typing import Any, Callable, Dict, List, Optional, Tuple, Union import pytorch_lightning as pl import torch @@ -11,35 +12,36 @@ from torchmetrics import Metric, MetricCollection from lighter.utils.collate import collate_fn_replace_corrupted -from lighter.utils.misc import ensure_list, get_name, hasarg, countargs +from lighter.utils.misc import countargs, ensure_list, get_name, hasarg from lighter.utils.model import reshape_pred_if_single_value_prediction class LighterSystem(pl.LightningModule): - - def __init__(self, - model: Module, - batch_size: int, - drop_last_batch: bool = False, - num_workers: int = 0, - pin_memory: bool = True, - optimizers: Optional[Union[Optimizer, List[Optimizer]]] = None, - schedulers: Optional[Union[Callable, List[Callable]]] = None, - criterion: Optional[Callable] = None, - cast_target_dtype_to: Optional[str] = None, - post_criterion_activation: Optional[str] = None, - patch_based_inferer: Optional[Callable] = None, - train_metrics: Optional[Union[Metric, List[Metric]]] = None, - val_metrics: Optional[Union[Metric, List[Metric]]] = None, - test_metrics: Optional[Union[Metric, List[Metric]]] = None, - train_dataset: Optional[Union[Dataset, List[Dataset]]] = None, - val_dataset: Optional[Union[Dataset, List[Dataset]]] = None, - test_dataset: Optional[Union[Dataset, List[Dataset]]] = None, - predict_dataset: Optional[Union[Dataset, List[Dataset]]] = None, - train_sampler: Optional[Sampler] = None, - val_sampler: Optional[Sampler] = None, - test_sampler: Optional[Sampler] = None, - predict_sampler: Optional[Sampler] = None) -> None: + def __init__( + self, + model: Module, + batch_size: int, + drop_last_batch: bool = False, + num_workers: int = 0, + pin_memory: bool = True, + optimizers: Optional[Union[Optimizer, List[Optimizer]]] = None, + schedulers: Optional[Union[Callable, List[Callable]]] = None, + criterion: Optional[Callable] = None, + cast_target_dtype_to: Optional[str] = None, + post_criterion_activation: Optional[str] = None, + patch_based_inferer: Optional[Callable] = None, + train_metrics: Optional[Union[Metric, List[Metric]]] = None, + val_metrics: Optional[Union[Metric, List[Metric]]] = None, + test_metrics: Optional[Union[Metric, List[Metric]]] = None, + train_dataset: Optional[Union[Dataset, List[Dataset]]] = None, + val_dataset: Optional[Union[Dataset, List[Dataset]]] = None, + test_dataset: Optional[Union[Dataset, List[Dataset]]] = None, + predict_dataset: Optional[Union[Dataset, List[Dataset]]] = None, + train_sampler: Optional[Sampler] = None, + val_sampler: Optional[Sampler] = None, + test_sampler: Optional[Sampler] = None, + predict_sampler: Optional[Sampler] = None, + ) -> None: """_summary_ Args: @@ -163,7 +165,6 @@ def forward(self, input: Union[torch.Tensor, List, Tuple]) -> Union[torch.Tensor else: return self.model(input, **kwargs) - def _base_step(self, batch: Tuple, batch_idx: int, mode: str) -> Union[Dict[str, Any], Any]: """Base step for all modes ('train', 'val', 'test', 'predict') @@ -177,7 +178,7 @@ def _base_step(self, batch: Tuple, batch_idx: int, mode: str) -> Union[Dict[str, Union[Dict[str, Any], Any]: For the training, validation and test step, it returns a dict containing loss, metrics, input, target, and pred. Loss will be `None` for the test step. Metrics will be `None` if no metrics are specified. - + For predict step, it returns pred only. """ input, target = batch if len(batch) == 2 else (batch[:-1], batch[-1]) @@ -209,16 +210,9 @@ def _base_step(self, batch: Tuple, batch_idx: int, mode: str) -> Union[Dict[str, # Calculate the metrics for the step step_metrics = getattr(self, f"{mode}_metrics")(pred, target) - return { - "loss": loss, - "metrics": step_metrics, - "input": input, - "target": target, - "pred": pred - } + return {"loss": loss, "metrics": step_metrics, "input": input, "target": target, "pred": pred} - def _calculate_loss(self, pred: Union[torch.Tensor, List, Tuple], - target: Union[torch.Tensor, None]) -> torch.Tensor: + def _calculate_loss(self, pred: Union[torch.Tensor, List, Tuple], target: Union[torch.Tensor, None]) -> torch.Tensor: """_summary_ Args: @@ -236,13 +230,15 @@ def _calculate_loss(self, pred: Union[torch.Tensor, List, Tuple], else: if not self._target_not_used_reported and not self.trainer.sanity_checking: self._target_not_used_reported = True - logger.info(f"The criterion `{get_name(self.criterion, True)}` " - "has no `target` argument. In such cases, the LighterSystem " - "passes only the predicted values to the criterion. " - "This is intended as a support for self-supervised " - "losses where target is not used. If this is not the " - "behavior you expected, redefine your criterion " - "so that it has a `target` argument.") + logger.info( + f"The criterion `{get_name(self.criterion, True)}` " + "has no `target` argument. In such cases, the LighterSystem " + "passes only the predicted values to the criterion. " + "This is intended as a support for self-supervised " + "losses where target is not used. If this is not the " + "behavior you expected, redefine your criterion " + "so that it has a `target` argument." + ) # Type not supported. if not isinstance(pred, (torch.Tensor, tuple, list, dict)): @@ -286,27 +282,28 @@ def _base_dataloader(self, mode: str) -> DataLoader: # varies in shape, preventing the data loader to stack them into a batch. batch_size = self.batch_size if self._patch_based_inferer is not None and mode in ["val", "test", "predict"]: - logger.info(f"Setting the general batch size to 1 for {mode} " - "mode because a patch-based inferer is used.") + logger.info(f"Setting the general batch size to 1 for {mode} " "mode because a patch-based inferer is used.") batch_size = 1 # A dataset can return None when a corrupted example occurs. This collate # function replaces None's with valid examples from the dataset. collate_fn = partial(collate_fn_replace_corrupted, dataset=dataset) - return DataLoader(dataset, - sampler=sampler, - shuffle=(mode == "train" and sampler is None), - batch_size=batch_size, - drop_last=self.drop_last_batch, - num_workers=self.num_workers, - pin_memory=self.pin_memory, - collate_fn=collate_fn) + return DataLoader( + dataset, + sampler=sampler, + shuffle=(mode == "train" and sampler is None), + batch_size=batch_size, + drop_last=self.drop_last_batch, + num_workers=self.num_workers, + pin_memory=self.pin_memory, + collate_fn=collate_fn, + ) def configure_optimizers(self) -> Dict: """LightningModule method. Returns optimizers and, if defined, schedulers. Returns: - Single optimizer: If only a optimizer is provided + Single optimizer: If only a optimizer is provided Tuple of dictionaries: a tuple of `dict` with keys `optimizer` and `lr_scheduler` """ if not self.optimizers: @@ -321,9 +318,8 @@ def configure_optimizers(self) -> Dict: optim_sched_paired = [] for optimizer, scheduler in zip(self.optimizers, self.schedulers): - optim_sched_paired.append({"optimizer": optimizer, - "lr_scheduler": scheduler}) - + optim_sched_paired.append({"optimizer": optimizer, "lr_scheduler": scheduler}) + return tuple(optim_sched_paired) def setup(self, stage: str) -> None: @@ -337,9 +333,16 @@ def setup(self, stage: str) -> None: # Stage-specific PyTorch Lightning methods. Defined dynamically so that the system # only has methods used in the stage and for which the configuration was provided. if not self._lightning_module_methods_defined: - del (self.train_dataloader, self.training_step, self.val_dataloader, - self.validation_step, self.test_dataloader, self.test_step, - self.predict_dataloader, self.predict_step) + del ( + self.train_dataloader, + self.training_step, + self.val_dataloader, + self.validation_step, + self.test_dataloader, + self.test_step, + self.predict_dataloader, + self.predict_step, + ) # `Trainer.tune()` calls the `self.setup()` method whenever it runs for a new # parameter, and deleting the above methods again breaks it. This flag prevents it. self._lightning_module_methods_defined = True diff --git a/lighter/utils/cli.py b/lighter/utils/cli.py index 667599e9..4c387d6b 100644 --- a/lighter/utils/cli.py +++ b/lighter/utils/cli.py @@ -1,6 +1,7 @@ +from typing import Any, Dict + import sys from functools import partial -from typing import Any, Dict import fire import yaml @@ -13,16 +14,17 @@ # Trainer methods calls in YAML format with support for command line arguments. # Waiting for https://github.com/Project-MONAI/MONAI/pull/5854#issuecomment-1384800886. trainer_methods = { - "fit": - yaml.safe_load(""" + "fit": yaml.safe_load( + """ fit: _method_: > $@trainer.fit(model=@fit#model, ckpt_path=@fit#ckpt_path) model: "@system" - ckpt_path: null"""), - "validate": - yaml.safe_load(""" + ckpt_path: null""" + ), + "validate": yaml.safe_load( + """ validate: _method_: > $@trainer.validate(model=@validate#model, @@ -30,17 +32,19 @@ verbose=@validate#verbose) model: "@system" ckpt_path: null - verbose: True"""), - "predict": - yaml.safe_load(""" + verbose: True""" + ), + "predict": yaml.safe_load( + """ predict: _method_: > $@trainer.predict(model=@predict#model, ckpt_path=@predict#ckpt_path) model: "@system" - ckpt_path: null"""), - "test": - yaml.safe_load(""" + ckpt_path: null""" + ), + "test": yaml.safe_load( + """ test: _method_: > $@trainer.test(model=@test#model, @@ -48,9 +52,10 @@ verbose=@test#verbose) model: "@system" ckpt_path: null - verbose: True"""), - "tune": - yaml.safe_load(""" + verbose: True""" + ), + "tune": yaml.safe_load( + """ tune: _method_: > $@trainer.tune(model=@tune#model, @@ -63,7 +68,8 @@ scale_batch_size_kwargs: null lr_find_kwargs: null method: fit - """), + """ + ), } diff --git a/lighter/utils/dynamic_imports.py b/lighter/utils/dynamic_imports.py index 2ea2fa89..e297a228 100644 --- a/lighter/utils/dynamic_imports.py +++ b/lighter/utils/dynamic_imports.py @@ -1,6 +1,7 @@ -import sys from typing import Any + import importlib +import sys from pathlib import Path from loguru import logger diff --git a/lighter/utils/misc.py b/lighter/utils/misc.py index bb7092c4..ea37b569 100644 --- a/lighter/utils/misc.py +++ b/lighter/utils/misc.py @@ -1,6 +1,7 @@ +from typing import Any, Callable, List + import inspect import sys -from typing import Any, Callable, List from loguru import logger @@ -31,14 +32,14 @@ def dot_notation_setattr(obj: Callable, attr: str, value: Any): attr (str): attribute name of the object. value (Any): attribute value to be set. """ - if '.' not in attr: + if "." not in attr: if not hasattr(obj, attr): logger.info(f"`{get_name(obj, True)}` has no attribute `{attr}`. Exiting.") sys.exit() setattr(obj, attr, value) # Solve recursively if the attribute is defined in dot-notation else: - obj_name, attr = attr.split('.', maxsplit=1) + obj_name, attr = attr.split(".", maxsplit=1) dot_notation_setattr(getattr(obj, obj_name), attr, value) diff --git a/lighter/utils/model.py b/lighter/utils/model.py index d7378ac6..e4a504ed 100644 --- a/lighter/utils/model.py +++ b/lighter/utils/model.py @@ -4,8 +4,7 @@ from lighter.utils.misc import dot_notation_setattr -def reshape_pred_if_single_value_prediction(pred: torch.Tensor, - target: torch.Tensor) -> torch.Tensor: +def reshape_pred_if_single_value_prediction(pred: torch.Tensor, target: torch.Tensor) -> torch.Tensor: """When the task is to predict a single value, pred and target dimensions often mismatch - dataloader returns the value in the (B) shape, while the network returns predictions in the (B, 1) shape, where the second dim is redundant. diff --git a/mkdocs.yml b/mkdocs.yml deleted file mode 100644 index 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"Suraj Pai ", + "Keno Bressem "] +license = "MIT" +repository = "https://github.com/lighter/lighter" +homepage = "https://github.com/lighter/lighter" + +# Keywords description https://python-poetry.org/docs/pyproject/#keywords +keywords = [] #! Update me +packages = [ + { include = "lighter" }, +] + +# Pypi classifiers: https://pypi.org/classifiers/ +classifiers = [ #! Update me + "Development Status :: 3 - Alpha", + "Intended Audience :: Developers", + "Operating System :: OS Independent", + "Topic :: Software Development :: Libraries :: Python Modules", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] + + + +[tool.poetry.dependencies] +python = "^3.8" +torch = "^1.13.1" +pandas = "^1.5.3" +torchvision = "^0.14.1" +pytorch-lightning = "^1.9.0" +fire = "^0.5.0" +loguru = "^0.6.0" +lightly = "^1.2.43" +torchmetrics = "^0.11.0" +py = "^1.11.0" +tensorboard = "^2.11.2" +monai-weekly = "^1.2.dev2305" + +[tool.poetry.group.dev.dependencies] +bandit = "^1.7.4" +black = {version = "^23.1a1", allow-prereleases = true} +isort = {extras = ["colors"], version = "^5.11.4"} +mypy = "^0.991" +mypy-extensions = "^0.4.3" +pre-commit = "^2.21.0" +pydocstyle = "^6.3.0" +pylint = "^2.15.10" +pytest = "^7.2.1" +pyupgrade = "^3.3.1" +safety = "^2.3.5" +coverage = "^7.0.5" +coverage-badge = "^1.1.0" +pytest-html = "^3.2.0" +pytest-cov = "^4.0.0" +aiohttp = "^3.8.3" +py = "^1.11.0" +poetry-bumpversion = "^0.3.0" +typing-extensions = "^4.4.0" + +[tool.black] +# https://github.com/psf/black +target-version = ["py38"] +line-length = 127 +color = true + +exclude = ''' +/( + \.git + | \.hg + | \.mypy_cache + | \.tox + | \.venv + | _build + | buck-out + | build + | dist + | env + | venv +)/ +''' + +[tool.isort] +# https://github.com/timothycrosley/isort/ +py_version = 38 +line_length = 127 + +known_typing = ["typing", "types", "typing_extensions", "mypy", "mypy_extensions"] +sections = ["FUTURE", "TYPING", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"] +include_trailing_comma = true +profile = "black" +multi_line_output = 3 +indent = 4 +color_output = true + +[tool.mypy] +# https://mypy.readthedocs.io/en/latest/config_file.html#using-a-pyproject-toml-file +python_version = 3.8 +pretty = true +show_traceback = true +color_output = true + +allow_redefinition = false +check_untyped_defs = true +disallow_any_generics = true +disallow_incomplete_defs = true +ignore_missing_imports = true +implicit_reexport = false +no_implicit_optional = true +show_column_numbers = true +show_error_codes = true +show_error_context = true +strict_equality = true +strict_optional = true +warn_no_return = true +warn_redundant_casts = true +warn_return_any = true +warn_unreachable = true +warn_unused_configs = true +warn_unused_ignores = true + + +[tool.pytest.ini_options] +# https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml +# Directories that are not visited by pytest collector: +norecursedirs =["hooks", "*.egg", ".eggs", "dist", "build", "docs", ".tox", ".git", "__pycache__"] +doctest_optionflags = ["NUMBER", "NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL"] + +# Extra options: +addopts = [ + "--strict-markers", + "--tb=short", + "--doctest-modules", + "--doctest-continue-on-failure", +] +# Markers to categorize tests +markers = [ + "slow: marks tests as slow (deselect with '-m \"not slow\"')", + "serial", +] + + +[tool.coverage.run] +source = ["tests"] + +[coverage.paths] +source = "lighter" + +[coverage.run] +branch = true + +[coverage.report] +fail_under = 50 +show_missing = true + + +[tool.pylint.'MESSAGES CONTROL'] +max-line-length = 127 +disable = """ + too-many-arguments, + not-callable +""" + +[tool.pylint.master] +fail-under=8 + +[tool.poetry_bumpversion.file."lighter/__init__.py"] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 023a02e4..00000000 --- a/requirements.txt +++ /dev/null @@ -1,11 +0,0 @@ -torch -torchvision -pytorch-lightning -fire -loguru -wandb -pandas -SimpleITK -monai -lightly -pandas \ No newline at end of file diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 8df6c850..00000000 --- a/setup.cfg +++ /dev/null @@ -1,71 +0,0 @@ -[metadata] -name = lighter -version = 0.0.1 -author = "ibro45" -# author-email = -url = https://github.com/ibro45/lighter -description = lighter description -long_description = file: README.md -long_description_content_type = text/markdown -license = mit -platforms = any -keywords = one, two -classifiers = - Development Status :: 3 - Alpha - Programming Language :: Python :: 3 :: Only - Intended Audience :: Science/Research -project_urls = - Documentation = https://lighter.readthedocs.io/en/latest/ - -[options] -zip_safe = False -packages = find: -include_package_data = True -#setup_requires = -# Add here dependencies of your project (semicolon/line-separated), e.g. -install_requires = - torch - torchvision - pytorch-lightning - hydra-core - omegaconf - wandb - loguru - mkdocs - -# The usage of test_requires is discouraged, see `Dependency Management` docs -# tests_require = pytest; pytest-cov -# Require a specific Python version, e.g. Python 2.7 or >= 3.4 -# python_requires = >=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.* - -[options.packages.find] -exclude = - docs - docker - tests - projects - - -[options.extras_require] -# Add here additional requirements for extra features, to install with: -# `pip install clinical-evaluation[PDF]` like: -# PDF = ReportLab; RXP -# Add here test requirements (semicolon/line-separated) -testing = - pytest - pytest-cov - -[options.entry_points] -console_scripts = - lighter = lighter.utils.cli:interface - -[yapf] -based_on_style = google -column_limit = 100 - -[pylint] -fail-under = 8 - -[pylint.typecheck] -generated-members=torch.*, cv2.* -good-names=x, y, z, i \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index 0ac365cb..00000000 --- a/setup.py +++ /dev/null @@ -1,13 +0,0 @@ -import sys - -from pkg_resources import VersionConflict, require -from setuptools import setup - -try: - require('setuptools>=38.3') -except VersionConflict: - print("Error: version of setuptools is too old (<38.3)!") - sys.exit(1) - -if __name__ == "__main__": - setup() \ No newline at end of file diff --git a/tests/integration/test_cifar.py b/tests/integration/test_cifar.py new file mode 100644 index 00000000..354d42e3 --- /dev/null +++ b/tests/integration/test_cifar.py @@ -0,0 +1,19 @@ +"""Tests for running CIFAR training to verify integrity of the pipeline""" +import pytest + +from lighter.utils.cli import run_trainer_method, trainer_methods + +test_overrides = "./tests/integration/test_overrides.yaml" + + +@pytest.mark.parametrize( + ("mode", "config_file"), + [("fit", "./projects/cifar10/experiments/monai_bundle_prototype.yaml")], +) +@pytest.mark.slow +def test_trainer_method(mode: str, config_file: str): + """Test trainer method for different mode configurations""" + kwargs = {"config_file": config_file, "args_file": test_overrides} + + func_return = run_trainer_method(trainer_methods[mode], **kwargs) + assert func_return == None diff --git a/tests/integration/test_overrides.yaml b/tests/integration/test_overrides.yaml new file mode 100644 index 00000000..fc5d92fa --- /dev/null +++ b/tests/integration/test_overrides.yaml @@ -0,0 +1,6 @@ +trainer#max_steps: 5 +trainer#num_sanity_val_steps: 0 +trainer#accelerator: cpu +system#batch_size: 16 +system#num_workers: 2 +trainer#callbacks: null diff --git a/tests/unit/test_dummy.py b/tests/unit/test_dummy.py new file mode 100644 index 00000000..757cdbb8 --- /dev/null +++ b/tests/unit/test_dummy.py @@ -0,0 +1,18 @@ +"""Tests for hello function.""" +import pytest + +from lighter.utils.misc import ensure_list + + +@pytest.mark.parametrize( + ("input", "result"), + [ + ([2, 3], [2, 3]), + (1, [1]), + ((2, 3), [2, 3]), + (None, []), + ], +) +def test_ensure_list(input, result): + """Example test with parametrization.""" + assert ensure_list(input) == result