diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..6bf86df --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,33 @@ +--- +name: Bug report +about: Create a bug report to help us improve +title: "Bug Summary" +labels: "bug" +assignees: "" +--- + +**Describe the bug** + + + +**To Reproduce** + +Steps to reproduce the behavior: + +1. ... +2. ... +3. ... + +**Expected behavior** + + + +**System [please complete the following information]:** + +- OS: e.g. [Ubuntu 18.04] +- Language Version: [e.g. Python 3.8] +- Virtual environment: [e.g. Conda] + +**Additional context** + + diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..fb6ac52 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,19 @@ +--- +name: Feature request +about: Suggest a new feature +title: "Feature Request Summary" +labels: "enhancement" +assignees: "" +--- + +**Is your feature request related to a problem? Please describe.** + + + +**Describe the solution you would like** + + + +**Additional context** + + diff --git a/.github/ISSUE_TEMPLATE/general_question.md b/.github/ISSUE_TEMPLATE/general_question.md new file mode 100644 index 0000000..c24b8c6 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/general_question.md @@ -0,0 +1,12 @@ +--- +name: General question +about: Ask a question about anything related to this project +title: "Question" +labels: "question" +assignees: "" +--- + +**Question** + + diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..bd55da9 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,45 @@ +version: 2 +updates: + - package-ecosystem: github-actions + directory: "/" + schedule: + interval: weekly + open-pull-requests-limit: 3 + target-branch: development + labels: + - DEPENDABOT + commit-message: + prefix: "[DEPENDABOT]" + + - package-ecosystem: pip + directory: "/.github/workflows" + schedule: + interval: weekly + open-pull-requests-limit: 3 + target-branch: development + labels: + - DEPENDABOT + commit-message: + prefix: "[DEPENDABOT]" + + - package-ecosystem: pip + directory: "/docs" + schedule: + interval: weekly + open-pull-requests-limit: 3 + target-branch: development + labels: + - DEPENDABOT + commit-message: + prefix: "[DEPENDABOT]" + + - package-ecosystem: pip + directory: "/" + schedule: + interval: weekly + open-pull-requests-limit: 3 + target-branch: development + labels: + - DEPENDABOT + commit-message: + prefix: "[DEPENDABOT]" diff --git a/.github/labels.yml b/.github/labels.yml new file mode 100644 index 0000000..c9f8456 --- /dev/null +++ b/.github/labels.yml @@ -0,0 +1,69 @@ +--- +# Labels names are important as they are used by Release Drafter to decide +# regarding where to record them in changelog or if to skip them. +# +# The repository labels will be automatically configured using this file and +# the GitHub Action https://github.com/marketplace/actions/github-labeler. +- name: breaking + description: Breaking Changes + color: bfd4f2 +- name: bug + description: Something isn't working + color: d73a4a +- name: build + description: Build System and Dependencies + color: bfdadc +- name: ci + description: Continuous Integration + color: 4a97d6 +- name: dependencies + description: Pull requests that update a dependency file + color: 0366d6 +- name: documentation + description: Improvements or additions to documentation + color: 0075ca +- name: duplicate + description: This issue or pull request already exists + color: cfd3d7 +- name: enhancement + description: New feature or request + color: a2eeef +- name: github_actions + description: Pull requests that update Github_actions code + color: "000000" +- name: good first issue + description: Good for newcomers + color: 7057ff +- name: help wanted + description: Extra attention is needed + color: 008672 +- name: invalid + description: This doesn't seem right + color: e4e669 +- name: performance + description: Performance + color: "016175" +- name: python + description: Pull requests that update Python code + color: 2b67c6 +- name: question + description: Further information is requested + color: d876e3 +- name: refactoring + description: Refactoring + color: ef67c4 +- name: removal + description: Removals and Deprecations + color: 9ae7ea +- name: style + description: Style + color: c120e5 +- name: testing + description: Testing + color: b1fc6f +- name: wontfix + description: This will not be worked on + color: ffffff +- name: skip-changelog + description: Changes that should be omitted from the release notes + color: ededed diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 0000000..0bafff6 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,22 @@ + + +**PR Checklist** + + + +- [ ] This comment contains a description of changes (with reason) +- [ ] Referenced issue is linked +- [ ] If you've fixed a bug or added code that should be tested, add tests! +- [ ] Documentation in `docs` is updated + +**Description of changes** + + + +**Technical details** + + + +**Additional context** + + diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml new file mode 100644 index 0000000..b9a8a33 --- /dev/null +++ b/.github/release-drafter.yml @@ -0,0 +1,54 @@ +name-template: "0.8.0 🌈" # <> +tag-template: 0.8.0 # <> +exclude-labels: + - "skip-changelog" + +categories: + - title: "🚀 Features" + labels: + - feature + - enhancement + - title: "🐛 Bug Fixes" + labels: + - fix + - bugfix + - bug + - title: "🧰 Maintenance" + label: chore + - title: ":package: Dependencies" + labels: + - dependencies + - build + - dependabot + - DEPENDABOT +version-resolver: + major: + labels: + - major + minor: + labels: + - minor + patch: + labels: + - patch + default: patch +autolabeler: + - label: chore + files: + - "*.md" + branch: + - '/docs{0,1}\/.+/' + - label: bug + branch: + - /fix\/.+/ + title: + - /fix/i + - label: enhancement + branch: + - /feature\/.+/ + body: + - "/JIRA-[0-9]{1,4}/" +template: | + ## Changes + + $CHANGES diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml new file mode 100644 index 0000000..b1d319f --- /dev/null +++ b/.github/workflows/build_package.yml @@ -0,0 +1,35 @@ +name: Build DrEvalPy Package + +on: [push, pull_request] + +jobs: + build: + runs-on: ${{ matrix.os }} + if: "!contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[ci skip]')" + strategy: + matrix: + os: [macos-latest, ubuntu-latest, windows-latest] + python: ["3.9", "3.10"] + + steps: + - uses: actions/checkout@v4 + name: Check out source-code repository + + - name: Setup Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python }} + + - name: Install Poetry + run: | + pip install poetry + poetry --version + + - name: Build package + run: poetry build --ansi + + - name: Install required twine packaging dependencies + run: pip install setuptools wheel twine + + - name: Check twine package + run: twine check dist/* diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml new file mode 100644 index 0000000..173926f --- /dev/null +++ b/.github/workflows/labeler.yml @@ -0,0 +1,19 @@ +name: Labeler + +on: + push: + branches: + - main + - master + +jobs: + labeler: + runs-on: ubuntu-latest + steps: + - name: Check out the repository + uses: actions/checkout@v4 + + - name: Run Labeler + uses: crazy-max/ghaction-github-labeler@v5.0.0 + with: + skip-delete: true diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml new file mode 100644 index 0000000..98413b6 --- /dev/null +++ b/.github/workflows/publish_docs.yml @@ -0,0 +1,36 @@ +name: Build Documentation + +on: [push] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + name: Check out source-code repository + + - name: Setup Python + uses: actions/setup-python@v5 + with: + python-version: 3.9 + + - name: Install pip + run: | + python -m pip install --upgrade pip + + - name: Install doc dependencies + run: | + pip install -r docs/requirements.txt + + - name: Build docs + run: | + cd docs + make html + + - name: Deploy + if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'}} + uses: peaceiris/actions-gh-pages@v4 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: ./docs/_build/html diff --git a/.github/workflows/release_drafter.yml b/.github/workflows/release_drafter.yml new file mode 100644 index 0000000..3c39582 --- /dev/null +++ b/.github/workflows/release_drafter.yml @@ -0,0 +1,19 @@ +name: Release Drafter +on: + push: + branches: + - development + pull_request: + branches: + - development + types: + - opened + - reopened + - synchronize +jobs: + update_release_draft: + runs-on: ubuntu-latest + steps: + - uses: release-drafter/release-drafter@v6 + env: + GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml new file mode 100644 index 0000000..d03ba5c --- /dev/null +++ b/.github/workflows/run_tests.yml @@ -0,0 +1,133 @@ +name: Run drevalpy Tests + +on: + push: + branches: + - development + - main + - "release/*" + pull_request: + branches: + - "*" + +jobs: + tests: + name: ${{ matrix.session }} ${{ matrix.python-version }} / ${{ matrix.os }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + include: + - { python-version: "3.10", os: ubuntu-latest, session: "pre-commit" } + - { python-version: "3.10", os: ubuntu-latest, session: "safety" } + - { python-version: "3.10", os: ubuntu-latest, session: "mypy" } + - { python-version: "3.10", os: ubuntu-latest, session: "tests" } + - { python-version: "3.10", os: windows-latest, session: "tests" } + - { python-version: "3.10", os: macos-latest, session: "tests" } + - { python-version: "3.10", os: ubuntu-latest, session: "typeguard" } + - { python-version: "3.10", os: ubuntu-latest, session: "xdoctest" } + - { python-version: "3.10", os: ubuntu-latest, session: "docs-build" } + + env: + NOXSESSION: ${{ matrix.session }} + + steps: + - name: Check out the repository + uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install Poetry + run: | + pipx install poetry + poetry --version + + - name: Install nox nox-poetry rich + run: | + pipx install nox + pipx inject nox nox-poetry + pipx inject nox rich + nox --version + + - name: Compute pre-commit cache key + if: matrix.session == 'pre-commit' + id: pre-commit-cache + shell: python + run: | + import hashlib + import sys + + python = "py{}.{}".format(*sys.version_info[:2]) + payload = sys.version.encode() + sys.executable.encode() + digest = hashlib.sha256(payload).hexdigest() + result = "${{ runner.os }}-{}-{}-pre-commit".format(python, digest[:8]) + + print("::set-output name=result::{}".format(result)) + + - name: Restore pre-commit cache + uses: actions/cache@v4.0.2 + if: matrix.session == 'pre-commit' + with: + path: ~/.cache/pre-commit + key: ${{ steps.pre-commit-cache.outputs.result }}-${{ hashFiles('.pre-commit-config.yaml') }} + restore-keys: | + ${{ steps.pre-commit-cache.outputs.result }}- + + - name: Run Nox + run: nox --force-color --python=${{ matrix.python-version }} + + - name: Upload coverage data + if: always() && matrix.session == 'tests' && matrix.os == 'ubuntu-latest' + uses: actions/upload-artifact@v4 + with: + name: coverage-data + path: ".coverage.*" + include-hidden-files: "true" + + - name: Upload documentation + if: matrix.session == 'docs-build' + uses: actions/upload-artifact@v4 + with: + name: docs + path: docs/_build + + coverage: + runs-on: ubuntu-latest + needs: tests + steps: + - name: Check out the repository + uses: actions/checkout@v4 + + - name: Set up Python 3.9 + uses: actions/setup-python@v5 + with: + python-version: 3.9 + + - name: Install Poetry + run: | + pipx install poetry + poetry --version + + - name: Install nox nox-poetry rich + run: | + pipx install nox + pipx inject nox nox-poetry + pipx inject nox rich + nox --version + + - name: Download coverage data + uses: actions/download-artifact@v4 + with: + name: coverage-data + + - name: Combine coverage data and display human readable report + run: nox --force-color --session=coverage + + - name: Create coverage report + run: nox --force-color --session=coverage -- xml -i + + - name: Upload coverage report + uses: codecov/codecov-action@v4.5.0 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..76dd8e8 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,64 @@ +repos: + - repo: local + hooks: + - id: black + name: black + entry: black + language: system + types: [python] + require_serial: true + - id: check-added-large-files + name: Check for added large files + entry: check-added-large-files + language: system + - id: check-toml + name: Check Toml + entry: check-toml + language: system + types: [toml] + - id: check-yaml + name: Check Yaml + entry: check-yaml + language: system + types: [yaml] + - id: end-of-file-fixer + name: Fix End of Files + entry: end-of-file-fixer + language: system + types: [text] + stages: [pre-commit, pre-push, manual] + exclude: docs/ + - id: flake8 + name: flake8 + entry: flake8 + language: system + types: [python] + require_serial: true + - id: pyupgrade + name: pyupgrade + description: Automatically upgrade syntax for newer versions. + entry: pyupgrade + language: system + types: [python] + args: [--py39-plus, --keep-runtime-typing] + - id: trailing-whitespace + name: Trim Trailing Whitespace + entry: trailing-whitespace-fixer + language: system + types: [text] + stages: [pre-commit, pre-push, manual] + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v2.5.1 + hooks: + - id: prettier + - repo: https://github.com/pycqa/isort + rev: 5.12.0 + hooks: + - id: isort + name: isort (python) + - id: isort + name: isort (cython) + types: [cython] + - id: isort + name: isort (pyi) + types: [pyi] diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000..24866dd --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,30 @@ +# .readthedocs.yaml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the OS, Python version and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.11" + # You can also specify other tool versions: + # nodejs: "19" + # rust: "1.64" + # golang: "1.19" + +# Build documentation in the "docs/" directory with Sphinx +sphinx: + configuration: docs/conf.py + +# Optionally build your docs in additional formats such as PDF and ePub +formats: all + +# Optional but recommended, declare the Python requirements required +# to build your documentation +# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html +python: + install: + - requirements: docs/requirements.txt diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..7671a00 --- /dev/null +++ b/README.rst @@ -0,0 +1,58 @@ +DrEvalPy: Python Cancer Cell Line Drug Response Prediction Suite +================================================================ + +|PyPI| |Python Version| |License| |Read the Docs| |Build| |Tests| |Codecov| |pre-commit| |Black| + +.. |PyPI| image:: https://img.shields.io/pypi/v/drevalpy.svg + :target: https://pypi.org/project/drevalpy/ + :alt: PyPI +.. |Python Version| image:: https://img.shields.io/pypi/pyversions/drevalpy + :target: https://pypi.org/project/drevalpy + :alt: Python Version +.. |License| image:: https://img.shields.io/github/license/daisybio/drevalpy + :target: https://opensource.org/licenses/GPL3 + :alt: License +.. |Read the Docs| image:: https://img.shields.io/readthedocs/drevalpy/latest.svg?label=Read%20the%20Docs + :target: https://drevalpy.readthedocs.io/ + :alt: Read the documentation at https://drevalpy.readthedocs.io/ +.. |Build| image:: https://github.com/daisybio/drevalpy/workflows/Build%20drevalpy%20Package/badge.svg + :target: https://github.com/daisybio/drevalpy/actions?workflow=Package + :alt: Build Package Status +.. |Tests| image:: https://github.com/daisybio/drevalpy/workflows/Run%20drevalpy%20Tests/badge.svg + :target: https://github.com/daisybio/drevalpy/actions?workflow=Tests + :alt: Run Tests Status +.. |Codecov| image:: https://codecov.io/gh/daisybio/drevalpy/branch/main/graph/badge.svg + :target: https://codecov.io/gh/daisybio/drevalpy + :alt: Codecov +.. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white + :target: https://github.com/pre-commit/pre-commit + :alt: pre-commit +.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg + :target: https://github.com/psf/black + :alt: Black + +Focus on Innovating Your Models — DrEval Handles the Rest! +- DrEval is a toolkit that ensures drug response prediction evaluations are statistically sound, biologically meaningful, and reproducible. +- Focus on model innovation while using our automated standardized evaluation protocols and preprocessing workflows. +- A flexible model interface supports all model types (e.g. Machine Learning, Stats, Network-based analyses) + +Use DrEval to Build Drug Response Models That Have an Impact + + 1. Maintained, up-to-date baseline catalog, no need to re-implement literature models + + 2. Gold standard datasets for benchmarking + + 3. Consistent application-driven evaluation + + 4. Ablation studies with permutation tests + + 5. Cross-study evaluation for generalization analysis + + 6. Optimized nextflow pipeline for fast experiments + + 7. Easy-to-use hyperparameter tuning + + 8. Paper-ready visualizations to display performance + +This project is a collaboration of the Technical University of Munich (TUM, Germany) +and the Freie Universität Berlin (FU, Germany). diff --git a/create_report.py b/create_report.py index 864e274..3fddf0e 100644 --- a/create_report.py +++ b/create_report.py @@ -11,13 +11,7 @@ RegressionSliderPlot, Violin, ) -from drevalpy.visualization.utils import ( - create_html, - create_index_html, - parse_results, - prep_results, - write_results, -) +from drevalpy.visualization.utils import create_html, create_index_html, parse_results, prep_results, write_results def create_output_directories(custom_id): @@ -344,12 +338,7 @@ def draw_per_grouping_algorithm_plots( all_files = [] for _, _, files in os.walk(f"results/{run_id}"): for file in files: - if file.endswith(".html") and file not in [ - "index.html", - "LPO.html", - "LCO.html", - "LDO.html", - ]: + if file.endswith(".html") and file not in ["index.html", "LPO.html", "LCO.html", "LDO.html"]: all_files.append(file) # PIPELINE: WRITE_HTML create_html( diff --git a/docs/API.rst b/docs/API.rst new file mode 100644 index 0000000..4165161 --- /dev/null +++ b/docs/API.rst @@ -0,0 +1,30 @@ +.. module:: drevalpy + +.. automodule:: drevalpy + :noindex: + +API +=== + +Import DrEvalPy using + +.. code-block:: python + + import drevalpy as dep + +.. + Models module: :code:`models` + ------------------------- + + .. module:: devalpy.models + + .. currentmodule:: drevalpy + + Available models + ~~~~~~~~~~~~~~~~ + + .. autosummary:: + :toctree: api/models + + models.baselines + models.BiGDRP \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..1ff9c24 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = python -msphinx +SPHINXPROJ = drevalpy +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/_key_contributors.rst b/docs/_key_contributors.rst new file mode 100644 index 0000000..83be277 --- /dev/null +++ b/docs/_key_contributors.rst @@ -0,0 +1,8 @@ +.. sidebar:: Key Contributors + + * `Judith Bernett `_: developer, maintainer + * `Pascal Iversen `_: developer, maintainer + * `Mario Picciani `_: developer + * `Markus List `_: advisor and PI of daisybio + * `Katharina Baum `_: advisor and PI of DILiS + * `Mathias Wilhelm `_: advisor and PI of wilhelmlab \ No newline at end of file diff --git a/docs/_static/custom_cookietemple.css b/docs/_static/custom_cookietemple.css new file mode 100644 index 0000000..88f80f1 --- /dev/null +++ b/docs/_static/custom_cookietemple.css @@ -0,0 +1,45 @@ +@import "basic.css"; + +.wy-nav-content { + max-width: 1200px; +} + +.wy-side-nav-search { + background-color: inherit; +} + +table.align-default { + text-align: left; +} + +.autosummary th:first-child, +.autosummary td:first-child { + min-width: 250px; +} + +.autosummary th:first-child, +.autosummary td:first-child { + min-width: 400px; +} + +.autosummary th:last-child, +.autosummary td:last-child { + width: 100%; +} + +.fixed-table { + margin-left: 0; +} + +.wy-table-responsive table th p, +.wy-table-responsive table td p { + white-space: normal; +} + +.autosummary { + margin-left: 0 !important; +} + +.date { + font-size: 50%; +} diff --git a/docs/_static/img/drevalpy.pdf b/docs/_static/img/drevalpy.pdf new file mode 100644 index 0000000..f662781 Binary files /dev/null and b/docs/_static/img/drevalpy.pdf differ diff --git a/docs/_static/img/drevalpy.png b/docs/_static/img/drevalpy.png new file mode 100644 index 0000000..cab3657 Binary files /dev/null and b/docs/_static/img/drevalpy.png differ diff --git a/docs/_static/img/drevalpy.svg b/docs/_static/img/drevalpy.svg new file mode 100644 index 0000000..9d64e7e --- /dev/null +++ b/docs/_static/img/drevalpy.svg @@ -0,0 +1,641 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Drug Response Suite + DrEvalPy + + + diff --git a/docs/_templates/autosummary/base.rst b/docs/_templates/autosummary/base.rst new file mode 100644 index 0000000..4ae6a2c --- /dev/null +++ b/docs/_templates/autosummary/base.rst @@ -0,0 +1,5 @@ +:github_url: {{ fullname | modurl }} + +{% extends "!autosummary/base.rst" %} + +.. http://www.sphinx-doc.org/en/stable/ext/autosummary.html#customizing-templates \ No newline at end of file diff --git a/docs/api/models/drevalpy.models.BiGDRP.rst b/docs/api/models/drevalpy.models.BiGDRP.rst new file mode 100644 index 0000000..ffd5a93 --- /dev/null +++ b/docs/api/models/drevalpy.models.BiGDRP.rst @@ -0,0 +1,6 @@ +drevalpy.models.BiGDRP +====================== + +.. automodule:: drevalpy.models.BiGDRP + + \ No newline at end of file diff --git a/docs/api/models/drevalpy.models.baselines.rst b/docs/api/models/drevalpy.models.baselines.rst new file mode 100644 index 0000000..9ccc1d0 --- /dev/null +++ b/docs/api/models/drevalpy.models.baselines.rst @@ -0,0 +1,6 @@ +drevalpy.models.baselines +========================= + +.. automodule:: drevalpy.models.baselines + + \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..7c31e3b --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,256 @@ +#!/usr/bin/env python +# mypy: ignore-errors +# drevalpy documentation build configuration file +# +# 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 inspect +import os +import sys +from datetime import datetime +from pathlib import Path + +from jinja2.defaults import DEFAULT_FILTERS + +sys.path.insert(0, os.path.abspath("../")) + + +# -- General configuration --------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones. + +# Add 'sphinx_automodapi.automodapi' if you want to build modules +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "sphinx_autodoc_typehints", + "sphinx.ext.intersphinx", + "sphinx_click", + "sphinx.ext.autosectionlabel", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +source_suffix = ".rst" + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "DrEvalPy" +author = "DrEvalpy development team" +copyright = f"{datetime.now():%Y}, daisybio at Technical University of Munich" + +# The version info for the project you're documenting, acts as replacement +# for |version| and |release|, also used in various other places throughout +# the built documents. +# +# The short X.Y version. +version = "0.0.1" +# The full version, including alpha/beta/rc tags. +release = "0.0.1" + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = "en" + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This patterns also effect to html_static_path and html_extra_path +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + + +# -- Options for HTML output ------------------------------------------- + +html_context = { + "display_github": True, # Integrate GitHub + "github_user": "daisybio", # Username + "github_repo": "drevalpy", # Repo name + "github_version": "development", # Version + "conf_py_path": "/docs/", # Path in the checkout to the docs root + "github_url": "https://github.com/daisybio/drevalpy/", +} + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "sphinx_rtd_theme" + +# The names of the Pygments (syntax highlighting) styles to use. +html_theme_options = {"pygment_light_style": "default", "pygment_dark_style": "lightbulp"} + +# Theme options are theme-specific and customize the look and feel of a +# theme further. For a list of options available for each theme, see the +# documentation. +# +html_theme_options = dict( + navigation_depth=4, + logo_only=True, +) +html_logo = "_static/img/drevalpy.png" + + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] + + +# -- Options for HTMLHelp output --------------------------------------- + +# Output file base name for HTML help builder. +htmlhelp_basename = "drevalpydoc" + + +# -- Options for LaTeX output ------------------------------------------ + +latex_elements = { + # The paper size ("letterpaper" or "a4paper"). + # + # "papersize": "letterpaper", + # The font size ("10pt", "11pt" or "12pt"). + # + # "pointsize": "10pt", + # Additional stuff for the LaTeX preamble. + # + # "preamble": "", + # Latex figure (float) alignment + # + # "figure_align": "htbp", +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass +# [howto, manual, or own class]). +latex_documents = [ + ( + master_doc, + "DrEvalPy.tex", + "DrEvalPy Documentation", + author, + "manual", + ), +] + + +# -- Options for manual page output ------------------------------------ + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ( + master_doc, + "DrEvalPy", + "DrEvalPy Documentation", + [author], + 1, + ) +] + +autodoc_typehints = "description" + + +autodoc_mock_imports = ["numpy", "sklearn", "pandas", "networkx", "yaml", "pytorch_lightning", "torch", "scipy"] + + +# -- Options for Texinfo output ---------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ( + master_doc, + "DrEvalPy", + "DrEvalPy Documentation", + author, + "DrEvalPy", + "One line description of project.", + "Miscellaneous", + ), +] + +html_css_files = [ + "custom_cookietemple.css", +] + +# -- Options for intersphinx mappings ---------------------------------- + +intersphinx_mapping = dict( + numpy=("https://numpy.org/doc/stable/", None), + pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), + python=("https://docs.python.org/3", None), + scipy=("https://docs.scipy.org/doc/scipy/", None), + sklearn=("https://scikit-learn.org/stable/", None), +) + + +# module path filter to create direct links to sources for autogenerated docs +# according to https://gist.github.com/flying-sheep/b65875c0ce965fbdd1d9e5d0b9851ef1 + + +def get_obj_module(qualname): + """Get a module/class/attribute and its original module by qualname.""" + modname = qualname + classname = None + attrname = None + while modname not in sys.modules: + attrname = classname + modname, classname = modname.rsplit(".", 1) + + # retrieve object and find original module name + if classname: + cls = getattr(sys.modules[modname], classname) + modname = cls.__module__ + obj = getattr(cls, attrname) if attrname else cls + else: + obj = None + + return obj, sys.modules[modname] + + +def get_linenos(obj): + """Get an object’s line numbers.""" + try: + lines, start = inspect.getsourcelines(obj) + except TypeError: # obj is an attribute or None + return None, None + else: + return start, start + len(lines) - 1 + + +project_dir = Path(__file__).parent.parent # project/docs/conf.py/../.. → project/ +github_url = "https://github.com/{github_user}/{github_repo}/tree/{github_version}".format_map(html_context) + + +def modurl(qualname): + """Get the full GitHub URL for some object’s qualname.""" + obj, module = get_obj_module(qualname) + path = Path(module.__file__).relative_to(project_dir) + start, end = get_linenos(obj) + fragment = f"#L{start}-L{end}" if start and end else "" + return f"{github_url}/{path}{fragment}" + + +# html_context doesn’t apply to autosummary templates ☹ +# and there’s no way to insert filters into those templates +# so we have to modify the default filters +DEFAULT_FILTERS["modurl"] = modurl + +# -- Options for autosectionlabel mappings ----------------------------- +autosectionlabel_prefix_document = True diff --git a/docs/contributing.rst b/docs/contributing.rst new file mode 100644 index 0000000..c4d7bf6 --- /dev/null +++ b/docs/contributing.rst @@ -0,0 +1,137 @@ +Contributor Guide +================= + +Thank you for your interest in improving this project. +This project is open-source under the `MIT license`_ and +highly welcomes contributions in the form of bug reports, feature requests, and pull requests. + +Here is a list of important resources for contributors: + +- `Source Code`_ +- `Documentation`_ +- `Issue Tracker`_ +- `Code of Conduct`_ + +.. _MIT license: https://opensource.org/licenses/MIT +.. _Source Code: https://github.com/daisybio/drevalpy +.. _Documentation: https://drevalpy.readthedocs.io/ +.. _Issue Tracker: https://github.com/daisybio/drevalpy/issues + +How to report a bug +------------------- + +Report bugs on the `Issue Tracker`_. + + +How to request a feature +------------------------ + +Request features on the `Issue Tracker`_. + + +How to set up your development environment +------------------------------------------ + +You need Python 3.9+ and the following tools: + +- Poetry_ +- Nox_ +- nox-poetry_ + +You can install them with: + +.. code:: console + + $ pip install poetry nox nox-poetry + +Install the package with development requirements: + +.. code:: console + + $ make install + +You can now run an interactive Python session, +or the command-line interface: + +.. code:: console + + $ poetry run python + $ poetry run drevalpy + +.. _Poetry: https://python-poetry.org/ +.. _Nox: https://nox.thea.codes/ +.. _nox-poetry: https://nox-poetry.readthedocs.io/ + + +How to test the project +----------------------- + +Run the full test suite: + +.. code:: console + + $ nox + +List the available Nox sessions: + +.. code:: console + + $ nox --list-sessions + +You can also run a specific Nox session. +For example, invoke the unit test suite like this: + +.. code:: console + + $ nox --session=tests + +Unit tests are located in the ``tests`` directory, +and are written using the pytest_ testing framework. + +.. _pytest: https://pytest.readthedocs.io/ + +How to build and view the documentation +--------------------------------------- + +This project uses Sphinx_ together with several extensions to build the documentation. +It further requires Pandoc_ to translate various formats. + +To install all required dependencies for the documentation run: + +.. code:: console + + $ pip install -r docs/requirements.txt + +Please note that drevalpy itself must also be installed. To build the documentation run: + +.. code:: console + + $ make html + +from inside the docs folder. The generated static HTML files can be found in the `_build/html` folder. +Simply open them with your favorite browser. + +.. _sphinx: https://www.sphinx-doc.org/en/master/ +.. _pandoc: https://pandoc.org/ + +How to submit changes +--------------------- + +Open a `pull request`_ to submit changes to this project against the ``development`` branch. + +Your pull request needs to meet the following guidelines for acceptance: + +- The Nox test suite must pass without errors and warnings. +- Include unit tests. This project maintains a high code coverage. +- If your changes add functionality, update the documentation accordingly. + +To run linting and code formatting checks before committing your change, you can install pre-commit as a Git hook by running the following command: + +.. code:: console + + $ nox --session=pre-commit -- install + +It is recommended to open an issue before starting work on anything. +This will allow a chance to talk it over with the owners and validate your approach. + +.. _pull request: https://github.com/daisybio/drevalpy/pulls diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..af27d94 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,26 @@ + +.. include:: readme.rst + +.. include:: _key_contributors.rst + +.. role:: small + +.. role:: smaller + +.. include:: quickstart.rst + +.. include:: news.rst + +.. toctree:: + :hidden: + :maxdepth: 2 + :caption: Contents: + + installation + usage + API + contributing + reference + +.. _github: https://github.com/daisybio/drevalpy + diff --git a/docs/installation.rst b/docs/installation.rst new file mode 100644 index 0000000..c1dd939 --- /dev/null +++ b/docs/installation.rst @@ -0,0 +1,31 @@ +.. highlight:: shell + +Installation +============ + +DrEvalPy can be installed on all three major platforms (Linux, MacOS, Windows). + +Install Python +~~~~~~~~~~~~~~ + +DrEvalPy requires python >=3.9 and <=3.11. Best practice is to use a clean conda environment (`Miniconda `_). +Follow the installation guide for your operating system, then create a new environment using + +.. code-block:: bash + + conda create -y -n drevalpy python==3.10 + + +Optional dependencies +~~~~~~~~~~~~~~~~~~~~~ + + +Installing DrEvalPy +~~~~~~~~~~~~~~~~~~~~~~ + +DrEvalPy is listed on the Python Package Index (PyPI) and can be installed with pip. Activate your conda environment (or skip this if you use a system wide python installation) and install the package (and optionally jupyterlab) using + +.. code-block:: bash + + conda activate drevalpy + pip install drevalpy jupyterlab diff --git a/docs/jobs.rst b/docs/jobs.rst new file mode 100644 index 0000000..5ef3195 --- /dev/null +++ b/docs/jobs.rst @@ -0,0 +1,41 @@ +Jobs +==== + +To run models from the catalog, you can run: + +.. code-block:: bash + + python run_suite.py --run_id my_first_run --models ElasticNet SimpleNeuralNetwork --dataset GDSC1 --test_mode LCO + +This will train and tune a neural network and an elastic net model on a subset of gene expression features and drug fingerprint features to predict IC50 values of the GDSC1 database. It will evaluate in "LCO" which is the leave-cell-line-out splitting strategy using 5 fold cross validation. +The results will be stored in + +.. code-block:: bash + + results/my_first_run/LCO + +You can visualize them using + +.. code-block:: bash + + python create_report.py --run_id my_first_run + +This will create an index.html file which you can open in your webbrowser. + +You can also run a drug response experiment using Python: + +.. code-block:: python + + from drevalpy import drug_response_experiment + + drug_response_experiment( + models=["MultiOmicsNeuralNetwork"], + baselines=["RandomForest"], + response_data="GDSC1", + metric="mse", + n_cv_splits=5, + test_mode="LPO", + run_id="my_second_run", + ) + +We recommend the use of our nextflow pipeline for computational demanding runs and for improved reproducibility. No knowledge of nextflow is required to run it. The nextflow pipeline is available here: `nf-core-drugresponseeval `_. \ No newline at end of file diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..a415832 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,36 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=python -msphinx +) +set SOURCEDIR=. +set BUILDDIR=_build +set SPHINXPROJ=drevalpy + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The Sphinx module was not found. Make sure you have Sphinx installed, + echo.then set the SPHINXBUILD environment variable to point to the full + echo.path of the 'sphinx-build' executable. Alternatively you may add the + echo.Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% + +:end +popd diff --git a/docs/news.rst b/docs/news.rst new file mode 100644 index 0000000..8a7c816 --- /dev/null +++ b/docs/news.rst @@ -0,0 +1,9 @@ +News +==== + +.. role:: date + :class: date + +.. + + -------------------------------------- diff --git a/docs/outputs.rst b/docs/outputs.rst new file mode 100644 index 0000000..493a084 --- /dev/null +++ b/docs/outputs.rst @@ -0,0 +1,7 @@ +Generated outputs +================= + +DrEvalPy creates a variety of files and groups them within the user defined output directory. The following tables provide an overview of all subdirectories and files created depending on the job that is executed. + +General directory structure +--------------------------- \ No newline at end of file diff --git a/docs/quickstart.rst b/docs/quickstart.rst new file mode 100644 index 0000000..309a0dc --- /dev/null +++ b/docs/quickstart.rst @@ -0,0 +1,9 @@ +Quickstart +---------- + +- Discuss usage, development and issues on `GitHub `_. +- Check the `Contributor Guide <./contributing.html>`_ if you want to participate in developing. + +.. + - Check our `tutorial notebook `_, the `usage principles <./usage.html>`_ or the `API <./API.html>`_. + - Consider citing `DrEvalPy <...>`_ along with original `references <./reference.html>`_. \ No newline at end of file diff --git a/docs/readme.rst b/docs/readme.rst new file mode 100644 index 0000000..6b2b3ec --- /dev/null +++ b/docs/readme.rst @@ -0,0 +1 @@ +.. include:: ../README.rst \ No newline at end of file diff --git a/docs/reference.rst b/docs/reference.rst new file mode 100644 index 0000000..7fda2d3 --- /dev/null +++ b/docs/reference.rst @@ -0,0 +1,4 @@ +How to cite +=========== + +If you want to cite DrEvalPy in your work, please use the following: \ No newline at end of file diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..d45dd64 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,4 @@ +sphinx-autobuild==2024.10.3 ; python_version >= "3.9" and python_version < "3.12" +sphinx-autodoc-typehints==1.25.3 ; python_version >= "3.9" and python_version < "3.12" +sphinx-click==6.0.0 ; python_version >= "3.9" and python_version < "3.12" +sphinx-rtd-theme==3.0.1 ; python_version >= "3.9" and python_version < "3.12" diff --git a/docs/usage.rst b/docs/usage.rst new file mode 100644 index 0000000..8473728 --- /dev/null +++ b/docs/usage.rst @@ -0,0 +1,11 @@ +Usage Principles +================ + +DrEvalPy provides a high-level API that can be easily executed with a single command by providing a config file. +The following outlines how to run a job with the high-level API, the three types of jobs available and examples for configuration and manual transformation of search results. + +.. toctree:: + :maxdepth: 1 + + jobs + outputs diff --git a/drevalpy/datasets/dataset.py b/drevalpy/datasets/dataset.py index 9f72c27..d653afa 100644 --- a/drevalpy/datasets/dataset.py +++ b/drevalpy/datasets/dataset.py @@ -246,12 +246,12 @@ def reduce_to(self, cell_line_ids: Optional[ArrayLike], drug_ids: Optional[Array def split_dataset( self, - n_cv_splits, - mode, - split_validation=True, - split_early_stopping=True, - validation_ratio=0.1, - random_state=42, + n_cv_splits: int, + mode: str, + split_validation: bool = True, + split_early_stopping: bool = True, + validation_ratio: float = 0.1, + random_state: int = 42, ) -> list[dict]: """ Splits the dataset into training, validation and test sets for cross-validation. @@ -270,7 +270,7 @@ def split_dataset( response = self.response if mode == "LPO": - cv_splits = leave_pair_out_cv( + cv_splits = _leave_pair_out_cv( n_cv_splits, response, cell_line_ids, @@ -283,7 +283,7 @@ def split_dataset( elif mode in ["LCO", "LDO"]: group = "cell_line" if mode == "LCO" else "drug" - cv_splits = leave_group_out_cv( + cv_splits = _leave_group_out_cv( group=group, n_cv_splits=n_cv_splits, response=response, @@ -299,7 +299,7 @@ def split_dataset( if split_validation and split_early_stopping: for split in cv_splits: - validation_es, early_stopping = split_early_stopping_data(split["validation"], test_mode=mode) + validation_es, early_stopping = _split_early_stopping_data(split["validation"], test_mode=mode) split["validation_es"] = validation_es split["early_stopping"] = early_stopping self.cv_splits = cv_splits @@ -400,7 +400,7 @@ def __hash__(self): def mask(self, mask: list[bool]) -> None: """ - Masks the dataset. + Removes rows from the dataset based on a boolean mask. :param mask: boolean mask """ @@ -440,7 +440,9 @@ def inverse_transform(self, response_transformation: TransformerMixin) -> None: self.predictions = response_transformation.inverse_transform(self.predictions.reshape(-1, 1)).squeeze() -def split_early_stopping_data(validation_dataset: DrugResponseDataset, test_mode: str) -> tuple[DrugResponseDataset, DrugResponseDataset]: +def _split_early_stopping_data( + validation_dataset: DrugResponseDataset, test_mode: str +) -> tuple[DrugResponseDataset, DrugResponseDataset]: """ Splits the validation dataset into a validation and an early stopping dataset. @@ -462,7 +464,7 @@ def split_early_stopping_data(validation_dataset: DrugResponseDataset, test_mode return validation_dataset, early_stopping_dataset -def leave_pair_out_cv( +def _leave_pair_out_cv( n_cv_splits: int, response: ArrayLike, cell_line_ids: ArrayLike, @@ -537,7 +539,7 @@ def leave_pair_out_cv( return cv_sets -def leave_group_out_cv( +def _leave_group_out_cv( group: str, n_cv_splits: int, response: ArrayLike, @@ -677,7 +679,9 @@ def randomize_features(self, views_to_randomize: Union[str, list], randomization feature view for this instance, for networks it is the degree distribution. """ if randomization_type not in ["permutation", "invariant"]: - raise AssertionError(f"Unknown randomization type {randomization_type!r}. Choose from 'permutation', 'invariant'.") + raise AssertionError( + f"Unknown randomization type {randomization_type!r}. Choose from 'permutation', 'invariant'." + ) if isinstance(views_to_randomize, str): views_to_randomize = [views_to_randomize] @@ -713,7 +717,8 @@ def randomize_features(self, views_to_randomize: Union[str, list], randomization else: raise ValueError( - f"No invariant randomization available for feature view " f"type {type(self.features[identifier][view])!r}." + f"No invariant randomization available for feature view " + f"type {type(self.features[identifier][view])!r}." ) self.features[identifier][view] = new_features @@ -759,14 +764,16 @@ def copy(self): """Returns a copy of the feature dataset.""" return FeatureDataset(features=copy.deepcopy(self.features)) - def add_features(self, other: "FeatureDataset") -> None: + def _add_features(self, other: "FeatureDataset") -> None: """ Adds features views from another dataset. Inner join (only common identifiers are kept). :param other: other dataset """ if len(set(self.view_names) & set(other.view_names)) != 0: - raise AssertionError("Trying to add features but feature views overlap. FeatureDatasets should be distinct.") + raise AssertionError( + "Trying to add features but feature views overlap. FeatureDatasets should be distinct." + ) if other.meta_info is not None: self.add_meta_info(other) @@ -844,7 +851,7 @@ def fit_transform_features(self, train_ids: ArrayLike, transformer: TransformerM self.features[identifier][view] = scaled_gene_expression return transformer - def apply(self, function: Callable, view: str): + def _apply(self, function: Callable, view: str): """Applies a function to the features of a view.""" for identifier in self.features: self.features[identifier][view] = function(self.features[identifier][view]) diff --git a/drevalpy/datasets/utils.py b/drevalpy/datasets/utils.py index 73ef9cf..09b166f 100644 --- a/drevalpy/datasets/utils.py +++ b/drevalpy/datasets/utils.py @@ -10,7 +10,7 @@ def download_dataset( - dataset: str, + dataset_name: str, data_path: str = "data", redownload: bool = False, ): @@ -22,18 +22,21 @@ def download_dataset( :param redownload: whether to redownload the data :return: """ - file_name = f"{dataset}.zip" + file_name = f"{dataset_name}.zip" file_path = os.path.join(data_path, file_name) - if os.path.exists(file_path) and not redownload: - print(f"{dataset} already exists, skipping download.") + extracted_folder_path = os.path.join(data_path, dataset_name) + + # Check if the extracted data exists and skip download if not redownloading + if os.path.exists(extracted_folder_path) and not redownload: + print(f"{dataset_name} is already extracted, skipping download.") else: url = "https://zenodo.org/doi/10.5281/zenodo.12633909" # Fetch the latest record - response = requests.get(url, timeout=10) + response = requests.get(url, timeout=60) if response.status_code != 200: raise requests.exceptions.HTTPError(f"Error fetching record: {response.status_code}") latest_url = response.links["linkset"]["url"] - response = requests.get(latest_url, timeout=10) + response = requests.get(latest_url, timeout=60) if response.status_code != 200: raise requests.exceptions.HTTPError(f"Error fetching record: {response.status_code}") data = response.json() @@ -45,10 +48,10 @@ def download_dataset( name_to_url = {file["key"]: file["links"]["self"] for file in data["files"]} file_url = name_to_url[file_name] # Download the file - print(f"Downloading {dataset} from {file_url}...") - response = requests.get(file_url, timeout=10) + print(f"Downloading {dataset_name} from {file_url}...") + response = requests.get(file_url, timeout=60) if response.status_code != 200: - raise requests.exceptions.HTTPError(f"Error downloading file {dataset}: " f"{response.status_code}") + raise requests.exceptions.HTTPError(f"Error downloading file {dataset_name}: " f"{response.status_code}") # Save the file with open(file_path, "wb") as f: @@ -60,7 +63,7 @@ def download_dataset( z.extract(member, data_path) os.remove(file_path) # Remove zip file after extraction - print(f"{dataset} data downloaded and extracted to {data_path}") + print(f"{dataset_name} data downloaded and extracted to {data_path}") def randomize_graph(original_graph: nx.Graph) -> nx.Graph: @@ -114,6 +117,9 @@ def permute_features( :return: permuted features """ return { - entity: {view: (features[entity][view] if view not in views_to_permute else features[other_entity][view]) for view in all_views} + entity: { + view: (features[entity][view] if view not in views_to_permute else features[other_entity][view]) + for view in all_views + } for entity, other_entity in zip(identifiers, np.random.permutation(identifiers), strict=True) } diff --git a/drevalpy/evaluation.py b/drevalpy/evaluation.py index 506875c..f522ccc 100644 --- a/drevalpy/evaluation.py +++ b/drevalpy/evaluation.py @@ -207,7 +207,9 @@ def get_mode(metric: str): elif metric in MAXIMIZATION_METRICS: mode = "max" else: - raise ValueError(f"Invalid metric: {metric}. Need to add metric to MINIMIZATION_METRICS or " f"MAXIMIZATION_METRICS?") + raise ValueError( + f"Invalid metric: {metric}. Need to add metric to MINIMIZATION_METRICS or " f"MAXIMIZATION_METRICS?" + ) return mode diff --git a/drevalpy/experiment.py b/drevalpy/experiment.py index 9cf235f..e4c9c0e 100644 --- a/drevalpy/experiment.py +++ b/drevalpy/experiment.py @@ -407,7 +407,9 @@ def handle_overwrite(path: str, overwrite: bool) -> None: os.makedirs(path, exist_ok=True) -def load_features(model: DRPModel, path_data: str, dataset: DrugResponseDataset) -> tuple[FeatureDataset, FeatureDataset]: +def load_features( + model: DRPModel, path_data: str, dataset: DrugResponseDataset +) -> tuple[FeatureDataset, FeatureDataset]: """Load and reduce cell line and drug features for a given dataset.""" cl_features = model.load_cell_line_features(data_path=path_data, dataset_name=dataset.dataset_name) drug_features = model.load_drug_features(data_path=path_data, dataset_name=dataset.dataset_name) @@ -469,7 +471,9 @@ def cross_study_prediction( train_dataset.add_rows(early_stopping_dataset) # remove rows which overlap in the training. depends on the test mode if test_mode == "LPO": - train_pairs = {f"{cl}_{drug}" for cl, drug in zip(train_dataset.cell_line_ids, train_dataset.drug_ids, strict=True)} + train_pairs = { + f"{cl}_{drug}" for cl, drug in zip(train_dataset.cell_line_ids, train_dataset.drug_ids, strict=True) + } dataset_pairs = [f"{cl}_{drug}" for cl, drug in zip(dataset.cell_line_ids, dataset.drug_ids, strict=True)] dataset.remove_rows([i for i, pair in enumerate(dataset_pairs) if pair in train_pairs]) @@ -726,7 +730,9 @@ def randomize_train_predict( cl_features, drug_features = load_features(model, path_data, train_dataset) if (view not in cl_features.get_view_names()) and (view not in drug_features.get_view_names()): - warnings.warn(f"View {view} not found in features. Skipping randomization test {test_name} " f"which includes this view.") + warnings.warn( + f"View {view} not found in features. Skipping randomization test {test_name} " f"which includes this view." + ) return cl_features_rand = cl_features.copy() if cl_features is not None else None drug_features_rand = drug_features.copy() if drug_features is not None else None @@ -750,7 +756,9 @@ def randomize_train_predict( test_dataset_rand.save(randomization_test_file) -def split_early_stopping(validation_dataset: DrugResponseDataset, test_mode: str) -> tuple[DrugResponseDataset, DrugResponseDataset]: +def split_early_stopping( + validation_dataset: DrugResponseDataset, test_mode: str +) -> tuple[DrugResponseDataset, DrugResponseDataset]: """ Split the validation dataset into a validation and early stopping dataset. @@ -1032,7 +1040,8 @@ def get_model_name_and_drug_id(model_name: str): model_name = name_split[0] if model_name not in SINGLE_DRUG_MODEL_FACTORY: raise AssertionError( - f"Model {model_name} not found in MODEL_FACTORY or SINGLE_DRUG_MODEL_FACTORY. " "Please add the model to the factory." + f"Model {model_name} not found in MODEL_FACTORY or SINGLE_DRUG_MODEL_FACTORY. " + "Please add the model to the factory." ) drug_id = name_split[1] diff --git a/drevalpy/models/SRMF/srmf.py b/drevalpy/models/SRMF/srmf.py index ca158dc..1881e2c 100644 --- a/drevalpy/models/SRMF/srmf.py +++ b/drevalpy/models/SRMF/srmf.py @@ -5,10 +5,7 @@ from drevalpy.datasets.dataset import DrugResponseDataset, FeatureDataset from drevalpy.models.drp_model import DRPModel -from drevalpy.models.utils import ( - load_and_reduce_gene_features, - load_drug_fingerprint_features, -) +from drevalpy.models.utils import load_and_reduce_gene_features, load_drug_fingerprint_features class SRMF(DRPModel): diff --git a/drevalpy/models/__init__.py b/drevalpy/models/__init__.py index 014ce07..44f5a5c 100644 --- a/drevalpy/models/__init__.py +++ b/drevalpy/models/__init__.py @@ -22,18 +22,9 @@ ] from .baselines.multi_omics_random_forest import MultiOmicsRandomForest -from .baselines.naive_pred import ( - NaiveCellLineMeanPredictor, - NaiveDrugMeanPredictor, - NaivePredictor, -) +from .baselines.naive_pred import NaiveCellLineMeanPredictor, NaiveDrugMeanPredictor, NaivePredictor from .baselines.singledrug_random_forest import SingleDrugRandomForest -from .baselines.sklearn_models import ( - ElasticNetModel, - GradientBoosting, - RandomForest, - SVMRegressor, -) +from .baselines.sklearn_models import ElasticNetModel, GradientBoosting, RandomForest, SVMRegressor from .simple_neural_network.multiomics_neural_network import MultiOmicsNeuralNetwork from .simple_neural_network.simple_neural_network import SimpleNeuralNetwork from .SRMF.srmf import SRMF diff --git a/drevalpy/models/baselines/naive_pred.py b/drevalpy/models/baselines/naive_pred.py index 5a2b05e..04dd7a0 100644 --- a/drevalpy/models/baselines/naive_pred.py +++ b/drevalpy/models/baselines/naive_pred.py @@ -195,7 +195,9 @@ def train( self.dataset_mean = np.mean(output.response) self.cell_line_means = {} - for cell_line_response, cell_line_feature in zip(unique(output.cell_line_ids), unique(cell_line_ids), strict=True): + for cell_line_response, cell_line_feature in zip( + unique(output.cell_line_ids), unique(cell_line_ids), strict=True + ): responses_cl = output.response[cell_line_feature == output.cell_line_ids] if len(responses_cl) > 0: # prevent nan response diff --git a/drevalpy/models/drp_model.py b/drevalpy/models/drp_model.py index fa1e7e3..c8fed41 100644 --- a/drevalpy/models/drp_model.py +++ b/drevalpy/models/drp_model.py @@ -286,7 +286,8 @@ def train( for i, drug in enumerate(drugs): if drug not in self.models: raise AssertionError( - f"Drug {drug} not in models. Maybe the CompositeDrugModel was not built or drug " f"missing from train data." + f"Drug {drug} not in models. Maybe the CompositeDrugModel was not built or drug " + f"missing from train data." ) print(f"Training model for drug {drug} ({i+1}/{len(drugs)})") output_mask = output.drug_ids == drug diff --git a/drevalpy/models/simple_neural_network/simple_neural_network.py b/drevalpy/models/simple_neural_network/simple_neural_network.py index ab409f2..4fc1815 100644 --- a/drevalpy/models/simple_neural_network/simple_neural_network.py +++ b/drevalpy/models/simple_neural_network/simple_neural_network.py @@ -63,7 +63,7 @@ def train( # Apply arcsinh transformation and scaling to gene expression features if "gene_expression" in self.cell_line_views: cell_line_input = cell_line_input.copy() - cell_line_input.apply(function=np.arcsinh, view="gene_expression") + cell_line_input._apply(function=np.arcsinh, view="gene_expression") self.gene_expression_scaler = cell_line_input.fit_transform_features( train_ids=np.unique(output.cell_line_ids), transformer=self.gene_expression_scaler, @@ -106,7 +106,7 @@ def predict( # Apply transformation to gene expression features before prediction if "gene_expression" in self.cell_line_views: cell_line_input = cell_line_input.copy() - cell_line_input.apply(function=np.arcsinh, view="gene_expression") + cell_line_input._apply(function=np.arcsinh, view="gene_expression") cell_line_input.transform_features( ids=np.unique(cell_line_ids), transformer=self.gene_expression_scaler, diff --git a/drevalpy/models/simple_neural_network/utils.py b/drevalpy/models/simple_neural_network/utils.py index f6eeb5b..45e8351 100644 --- a/drevalpy/models/simple_neural_network/utils.py +++ b/drevalpy/models/simple_neural_network/utils.py @@ -37,9 +37,7 @@ def __init__( self.drug_input = drug_input for cl_view in self.cell_line_views: if cl_view not in cell_line_input.view_names: - raise AssertionError( - f"Cell line view {cl_view} not found in cell line input" - ) + raise AssertionError(f"Cell line view {cl_view} not found in cell line input") for d_view in self.drug_views: if d_view not in drug_input.view_names: raise AssertionError(f"Drug view {d_view} not found in drug input") @@ -67,13 +65,9 @@ def __getitem__(self, idx): if drug_features is None: drug_features = self.drug_input.features[drug_id][d_view] else: - drug_features = np.concatenate( - (drug_features, self.drug_input.features[drug_id][d_view]) - ) + drug_features = np.concatenate((drug_features, self.drug_input.features[drug_id][d_view])) if not isinstance(cell_line_features, np.ndarray): - raise TypeError( - f"Cell line features for {cell_line_id} are not numpy array" - ) + raise TypeError(f"Cell line features for {cell_line_id} are not numpy array") if not isinstance(drug_features, np.ndarray): raise TypeError(f"Drug features for {drug_id} are not numpy array") data = np.concatenate((cell_line_features, drug_features)) @@ -156,7 +150,7 @@ def fit( shuffle=True, num_workers=num_workers, persistent_workers=True, - drop_last=True, # to avoid batch norm errors, if last batch is smaller than batch_size, it is not processed + drop_last=True # to avoid batch norm errors, if last batch is smaller than batch_size, it is not processed ) val_loader = None @@ -180,9 +174,7 @@ def fit( # Train the model monitor = "train_loss" if (val_loader is None) else "val_loss" - early_stop_callback = EarlyStopping( - monitor=monitor, mode="min", patience=patience - ) + early_stop_callback = EarlyStopping(monitor=monitor, mode="min", patience=patience) name = "version-" + "".join( [random.choice("0123456789abcdef") for i in range(20)] ) # preventing conflicts of filenames @@ -194,9 +186,7 @@ def fit( filename=name, ) - progress_bar = TQDMProgressBar( - refresh_rate=trainer_params["progress_bar_refresh_rate"] - ) + progress_bar = TQDMProgressBar(refresh_rate=trainer_params["progress_bar_refresh_rate"]) trainer_params_copy = trainer_params.copy() del trainer_params_copy["progress_bar_refresh_rate"] @@ -210,9 +200,7 @@ def fit( self.checkpoint_callback, progress_bar, ], - default_root_dir=os.path.join( - os.getcwd(), "nn_baseline_checkpoints/lightning_logs/" + name - ), + default_root_dir=os.path.join(os.getcwd(), "nn_baseline_checkpoints/lightning_logs/" + name), **trainer_params_copy, ) if val_loader is None: @@ -251,15 +239,11 @@ def initialize_model(self, x): :return: """ n_features = x.size(1) - self.fully_connected_layers.append( - nn.Linear(n_features, self.n_units_per_layer[0]) - ) + self.fully_connected_layers.append(nn.Linear(n_features, self.n_units_per_layer[0])) self.batch_norm_layers.append(nn.BatchNorm1d(self.n_units_per_layer[0])) for i in range(1, len(self.n_units_per_layer)): - self.fully_connected_layers.append( - nn.Linear(self.n_units_per_layer[i - 1], self.n_units_per_layer[i]) - ) + self.fully_connected_layers.append(nn.Linear(self.n_units_per_layer[i - 1], self.n_units_per_layer[i])) self.batch_norm_layers.append(nn.BatchNorm1d(self.n_units_per_layer[i])) self.fully_connected_layers.append(nn.Linear(self.n_units_per_layer[-1], 1)) diff --git a/drevalpy/models/utils.py b/drevalpy/models/utils.py index a4c95b1..d94d800 100644 --- a/drevalpy/models/utils.py +++ b/drevalpy/models/utils.py @@ -11,6 +11,7 @@ import pandas as pd from drevalpy.datasets.dataset import FeatureDataset +from drevalpy.datasets.utils import download_dataset def load_cl_ids_from_csv(path: str, dataset_name: str) -> FeatureDataset: @@ -44,6 +45,7 @@ def load_and_reduce_gene_features( if dataset_name == "Toy_Data": cl_features = load_toy_features(data_path, "cell_line") dataset_name = "GDSC1" + download_dataset(dataset_name=dataset_name, data_path=data_path, redownload=False) else: ge = pd.read_csv(f"{data_path}/{dataset_name}/{feature_type}.csv", index_col=0) cl_features = FeatureDataset( @@ -71,7 +73,8 @@ def load_and_reduce_gene_features( ) else: raise ValueError( - f"The following genes are missing from the dataset {dataset_name} for {feature_type}: " f"{', '.join(missing_genes_list)}" + f"The following genes are missing from the dataset {dataset_name} for {feature_type}: " + f"{', '.join(missing_genes_list)}" ) # Only proceed with genes that are available @@ -126,7 +129,9 @@ def load_drug_fingerprint_features(data_path: str, dataset_name: str) -> Feature f"{data_path}/{dataset_name}/drug_fingerprints/" "drug_name_to_demorgan_128_map.csv", index_col=0, ).T - return FeatureDataset(features={drug: {"fingerprints": fingerprints.loc[drug].values} for drug in fingerprints.index}) + return FeatureDataset( + features={drug: {"fingerprints": fingerprints.loc[drug].values} for drug in fingerprints.index} + ) def get_multiomics_feature_dataset( @@ -169,7 +174,7 @@ def get_multiomics_feature_dataset( dataset_name=dataset_name, ) for fd in [me_dataset, mu_dataset, cnv_dataset]: - ge_dataset.add_features(fd) + ge_dataset._add_features(fd) return ge_dataset diff --git a/drevalpy/utils.py b/drevalpy/utils.py index 43e678f..1caadd3 100644 --- a/drevalpy/utils.py +++ b/drevalpy/utils.py @@ -204,13 +204,17 @@ def check_arguments(args): # TODO Allow for custom randomization tests maybe via config file if args.randomization_mode[0] != "None": if not all(randomization in ["SVCC", "SVRC", "SVSC", "SVRD"] for randomization in args.randomization_mode): - raise AssertionError("At least one invalid randomization mode. Available randomization modes are SVCC, " "SVRC, SVSC, SVRD") + raise AssertionError( + "At least one invalid randomization mode. Available randomization modes are SVCC, " "SVRC, SVSC, SVRD" + ) if args.curve_curator: raise NotImplementedError("CurveCurator not implemented") if args.response_transformation not in ["None", "standard", "minmax", "robust"]: raise AssertionError("Invalid response_transformation. Choose from None, standard, minmax, robust") if args.optim_metric not in AVAILABLE_METRICS: - raise AssertionError(f"Invalid optim_metric for hyperparameter tuning. Choose from" f" {list(AVAILABLE_METRICS.keys())}") + raise AssertionError( + f"Invalid optim_metric for hyperparameter tuning. Choose from" f" {list(AVAILABLE_METRICS.keys())}" + ) def main(args): diff --git a/drevalpy/visualization/critical_difference_plot.py b/drevalpy/visualization/critical_difference_plot.py index 309d0ce..936cc19 100644 --- a/drevalpy/visualization/critical_difference_plot.py +++ b/drevalpy/visualization/critical_difference_plot.py @@ -417,7 +417,9 @@ def wilcoxon_holm(alpha=0.05, df_perf=None): # get the list of classifiers who have been tested on nb_max_datasets classifiers = list(df_counts.loc[df_counts["count"] == max_nb_datasets]["classifier_name"]) # test the null hypothesis using friedman before doing a post-hoc analysis - friedman_p_value = friedmanchisquare(*(np.array(df_perf.loc[df_perf["classifier_name"] == c]["accuracy"]) for c in classifiers))[1] + friedman_p_value = friedmanchisquare( + *(np.array(df_perf.loc[df_perf["classifier_name"] == c]["accuracy"]) for c in classifiers) + )[1] if friedman_p_value >= alpha: # then the null hypothesis over the entire classifiers cannot be rejected print("the null hypothesis over the entire classifiers cannot be rejected") @@ -469,7 +471,9 @@ def wilcoxon_holm(alpha=0.05, df_perf=None): break # compute the average ranks to be returned (useful for drawing the cd diagram) # sort the dataframe of performances - sorted_df_perf = df_perf.loc[df_perf["classifier_name"].isin(classifiers)].sort_values(["classifier_name", "dataset_name"]) + sorted_df_perf = df_perf.loc[df_perf["classifier_name"].isin(classifiers)].sort_values( + ["classifier_name", "dataset_name"] + ) # get the rank data rank_data = np.array(sorted_df_perf["accuracy"]).reshape(m, max_nb_datasets) diff --git a/drevalpy/visualization/heatmap.py b/drevalpy/visualization/heatmap.py index 22ae652..c3ae8b2 100644 --- a/drevalpy/visualization/heatmap.py +++ b/drevalpy/visualization/heatmap.py @@ -77,7 +77,9 @@ def __draw_subplots__(self, plot_setting): colorscale = "Blues" elif plot_setting == "correlations": corr_columns = [ - col for col in self.df.columns if "Pearson" in col or "Spearman" in col or "Kendall" in col or "Partial_Correlation" in col + col + for col in self.df.columns + if "Pearson" in col or "Spearman" in col or "Kendall" in col or "Partial_Correlation" in col ] corr_columns.sort() dt = self.df[corr_columns] diff --git a/drevalpy/visualization/utils.py b/drevalpy/visualization/utils.py index 90003af..df82e5e 100644 --- a/drevalpy/visualization/utils.py +++ b/drevalpy/visualization/utils.py @@ -69,7 +69,9 @@ def parse_results(path_to_results: str): model_name, ) = evaluate_file(pred_file=file, test_mode=lpo_lco_ldo, model_name=algorithm) - evaluation_results = overall_eval if evaluation_results is None else pd.concat([evaluation_results, overall_eval]) + evaluation_results = ( + overall_eval if evaluation_results is None else pd.concat([evaluation_results, overall_eval]) + ) true_vs_pred = t_vs_p if true_vs_pred is None else pd.concat([true_vs_pred, t_vs_p]) if eval_results_per_drug is not None: @@ -199,14 +201,16 @@ def prep_results(eval_results, eval_results_per_drug, eval_results_per_cell_line new_columns.index = eval_results.index eval_results = pd.concat([new_columns.drop("split", axis=1), eval_results], axis=1) if eval_results_per_drug is not None: - eval_results_per_drug[["algorithm", "rand_setting", "LPO_LCO_LDO", "split", "CV_split"]] = eval_results_per_drug["model"].str.split( - "_", expand=True + eval_results_per_drug[["algorithm", "rand_setting", "LPO_LCO_LDO", "split", "CV_split"]] = ( + eval_results_per_drug["model"].str.split("_", expand=True) ) if eval_results_per_cell_line is not None: - eval_results_per_cell_line[["algorithm", "rand_setting", "LPO_LCO_LDO", "split", "CV_split"]] = eval_results_per_cell_line[ - "model" - ].str.split("_", expand=True) - t_vs_p[["algorithm", "rand_setting", "LPO_LCO_LDO", "split", "CV_split"]] = t_vs_p["model"].str.split("_", expand=True) + eval_results_per_cell_line[["algorithm", "rand_setting", "LPO_LCO_LDO", "split", "CV_split"]] = ( + eval_results_per_cell_line["model"].str.split("_", expand=True) + ) + t_vs_p[["algorithm", "rand_setting", "LPO_LCO_LDO", "split", "CV_split"]] = t_vs_p["model"].str.split( + "_", expand=True + ) return ( eval_results, diff --git a/drevalpy/visualization/violin.py b/drevalpy/visualization/violin.py index cb143a2..7e19cc7 100644 --- a/drevalpy/visualization/violin.py +++ b/drevalpy/visualization/violin.py @@ -54,7 +54,13 @@ def __draw__(self) -> None: args=[ { "visible": [False] * self.count_r2 - + [True] * (self.count_pearson + self.count_spearman + self.count_kendall + self.count_partial_correlation) + + [True] + * ( + self.count_pearson + + self.count_spearman + + self.count_kendall + + self.count_partial_correlation + ) + [False] * (self.count_mse + self.count_rmse + self.count_mae) }, {"title": "All Correlations"}, diff --git a/model_checkpoints/README.md b/model_checkpoints/README.md deleted file mode 100644 index 2570ab6..0000000 --- a/model_checkpoints/README.md +++ /dev/null @@ -1 +0,0 @@ -This directory is used for saving the trained models. diff --git a/noxfile.py b/noxfile.py new file mode 100644 index 0000000..cd2def8 --- /dev/null +++ b/noxfile.py @@ -0,0 +1,217 @@ +"""Nox sessions.""" + +import os +import shlex +import shutil +import sys +from pathlib import Path +from textwrap import dedent + +import nox +from rich import print + +try: + from nox_poetry import Session, session +except ImportError: + print("[bold red]Did not find nox-poetry installed in your current environment!") + print("[bold blue]Try installing it using [bold green]pip install nox-poetry [bold blue]! ") + sys.exit(1) + +package = "drevalpy" +python_versions = ["3.10", "3.11"] +nox.options.sessions = ( + "pre-commit", + "safety", + "mypy", + "tests", + "xdoctest", + "docs-build", +) + + +def activate_virtualenv_in_precommit_hooks(session: Session) -> None: + """Activate virtualenv in hooks installed by pre-commit. + + This function patches git hooks installed by pre-commit to activate the + session's virtual environment. This allows pre-commit to locate hooks in + that environment when invoked from git. + + :param session: The Session object. + """ + assert session.bin is not None # noqa: S101 + + # Only patch hooks containing a reference to this session's bindir. Support + # quoting rules for Python and bash, but strip the outermost quotes so we + # can detect paths within the bindir, like /python. + bindirs = [ + bindir[1:-1] if bindir[0] in "'\"" else bindir for bindir in (repr(session.bin), shlex.quote(session.bin)) + ] + + virtualenv = session.env.get("VIRTUAL_ENV") + if virtualenv is None: + return + + headers = { + # pre-commit < 2.16.0 + "python": f"""\ + import os + os.environ["VIRTUAL_ENV"] = {virtualenv!r} + os.environ["PATH"] = os.pathsep.join(( + {session.bin!r}, + os.environ.get("PATH", ""), + )) + """, + # pre-commit >= 2.16.0 + "bash": f"""\ + VIRTUAL_ENV={shlex.quote(virtualenv)} + PATH={shlex.quote(session.bin)}"{os.pathsep}$PATH" + """, + # pre-commit >= 2.17.0 on Windows forces sh shebang + "/bin/sh": f"""\ + VIRTUAL_ENV={shlex.quote(virtualenv)} + PATH={shlex.quote(session.bin)}"{os.pathsep}$PATH" + """, + } + + hookdir = Path(".git") / "hooks" + if not hookdir.is_dir(): + return + + for hook in hookdir.iterdir(): + if hook.name.endswith(".sample") or not hook.is_file(): + continue + + if not hook.read_bytes().startswith(b"#!"): + continue + + text = hook.read_text() + + if not any(Path("A") == Path("a") and bindir.lower() in text.lower() or bindir in text for bindir in bindirs): + continue + + lines = text.splitlines() + + for executable, header in headers.items(): + if executable in lines[0].lower(): + lines.insert(1, dedent(header)) + hook.write_text("\n".join(lines)) + break + + +@session(name="pre-commit", python=python_versions) +def precommit(session: Session) -> None: + """Lint using pre-commit.""" + args = session.posargs or ["run", "--all-files"] + session.install( + "black", + "flake8", + "flake8-bandit", + "flake8-bugbear", + "flake8-docstrings", + "darglint", + "flake8-rst-docstrings", + "isort", + "pep8-naming", + "pre-commit", + "pre-commit-hooks", + "pyupgrade", + ) + session.run("pre-commit", *args) + if args and args[0] == "install": + activate_virtualenv_in_precommit_hooks(session) + + +@session(python=python_versions) +def safety(session: Session) -> None: + """Scan dependencies for insecure packages.""" + to_ignore = "--ignore=70612" + requirements = session.poetry.export_requirements() + session.install("safety") + session.run("safety", "check", "--full-report", f"--file={requirements}", to_ignore) + + +@session(python=python_versions) +def mypy(session: Session) -> None: + """Type-check using mypy.""" + args = session.posargs or ["drevalpy", "tests", "docs/conf.py"] + session.install(".") + session.install("mypy", "pytest", "types-requests", "types-attrs") + session.run("mypy", *args) + + +@session(python=python_versions) +def tests(session: Session) -> None: + """Run the test suite.""" + session.install(".") + session.install("coverage[toml]", "pytest", "pygments") + try: + session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs) + finally: + if session.interactive: + session.notify("coverage") + + +@session +def coverage(session: Session) -> None: + """Produce the coverage report.""" + # Do not use session.posargs unless this is the only session. + nsessions = len(session._runner.manifest) # type: ignore[attr-defined] + has_args = session.posargs and nsessions == 1 + args = session.posargs if has_args else ["report", "-i"] + + session.install("coverage[toml]") + + if not has_args and any(Path().glob(".coverage.*")): + session.run("coverage", "combine") + + session.run("coverage", *args) + + +@session(python=python_versions) +def typeguard(session: Session) -> None: + """Runtime type checking using Typeguard.""" + session.install(".") + session.install("pytest", "typeguard", "pygments") + session.run("pytest", f"--typeguard-packages={package}", *session.posargs) + + +@session(python=python_versions) +def xdoctest(session: Session) -> None: + """Run examples with xdoctest.""" + args = session.posargs or ["all"] + session.install(".") + session.install("xdoctest[colors]") + session.run("python", "-m", "xdoctest", package, *args) + + +@session(name="docs-build", python=python_versions) +def docs_build(session: Session) -> None: + """Build the documentation.""" + args = session.posargs or ["docs", "docs/_build"] + session.install("-r", "./docs/requirements.txt") + + build_dir = Path("docs", "_build") + if build_dir.exists(): + shutil.rmtree(build_dir) + + session.run("sphinx-build", *args) + + +@session(python=python_versions) +def docs(session: Session) -> None: + """Build and serve the documentation with live reloading on file changes.""" + args = session.posargs or ["--open-browser", "docs", "docs/_build"] + session.install(".") + session.install( + "sphinx", + "sphinx-autobuild", + "sphinx-click", + "sphinx-rtd-theme", + "sphinx-rtd-dark-mode", + ) + + build_dir = Path("docs", "_build") + if build_dir.exists(): + shutil.rmtree(build_dir) + + session.run("sphinx-autobuild", *args) diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..8bdd8d7 --- /dev/null +++ b/poetry.lock 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"3.9" and python_version < "3.12" +exceptiongroup==1.2.2 ; python_version >= "3.9" and python_version < "3.11" +filelock==3.16.1 ; python_version >= "3.9" and python_version < "3.12" +flake8-bandit==4.1.1 ; python_version >= "3.9" and python_version < "3.12" +flake8-bugbear==24.8.19 ; python_version >= "3.9" and python_version < "3.12" +flake8-docstrings==1.7.0 ; python_version >= "3.9" and python_version < "3.12" +flake8-rst-docstrings==0.3.0 ; python_version >= "3.9" and python_version < "3.12" +flake8==7.1.1 ; python_version >= "3.9" and python_version < "3.12" +flaky==3.8.1 ; python_version >= "3.9" and python_version < "3.12" +fonttools==4.54.1 ; python_version >= "3.9" and python_version < "3.12" +frozenlist==1.4.1 ; python_version >= "3.9" and python_version < "3.12" +fsspec==2024.9.0 ; python_version >= "3.9" and python_version < "3.12" +fsspec[http]==2024.9.0 ; python_version >= "3.9" and python_version < "3.12" +h11==0.14.0 ; python_version >= "3.9" and python_version < "3.12" +identify==2.6.1 ; python_version >= "3.9" and python_version < "3.12" +idna==3.10 ; python_version >= "3.9" and python_version < "3.12" +imagesize==1.4.1 ; python_version >= "3.9" and python_version < "3.12" +importlib-metadata==8.5.0 ; python_version >= "3.9" and python_version < "3.10" +importlib-resources==6.4.5 ; python_version >= "3.9" and python_version < "3.10" +iniconfig==2.0.0 ; python_version >= "3.9" and python_version < "3.12" +isort==5.13.2 ; python_version >= "3.9" and python_version < "3.12" +jinja2==3.1.4 ; python_version >= "3.9" and python_version < "3.12" +joblib==1.4.2 ; python_version >= "3.9" and python_version < "3.12" +kiwisolver==1.4.7 ; python_version >= "3.9" and python_version < "3.12" +lightning-utilities==0.11.7 ; python_version >= "3.9" and python_version < "3.12" +markdown-it-py==3.0.0 ; python_version >= "3.9" and python_version < "3.12" +markupsafe==3.0.1 ; python_version >= "3.9" and python_version < "3.12" +matplotlib==3.9.2 ; python_version >= "3.9" and python_version < "3.12" +mccabe==0.7.0 ; python_version >= "3.9" and python_version < "3.12" +mdurl==0.1.2 ; python_version >= "3.9" and python_version < "3.12" +mpmath==1.3.0 ; python_version >= "3.9" and python_version < "3.12" +multidict==6.1.0 ; python_version >= "3.9" and python_version < "3.12" +mypy-extensions==1.0.0 ; python_version >= "3.9" and python_version < "3.12" +networkx==3.2.1 ; python_version >= "3.9" and python_version < "3.12" +nodeenv==1.9.1 ; python_version >= "3.9" and python_version < "3.12" +nox-poetry==1.0.3 ; python_version >= "3.9" and python_version < "3.12" +nox==2024.10.9 ; python_version >= "3.9" and python_version < "3.12" +numpy==1.24.4 ; python_version >= "3.9" and python_version < "3.12" +nvidia-cublas-cu12==12.1.3.1 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-cuda-cupti-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-cuda-nvrtc-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-cuda-runtime-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-cudnn-cu12==9.1.0.70 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-cufft-cu12==11.0.2.54 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-curand-cu12==10.3.2.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-cusolver-cu12==11.4.5.107 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-cusparse-cu12==12.1.0.106 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-nccl-cu12==2.20.5 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-nvjitlink-cu12==12.6.77 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +nvidia-nvtx-cu12==12.1.105 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version >= "3.9" and python_version < "3.12" +packaging==24.1 ; python_version >= "3.9" and python_version < "3.12" +pandas-flavor==0.6.0 ; python_version >= "3.9" and python_version < "3.12" +pandas==2.2.3 ; python_version >= "3.9" and python_version < "3.12" +pathspec==0.12.1 ; python_version >= "3.9" and python_version < "3.12" +patsy==0.5.6 ; python_version >= "3.9" and python_version < "3.12" +pbr==6.1.0 ; python_version >= "3.9" and python_version < "3.12" +pillow==11.0.0 ; python_version >= "3.9" and python_version < "3.12" +pingouin==0.5.5 ; python_version >= "3.9" and python_version < "3.12" +platformdirs==4.3.6 ; python_version >= "3.9" and python_version < "3.12" +pluggy==1.5.0 ; python_version >= "3.9" and python_version < "3.12" +pre-commit-hooks==5.0.0 ; python_version >= "3.9" and python_version < "3.12" +pre-commit==4.0.1 ; python_version >= "3.9" and python_version < "3.12" +propcache==0.2.0 ; python_version >= "3.9" and python_version < "3.12" +pycodestyle==2.12.1 ; python_version >= "3.9" and python_version < "3.12" +pydocstyle==6.3.0 ; python_version >= "3.9" and python_version < "3.12" +pyflakes==3.2.0 ; python_version >= "3.9" and python_version < "3.12" +pygments==2.18.0 ; python_version >= "3.9" and python_version < "3.12" +pyparsing==3.2.0 ; python_version >= "3.9" and python_version < "3.12" +pytest==8.3.3 ; python_version >= "3.9" and python_version < "3.12" +python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_version < "3.12" +pytorch-lightning==2.4.0 ; python_version >= "3.9" and python_version < "3.12" +pytz==2024.2 ; python_version >= "3.9" and python_version < "3.12" +pyupgrade==3.18.0 ; python_version >= "3.9" and python_version < "3.12" +pyyaml==6.0.2 ; python_version >= "3.9" and python_version < "3.12" +requests==2.32.3 ; python_version >= "3.9" and python_version < "3.12" +restructuredtext-lint==1.4.0 ; python_version >= "3.9" and python_version < "3.12" +rich==13.9.2 ; python_version >= "3.9" and python_version < "3.12" +ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.9" +ruamel-yaml==0.18.6 ; python_version >= "3.9" and python_version < "3.12" +scikit-learn==1.5.2 ; python_version >= "3.9" and python_version < "3.12" +scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.12" +seaborn==0.13.2 ; python_version >= "3.9" and python_version < "3.12" +setuptools==75.1.0 ; python_version >= "3.9" and python_version < "3.12" +six==1.16.0 ; python_version >= "3.9" and python_version < "3.12" +sniffio==1.3.1 ; python_version >= "3.9" and python_version < "3.12" +snowballstemmer==2.2.0 ; python_version >= "3.9" and python_version < "3.12" +sphinx-autobuild==2024.10.3 ; python_version >= "3.9" and python_version < "3.12" +sphinx-autodoc-typehints==1.25.3 ; python_version >= "3.9" and python_version < "3.12" +sphinx-click==6.0.0 ; python_version >= "3.9" and python_version < "3.12" +sphinx-rtd-theme==3.0.1 ; python_version >= "3.9" and python_version < "3.12" +sphinx==7.4.7 ; python_version >= "3.9" and python_version < "3.12" +sphinxcontrib-applehelp==2.0.0 ; python_version >= "3.9" and python_version < "3.12" +sphinxcontrib-devhelp==2.0.0 ; python_version >= "3.9" and python_version < "3.12" +sphinxcontrib-htmlhelp==2.1.0 ; python_version >= "3.9" and python_version < "3.12" +sphinxcontrib-jquery==4.1 ; python_version >= "3.9" and python_version < "3.12" +sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.9" and python_version < "3.12" +sphinxcontrib-qthelp==2.0.0 ; python_version >= "3.9" and python_version < "3.12" +sphinxcontrib-serializinghtml==2.0.0 ; python_version >= "3.9" and python_version < "3.12" +starlette==0.40.0 ; python_version >= "3.9" and python_version < "3.12" +statsmodels==0.14.4 ; python_version >= "3.9" and python_version < "3.12" +stevedore==5.3.0 ; python_version >= "3.9" and python_version < "3.12" +sympy==1.13.3 ; python_version >= "3.9" and python_version < "3.12" +tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.12" +threadpoolctl==3.5.0 ; python_version >= "3.9" and python_version < "3.12" +tokenize-rt==6.0.0 ; python_version >= "3.9" and python_version < "3.12" +tomli==2.0.2 ; python_version >= "3.9" and python_version < "3.11" +tomlkit==0.13.2 ; python_version >= "3.9" and python_version < "3.12" +torch==2.4.1 ; python_version >= "3.9" and python_version < "3.12" +torchmetrics==1.4.3 ; python_version >= "3.9" and python_version < "3.12" +tqdm==4.66.5 ; python_version >= "3.9" and python_version < "3.12" +triton==3.0.0 ; platform_system == "Linux" and platform_machine == "x86_64" and python_version < "3.12" and python_version >= "3.9" +typing-extensions==4.12.2 ; python_version >= "3.9" and python_version < "3.12" +tzdata==2024.2 ; python_version >= "3.9" and python_version < "3.12" +urllib3==2.2.3 ; python_version >= "3.9" and python_version < "3.12" +uvicorn==0.31.1 ; python_version >= "3.9" and python_version < "3.12" +virtualenv==20.26.6 ; python_version >= "3.9" and python_version < "3.12" +watchfiles==0.24.0 ; python_version >= "3.9" and python_version < "3.12" +websockets==13.1 ; python_version >= "3.9" and python_version < "3.12" +xarray==2024.7.0 ; python_version >= "3.9" and python_version < "3.12" +yarl==1.15.2 ; python_version >= "3.9" and python_version < "3.12" +zipp==3.20.2 ; python_version >= "3.9" and python_version < "3.10" diff --git a/tests/individual_models/conftest.py b/tests/individual_models/conftest.py new file mode 100644 index 0000000..edf7f9b --- /dev/null +++ b/tests/individual_models/conftest.py @@ -0,0 +1,44 @@ +import os +import pickle +import tempfile +import zipfile + +import pytest +import requests + +from drevalpy.datasets.dataset import DrugResponseDataset, FeatureDataset + + +@pytest.fixture(scope="session") +def sample_dataset() -> tuple[DrugResponseDataset, FeatureDataset, FeatureDataset]: + seconds = 30 + url = "https://zenodo.org/doi/10.5281/zenodo.12633909" + # Fetch the latest record + response = requests.get(url, timeout=seconds) + latest_url = response.links["linkset"]["url"] + response = requests.get(latest_url, timeout=seconds) + data = response.json() + name_to_url = {file["key"]: file["links"]["self"] for file in data["files"]} + tmpdir = tempfile.TemporaryDirectory() + toy_data_url = name_to_url["Toy_Data.zip"] + response = requests.get(toy_data_url, timeout=seconds) + file_path = os.path.join(tmpdir.name, "Toy_Data.zip") + + print(f"Loading Toy Dataset from Zenodo, from {data['created']}") + + with open(file_path, "wb") as f: + f.write(response.content) + + with zipfile.ZipFile(file_path, "r") as zip_ref: + zip_ref.extractall(tmpdir.name) + + with open(os.path.join(tmpdir.name, "Toy_Data", "toy_data_drp_dataset.pkl"), "rb") as f: + drug_response = pickle.load(f) + with open(os.path.join(tmpdir.name, "Toy_Data", "toy_data_cl_features.pkl"), "rb") as f: + cell_line_features = pickle.load(f) + with open( + os.path.join(tmpdir.name, "Toy_Data", "toy_data_drug_features.pkl"), + "rb", + ) as f: + drug_features = pickle.load(f) + return drug_response, cell_line_features, drug_features diff --git a/tests/test_dataset.py b/tests/test_dataset.py index dbccdd6..42b23ec 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -227,14 +227,10 @@ def test_split_response_dataset(mode, split_validation): "validation_es", "early_stopping", ]: - validation_pairs = set( - zip( - split[val_es].cell_line_ids, - split[val_es].drug_ids, - strict=True, - ) - ) - assert validation_pairs.isdisjoint(test_pairs) # Check for disjointness between validation and test pairs + validation_pairs = set(zip(split[val_es].cell_line_ids, split[val_es].drug_ids, strict=True)) + assert validation_pairs.isdisjoint( + test_pairs + ) # Check for disjointness between validation and test pairs tempdir = tempfile.TemporaryDirectory() dataset.save_splits(path=tempdir.name) diff --git a/tests/test_drp_model.py b/tests/test_drp_model.py index 052f5f7..9d059c3 100644 --- a/tests/test_drp_model.py +++ b/tests/test_drp_model.py @@ -257,7 +257,9 @@ def test_get_multiomics_feature_dataset(gene_list): assert np.all(common_cls == ["22Rv1", "CAL-120"]) assert len(dataset.meta_info) == 4 if gene_list is None: - assert np.all(dataset.meta_info["gene_expression"] == ["TSPAN6", "TNMD", "BRCA1", "SCYL3", "HDAC1", "INSIG1", "FOXO3"]) + assert np.all( + dataset.meta_info["gene_expression"] == ["TSPAN6", "TNMD", "BRCA1", "SCYL3", "HDAC1", "INSIG1", "FOXO3"] + ) for key in dataset.meta_info: assert len(dataset.meta_info[key]) == 7 elif gene_list == "landmark_genes": diff --git a/tests/test_evaluation.py b/tests/test_evaluation.py index e0fc21c..d50486a 100644 --- a/tests/test_evaluation.py +++ b/tests/test_evaluation.py @@ -5,13 +5,7 @@ from sklearn.metrics import mean_absolute_error, mean_squared_error, r2_score from drevalpy.datasets.dataset import DrugResponseDataset -from drevalpy.evaluation import ( - evaluate, - kendall, - partial_correlation, - pearson, - spearman, -) +from drevalpy.evaluation import evaluate, kendall, partial_correlation, pearson, spearman def test_evaluate(): diff --git a/tests/test_run_suite.py b/tests/test_run_suite.py index 5d6062d..014ee79 100644 --- a/tests/test_run_suite.py +++ b/tests/test_run_suite.py @@ -22,11 +22,11 @@ "randomization_mode": ["SVRC"], "randomization_type": "permutation", "n_trials_robustness": 2, - "cross_study_datasets": ["GDSC2"], + "cross_study_datasets": ["GDSC1"], "curve_curator": False, "overwrite": False, "optim_metric": "RMSE", - "n_cv_splits": 5, + "n_cv_splits": 2, "response_transformation": "None", "multiprocessing": False, "path_data": "../data", @@ -73,9 +73,14 @@ def test_run_suite(args): assert "predictions" in evaluation_results.rand_setting.unique() if len(args.randomization_mode) > 0: for rand_setting in args.randomization_mode: - assert any(setting.startswith(f"randomize-{rand_setting}") for setting in evaluation_results.rand_setting.unique()) + assert any( + setting.startswith(f"randomize-{rand_setting}") for setting in evaluation_results.rand_setting.unique() + ) if args.n_trials_robustness > 0: - assert any(setting.startswith(f"robustness-{args.n_trials_robustness}") for setting in evaluation_results.rand_setting.unique()) + assert any( + setting.startswith(f"robustness-{args.n_trials_robustness}") + for setting in evaluation_results.rand_setting.unique() + ) assert all(test_mode in evaluation_results.LPO_LCO_LDO.unique() for test_mode in args.test_mode) assert evaluation_results.CV_split.astype(int).max() == (args.n_cv_splits - 1) assert evaluation_results.Pearson.astype(float).max() > 0.5