Merge branch 'main' of github.com:daisybio/drevalpy

Author: JudithBernett

.github/workflows/build_package.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python: ["3.9", "3.10"]
+        python: ["3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/publish-docker.yml

@@ -2,9 +2,6 @@ name: Create and publish a Docker image
 
 # Configures this workflow to run every time a release is published
 on:
-  push:
-    branches:
-      - main
   release:
     types: [published]
 

.github/workflows/publish_docs.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.11"
 
       - name: Install pip
         run: |

.github/workflows/python-package.yml

@@ -5,7 +5,7 @@ name: Python package
 
 on:
   pull_request:
-    types: [opened, reopened]
+    branches: [main, development]
   release:
     types: [published]
 
@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11", "3.12"]
 
     steps:
       - name: Check out the repository
@@ -44,6 +44,3 @@ jobs:
           poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --ignore W503,D212
-      - name: Test with pytest
-        run: |
-          poetry run pytest

.github/workflows/python-publish.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Build package
         run: python -m build
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@15c56dba361d8335944d31a2ecd17d700fc7bcbc
+        uses: pypa/gh-action-pypi-publish@67339c736fd9354cd4f8cb0b744f2b82a74b5c70
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/run_tests.yml

@@ -16,14 +16,14 @@ jobs:
       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: ubuntu-latest, session: "typeguard" }
-          - { python-version: "3.10", os: ubuntu-latest, session: "xdoctest" }
-          - { python-version: "3.10", os: ubuntu-latest, session: "docs-build" }
+          - { python-version: "3.11", os: ubuntu-latest, session: "pre-commit" }
+          - { python-version: "3.11", os: ubuntu-latest, session: "safety" }
+          - { python-version: "3.11", os: ubuntu-latest, session: "mypy" }
+          - { python-version: "3.11", os: ubuntu-latest, session: "tests" }
+          - { python-version: "3.11", os: windows-latest, session: "tests" }
+          - { python-version: "3.11", os: ubuntu-latest, session: "typeguard" }
+          - { python-version: "3.11", os: ubuntu-latest, session: "xdoctest" }
+          - { python-version: "3.11", os: ubuntu-latest, session: "docs-build" }
 
     env:
       NOXSESSION: ${{ matrix.session }}
@@ -40,6 +40,7 @@ jobs:
       - name: Install Poetry
         run: |
           pipx install poetry
+          pipx inject poetry poetry-plugin-export
           poetry --version
 
       - name: Install nox nox-poetry rich
@@ -65,7 +66,7 @@ jobs:
           print("::set-output name=result::{}".format(result))
 
       - name: Restore pre-commit cache
-        uses: actions/cache@v4.1.2
+        uses: actions/cache@v4.2.0
         if: matrix.session == 'pre-commit'
         with:
           path: ~/.cache/pre-commit
@@ -98,14 +99,15 @@ jobs:
       - name: Check out the repository
         uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Install Poetry
         run: |
           pipx install poetry
+          pipx inject poetry poetry-plugin-export
           poetry --version
 
       - name: Install nox nox-poetry rich
@@ -127,6 +129,6 @@ jobs:
         run: nox --force-color --session=coverage -- xml -i
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v5.0.2
+        uses: codecov/codecov-action@v5.1.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.readthedocs.yml

@@ -28,3 +28,5 @@ formats: all
 python:
   install:
     - requirements: docs/requirements.txt
+    - method: pip
+      path: .

Dockerfile

@@ -40,7 +40,6 @@ COPY drevalpy ./drevalpy
 COPY create_report.py ./
 COPY README.md ./
 COPY run_suite.py ./
-COPY setup.py ./
 COPY pyproject.toml ./
 COPY poetry.lock ./
 

README.md

@@ -1,5 +1,13 @@
 # DrEvalPy: Python Cancer Cell Line Drug Response Prediction Suite
 
+[![PyPI version](https://img.shields.io/pypi/v/drevalpy.svg)](https://pypi.org/project/drevalpy/)
+![Python versions](https://img.shields.io/pypi/pyversions/drevalpy)
+[![License](https://img.shields.io/github/license/daisybio/drevalpy)](https://opensource.org/licenses/GPL3)
+[![Read the Docs](https://img.shields.io/readthedocs/drevalpy/latest.svg?label=Read%20the%20Docs)](https://drevalpy.readthedocs.io/)
+[![Test status](https://github.com/daisybio/drevalpy/actions/workflows/run_tests.yml/badge.svg)](https://github.com/daisybio/drevalpy/actions?workflow=Tests)
+[![Precommit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/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.
@@ -8,7 +16,7 @@ Focus on Innovating Your Models — DrEval Handles the Rest!
 
 By contributing your model to the DrEval catalog, you can increase your work's exposure, reusability, and transferability.
 
-![DrEval](https://github.com/daisybio/drevalpy/blob/main/assets/dreval.png)
+![DrEval](assets/dreval.png)
 
 Use DrEval to Build Drug Response Models That Have an Impact
 
@@ -39,22 +47,32 @@ Using pip:
 pip install drevalpy
 ```
 
-From Source:
+Using docker:
+
+```bash
+docker pull ghcr.io/daisybio/drevalpy:main
+```
+
+From source:
 
 ```bash
-conda env create -f models/SimpleNeuralNetwork/env.yml
-pip install .
+git clone https://github.com/daisybio/drevalpy.git
+cd drevalpy
+pip install poetry
+poetry install
 ```
 
 ## Quickstart
 
 To run models from the catalog, you can run:
 
 ```bash
-python run_suite.py --run_id my_first_run --models ElasticNet SimpleNeuralNetwork --dataset GDSC1 --test_mode LCO
+python run_suite.py --run_id my_first_run --models ElasticNet SimpleNeuralNetwork --dataset GDSC2 --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.
+This will train and tune a neural network and an elastic net model on gene expression features and drug fingerprint
+features to predict IC50 values of the GDSC2 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
 
 ```bash