Fixed MOLIR, also pushing current state of documentation

.github/workflows/publish_docs.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          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

.readthedocs.yml

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

Dockerfile

@@ -6,15 +6,11 @@ FROM python:3.10-buster as builder
 
 RUN pip install poetry==1.8.4
 
-# POETRY_VIRTUALENVS_CREATE=1: Makes sure that environment will be as isolated as possible and above all that
-# installation will not mess up with the system Python or, even worse, with Poetry itself.
 # POETRY_CACHE_DIR: When removing the cache folder, make sure this is done in the same RUN command. If it’s done in a
 # separate RUN command, the cache will still be part of the previous Docker layer (the one containing poetry install )
 # effectively rendering your optimization useless.
 
 ENV POETRY_NO_INTERACTION=1 \
-    POETRY_VIRTUALENVS_IN_PROJECT=1 \
-    POETRY_VIRTUALENVS_CREATE=1 \
     POETRY_CACHE_DIR=/tmp/poetry_cache
 
 WORKDIR /root
@@ -34,10 +30,9 @@ FROM python:3.10-slim-buster as runtime
 LABEL image.author.name="Judith Bernett"
 LABEL image.author.email="judith.bernett@tum.de"
 
-ENV VIRTUAL_ENV=/root/.venv \
-    PATH="/root/.venv/bin:$PATH"
-
-COPY --from=builder ${VIRTUAL_ENV} ${VIRTUAL_ENV}
+# Copy installed dependencies from the builder image
+COPY --from=builder /usr/local/lib/python3.10/site-packages /usr/local/lib/python3.10/site-packages
+COPY --from=builder /usr/local/bin /usr/local/bin
 
 # Copy all relevant code
 
@@ -51,3 +46,6 @@ COPY poetry.lock ./
 
 # Install drevalpy
 RUN pip install .
+
+# Nextflow needs the command ps to be available
+RUN apt-get update && apt-get install -y procps && rm -rf /var/lib/apt/lists/*

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

docs/API.rst

@@ -0,0 +1,59 @@
+API
+===
+
+Import DrEvalPy using
+
+.. code-block:: python
+
+   import drevalpy as dep
+
+Subpackages
+-----------
+
+DrEvalPy consists of three major subpackages:
+
+* Datasets
+* Models
+* Visualization
+
+.. toctree::
+   :maxdepth: 3
+
+   drevalpy.datasets
+   drevalpy.models
+   drevalpy.visualization
+
+Other functions
+---------------
+
+Major functions for running the experiment
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: drevalpy.experiment
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Evaluation functions
+~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: drevalpy.evaluation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Utility functions
+~~~~~~~~~~~~~~~~~
+
+.. automodule:: drevalpy.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Pipeline function decorator
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: drevalpy.pipeline_function
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_key_contributors.rst

@@ -1,8 +1,8 @@
 .. sidebar:: Key Contributors
 
-   * `Judith Bernett <https://github.com/JudithBernett>`_: developer, maintainer
-   * `Pascal Iversen <https://github.com/PascalIversen>`_: developer, maintainer
-   * `Mario Picciani <https://github.com/picciama>`_: developer
-   * `Markus List <https://github.com/mlist>`_: advisor and PI of daisybio
-   * `Katharina Baum <https://github.com/kathbaum>`_: advisor and PI of DILiS
-   * `Mathias Wilhelm <https://github.com/mwilhelm42>`_: advisor and PI of wilhelmlab
+   * `Judith Bernett <https://github.com/JudithBernett>`_: Developer, Maintainer
+   * `Pascal Iversen <https://github.com/PascalIversen>`_: Developer, Maintainer
+   * `Mario Picciani <https://github.com/picciama>`_: Developer
+   * `Markus List <https://github.com/mlist>`_: Advisor and PI of Data Science in Systems Biology, TUM
+   * `Katharina Baum <https://github.com/kathbaum>`_: Advisor and PI of Data Integration in the Life Sciences, FU Berlin
+   * `Mathias Wilhelm <https://github.com/mwilhelm42>`_: Advisor and PI of Computational Mass Spectrometry, TUM

docs/_static/custom_cookietemple.css

@@ -43,3 +43,7 @@ table.align-default {
 .date {
   font-size: 50%;
 }
+
+a:visited {
+  color: #a63a85;
+}

docs/conf.py

@@ -49,7 +49,7 @@
 # General information about the project.
 project = "DrEvalPy"
 author = "DrEvalpy development team"
-copyright = f"{datetime.now():%Y}, daisybio at Technical University of Munich"
+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
@@ -100,7 +100,7 @@
 # documentation.
 #
 html_theme_options = dict(
-    navigation_depth=4,
+    navigation_depth=6,
     logo_only=True,
 )
 html_logo = "_static/img/drevalpy.png"
@@ -166,7 +166,8 @@
 autodoc_typehints = "description"
 
 
-autodoc_mock_imports = ["numpy", "sklearn", "pandas", "networkx", "yaml", "pytorch_lightning", "torch", "scipy"]
+# autodoc_mock_imports = ["numpy", "sklearn", "pandas", "networkx", "yaml", "pytorch_lightning", "torch", "scipy",
+#                        "copy", "os", "abc", "pathlib", "typing"]
 
 
 # -- Options for Texinfo output ----------------------------------------

docs/contributing.rst

@@ -2,7 +2,7 @@ Contributor Guide
 =================
 
 Thank you for your interest in improving this project.
-This project is open-source under the `MIT license`_ and
+This project is open-source under the `GPL-3 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:
@@ -11,7 +11,7 @@ Here is a list of important resources for contributors:
 - `Documentation`_
 - `Issue Tracker`_
 
-.. _MIT license: https://opensource.org/licenses/MIT
+.. _GPL-3 license: https://opensource.org/license/gpl-3-0
 .. _Source Code: https://github.com/daisybio/drevalpy
 .. _Documentation: https://drevalpy.readthedocs.io/
 .. _Issue Tracker: https://github.com/daisybio/drevalpy/issues
@@ -31,39 +31,19 @@ Request features on the `Issue Tracker`_.
 How to set up your development environment
 ------------------------------------------
 
-You need Python 3.9+ and the following tools:
+You need Python 3.10+ and Poetry_ to set up your development environment.
 
-- Poetry_
-- Nox_
-- nox-poetry_
-
-You can install them with:
-
-.. code:: console
-
-    $ pip install poetry nox nox-poetry
-
-Install the package with development requirements:
+.. _Poetry: https://python-poetry.org/
 
-.. code:: console
 
-   $ make install
+How to test the project
+-----------------------
 
-You can now run an interactive Python session,
-or the command-line interface:
+For this, you need to install nox and nox-poetry:
 
 .. 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
------------------------
+   $ pip install nox nox-poetry
 
 Run the full test suite:
 
@@ -93,7 +73,6 @@ 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:
 
@@ -111,7 +90,6 @@ from inside the docs folder. The generated static HTML files can be found in the
 Simply open them with your favorite browser.
 
 .. _sphinx: https://www.sphinx-doc.org/en/master/
-.. _pandoc: https://pandoc.org/
 
 How to submit changes
 ---------------------

docs/drevalpy.datasets.rst

@@ -0,0 +1,35 @@
+Datasets
+=========================
+
+Dataset module
+--------------
+
+.. automodule:: drevalpy.datasets.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Loaders
+-------
+
+.. automodule:: drevalpy.datasets.loader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+CurveCurator
+------------
+
+.. automodule:: drevalpy.datasets.curvecurator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Utility functions
+-----------------
+
+.. automodule:: drevalpy.datasets.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+