Merge pull request #187 from HelikarLab/purge_r

Purge R code

Author: JoshLoecker

.dockerignore

@@ -5,3 +5,4 @@ main/src/tests
 **/.ipynb_checkpoints/
 README.md
 LICENSE
+/.venv

.github/workflows/continuous_integration.yml

@@ -0,0 +1,84 @@
+name: Continuous Integration
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Create Virtual Environment
+        run: uv venv
+
+      - name: Install Jupyter
+        run: uv pip install jupyter nbconvert
+
+      - name: Strip Notebook Output
+        run: uv run jupyter nbconvert --clear-output --inplace "main/COMO.ipynb"
+
+      - name: Format Python Imports
+        uses: astral-sh/ruff-action@v1
+        with:
+          args: "check --fix --select I"
+
+      - name: Format code
+        uses: astral-sh/ruff-action@v1
+        with:
+          args: "format"
+
+      - name: Format Notebook
+        uses: astral-sh/ruff-action@v1
+        with:
+          args: "format main/COMO.ipynb"
+
+      - name: Commit Changes
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "style: format code, Jupyter Notebook(s), and Python imports with `ruff`"
+          file_pattern: "main/como/*.py"
+
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Check Lint
+        uses: astral-sh/ruff-action@v1
+        with:
+          args: "check --no-fix --verbose"
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.10" ]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: "true"
+          cache-suffix: "${{ matrix.python-version }}"
+          cache-dependency-glob: 'uv.lock'
+
+      - name: Install Dependencies
+        run: uv sync --python "${{ matrix.python-version }}" --all-extras --dev
+
+      - name: Run tests
+        run: uv run --python "${{ matrix.python-version }}" pytest --cov --junitxml=junit.xml -o junit_family=legacy
+
+      - name: Cache Clear
+        run: uv cache prune --ci

.github/workflows/unit_tests.yml

@@ -12,14 +12,13 @@ docs/_site
 docs/Gemfile.lock
 
 # COMO-specific files
+.hypothesis
 **/*.Rout
 main/logs/
-main/data/results/
-main/data/config_sheets/*_data_inputs_auto.xlsx
 main/data/gene_info.csv
 main/data/Repurposing_Hub_Preproc.tsv
-main/microarray.db
-main/data/config_sheets/*
-main/data/GSE*_RAW
-main/data/gpl*entrez.csv
-main/src/microarray.db
+main/data/results/
+main/data/config_sheets
+
+# COMO data
+main/data/data_matrices

.gitignore

@@ -0,0 +1,8 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/opensource-nepal/commitlint
+    rev: v1.2.0
+    hooks:
+    -   id: commitlint
+        name: Commit Lint

.pre-commit-config.yaml

@@ -1,27 +1,12 @@
-FROM jupyter/r-notebook:latest as builder
+FROM python:3.10 AS app
 
-COPY environment.yaml "${HOME}/environment.yaml"
-COPY --chown=1000:100 main "${HOME}/main"
-
-# Install python-related items
-# Remove "python" from the pinned file so we can install our own version
-RUN sed -i '/^python/d' /opt/conda/conda-meta/pinned && \
-    echo "auto_activate_base: true" >> "${HOME}/.condarc" && \
-    jupyter trust "${HOME}/main/COMO.ipynb" && \
-    echo "c.ServerApp.ip = '0.0.0.0'" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
-    echo "c.ServerApp.root_dir = '${HOME}/main'" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
-    echo "c.ServerApp.token = ''" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
-    echo "c.ServerApp.password = ''" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
-    mamba config --quiet --add channels conda-forge && \
-    mamba config --quiet --add channels bioconda && \
-    mamba config --quiet --add channels r && \
-    rm -rf "${HOME}/main/tests"  # Tests not required for running COMO
-
-# Update base environment
-RUN mamba env update --name=base --file="${HOME}/environment.yaml" && \
-    R -e "devtools::install_github('babessell1/zFPKM')" && \
-    pip cache purge && \
-    mamba clean --all --yes
+WORKDIR /app
+ENV PATH="/app/.venv/bin:$PATH"
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+COPY --chown=1000:100 main /app/main/
+COPY --chown=1000:100 pyproject.toml /app/pyproject.toml
 
+RUN uv sync && uv pip install jupyterlab
 EXPOSE 8888
-VOLUME /home/joyvan/main/data/local_files
+VOLUME "/app/main/data/local_files"
+CMD ["jupyter", "lab", "--allow-root", "--no-browser", "--ip=0.0.0.0", "--port=8888", "--notebook-dir=/app/main", "--NotebookApp.token=''", "--NotebookApp.password=''"]

Dockerfile

@@ -3,6 +3,8 @@
 ![GitHub release (with filter)](https://img.shields.io/github/v/release/HelikarLab/COMO?filter=v*-master&style=for-the-badge&color=blue)
 ![GitHub Workflow Status (with event)](https://img.shields.io/github/actions/workflow/status/HelikarLab/COMO/unit_tests.yml?style=for-the-badge&logo=pytest&logoColor=white&label=Tests)
 ![GitHub Workflow Status (with event)](https://img.shields.io/github/actions/workflow/status/HelikarLab/COMO/container_build.yml?style=for-the-badge&logo=docker&logoColor=white&label=Docker%20Build)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+
 
 # Setting up COMO
 

README.md

@@ -0,0 +1,9 @@
+services:
+  como:
+    image: ghcr.io/helikarlab/como:latest
+    container_name: como
+    ports:
+      - "8888:8888"
+    volumes:
+      # Map "[LOCAL_DIRECTORY]/local_files to /app/main/data/local_files
+      - "$(pwd)/local_files:/app/main/data/local_files"