Buscar pip packaging

.github/workflows/ci.yml

@@ -0,0 +1,85 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      - name: Install dependencies
+        run: poetry install -E dev --no-interaction
+
+      - name: Run pre-commit (required)
+        run: poetry run pre-commit run --all-files --show-diff-on-failure
+
+  test-build:
+    needs: pre-commit
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      - name: Install dependencies
+        run: poetry install -E dev --no-interaction
+
+      - name: Run tests with coverage (Ubuntu 3.12)
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        run: poetry run pytest --cov=buscar --cov-report=term-missing --cov-report=xml
+
+      - name: Upload coverage artifact
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml
+
+      - name: Run tests
+        if: matrix.os != 'ubuntu-latest' || matrix.python-version != '3.12'
+        run: poetry run pytest
+
+      - name: Build package
+        run: poetry build
+
+      - name: Validate wheel import
+        shell: bash
+        run: |
+          poetry run python -m pip install --upgrade pip
+          poetry run python -m pip install dist/*.whl
+          poetry run python -c "import buscar; print(buscar.__name__)"

.gitignore

@@ -166,6 +166,8 @@ data/
 
 # ignoring prototype files
 _*
+!**/__init__.py
+!**/__main__.py
 
 # ignoring results files as they are generated when running the notebooks
 # also to prevent storing large datasets
@@ -176,3 +178,6 @@ results/
 
 # ignore .vscode settings
 .vscode/
+
+# ignore analytical notebooks
+notebooks*

.pre-commit-config.yaml

@@ -7,6 +7,7 @@ repos:
     rev: v6.0.0
     hooks:
     -   id: check-yaml
+        exclude: ^recipe/meta\.yaml$
     -   id: check-json
     -   id: check-merge-conflict
     -   id: check-added-large-files
@@ -35,7 +36,7 @@ repos:
 
   # Ruff for linting and formatting Python files
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
+    rev: v0.15.5
     hooks:
     -   id: ruff-check
         args: ["--fix"]

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Erik Serrano
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -23,44 +23,58 @@ buscar has 5 main modules:
 | ------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | Signatures    | Identifies morphological features between two profiles (e.g., healthy vs. disease). Features altered by perturbations are "on-morphology signatures"; unchanged features are "off-morphological features." This distinction helps pinpoint impacted features and track off-target effects. |
 | Heterogeneity | Assesses heterogeneity within single-cell populations using (1) dimensionality reduction (e.g., UMAP or PCA), and (2) clustering. Cells are mapped back to their original space to assign cluster labels.                                                                                  |
-| Refinement    | Evaluates clusters from the Heterogeneity module to remove uninformative or small clusters (e.g., those with few cells), which can skew phenotypic measurements due to label imbalance.                                                                                                    |
 | Activity      | Measures the phenotypic activity of selected treatment groups versus controls using both on-morphology and off-morphological signatures. Produces two scores: one for on-morphology activity, and one for off-morphology activity.                                                         |
 | Hits          | Identifies compounds that perform well based on both on-morphology and off-morphological activity scores from the Activity module.                                                                                                                                                         |
 
 ## How to install
 
-### 1. Clone the Repository
+### Option 1: Use Buscar (pip install)
 
-Start by cloning the buscar repository and navigating into the project directory:
+If you only want to use the package, install it directly from PyPI:
+
+```bash
+python -m pip install buscar
+```
+
+### Option 2: Develop Buscar (clone + Poetry)
+
+If you want to modify code, run tests, or contribute:
+
+1. Clone the repository
 
 ```bash
 git clone https://github.com/WayScience/buscar.git
 cd buscar
 ```
 
-### 2. Set Up a Conda Environment
-
-Create and activate a dedicated Conda environment for buscar:
+2. Create a Python 3.10+ environment
 
 ```bash
 conda create -n buscar python=3.12
 conda activate buscar
 ```
 
-### 3. Install Poetry
-
-Install Poetry within your Conda environment to manage project dependencies:
+3. Install Poetry
 
 ```bash
-conda install poetry
+conda install -c conda-forge poetry
 ```
 
-### 4. Install Project Dependencies
+4. Run tests
+
+```bash
+poetry run pytest
+```
 
-With Poetry installed and your environment activated, install all required dependencies:
+Run tests with coverage:
 
 ```bash
-poetry install
+poetry run pytest --cov=buscar --cov-report=term-missing
 ```
 
-This command will set up all packages as specified in the `pyproject.toml` and `poetry.lock` files.
+5. Build and install wheel with pip (optional release check)
+
+```bash
+poetry build
+pip install dist/*.whl
+```