codecov to CI

.github/workflows/ci.yml

@@ -7,24 +7,41 @@ on:
     branches: [main]
 
 jobs:
-  deploy:
+  pre-commit:
     runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/[email protected]
+
+  build:
+    needs: [pre-commit]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11.8"]
     steps:
       #----------------------------------------------
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v3
-      - name: Set up python
+        uses: actions/checkout@v4
+      - name: Set up python ${{ matrix.python-version }}
         id: setup-python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: ${{ matrix.python-version }}
+
       #----------------------------------------------
       #         install & configure poetry
       #----------------------------------------------
       - name: Install Poetry
         uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
       #----------------------------------------------
       #       load cached venv if cache exists
       #----------------------------------------------
@@ -34,16 +51,37 @@ jobs:
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+
       #----------------------------------------------
       # install dependencies if cache does not exist
       #----------------------------------------------
       - name: Install dependencies
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install
+        run: poetry install --all-extras --no-interaction
+
       #----------------------------------------------
-      #              run test suite
+      #              perform tasks
       #----------------------------------------------
       - name: Tests
-        run: poetry run pytest
+        run: poetry run pytest --cov
+
       - name: Deploy doc
+        if: contains(github.ref, 'tags')
         run: poetry run mkdocs gh-deploy --force
+
+      - name: Upload results to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  # publish:
+  #   needs: [build]
+  #   if: contains(github.ref, 'tags')
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v3
+  #     - name: Build and publish to pypi
+  #       uses: JRubics/[email protected]
+  #       with:
+  #         python_version: "3.10"
+  #         pypi_token: ${{ secrets.PYPI_TOKEN }}

README.md

@@ -3,6 +3,8 @@
 </p>
 <!-- TODO: when it becomes public: https://raw.githubusercontent.com/MICS-Lab/novae/main/docs/assets/banner.png -->
 
+<div align="center">
+
 [![PyPI](https://img.shields.io/pypi/v/novae.svg)](https://pypi.org/project/novae)
 [![Downloads](https://static.pepy.tech/badge/novae)](https://pepy.tech/project/novae)
 [![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://mics-lab.github.io/novae)
@@ -11,6 +13,8 @@
 [![License](https://img.shields.io/pypi/l/novae.svg)](https://github.com/MICS-Lab/novae/blob/main/LICENSE)
 [![Imports: isort](https://img.shields.io/badge/imports-isort-blueviolet)](https://pycqa.github.io/isort/)
 
+</div>
+
 <p align="center"><b><i>
   💫 Graph-based foundation model for spatial transcriptomics data
 </b></i></p>

novae/module/augment.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import lightning as L
 import torch
 from torch.distributions import Exponential

novae/monitor/log.py

@@ -1,12 +1,14 @@
+from __future__ import annotations
+
 import io
 
 import matplotlib.pyplot as plt
-from PIL import Image
-
 import wandb
+from PIL import Image
 
 
 def log_plt_figure(name: str):
+
     img_buf = io.BytesIO()
     plt.savefig(img_buf, format="png", bbox_inches="tight")
     wandb.log({name: wandb.Image(Image.open(img_buf))})

novae/plot/_heatmap.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import matplotlib.patches as mpatches
 import matplotlib.pyplot as plt
 import numpy as np

novae/utils/_correct.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pandas as pd
 from anndata import AnnData

novae/utils/_data.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 from pathlib import Path
 

novae/utils/_docs.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 _format_doc_dict = {
     "adata": "An `AnnData` object, or a list of `AnnData` objects. Optional if the model was initialized with `adata`.",
     "slide_key": "Optional key of `adata.obs` containing the ID of each slide. Not needed if each `adata` is a slide.",

novae/utils/_mode.py

@@ -1,3 +1,6 @@
+from __future__ import annotations
+
+
 class Mode:
     """Novae mode class, used to store states variables related to training and inference."""