incorporating pre-commit checks (#48)

* formatted everything with ruff
* incorporating pre-commit checks

.github/workflows/docs.yml

@@ -27,8 +27,8 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Install Package
-        run: | 
-         pip install . 
+        run: |
+         pip install .
 
       - name: Install Pandoc
         run: sudo apt-get install -y pandoc

.github/workflows/test_pinned_deps.yml

@@ -36,6 +36,9 @@ jobs:
       - name: Install package
         run: pip install .
 
+      - name: Pre-commit checks
+        run: pre-commit run --all-files
+
       - name: Check Versions of Dependencies
         run: pip freeze
 
@@ -47,5 +50,3 @@ jobs:
         run: coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-
-

.github/workflows/test_unpinned_deps.yml

@@ -40,4 +40,3 @@ jobs:
 
       - name: Pytest
         run: pytest
-

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: 'tests/test_data/.*'
+
+      - id: end-of-file-fixer
+        exclude: 'tests/test_data/.*'
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.6
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+        exclude: 'tests/test_data/.*'
+
+      - id: ruff-format
+        exclude: 'tests/test_data/.*'

README.md

@@ -2,7 +2,7 @@
 [![Coverage Status](https://coveralls.io/repos/github/raphael-group/paste3/badge.svg?branch=main)](https://coveralls.io/github/raphael-group/paste3?branch=main)
 [![Docs](https://github.com/raphael-group/paste3/actions/workflows/docs.yml/badge.svg)](https://raphael-group.github.io/paste3/)
 
-(Note: This repository integrates Paste and Paste 2, and is a work in progress) 
+(Note: This repository integrates Paste and Paste 2, and is a work in progress)
 # PASTE
 
 ![PASTE Overview](https://github.com/raphael-group/paste/blob/main/docs/source/_static/images/paste_overview.png)
@@ -27,9 +27,9 @@ Additional examples and the code to reproduce the paper's analyses can be found
 
 ### Installation
 
-The easiest way is to install PASTE on pypi: https://pypi.org/project/paste-bio/. 
+The easiest way is to install PASTE on pypi: https://pypi.org/project/paste-bio/.
 
-`pip install paste-bio` 
+`pip install paste-bio`
 
 Or you can install PASTE on bioconda: https://anaconda.org/bioconda/paste-bio.
 
@@ -38,14 +38,14 @@ Or you can install PASTE on bioconda: https://anaconda.org/bioconda/paste-bio.
 Check out Tutorial.ipynb for an example of how to use PASTE.
 
 Alternatively, you can clone the respository and try the following example in a
-notebook or the command line. 
+notebook or the command line.
 
 ### Quick Start
 
 To use PASTE we require at least two slices of spatial-omics data (both
 expression and coordinates) that are in
 anndata format (i.e. read in by scanpy/squidpy). We have included a breast
-cancer dataset from [1] in the [sample_data folder](tests/data/input/) of this repo 
+cancer dataset from [1] in the [sample_data folder](tests/data/input/) of this repo
 that we will use as an example below to show how to use PASTE.
 
 ```python
@@ -79,7 +79,7 @@ slice1, slice2 = slices
 # Pairwise align the slices
 pi12 = pst.pairwise_align(slice1, slice2)
 
-# To visualize the alignment you can stack the slices 
+# To visualize the alignment you can stack the slices
 # according to the alignment pi
 slices, pis = [slice1, slice2], [pi12]
 new_slices = pst.stack_slices_pairwise(slices, pis)
@@ -106,11 +106,11 @@ initial_slice = slice1.copy()
 slices = [slice1, slice2]
 lmbda = len(slices) * [1 / len(slices)]  # set hyperparameter to be uniform
 
-## Possible to pass in an initial pi (as keyword argument pis_init) 
+## Possible to pass in an initial pi (as keyword argument pis_init)
 ## to improve performance, see Tutorial.ipynb notebook for more details.
 center_slice, pis = pst.center_align(initial_slice, slices, lmbda)
 
-## The low dimensional representation of our center slice is held 
+## The low dimensional representation of our center slice is held
 ## in the matrices W and H, which can be used for downstream analyses
 W = center_slice.uns['paste_W']
 H = center_slice.uns['paste_H']
@@ -121,13 +121,13 @@ PASTE now is compatible with gpu via Pytorch. All we need to do is add the follo
 ```
 pi12 = pst.pairwise_align(slice1, slice2, backend = ot.backend.TorchBackend(), use_gpu = True)
 
-center_slice, pis = pst.center_align(initial_slice, slices, lmbda, backend = ot.backend.TorchBackend(), use_gpu = True) 
+center_slice, pis = pst.center_align(initial_slice, slices, lmbda, backend = ot.backend.TorchBackend(), use_gpu = True)
 ```
 For more details, see the GPU section of the [Tutorial notebook](docs/source/notebooks/getting-started.ipynb).
 
 ### Command Line
 
-We provide the option of running PASTE from the command line. 
+We provide the option of running PASTE from the command line.
 
 First, clone the repository:
 
@@ -162,7 +162,7 @@ Note: `pairwise` will return pairwise alignment between each consecutive pair of
 
 Added sample spatial transcriptomics dataset consisting of four breast cancer slice courtesy of:
 
-[1] Ståhl, Patrik & Salmén, Fredrik & Vickovic, Sanja & Lundmark, Anna & Fernandez Navarro, Jose & Magnusson, Jens & Giacomello, Stefania & Asp, Michaela & Westholm, Jakub & Huss, Mikael & Mollbrink, Annelie & Linnarsson, Sten & Codeluppi, Simone & Borg, Åke & Pontén, Fredrik & Costea, Paul & Sahlén, Pelin Akan & Mulder, Jan & Bergmann, Olaf & Frisén, Jonas. (2016). Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 353. 78-82. 10.1126/science.aaf2403. 
+[1] Ståhl, Patrik & Salmén, Fredrik & Vickovic, Sanja & Lundmark, Anna & Fernandez Navarro, Jose & Magnusson, Jens & Giacomello, Stefania & Asp, Michaela & Westholm, Jakub & Huss, Mikael & Mollbrink, Annelie & Linnarsson, Sten & Codeluppi, Simone & Borg, Åke & Pontén, Fredrik & Costea, Paul & Sahlén, Pelin Akan & Mulder, Jan & Bergmann, Olaf & Frisén, Jonas. (2016). Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 353. 78-82. 10.1126/science.aaf2403.
 
 Note: Original data is (.tsv), but we converted it to (.csv).
 

docs/paste3/installation.md

@@ -1,28 +1,28 @@
-# Setting up the environment 
+# Setting up the environment
 
-1. Clone the repository and enter it: 
+1. Clone the repository and enter it:
 ```shell
   git clone [email protected]:raphael-group/paste3.git
   cd paste3
 ```
-2. Create and activate a conda environment using the provided `environment.yml` file: 
+2. Create and activate a conda environment using the provided `environment.yml` file:
 ```shell
    conda env create --file environment.yml
    conda activate paste
 ```
-The command prompt will change to indicate the new conda environment by prepending `(paste)`. 
-3. When you are done using the package, deactivate the `paste` environment and return to `(base)` by entering the following command: 
+The command prompt will change to indicate the new conda environment by prepending `(paste)`.
+3. When you are done using the package, deactivate the `paste` environment and return to `(base)` by entering the following command:
 ```shell
 conda deactivate
 ```
 
-# Installation 
+# Installation
 
 1. Enter the `paste3` repository cloned before setting up the environment
 ```shell
 cd paste3
 ```
 2. Install the package:
 ```shell
-pip install . 
-```
+pip install .
+```

docs/source/api.rst

@@ -70,4 +70,3 @@ Miscellaneous
 
    helper.filter_for_common_genes
    helper.match_spots_using_spatial_heuristic
-

docs/source/conf.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 import sys
 import os
+
 HERE = Path(__file__).parent
 sys.path.insert(0, os.path.abspath(HERE.parent.parent))
 
@@ -12,34 +13,34 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'paste3'
-copyright = '2022, Raphael Lab'
-author = 'Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J. Raphael'
+project = "paste3"
+copyright = "2022, Raphael Lab"
+author = "Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J. Raphael"
 
 # The full version, including alpha/beta/rc tags
-release = '1.2.0'
+release = "1.2.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
     "myst_parser",
-    'sphinx.ext.autosummary',
+    "sphinx.ext.autosummary",
     "sphinx.ext.autodoc",
-    'sphinx.ext.napoleon',
+    "sphinx.ext.napoleon",
     "sphinx_autodoc_typehints",
     "nbsphinx",
     "sphinx_gallery.load_style",
-    "sphinx.ext.viewcode"
+    "sphinx.ext.viewcode",
 ]
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 exclude_patterns = []
 
-language = 'python'
+language = "python"
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = "sphinx_rtd_theme"
-html_static_path = ['_static']
+html_static_path = ["_static"]

docs/source/index.rst

@@ -37,5 +37,3 @@ You can view PASTE `preprint <https://www.biorxiv.org/content/10.1101/2021.03.16
    paste3/installation.md
    api
    tutorial
-
-