Switch to pyproject, add requirements, remove docker

Author: tsmbland

.github/workflows/binder.yaml

@@ -5,24 +5,30 @@ on:
     branches:
       - master
   pull_request:
+  workflow_call:
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ windows-latest, ubuntu-latest, macos-latest ]
+        python-version: [ "3.8", "3.11" ]
 
     steps:
       - uses: actions/checkout@v3
 
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.7'
+          python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          pip install .[dev]
 
       - name: Test with pytest
         run: |

.github/workflows/test.yaml

@@ -16,3 +16,5 @@ dist/
 # IPython notebooks
 .ipynb_checkpoints
 
+# Virtual environment
+.venv

.gitignore

@@ -18,19 +18,23 @@ Python implementation of SAIBR: a simple, platform independent protocol for spec
 
 ## Tutorial notebook
 
-Please see the [tutorial notebook](https://nbviewer.org/github/goehringlab/saibr_python/blob/master/scripts/SAIBRdemonstration.ipynb) for instructions on usage.
+As a first step, I would recommend checking out the [tutorial notebook](https://nbviewer.org/github/goehringlab/saibr_python/blob/master/scripts/SAIBRdemonstration.ipynb). This can be run in the cloud using Binder (please note that it may take several minutes to open the notebook):
 
-To run interactively in the cloud with Binder, click here: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/goehringlab/saibr_python/HEAD?filepath=%2Fscripts/SAIBRdemonstration.ipynb)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/goehringlab/saibr_python/HEAD?filepath=%2Fscripts/SAIBRdemonstration.ipynb)
 
-(The notebook may take a few minutes to open)
+To run locally, download the code and install the relevant requirements (requirements.txt) in a virtual environment.
 
 
 ## Install instructions
 
-To explore further and incorporate into your own analysis pipelines, you can install the package using pip:
+To explore further and incorporate into your own analysis pipelines, you can install the package from PyPI using pip:
 
     pip install saibr
 
+If you want to make changes to the code you can download/clone this folder, navigate to it, and run:
+
+    pip install -e .[dev]
+
 
 ## Citation
 

README.md

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools"]
+
+[tool.setuptools]
+packages = ["saibr"]
+
+[project]
+name = "saibr"
+description = "Python implementation of SAIBR: a tool for performing spectral autofluorescence correction on biological images"
+readme = "README.md"
+version = "0.1.6"
+license = {file = "LICENSE"}
+authors = [
+    { name = "Tom Bland", email = "tom_bland@hotmail.co.uk" },
+]
+dependencies = [
+    "numpy",
+    "matplotlib",
+    "scipy",
+    "ipywidgets",
+    "scikit-learn",
+    "scikit-image",
+    "jupyter",
+    "opencv-python",
+]
+
+[project.urls]
+Documentation = "https://saibr.readthedocs.io/en/latest/"
+Source = "https://github.com/goehringlab/saibr_python"
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pre-commit",
+    "black",
+    "pip-tools",
+    "pytest-cov",
+]
+
+doc = [
+    "sphinx_rtd_theme==1.0.0",
+]
+