Merge pull request #4 from lowe-lab-ucl/refactor

Refactor

.github/workflows/linting.yml

@@ -0,0 +1,35 @@
+name: Linting
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v3
+
+      - name: Cache pre-commit
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: Set up python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+          cache-dependency-path: "pyproject.toml"
+
+      - name: Install dependencies
+        run: |-
+          python -m pip install pre-commit
+          pre-commit install
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files --color always

.github/workflows/test.yml

@@ -0,0 +1,36 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - "**.md"
+      - "**.rst"
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v3
+
+      - name: Set up python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "pyproject.toml"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest
+
+      - name: Install umetrics
+        run: |
+          pip install -e .
+      - name: Run tests
+        run: |
+          pytest

.gitignore

@@ -1,3 +1,6 @@
+*.ipynb_checkpoints
+*.egg-info/
 .DS_Store
-umetrics/__pycache__
-notebooks/.ipynb_checkpoints
+__pycache__
+notebooks/
+_version.py

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.262
+      hooks:
+        - id: ruff
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: check-case-conflict
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-merge-conflict
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: trailing-whitespace
+            args: [--markdown-linebreak-ext=md]
+    - repo: https://github.com/psf/black
+      rev: 23.3.0
+      hooks:
+          - id: black
+    - repo: https://github.com/pappasam/toml-sort
+      rev: v0.23.0
+      hooks:
+        - id: toml-sort-fix

README.md

@@ -20,7 +20,7 @@ TODO:
 ### Single image usage
 
 ```python
-import umetrics
+import umetrix
 from skimage.io import imread
 
 y_true = imread('true.tif')
@@ -29,7 +29,12 @@ y_pred = imread('pred.tif')
 
 # can now make the calculation strict, by only considering objects that have
 # an IoU above a theshold as being true positives
-result = umetrics.calculate(y_true, y_pred, strict=True, iou_threshold=0.5)
+result = umetrix.calculate(
+    y_true,
+    y_pred,
+    strict=True,
+    iou_threshold=0.5
+)
 
 print(result.results)
 ```
@@ -56,14 +61,16 @@ localization_error: 0.010
 ### Batch processing
 
 ```python
-import umetrics
+import umetrix
 
 # provide a list of file pairs ('true', 'prediction')
-files = [('true0.tif', 'pred0.tif'),
-         ('true1.tif', 'pred1.tif'),
-         ('true2.tif', 'pred2.tif')]
+files = [
+    ('true0.tif', 'pred0.tif'),
+    ('true1.tif', 'pred1.tif'),
+    ('true2.tif', 'pred2.tif')
+]
 
-batch_result = umetrics.batch(files)
+batch_result = umetrix.batch(files)
 ```
 
 Returns aggregate statistics over the batch. Jaccard index is calculated over
@@ -79,8 +86,8 @@ $ git clone https://github.com/quantumjot/unet_segmentation_metrics.git
 
 2. (Optional, but advised) Create a conda environment:
 ```sh
-$ conda create -n umetrics python=3.7
-$ conda activate umetrics
+$ conda create -n umetrix python=3.9
+$ conda activate umetrix
 ```
 
 3. Install the package

pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "umetrix"
+authors = [
+  {name = "Alan R. Lowe", email = "[email protected]"}
+]
+description = "UNet Segmentation Metrics"
+readme = "README.md"
+requires-python = ">=3.8"
+keywords = ["image analysis"]
+license = {text = "BSD-3-Clause"}
+classifiers = [
+  "Programming Language :: Python :: 3"
+]
+dependencies = [
+  "matplotlib",
+  "numpy",
+  "pandas",
+  "scikit-learn",
+  "scikit-image>=0.20.0" # to include the spacing argument in regionprops
+]
+dynamic = ["version"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["umetrix*"]
+
+[tool.setuptools_scm]
+local_scheme = "no-local-version"
+write_to = "src/umetrix/_version.py"

src/umetrix/__init__.py

@@ -0,0 +1 @@
+from .core import calculate, batch  # NOQA: F401