Merge pull request #10 from bluemindai/fitzjalen-patch-3

Make CI

.github/workflows/makefile.yml

@@ -0,0 +1,33 @@
+name: CI Workflow
+
+on:
+  push:
+    branches: [ master, main ]
+  pull_request:
+    branches: [ master, main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.x
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Install OpenBLAS dependencies
+        run: sudo apt-get update && sudo apt-get install -y libopenblas-dev liblapack-dev
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install meson ninja
+          pip install -e .
+
+      - name: Run Makefile target (pre-commit and tests)
+        run: |
+          make all

Makefile

@@ -1,6 +1,8 @@
 .PHONY: all
-all: test
-
+all: pre-commit test
+.PHONY: pre-commit
+pre-commit:
+	pre-commit run --all-files
 .PHONY: test
 test:
 	coverage run -m unittest discover -s tests

README.md

@@ -9,6 +9,28 @@ It simplifies the tasks of loading, transforming, analyzing, and visualizing dat
 
 Read more about available modules [here](documents/readme_modules.md)
 
+## Installation
+
+Optimed is available via [PyPI](https://pypi.org/project/optimed/), which makes installation quick and easy. Follow the steps below to install the package for your desired setup.
+
+### 1. Standard Installation (CPU Only)
+
+For most users who do not require GPU acceleration, install the core package with:
+
+```bash
+pip install optimed
+```
+
+### 2. GPU-Accelerated Installation
+
+To leverage GPU capabilities for faster processing, install Optimed with GPU support:
+
+```bash
+pip install optimed[gpu]
+```
+
+> **Note:** Ensure you have a compatible GPU and have installed the necessary drivers and libraries (such as CUDA) to enable GPU acceleration.
+
 # Contributing
 Optimed welcomes your contributions!<br>
 Thanks so much to all of our amazing contributors!

pyproject.toml

@@ -12,11 +12,10 @@ authors = [
     { name = "Roman Fitzjalen", email = "[email protected]" }
 ]
 dependencies = [
-    "cupy-cuda12x==13.0.0; platform_system != 'Darwin'",
-    "pylibraft-cu12==24.8.1; platform_system != 'Darwin'",
     "numpy==1.26.3",
     "nibabel==5.2.1",
-    "SimpleITK==2.3.1",
+    "slicerio==1.1.2",
+    "SimpleITK==2.4.1",
     "pyyaml==6.0.2",
     "xmltodict==0.14.2",
     "scipy==1.13.1",
@@ -25,6 +24,7 @@ dependencies = [
     "scikit-image==0.24.0",
     "psutil==5.9.8",
     "vtk==9.4.1",
+    "coverage==7.6.12",
     "pre-commit==4.1.0"
 ]
 requires-python = ">=3.9"
@@ -43,3 +43,9 @@ exclude = [".venv-optimed", ".vscode", ".history", "local", ".github"]
 
 [tool.codespell]
 skip = '.git,*.pdf,*.svg'
+
+[project.optional-dependencies]
+gpu = [
+    "cupy-cuda12x==13.0.0; platform_system != 'Darwin'",
+    "pylibraft-cu12==24.8.1; platform_system != 'Darwin'"
+]

requirements.txt

@@ -4,7 +4,8 @@ cupy-cuda12x==13.0.0
 pylibraft-cu12==24.8.1 
 numpy==1.26.3
 nibabel==5.2.1
-SimpleITK==2.3.1
+slicerio==1.1.2
+SimpleITK==2.4.1
 pyyaml==6.0.2
 xmltodict==0.14.2
 scipy==1.13.1
@@ -13,4 +14,5 @@ joblib==1.4.2
 scikit-image==0.24.0
 psutil==5.9.8
 vtk==9.4.1
+coverage==7.6.12
 pre-commit==4.1.0