radstract 1.0.0__tar.gz

radstract-1.0.0/.github/workflows/gh-pages.yml

@@ -0,0 +1,67 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Install dependencies
+        run: uv sync --all-groups
+
+      - name: Build docs with pdoc
+        run: uv run pdoc -d numpy -o docs radstract
+
+      - name: Build package
+        run: uv build
+
+      - name: Include build artifacts in docs
+        run: |
+          mkdir -p docs/downloads
+          cp -r dist/* docs/downloads/
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

radstract-1.0.0/.github/workflows/lint-and-test.yml

@@ -0,0 +1,49 @@
+name: Lint & Test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  lint-and-test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        version: "latest"
+
+    - name: Set up Python
+      run: uv python install
+
+    - name: Install dependencies
+      run: |
+        uv sync --all-groups
+        uv add poethepoet
+
+    - name: Check code formatting with black
+      run: |
+        uv run poe format --check
+
+    - name: Generate test data
+      run: |
+        uv run poe testgen
+
+    - name: Run tests
+      run: |
+        sudo rm -rf tmp/*
+        uv run poe test_all
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }} # Set this in your repository secrets
+        files: coverage.xml
+        name: code-coverage-report
+        fail_ci_if_error: true

radstract-1.0.0/.github/workflows/pypi-release.yml

@@ -0,0 +1,68 @@
+name: PyPI Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        version: "latest"
+
+    - name: Set up Python
+      run: uv python install
+
+    - name: Install dependencies
+      run: |
+        uv sync --all-groups
+        uv add poethepoet
+
+    - name: Generate test data
+      run: |
+        uv run poe testgen
+
+    - name: Run tests
+      run: |
+        sudo rm -rf tmp/*
+        uv run poe test_all
+
+  release:
+    needs: test
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/radstract
+    permissions:
+      id-token: write
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+      with:
+        version: "latest"
+
+    - name: Set up Python
+      run: uv python install
+
+    - name: Update version from tag
+      run: |
+        TAG=${GITHUB_REF#refs/tags/v}
+        sed -i "s/version = \".*\"/version = \"$TAG\"/" pyproject.toml
+
+    - name: Build package
+      run: uv build
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        print-hash: true

radstract-1.0.0/.gitignore

@@ -0,0 +1,19 @@
+# editor settings
+.idea
+.vscode
+_darcs
+
+# python
+.coverage
+__pycache__
+.pytest_cache
+
+# pdoc
+/docs
+
+# examples
+/debug
+
+# tests
+/tests/test_data
+.venv

radstract-1.0.0/LICENSE

@@ -0,0 +1,202 @@
+
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+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
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+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
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+   Copyright 2024 Adam McArthur
+
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+
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+
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+   See the License for the specific language governing permissions and
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radstract-1.0.0/PKG-INFO

@@ -0,0 +1,101 @@
+Metadata-Version: 2.4
+Name: radstract
+Version: 1.0.0
+Author-email: Sharpz7 <adam.mcarthur62@gmail.com>
+License: Apache-2.0
+License-File: LICENSE
+Requires-Python: <4.0,>=3.10
+Requires-Dist: black>=25.1.0
+Requires-Dist: importlib-metadata>=7.1.0
+Requires-Dist: licensecheck>=2023.5.2
+Requires-Dist: matplotlib>=3.8.2
+Requires-Dist: nibabel==5.2.1
+Requires-Dist: numpy==1.26.4
+Requires-Dist: opencv-python>=4.9.0.80
+Requires-Dist: pdoc>=14.4.0
+Requires-Dist: pillow>=11.0.0
+Requires-Dist: pydicom>=3.0.1
+Requires-Dist: pylibjpeg-openjpeg>=2.2.1
+Requires-Dist: pylibjpeg>=2.0.1
+Requires-Dist: pytest-cov>=5.0.0
+Requires-Dist: pytest-mock>=3.14.0
+Requires-Dist: pytest-xdist>=3.6.1
+Requires-Dist: pytest>=8.1.1
+Requires-Dist: scikit-image>=0.24.0
+Requires-Dist: simpleitk>=2.4.0
+Requires-Dist: sympy>=1.12
+Requires-Dist: trimesh>=4.0.5
+Requires-Dist: vulture>=2.11
+Requires-Dist: weasyprint>=65.1
+Description-Content-Type: text/markdown
+
+[![Lint & Test](https://github.com/radoss-org/radstract/actions/workflows/lint-and-test.yml/badge.svg)](https://github.com/radoss-org/radstract/actions/workflows/lint-and-test.yml)
+[![codecov](https://codecov.io/gh/radoss-org/radstract/graph/badge.svg?token=AAC82LNAKU)](https://codecov.io/gh/radoss-org/radstract)
+
+## Radstract
+
+Radstract is python library containing shared code for RadOSS projects.
+
+It has a range of subpackages for different tasks:
+- Data: For data/image manipulation and conversion functions
+- Analysis: For different methods of analyzing the data, from nifti and dicom files
+- Math: For different mathematical functions and operations
+- Datasets: for converting and working with different datasets (Huggingface etc)
+
+Feel free to use this code in your own projects, and if you have any questions or suggestions, please feel free to open an issue.
+
+## Installation
+
+```bash
+pip install git+https://github.com/radoss-org/radstract.git
+```
+
+See examples here for a quickstart: https://github.com/radoss-org/Radstract/tree/main/examples
+
+## Docs
+
+Docs can be viewed at https://radoss-org.github.io/radstract/radstract.html
+
+## Examples
+
+See examples here: https://github.com/radoss-org/Radstract/tree/main/examples
+
+
+## Developer Guide
+
+You can clone the repository and install the dependencies with the following command:
+
+```bash
+git clone https://github.com/radoss-org/radstract.git
+```
+
+You can then install retuve with poetry, and then run the tests:
+
+```bash
+# Needed for the scripts
+pip install poethepoet
+
+cd retuve
+poetry install
+
+# Generate the test data
+poe testgen
+
+# Run all tests, including examples.
+poe test_all
+
+# Get info on all other dev scripts
+poe help
+```
+
+## Acknowledgments
+
+Data for the examples and tests is from https://github.com/radoss-org/radoss-creative-commons.
+
+Please see this repo for attribution and licensing information.
+
+- **Shape Distribution Models** From https://graphics.stanford.edu/courses/cs468-08-fall/pdf/osada.pdf
+
+## License
+
+This project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.

radstract-1.0.0/README.md

@@ -0,0 +1,70 @@
+[![Lint & Test](https://github.com/radoss-org/radstract/actions/workflows/lint-and-test.yml/badge.svg)](https://github.com/radoss-org/radstract/actions/workflows/lint-and-test.yml)
+[![codecov](https://codecov.io/gh/radoss-org/radstract/graph/badge.svg?token=AAC82LNAKU)](https://codecov.io/gh/radoss-org/radstract)
+
+## Radstract
+
+Radstract is python library containing shared code for RadOSS projects.
+
+It has a range of subpackages for different tasks:
+- Data: For data/image manipulation and conversion functions
+- Analysis: For different methods of analyzing the data, from nifti and dicom files
+- Math: For different mathematical functions and operations
+- Datasets: for converting and working with different datasets (Huggingface etc)
+
+Feel free to use this code in your own projects, and if you have any questions or suggestions, please feel free to open an issue.
+
+## Installation
+
+```bash
+pip install git+https://github.com/radoss-org/radstract.git
+```
+
+See examples here for a quickstart: https://github.com/radoss-org/Radstract/tree/main/examples
+
+## Docs
+
+Docs can be viewed at https://radoss-org.github.io/radstract/radstract.html
+
+## Examples
+
+See examples here: https://github.com/radoss-org/Radstract/tree/main/examples
+
+
+## Developer Guide
+
+You can clone the repository and install the dependencies with the following command:
+
+```bash
+git clone https://github.com/radoss-org/radstract.git
+```
+
+You can then install retuve with poetry, and then run the tests:
+
+```bash
+# Needed for the scripts
+pip install poethepoet
+
+cd retuve
+poetry install
+
+# Generate the test data
+poe testgen
+
+# Run all tests, including examples.
+poe test_all
+
+# Get info on all other dev scripts
+poe help
+```
+
+## Acknowledgments
+
+Data for the examples and tests is from https://github.com/radoss-org/radoss-creative-commons.
+
+Please see this repo for attribution and licensing information.
+
+- **Shape Distribution Models** From https://graphics.stanford.edu/courses/cs468-08-fall/pdf/osada.pdf
+
+## License
+
+This project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.

radstract-1.0.0/examples/_test.py

@@ -0,0 +1,94 @@
+# Copyright 2024 Adam McArthur
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os
+import subprocess
+
+import pytest
+
+BLACKLIST = []
+
+
+# Dynamically collect scripts for testing
+def collect_scripts():
+    examples_dir = os.path.dirname(__file__)
+    module_dir = os.path.abspath(
+        os.path.join(examples_dir, "..")
+    )  # Assuming your module is one level up from the examples directory
+
+    scripts = []
+    for root, _, files in os.walk(examples_dir):
+        for file in files:
+            if file.endswith(".py") and file not in BLACKLIST:
+                scripts.append((os.path.join(root, file), module_dir))
+    return scripts
+
+
+# Dynamically create test functions for pytest
+scripts = collect_scripts()
+for i, (script_path, module_dir) in enumerate(scripts):
+    # test_name should be derived from the script name
+    test_name = f'test_{script_path.split("/")[-1].replace(".py", "").replace("_", "")}'
+
+    # divide i to fit into 4 groups
+    group_no = i % 8 + 1
+
+    def create_test(script_path, module_dir, temp_dir):
+        @pytest.mark.xdist_group(name=f"group{group_no}")
+        def test():
+            try:
+                # Capture the initial state of the directory
+                initial_files = set(os.listdir(temp_dir))
+
+                # Set up the environment
+                env = os.environ.copy()
+                env["PYTHONPATH"] = module_dir
+
+                # Run the script
+                subprocess.run(
+                    ["python", script_path],
+                    check=True,
+                    env=env,
+                )
+
+                # Capture the state of the directory after the script runs
+                final_files = set(os.listdir(temp_dir))
+
+                # Identify new files created during script execution
+                new_files = final_files - initial_files
+
+                # Filter only files with the specified extensions
+                target_extensions = {".html", ".mp4", ".jpg", ".png"}
+                files_to_remove = [
+                    file_name
+                    for file_name in new_files
+                    if os.path.splitext(file_name)[1].lower()
+                    in target_extensions
+                ]
+
+                # Delete the filtered files
+                for file_name in files_to_remove:
+                    file_path = os.path.join(temp_dir, file_name)
+                    if os.path.isfile(file_path):
+                        os.remove(file_path)
+
+            except subprocess.CalledProcessError as e:
+                pytest.fail(
+                    f"Script failed: {script_path}\nError message: {e}"
+                )
+
+        return test
+
+    # Add the test function to the global scope
+    globals()[test_name] = create_test(script_path, module_dir, "./")