DeepSDFStruct 1.7.2__tar.gz

deepsdfstruct-1.7.2/.deepsource.toml

@@ -0,0 +1,10 @@
+version = 1
+
+[[analyzers]]
+name = "python"
+
+  [analyzers.meta]
+  runtime_version = "3.x.x"
+
+[[code_formatters]]
+name = "black"

deepsdfstruct-1.7.2/.github/copilot-instructions.md

@@ -0,0 +1,5 @@
+# Copilot Instructions
+
+## Lock files
+
+Never modify or touch lock files (e.g., `uv.lock`, `package-lock.json`, `poetry.lock`). These files are managed by their respective package managers and should not be edited manually or as part of automated changes.

deepsdfstruct-1.7.2/.github/workflows/copilot-setup-steps.yml

@@ -0,0 +1,43 @@
+name: "Copilot Setup Steps"
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    # Set the permissions to the lowest permissions possible needed for your steps.
+    # Copilot will be given its own token for its operations.
+    permissions:
+      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission.
+      # If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
+      contents: read
+
+    # You can define any steps you want, and they will run before the agent starts.
+    # If you do not check out your code, Copilot will do this for you.
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12 
+
+      - name: Setup UV with cache
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Sync dependencies with uv
+        run: uv sync 

deepsdfstruct-1.7.2/.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+name: Create Docs
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Setup UV with cache
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Sync dependencies with uv
+        run: uv sync --extra docs --no-editable
+
+      - name: Create Docs
+        run: |
+          uv run sphinx-autogen -o docs/source/generated docs/api_reference.rst
+          uv run make -C docs html
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html

deepsdfstruct-1.7.2/.github/workflows/publish.yml

@@ -0,0 +1,56 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  test:
+    uses: ./.github/workflows/test.yml
+    secrets: inherit
+
+  publish:
+    needs: test
+
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Verify tag format
+        run: |
+          [[ "$GITHUB_REF_NAME" =~ ^v[0-9]+\.[0-9]+\.[0-9]+$ ]]
+
+      - name: Verify package version
+        shell: bash
+        run: |
+          TAG="${GITHUB_REF_NAME#v}"
+
+          VERSION=$(uv version --short)
+
+          echo "Tag:     $TAG"
+          echo "Version: $VERSION"
+
+          if [ "$TAG" != "$VERSION" ]; then
+            echo "::error::Git tag ($TAG) does not match package version ($VERSION)"
+            exit 1
+          fi
+
+      - run: uv sync
+
+      - run: uv build
+
+      - run: uv publish

deepsdfstruct-1.7.2/.github/workflows/test.yml

@@ -0,0 +1,76 @@
+name: Test Python Package
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_call:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+
+    env:
+      HF_HOME: ${{ github.workspace }}/.cache/huggingface
+      HF_HUB_CACHE: ${{ github.workspace }}/.cache/huggingface/hub
+      HF_HUB_DOWNLOAD_TIMEOUT: "60"
+      HF_HUB_ETAG_TIMEOUT: "30"
+      HF_TOKEN: ${{ secrets.HF_TOKEN }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup UV with cache
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Cache huggingface
+        id: hf-cache
+        uses: actions/cache@v4
+        with:
+          path: ${{ github.workspace }}/.cache/huggingface
+          key: huggingface-${{ hashFiles('pyproject.toml') }}
+          restore-keys: |
+            huggingface-
+
+      - name: Ensure Hugging Face cache directories exist
+        run: |
+          mkdir -p "$HF_HUB_CACHE"
+
+      - name: Show Hugging Face cache status
+        run: |
+          echo "hf-cache-hit=${{ steps.hf-cache.outputs.cache-hit }}"
+          echo "HF_HOME=$HF_HOME"
+          ls -la "$(dirname "$HF_HOME")" || true
+          du -sh "$HF_HOME" || true
+          du -sh "$HF_HUB_CACHE" || true
+
+      - name: Sync dependencies with uv
+        run: uv sync
+
+      - name: Run tests
+        run: uv run pytest --cov=DeepSDFStruct --cov-report=term-missing --cov-report=xml tests
+
+      - name: Show Hugging Face cache after tests
+        if: always()
+        run: |
+          echo "Post-test Hugging Face cache usage"
+          du -sh "$HF_HOME" || true
+          du -sh "$HF_HUB_CACHE" || true
+
+      - name: Coveralls
+        if: matrix.python-version == '3.13' && matrix.os == 'ubuntu-latest'
+        uses: coverallsapp/github-action@v2

deepsdfstruct-1.7.2/.gitignore

@@ -0,0 +1,132 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Virtual environments
+venv/
+env/
+.venv/
+ENV/
+env.bak/
+venv.bak/
+.python-version
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+
+# Pytest
+.pytest_cache/
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pylint
+pylint-report.txt
+pylint-global.txt
+
+# Bandit
+bandit.json
+
+# PyCharm / VSCode
+.idea/
+.vscode/
+*.code-workspace
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# macOS
+.DS_Store
+
+# Windows
+Thumbs.db
+ehthumbs.db
+Desktop.ini
+
+# VS Code
+.vscode/
+
+# ruff
+.ruff_cache
+
+# Editor backups
+*~
+*.swp
+*.swo
+
+# Pytorch intermediate files
+*.pth 
+!latest.pth
+
+# Files generated during testing
+DeepSDFStruct/trained_models/test_experiment/**/latest.pth
+DeepSDFStruct/trained_models/test_experiment_hierarchical/**/latest.pth
+DeepSDFStruct/trained_models/test_experiment/**/Logs.png
+DeepSDFStruct/trained_models/test_experiment_hierarchical/**/Logs.png
+DeepSDFStruct/trained_models/**/Reconstructions/*
+training_data
+tests/tmp_outputs
+*.vtk
+
+# doc temp files
+docs/_build
+docs/source/generated
+
+# work in progress files
+wip
+examples
+reconstruction
+todo
+
+# confidential files
+confidential*
+
+# slurm files
+slurm-*.out
+
+# intermediate model runs
+mlruns

deepsdfstruct-1.7.2/.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.5.1
+    hooks:
+    -   id: black

deepsdfstruct-1.7.2/AGENT_INSTRUCTIONS.md

@@ -0,0 +1,17 @@
+AGENT_INSTRUCTIONS.md
+# Agent Instructions
+
+This file contains specific instructions for agents working in this environment.
+
+## Running Python Code
+
+In order to run python code, use 'uv run python [your commmand]'
+
+NEVER append 2>&1 to your commands
+## Context
+
+This project uses uv for Python dependency management. Always wrap python commands with 'uv run' to ensure proper environment setup.
+
+## Formatting
+always run black on the files that you touched or generated to keep aligned with the repository formatting.
+