Updated build system, github workflow, and switched to uv

.github/workflows/run_tests.yaml

@@ -10,25 +10,30 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Install `poetry` 
+      - uses: actions/checkout@v4
+
+      - name: Install uv
         run: |
-          pipx install poetry
-          poetry --version
+          curl -Ls https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'poetry'
+
       - name: Install package
-        run: |
-          poetry install
+        run: uv sync
+
       - name: Run linter
         run: |
-          poetry run flake8 torch_topological
+          source .venv/bin/activate
+          flake8 torch_topological
+
       - name: Run tests
         run: |
-          poetry run pytest
+          source .venv/bin/activate
+          pytest

.gitignore

@@ -1,8 +1,59 @@
 *~
 
-*.pyc
 *.swp
 
 /data/
-/dist/
+
+# Byte-compiled / optimized / DLL files
 __pycache__/
+*.py[codz]
+*$py.class
+
+# Distribution / packaging
+build/
+dist/
+wheels/
+*.egg-info/
+*.egg
+
+# Unit test
+.pytest_cache/
+
+# Sphinx documentation
+docs/build/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Environments
+.envrc
+.venv
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+.vscode/*
+!*.code-workspace
+# Built Visual Studio Code Extensions
+*.vsix
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+

pyproject.toml

@@ -7,30 +7,38 @@ authors = [
 ]
 license = "BSD-3-Clause"
 readme = "README.md"
-include = ["README.md"]
+requires-python = ">=3.9,<4"
 
-[tool.poetry.dependencies]
-python = ">=3.9"
-matplotlib = "^3.5.0"
-giotto-ph = "^0.2.0"
-torch = ">=1.12.0"
-gudhi = "^3.4.1"
-POT = "^0.9.0"
+dependencies = [
+    "matplotlib>=3.5",
+    "giotto-ph>=0.2",
+    "torch>=1.12",
+    "gudhi>=3.4",
+    "POT>=0.9",
+]
+
+[tool.uv]
+prerelease = "allow"
+index-strategy = "unsafe-best-match"
+dev-dependencies = [
+    "pytest>=5.2",
+    "Sphinx>=4.3",
+    "sphinx-rtd-theme>=1.0",
+    "tqdm>=4.62",
+    "torchvision>=0.11",
+    "flake8>=4.0",
+]
 
-[tool.poetry.dev-dependencies]
-pytest = ">=5.2"
-Sphinx = ">=4.3.1"
-sphinx-rtd-theme = "^1.0.0"
-tqdm = "^4.62.3"
-torchvision = ">=0.11.2"
-flake8 = "^4.0.1"
 
 [tool.black]
 line-length = 79
 
 [build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+py-modules = ['torch_topological']
 
 [project.urls]
 homepage = "https://github.com/aidos-lab/pytorch-topological"

torch_topological/examples/alpha_complex_pd.py

@@ -46,12 +46,12 @@
         pers_info = alpha_complex(X)
         pers_info = selector(pers_info)
 
-        data=pers_info[0].diagram
+        data = pers_info[0].diagram
         data = data.detach().cpu().numpy()
         ax.clear()
         plt.xlabel("Birth")
         plt.ylabel("Death")
-        ax.plot(data[:, 0], data[:, 1], 'ro', [0,0.8], [0,0.8], 'k-')
+        ax.plot(data[:, 0], data[:, 1], 'ro', [0, 0.8], [0, 0.8], 'k-')
         plt.pause(0.2)
 
         # Evaluate the loss; notice that we want to *maximise* it in

torch_topological/nn/weighted_euler_characteristic_transform.py

@@ -234,8 +234,8 @@ def _obtainDirection(self):
         return torch.tensor([x, y, z], dtype=torch.double)
 
     def _genSquares(self, x):
-        """Obtains coordinates and values of the adjacent squares in the 3D tensor
-        Input: x - 3D tensor"""
+        """Obtains coordinates and values of the adjacent squares in the 3D
+        tensor. Input: x - 3D tensor"""
         device = x.device
         arr = torch.clone(x)
         arr = arr.unsqueeze(0).float()
@@ -311,8 +311,8 @@ def _genSquares(self, x):
         return coords.float(), sqVals
 
     def _genCubes(self, x):
-        """Obtains coordinates and values of the adjacent cubes in the 3D tensor
-        Input: x - 3D tensor"""
+        """Obtains coordinates and values of the adjacent cubes in the 3D
+        tensor. Input: x - 3D tensor"""
         device = x.device
         x_ = torch.clone(x)
         x_ = x_.unsqueeze(0).unsqueeze(0).float()
@@ -387,8 +387,8 @@ def _genVertices(self, x):
         return torch.transpose(torch.nonzero(x), 0, 1).float()
 
     def _genEdges(self, x):
-        """Obtains coordinates and values of the adjacent edges in the 3D tensor
-        Input: x - 3D tensor"""
+        """Obtains coordinates and values of the adjacent edges in the 3D
+        tensor. Input: x - 3D tensor"""
         device = x.device
         arr = torch.clone(x)
         arr = arr.unsqueeze(0).float()