Migrate to uv

.github/workflows/code_checks.yml

@@ -1,4 +1,7 @@
 name: code checks
+permissions:
+  contents: read
+  pull-requests: write
 
 on:
   push:
@@ -9,7 +12,7 @@ on:
       - .github/workflows/code_checks.yml
       - .github/workflows/integration_tests.yml
       - '**.py'
-      - poetry.lock
+      - uv.lock
       - pyproject.toml
       - '**.ipynb'
   pull_request:
@@ -19,7 +22,7 @@ on:
       - .pre-commit-config.yaml
       - .github/workflows/code_checks.yml
       - '**.py'
-      - poetry.lock
+      - uv.lock
       - pyproject.toml
       - '**.ipynb'
 
@@ -28,20 +31,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/[email protected]
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
+      - name: Install uv
+        uses: astral-sh/setup-uv@4db96194c378173c656ce18a155ffc14a9fc4355
         with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - uses: actions/[email protected]
+          # Install a specific version of uv.
+          version: "0.7.20"
+          enable-cache: true
+      - name: "Set up Python"
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38
         with:
-          python-version: '3.10'
-          cache: 'poetry'
+          python-version-file: ".python-version"
+      - name: Install the project
+        run: uv sync --dev --all-extras
       - name: Install dependencies and check code
         run: |
-          poetry env use '3.10'
           source .venv/bin/activate
-          poetry install --with test --all-extras
           pre-commit run --all-files
       - name: pip-audit (gh-action-pip-audit)
         uses: pypa/[email protected]

.github/workflows/docs.yml

@@ -1,4 +1,7 @@
 name: docs
+permissions:
+  contents: read
+  pull-requests: write
 
 on:
   pull_request:
@@ -14,22 +17,27 @@ jobs:
           submodules: 'true'
           fetch-depth: 0
 
-      - name: Install poetry
-        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-
-      - uses: actions/[email protected]
+      - name: Install uv
+        uses: astral-sh/setup-uv@4db96194c378173c656ce18a155ffc14a9fc4355
         with:
-          python-version: '3.10'
-          cache: 'poetry'
+          # Install a specific version of uv.
+          version: "0.7.20"
+          enable-cache: true
 
-      - name: Install dependencies
+      - name: "Set up Python"
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38
+        with:
+          python-version-file: ".python-version"
+      - name: Install the project
+        run: uv sync --dev --group docs
+      - name: Install dependencies and check code
         run: |
-          poetry env use '3.10'
-          poetry install --with docs,test --all-extras
+          source .venv/bin/activate
+          pre-commit run --all-files
 
       - name: Build docs
         run: |
-          source $(poetry env info --path)/bin/activate
+          source .venv/bin/activate
           cd docs
           rm -rf source/reference/api/_autosummary
           if [[ "${{ github.event_name == 'pull_request' && github.event.pull_request.merged == true && contains(github.event.pull_request.labels.*.name, 'release') }}" == "true" ]]; then

.github/workflows/integration_tests.yml

@@ -13,7 +13,7 @@ on:
       - '**.html'
       - '**.jinja'
       - '**.js'
-      - poetry.lock
+      - uv.lock
       - pyproject.toml
       - '**.rst'
       - '**.md'
@@ -30,7 +30,7 @@ on:
       - '**.html'
       - '**.jinja'
       - '**.js'
-      - poetry.lock
+      - uv.lock
       - pyproject.toml
       - '**.rst'
       - '**.md'
@@ -41,20 +41,23 @@ jobs:
     runs-on: [self-hosted, gpu, db, cyclops]
     steps:
       - uses: actions/[email protected]
-      - name: Install poetry
-        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/[email protected]
+      - name: Install uv
+        uses: astral-sh/setup-uv@4db96194c378173c656ce18a155ffc14a9fc4355
         with:
-          python-version: '3.10'
-          cache: 'poetry'
-      - name: Install dependencies and check code
+          # Install a specific version of uv.
+          version: "0.7.20"
+          enable-cache: true
+      - name: "Set up Python"
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38
+        with:
+          python-version-file: ".python-version"
+      - name: Install project and check code
         run: |
           export PATH=/opt/openmpi-4.1.5/bin:$PATH
           export LD_LIBRARY_PATH=/opt/openmpi-4.1.5/lib:$LD_LIBRARY_PATH
           ompi_info
-          poetry env use '3.10'
-          source $(poetry env info --path)/bin/activate
-          env MPICC=/opt/openmpi-4.1.5/bin/mpicc poetry install --with dev,test --all-extras
+          env MPICC=/opt/openmpi-4.1.5/bin/mpicc uv sync --all-extras --dev --group test
+          source .venv/bin/activate
           mpirun -n 2 python -m pytest --only-mpi
           pytest -m integration_test --cov-report term --cov-report xml:./coverage.xml --cov=cyclops -n auto --dist loadscope
       - name: Upload coverage to Codecov

.github/workflows/package.yml

@@ -29,9 +29,10 @@ jobs:
       - uses: actions/[email protected]
       - name: Install pip
         run: python3 -m pip install --upgrade pip
-      - uses: actions/[email protected]
+      - name: "Set up Python"
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38
         with:
-          python-version: '3.10'
+          python-version-file: ".python-version"
       - name: Install package and test import
         run: |
           pip install -e .

.github/workflows/publish.yml

@@ -1,4 +1,7 @@
 name: publish package
+permissions:
+  contents: read
+  pull-requests: write
 
 on:
   release:
@@ -13,13 +16,25 @@ jobs:
           sudo apt-get update
           sudo apt-get install libcurl4-openssl-dev libssl-dev
       - uses: actions/[email protected]
-      - name: Install poetry
-        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/[email protected]
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@4db96194c378173c656ce18a155ffc14a9fc4355
+        with:
+          # Install a specific version of uv.
+          version: "0.7.20"
+          enable-cache: true
+
+      - name: "Set up Python"
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38
         with:
-          python-version: '3.10'
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --all-extras
+
       - name: Build package
-        run: poetry build
+        run: uv build
+
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
         with:

.github/workflows/unit_tests.yml

@@ -11,7 +11,7 @@ on:
       - '**.html'
       - '**.jinja'
       - '**.js'
-      - poetry.lock
+      - uv.lock
       - pyproject.toml
   pull_request:
     branches:
@@ -23,25 +23,28 @@ on:
       - '**.html'
       - '**.jinja'
       - '**.js'
-      - poetry.lock
+      - uv.lock
       - pyproject.toml
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/[email protected]
-      - name: Install dependencies, run unit tests and coverage report
-        run: python3 -m pip install --upgrade pip && python3 -m pip install poetry
-      - uses: actions/[email protected]
+      - name: Install uv
+        uses: astral-sh/setup-uv@4db96194c378173c656ce18a155ffc14a9fc4355
         with:
-          python-version: '3.10'
-          cache: 'poetry'
+          # Install a specific version of uv.
+          version: "0.7.20"
+          enable-cache: true
+      - name: "Set up Python"
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38
+        with:
+          python-version-file: ".python-version"
+      - name: Install the project
+        run: uv sync --dev
       - run: |
-          python3 -m pip install --upgrade pip && python3 -m pip install poetry
-          poetry env use '3.10'
-          source $(poetry env info --path)/bin/activate
-          poetry install --with test --all-extras
+          source .venv/bin/activate
           pytest -m "not integration_test" --cov-report term --cov-report xml:./coverage.xml --cov=cyclops -n auto --dist loadscope
       - name: Upload coverage to Codecov
         uses: Wandalen/[email protected]

.gitignore

@@ -1,7 +1,6 @@
 *__pycache__*
 *.log
 docs/build
-.python-version
 *.DS_Store
 htmlcov
 .coverage

.pre-commit-config.yaml

@@ -55,14 +55,14 @@ repos:
       files: "^cyclops/"
       language: system
 
-  - repo: local
-    hooks:
-    - id: pytest
-      name: pytest
-      entry: python3 -m pytest -m "not integration_test" -n auto --dist loadscope
-      language: system
-      pass_filenames: false
-      always_run: true
+  # - repo: local
+  #   hooks:
+  #   - id: pytest
+  #     name: pytest
+  #     entry: python3 -m pytest -m "not integration_test" -n auto --dist loadscope
+  #     language: system
+  #     pass_filenames: false
+  #     always_run: true
 
 ci:
     autofix_commit_msg: |
@@ -73,5 +73,5 @@ ci:
     autoupdate_branch: ''
     autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
     autoupdate_schedule: weekly
-    skip: [pytest,doctest,nbstripout,mypy]
+    skip: [doctest,nbstripout,mypy]
     submodules: false

.python-version

@@ -0,0 +1 @@
+3.11

README.md

@@ -53,29 +53,29 @@ below.
 
 ## 🧑🏿‍💻 Developing
 
-### Using poetry
+### Using uv
 
 The development environment can be set up using
-[poetry](https://python-poetry.org/docs/#installation). Hence, make sure it is
+[uv](https://github.com/astral-sh/uv?tab=readme-ov-file#installation). Hence, make sure it is
 installed and then run:
 
 ```bash
-python3 -m poetry install
-source $(poetry env info --path)/bin/activate
+uv sync
+source .venv/bin/activate
 ```
 
 In order to install dependencies for testing (codestyle, unit tests, integration tests),
 run:
 
 ```bash
-python3 -m poetry install --with test
+uv sync --group test
 ```
 
 API documentation is built using [Sphinx](https://www.sphinx-doc.org/en/master/) and
 can be locally built by:
 
 ```bash
-python3 -m poetry install --with docs
+uv sync --group docs
 cd docs
 make html SPHINXOPTS="-D nbsphinx_allow_errors=True"
 ```
@@ -89,7 +89,7 @@ guidelines.
 
 ## 📚 [Documentation](https://vectorinstitute.github.io/cyclops/)
 
-If you need to build the documentations locally, make sure to install ``Pandoc`` in addition to ``docs`` poetry group.
+If you need to build the documentations locally, make sure to install ``Pandoc`` in addition to ``docs`` dependency group.
 
 
 ## 📓 Notebooks

cyclops/data/aggregate.py

@@ -761,4 +761,4 @@ def timestamp_ffill_agg(
     if fill_nan is not None:
         arr = np.nan_to_num(arr, nan=fill_nan)
 
-    return arr
+    return arr  # type: ignore[no-any-return]

cyclops/data/utils.py

@@ -13,7 +13,7 @@
 )
 
 import pandas as pd
-import PIL
+import PIL.Image
 import psutil
 from datasets import Dataset, DatasetDict
 from datasets.features import (

cyclops/evaluate/metrics/experimental/distributed_backends/torch_distributed.py

@@ -53,7 +53,7 @@ def world_size(self) -> int:
     def _simple_all_gather(self, data: Tensor) -> List[Tensor]:
         """Gather tensors of the same shape from all processes."""
         gathered_data = [torch.zeros_like(data) for _ in range(self.world_size)]
-        torch_dist.all_gather(gathered_data, data)  # type: ignore[no-untyped-call]
+        torch_dist.all_gather(gathered_data, data)
         return gathered_data
 
     def all_gather(self, data: Tensor) -> List[Tensor]:  # type: ignore[override]
@@ -77,7 +77,7 @@ def all_gather(self, data: Tensor) -> List[Tensor]:  # type: ignore[override]
         # gather sizes of all tensors
         local_size = torch.tensor(data.shape, device=data.device)
         local_sizes = [torch.zeros_like(local_size) for _ in range(self.world_size)]
-        torch_dist.all_gather(local_sizes, local_size)  # type: ignore[no-untyped-call]
+        torch_dist.all_gather(local_sizes, local_size)
         max_size = torch.stack(local_sizes).max(dim=0).values
         all_sizes_equal = all(all(ls == max_size) for ls in local_sizes)
 
@@ -93,7 +93,7 @@ def all_gather(self, data: Tensor) -> List[Tensor]:  # type: ignore[override]
             pad_dims.append(val.item())
         data_padded = torch.nn.functional.pad(data, pad_dims)
         gathered_data = [torch.zeros_like(data_padded) for _ in range(self.world_size)]
-        torch_dist.all_gather(gathered_data, data_padded)  # type: ignore[no-untyped-call]
+        torch_dist.all_gather(gathered_data, data_padded)
         for idx, item_size in enumerate(local_sizes):
             slice_param = [slice(dim_size) for dim_size in item_size]
             gathered_data[idx] = gathered_data[idx][slice_param]

cyclops/evaluate/metrics/experimental/functional/auroc.py

@@ -234,7 +234,7 @@ def _reduce_auroc(
 
     """
     if apc.is_array_api_obj(fpr) and apc.is_array_api_obj(tpr):
-        res = _auc_compute(fpr, tpr, 1.0, axis=1)  # type: ignore
+        res = _auc_compute(fpr, tpr, 1.0, axis=1)
     else:
         res = xp.stack(
             [_auc_compute(x, y, 1.0) for x, y in zip(fpr, tpr)],  # type: ignore

cyclops/evaluate/metrics/experimental/functional/average_precision.py

@@ -229,7 +229,7 @@ def _reduce_average_precision(
     """
     if apc.is_array_api_obj(precision) and apc.is_array_api_obj(recall):
         avg_prec = -xp.sum(
-            (recall[:, 1:] - recall[:, :-1]) * precision[:, :-1],  # type: ignore
+            (recall[:, 1:] - recall[:, :-1]) * precision[:, :-1],
             axis=1,
             dtype=xp.float32,
         )