update readme and fix CI

.github/test_conda_env.yml

@@ -1,4 +1,4 @@
-name: test
+name: dbscan1d
 channels:
   - conda-forge
   - defaults

.github/workflows/lint.yml

@@ -0,0 +1,30 @@
+# Lint the code using the defined pre-commits
+name: LintCode
+on: [push]
+
+jobs:
+  lint_code:
+    runs-on: ubuntu-latest
+
+    # only run if CI isn't turned off
+    if: github.event_name == 'push' || !contains(github.event.pull_request.labels.*.name, 'no_ci')
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: "get tags"
+        run: |
+          git fetch --tags --force # Retrieve annotated tags.
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: install linting packages
+        run: uv tool install pre-commit
+
+      - name: run all precommits
+        run: uv run pre-commit run --all

.github/workflows/release_published.yml

@@ -9,27 +9,25 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniconda-version: 'latest'
-          python-version: "3.11"
-          activate-environment: test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
-
-      - name: install
-        shell: bash -l {0}
+      - name: "get tags"
         run: |
-          pip install -e .[dev]
+          git fetch --tags --force # Retrieve annotated tags.
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
 
       - name: create dists
         shell: bash -l {0}
         run: |
-          python -m pip install build
-          python -m build
+          uv build
 
       - name: publish package
         uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/runtests.yml

@@ -1,58 +1,79 @@
-name: validate
-on: [push]
+# Run full test suite using conda env and all optional deps.
+name: TestCode
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+    branches:
+    - master
+    paths:
+      - 'pyproject.toml'
+      - '**.py'
+      - '.github/workflows/*.yml'
 
-jobs:
-  # Simply applies flake8 to code using pre-commit
-  lint_code:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v1
-
-      - name: Setup conda
-        uses: s-weigand/setup-conda@v1
-        with:
-          python-version: "3.10"
 
-      - name: install linting packages
-        run: pip install pre-commit
-
-      - name: run all precommits
-        run: pre-commit run --all
+# Cancel previous runs when this one starts.
+concurrency:
+  group: TestCode-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
 
+jobs:
   # Runs the tests on combinations of the supported python/os matrix.
   test_code:
+
+    timeout-minutes: 25
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ['3.10', '3.11', "3.12"]
+
+    # only run if CI isn't turned off
+    if: github.event_name == 'push' || !contains(github.event.pull_request.labels.*.name, 'no_ci')
+
+    env:
+      # set conda environment file with dependencies
+      env_file: "test_conda_env.yml"
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniconda-version: 'latest'
-          python-version: ${{ matrix.python-version }}
-          activate-environment: test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
-
-      - name: install
-        shell: bash -l {0}
+      - name: "get tags"
         run: |
-          pip install -e .
+          git fetch --tags --force # Retrieve annotated tags.
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
 
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      # Print out the package info for current environment
       - name: print package info
-        shell: bash -l {0}
+        shell: bash -el {0}
         run: |
-          conda info -a
-          conda list
+          uv pip list
 
-      # Runs test suite and calculates coverage
-      - name: run test suite
-        shell: bash -l {0}
-        run: |
-          pytest tests
+      - name: Run tests
+        # For example, using `pytest`
+        run: uv run pytest -s --cov dbscan1d --cov-append --cov-report=xml
+
+      # Upload coverage files
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: false
+          files: ./coverage.xml
+          flags: unittests
+          name: PR_tests
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+
+# This is a very useful step for debugging, it allows you to ssh into the CI
+# machine (https://github.com/marketplace/actions/debugging-with-tmate).
+#
+#- name: Setup tmate session
+#  uses: mxschmitt/action-tmate@v3

.gitignore

@@ -88,3 +88,6 @@ docs/quickref/stubs
 
 # mypy
 .mypy_cache
+
+# uv
+uv.lock

.pre-commit-config.yaml

@@ -1,38 +1,27 @@
+exclude: scripts/
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.3.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
-    -   id: trailing-whitespace
+    -   id: check-merge-conflict
     -   id: mixed-line-ending
         args: ['--fix=lf']
--   repo: https://github.com/psf/black
-    rev: 22.6.0
+
+    # Ruff is a replacement for flake8 and many other linters (much faster too)
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.1
     hooks:
-    -   id: black
--   repo: https://github.com/PyCQA/flake8
-    rev: 3.8.3
+    -   id: ruff
+        args: ["--fix"]
+        # Run the formatter.
+    -   id: ruff-format
+
+    # ensures __future__ import annotations at top of files which require it
+    # for the typing features they are using.
+-   repo: https://github.com/frostming/fix-future-annotations
+    rev: 0.5.0
     hooks:
-    -   id: flake8
-        additional_dependencies:
-          - flake8-black
-          - flake8-breakpoint
-          - flake8-docstrings
--   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        name: isort (python)
-        args: ["--profile", "black"]
-      - id: isort
-        name: isort (cython)
-        types: [cython]
-      - id: isort
-        name: isort (pyi)
-        types: [pyi]
--   repo: https://github.com/kynan/nbstripout
-    rev: 0.3.9
-    hooks:
-    -   id: nbstripout
-        files: ".ipynb"
+    -   id: fix-future-annotations

README.md

@@ -24,7 +24,7 @@ It only requires numpy.
 
 ## Quickstart
 dbscan1d is designed to be interchangable with sklearn's implementation in almost
-all cases. The exception is that the `weights` parameter is not yet supported.
+all cases.
 
 ```python
 from sklearn.datasets import make_blobs