try fix ci using uv

.github/test_conda_env.yml

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

.github/workflows/lint.yml

@@ -0,0 +1,19 @@
+# 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: install linting packages
+        run: pip install pre-commit --break-system-packages
+
+      - name: run all precommits
+        run: pre-commit run --all

.github/workflows/release_published.yml

@@ -9,16 +9,17 @@ 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: "get tags"
+        run: |
+          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
         shell: bash -l {0}

.github/workflows/runtests.yml

@@ -1,32 +1,40 @@
-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: ["3.9", "3.10", "3.11", "3.12"]
+        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@v4
@@ -35,28 +43,40 @@ jobs:
         run: |
           git fetch --tags --force # Retrieve annotated tags.
 
-      - 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: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: install dbscan1d
+        shell: bash -el {0}
         run: |
-          pip install -e .
+          python -m pip install -e ".[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
+        shell: bash -el {0}
+        run: python -m 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

tests/test_dbscan1d.py

@@ -235,16 +235,16 @@ def test_issue_7(self, issue_7_array):
         # also test indices of core points
         assert np.all(dbs_1.core_sample_indices_ == dbs_2.core_sample_indices_)
 
-
-def test_sample_weights() -> None:
-    x = np.asarray([0.1, 0.2, 0.3, 0.1, 0.2, 0.3, 0.1, 0.2, 0.3, 1.1, 1.2])
-    labels = DBSCAN1D(eps=0.5, min_samples=3).fit_predict(x)
-    assert np.all(labels[:9] == 0)
-    assert np.all(labels[-2:] == -1)
-
-    weight = np.ones_like(x)
-    weight[-1] = 1.2
-    weight[-2] = 1.8
-    labels = DBSCAN1D(eps=0.5, min_samples=3).fit_predict(x, sample_weight=weight)
-    assert np.all(labels[:9] == 0)
-    assert np.all(labels[-2:] == 1)
+    def test_sample_weights(self) -> None:
+        """Test case for sample weights ."""
+        x = np.asarray([0.1, 0.2, 0.3, 0.1, 0.2, 0.3, 0.1, 0.2, 0.3, 1.1, 1.2])
+        labels = DBSCAN1D(eps=0.5, min_samples=3).fit_predict(x)
+        assert np.all(labels[:9] == 0)
+        assert np.all(labels[-2:] == -1)
+
+        weight = np.ones_like(x)
+        weight[-1] = 1.2
+        weight[-2] = 1.8
+        labels = DBSCAN1D(eps=0.5, min_samples=3).fit_predict(x, sample_weight=weight)
+        assert np.all(labels[:9] == 0)
+        assert np.all(labels[-2:] == 1)