[MNT] Fixing CI issues and separate doctests from regular CI runners (#2902)

* trying to fix CI stuff

* use numba in codecov

* try cov

* no cov

* doctest-plus

* doctest-plus

* addopts

* dedicated doctest test

* periodic

Author: MatthewMiddlehurst

.github/actions/cpu_all_extras/action.yml

@@ -15,7 +15,7 @@ runs:
   using: "composite"
   steps:
     - name: Install CPU TensorFlow
-      if: ${{ runner.os == 'Linux' && inputs.python_version != '3.13' }}
+      if: ${{ runner.os == 'Linux' && inputs.python_version != '3.13.5' }}
       uses: nick-fields/retry@v3
       with:
         timeout_minutes: 30

.github/workflows/periodic_tests.yml

@@ -163,7 +163,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macOS-14, windows-2022 ]
-        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13.5" ]
 
     steps:
       - name: Checkout
@@ -178,7 +178,7 @@ jobs:
         if: runner.os == 'Linux'
         uses: pierotofy/set-swap-space@v1.0
         with:
-          swap-size-gb: 10
+          swap-size-gb: 8
 
       - name: Use numba cache to set env variables but not restore cache
         uses: ./.github/actions/numba_cache
@@ -208,6 +208,40 @@ jobs:
           # Save cache with the current date (ENV set in numba_cache action)
           key: numba-pytest-${{ runner.os }}-${{ matrix.python-version}}-${{ env.CURRENT_DATE }}
 
+  doctests:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - if: ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'no numba cache') }}
+        name: Use numba cache to set env variables but not restore cache
+        uses: ./.github/actions/numba_cache
+        with:
+          cache_name: "doctests"
+          runner_os: ${{ runner.os }}
+          python_version: "3.12"
+          restore_cache: "false"
+
+      - name: Install aeon and dependencies
+        uses: nick-fields/retry@v3
+        with:
+          timeout_minutes: 30
+          max_attempts: 3
+          command: python -m pip install .[all_extras,dev]
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: python -m pytest -n logical --doctest-only
+
   codecov:
     runs-on: ubuntu-24.04
 

.github/workflows/pr_examples.yml

@@ -41,7 +41,8 @@ jobs:
           runner_os: ${{ runner.os }}
           python_version: "3.12"
 
-      - uses: ./.github/actions/cpu_all_extras
+      - name: Install aeon and dependencies
+        uses: ./.github/actions/cpu_all_extras
         with:
           additional_extras: "dev,binder"
 

.github/workflows/pr_pytest.yml

@@ -55,7 +55,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macOS-14, windows-2022 ]
-        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13.5" ]
         # skip python versions unless the PR has the 'full pytest actions' label
         pr-testing:
           - ${{ (github.event_name == 'pull_request' && !contains(github.event.pull_request.labels.*.name, 'full pytest actions')) }}
@@ -76,7 +76,7 @@ jobs:
         if: runner.os == 'Linux'
         uses: pierotofy/set-swap-space@v1.0
         with:
-          swap-size-gb: 10
+          swap-size-gb: 8
 
       - if: ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'no numba cache') }}
         name: Restore numba cache
@@ -86,7 +86,8 @@ jobs:
           runner_os: ${{ runner.os }}
           python_version: ${{ matrix.python-version }}
 
-      - uses: ./.github/actions/cpu_all_extras
+      - name: Install aeon and dependencies
+        uses: ./.github/actions/cpu_all_extras
         with:
           python_version: ${{ matrix.python-version }}
           additional_extras: "dev"
@@ -98,6 +99,38 @@ jobs:
         # run the full test suit if a PR has the 'full pytest actions' label
         run: python -m pytest -n logical --prtesting ${{ github.event_name == 'pull_request' && !contains(github.event.pull_request.labels.*.name, 'full pytest actions') }}
 
+  doctests:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - if: ${{ github.event_name != 'pull_request' || !contains(github.event.pull_request.labels.*.name, 'no numba cache') }}
+        name: Restore numba cache
+        uses: ./.github/actions/numba_cache
+        with:
+          cache_name: "doctests"
+          runner_os: ${{ runner.os }}
+          python_version: "3.12"
+
+      - name: Install aeon and dependencies
+        uses: ./.github/actions/cpu_all_extras
+        with:
+          additional_extras: "dev"
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Run tests
+        run: python -m pytest -n logical --doctest-only
+
+
   codecov:
     # run the code coverage job if a PR has the 'codecov actions' label
     if: ${{ github.event_name != 'pull_request' || contains(github.event.pull_request.labels.*.name, 'codecov actions') }}
@@ -116,7 +149,8 @@ jobs:
       - name: Disable Numba JIT
         run: echo "NUMBA_DISABLE_JIT=1" >> $GITHUB_ENV
 
-      - uses: ./.github/actions/cpu_all_extras
+      - name: Install aeon and dependencies
+        uses: ./.github/actions/cpu_all_extras
         with:
           additional_extras: "unstable_extras,dev"
 

.github/workflows/release.yml

@@ -54,7 +54,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macOS-14, windows-2022 ]
-        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13.5" ]
 
     steps:
       - name: Checkout
@@ -69,7 +69,7 @@ jobs:
         if: runner.os == 'Linux'
         uses: pierotofy/set-swap-space@v1.0
         with:
-          swap-size-gb: 10
+          swap-size-gb: 8
 
       - uses: actions/download-artifact@v4
         with:

aeon/transformations/collection/dictionary_based/_borf.py

@@ -615,7 +615,7 @@ def _sax(
     )
     global_std = np.std(a)
     if global_std == 0:
-        return np.zeros((n_windows, word_length), dtype=np.uint8)
+        return np.zeros((n_windows, word_length), dtype=np.uint16)
     seg_size = window_size // word_length
     n_windows = _get_n_windows(
         sequence_size=a.size, window_size=window_size, dilation=dilation, stride=stride
@@ -646,7 +646,7 @@ def _sax(
                 sigma_global=global_std,
                 sigma_threshold=min_window_to_signal_std_ratio,
             )
-    return np.digitize(out, bins).astype(np.uint8)
+    return np.digitize(out, bins).astype(np.uint16)
 
 
 @nb.njit(fastmath=True, cache=True)

pyproject.toml

@@ -87,17 +87,16 @@ unstable_extras = [
 
 # development dependencies
 dev = [
-    "backoff",
-    "httpx",
     "pre-commit",
     "pytest",
     "pytest-cov",
+    "pytest-doctestplus",
     "pytest-mock",
     "pytest-randomly",
+    "pytest-remotedata",
+    "pytest-rerunfailures",
     "pytest-timeout",
     "pytest-xdist[psutil]",
-    "pytest-rerunfailures",
-    "wheel",
 ]
 binder = [
     "notebook",
@@ -166,21 +165,24 @@ convention = "numpy"
 mypy_path = "aeon/"
 
 [tool.pytest.ini_options]
-# ignore certain folders and pytest warnings
 testpaths = "aeon"
-addopts = '''
-    --doctest-modules
-    --durations 20
-    --timeout 600
-    --showlocals
-    --dist worksteal
-    --reruns 2
-    --only-rerun "crashed while running"
-    --only-rerun "zipfile.BadZipFile"
-    --only-rerun "accessible `.keras` zip file."
-'''
-filterwarnings = '''
-    ignore::UserWarning
-    ignore:numpy.dtype size changed
-    ignore:numpy.ufunc size changed
-'''
+doctest_optionflags = [
+    "NORMALIZE_WHITESPACE",
+    "ELLIPSIS",
+    "FLOAT_CMP",
+]
+addopts = [
+    "--durations=20",
+    "--timeout=600",
+    "--showlocals",
+    "--dist=worksteal",
+    "--reruns=3",
+    "--reruns-delay=3",
+    "--rerun-except=Error",
+    "--rerun-except=Exception",
+]
+filterwarnings = [
+    "ignore::UserWarning",
+    "ignore:numpy.dtype size changed",
+    "ignore:numpy.ufunc size changed",
+]