Remove numba, fix CI

.github/workflows/build-sdist.yml

@@ -2,15 +2,6 @@ name: build-sdist
 
 on:
   workflow_call:
-    inputs:
-      mock:
-        required: false
-        type: boolean
-        default: false
-      upload_artifacts:
-        required: false
-        type: boolean
-        default: false
 
 env:
   MODULE_NAME: imops
@@ -22,31 +13,18 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Mock sdist
-        if: ${{ inputs.mock }}
-        run: |
-          mkdir -p dist
-          echo "Create mock sdist" > "dist/mock_sdist.tar.gz"
-
       - name: Set up Python 3.9
-        if: ${{ inputs.mock == false }}
         uses: actions/setup-python@v5
         with:
           python-version: 3.9
 
       - name: Build
-        if: ${{ inputs.mock == false }}
         run: |
           pip install build wheel
           python -m build --sdist
 
       - name: Upload sdist
-        if: ${{ inputs.upload_artifacts }}
         uses: actions/upload-artifact@v4
         with:
           name: sdist
           path: dist/*.tar.gz
-
-      - name: Cleanup all local files
-        if: ${{ inputs.mock }}
-        run: rm -rf dist

.github/workflows/build-wheels.yml

@@ -10,14 +10,6 @@ on:
         required: false
         type: string
         default: ""
-      mock:
-        required: false
-        type: boolean
-        default: false
-      upload_artifacts:
-        required: false
-        type: boolean
-        default: false
 
 env:
   MODULE_NAME: imops
@@ -26,43 +18,34 @@ jobs:
   build_wheels:
     strategy:
       matrix:
-        os: [ ubuntu-22.04, windows-2022, macOS-13 ]
+        os: [ ubuntu-22.04, windows-2022, macOS-15 ]
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
 
-      - name: Mock wheels
-        if: ${{ inputs.mock }}
-        run: |
-          New-Item -ItemType Directory -Force -Path wheelhouse | Out-Null
-          "Create mock wheels" | Out-File -Encoding ascii "wheelhouse/mock_wheels_${{ matrix.os }}.whl"
-        shell: pwsh
-
       - name: Set up Python 3.9
-        if: ${{ inputs.mock == false }}
         uses: actions/setup-python@v5
         with:
           python-version: '3.9'
 
       - name: Install cibuildwheel
-        if: ${{ inputs.mock == false }}
         run: python -m pip install cibuildwheel==2.17.0
 
       - name: Install llvm for mac
-        if: ${{ matrix.os == 'macOS-13' && inputs.mock == false }}
+        if: ${{ matrix.os == 'macOS-15' }}
         run: |
           brew install llvm
 
       - name: Install g++-11 for ubuntu
-        if: ${{ matrix.os == 'ubuntu-22.04' && inputs.mock == false }}
+        if: ${{ matrix.os == 'ubuntu-22.04' }}
         id: install_cc
         uses: rlalik/setup-cpp-compiler@master
         with:
           compiler: g++-11
 
       - name: Check compilers for ubuntu
-        if: ${{ matrix.os == 'ubuntu-22.04' && inputs.mock == false }}
+        if: ${{ matrix.os == 'ubuntu-22.04' }}
         run: |
           ls /usr/bin/gcc*
           ls /usr/bin/g++*
@@ -72,7 +55,6 @@ jobs:
           gcc --version
 
       - name: Build wheels
-        if: ${{ inputs.mock == false }}
         run: |
           python -m pip install --upgrade pip
           python -m pip install build wheel
@@ -88,13 +70,7 @@ jobs:
             fi
 
       - name: Upload wheels
-        if: ${{ inputs.upload_artifacts }}
         uses: actions/upload-artifact@v4
         with:
           name: wheels-${{ matrix.os }}
-          path: ./wheelhouse/*.whl
-
-      - name: Cleanup all local files
-        if: ${{ inputs.mock }}
-        run: Remove-Item -Recurse -Force wheelhouse
-        shell: pwsh
+          path: ./wheelhouse/*.whl

.github/workflows/release.yml

@@ -36,13 +36,10 @@ jobs:
     needs: [ check_version ]
     with:
       cibw_build: cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*
-      upload_artifacts: true
 
   build_sdist:
     uses: ./.github/workflows/build-sdist.yml
     needs: [ check_version ]
-    with:
-      upload_artifacts: true
 
   release:
     needs: [ build_wheels, build_sdist ]
@@ -53,7 +50,15 @@ jobs:
         with:
           path: dist
 
+      - name: Flatten dist directory
+        run: |
+          shopt -s globstar
+          mkdir -p flat
+          cp dist/**/* flat/ || true
+          rm -rf dist
+          mv flat dist
+
       - name: Publish to PyPi
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test-release.yml

@@ -0,0 +1,40 @@
+name: Test release
+
+on: [ pull_request ]
+
+env:
+  MODULE_NAME: imops
+
+jobs:
+  build_wheels:
+    uses: ./.github/workflows/build-wheels.yml
+    with:
+      cibw_build: cp37-* cp39-* cp312-*
+      cibw_skip: "*manylinux_x86_64 *musllinux_x86_64"
+
+  build_sdist:
+    uses: ./.github/workflows/build-sdist.yml
+
+  publish_testpypi:
+    needs: [ build_wheels, build_sdist ]
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+
+      - name: Flatten dist directory
+        run: |
+          shopt -s globstar
+          mkdir -p flat
+          cp dist/**/* flat/ || true
+          rm -rf dist
+          mv flat dist
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          skip-existing: true

.github/workflows/tests.yml

@@ -45,12 +45,10 @@ jobs:
 
       - name: Test with pytest
         run: |
-          pytest tests -m "not nonumba" --junitxml=reports/junit-${{ matrix.python-version }}.xml --cov="$MODULE_PARENT/$MODULE_NAME" --cov-report=xml --cov-branch
-          pip uninstall numba -y
-          pytest tests/test_backend.py -m nonumba
+          pytest tests -n 2 --junitxml=reports/junit-${{ matrix.python-version }}.xml --cov="$MODULE_PARENT/$MODULE_NAME" --cov-report=xml --cov-branch
       - name: Generate coverage report
         run: |
-          coverage xml -o reports/coverage-${{ matrix.python-version }}.xml --omit=imops/src/_numba_zoom.py
+          coverage xml -o reports/coverage-${{ matrix.python-version }}.xml
           sed -i -e "s|$MODULE_PARENT/||g" reports/coverage-${{ matrix.python-version }}.xml
           sed -i -e "s|$(echo $MODULE_PARENT/ | tr "/" .)||g" reports/coverage-${{ matrix.python-version }}.xml
 

README.md

@@ -13,24 +13,23 @@ Efficient parallelizable algorithms for multidimensional arrays to speed up your
 
 ```shell
 pip install imops  # default install with Cython backend
-pip install imops[numba]  # additionally install Numba backend
 ```
 
 # How fast is it?
 
 Time comparisons (ms) for Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz using 8 threads. All inputs are C-contiguous NumPy arrays. For morphology functions `bool` dtype is used and `float64` for all others.
-| function / backend   |  Scipy()  |  Cython(fast=False)  |  Cython(fast=True)  |  Numba()  |
-|:----------------------:|:-----------:|:----------------------:|:---------------------:|:-----------:|
-| `zoom(..., order=0)` |   2072    |         1114         |         **867**         |   3590    |
-| `zoom(..., order=1)` |   6527    |         596          |         **575**         |   3757    |
-| `interp1d`           |    780    |         149          |         **146**         |    420    |
-| `radon`              |   59711   |         5982         |        **4837**         |      -     |
-| `inverse_radon`      |   52928   |         8254         |        **6535**         |         -  |
-| `binary_dilation`    |   2207    |         310          |         **298**         |        -   |
-| `binary_erosion`     |   2296    |         326          |         **304**         |        -   |
-| `binary_closing`     |   4158    |         544          |         **469**         |        -   |
-| `binary_opening`     |   4410    |         567          |         **522**         |        -   |
-| `center_of_mass`     |   2237    |          **64**          |         **64**          |        -   |
+| function / backend   |  Scipy()  |  Cython(fast=False)  |  Cython(fast=True)  |
+|:----------------------:|:-----------:|:----------------------:|:---------------------:|
+| `zoom(..., order=0)` |   2072    |         1114         |         **867**         |
+| `zoom(..., order=1)` |   6527    |         596          |         **575**         |
+| `interp1d`           |    780    |         149          |         **146**         |
+| `radon`              |   59711   |         5982         |        **4837**         |
+| `inverse_radon`      |   52928   |         8254         |        **6535**         |
+| `binary_dilation`    |   2207    |         310          |         **298**         |
+| `binary_erosion`     |   2296    |         326          |         **304**         |
+| `binary_closing`     |   4158    |         544          |         **469**         |
+| `binary_opening`     |   4410    |         567          |         **522**         |
+| `center_of_mass`     |   2237    |          **64**          |         **64**          |
 
 We use [`airspeed velocity`](https://asv.readthedocs.io/en/stable/) to benchmark our code. For detailed results visit [benchmark page](https://neuro-ml.github.io/imops/benchmarks/).
 
@@ -121,36 +120,33 @@ labeled, num_components = label(x, background=1, return_num=True)
 # Backends
 For all heavy image routines except `label` you can specify which backend to use. Backend can be specified by a string or by an instance of `Backend` class. The latter allows you to customize some backend options:
 ```python
-from imops import Cython, Numba, Scipy, zoom
+from imops import Cython, Scipy, zoom
 
 y = zoom(x, 2, backend='Cython')
 y = zoom(x, 2, backend=Cython(fast=False))  # same as previous
 y = zoom(x, 2, backend=Cython(fast=True))  # -ffast-math compiled cython backend
 y = zoom(x, 2, backend=Scipy())  # use scipy original implementation
-y = zoom(x, 2, backend='Numba')
-y = zoom(x, 2, backend=Numba(parallel=True, nogil=True, cache=True))  # same as previous
 ```
 Also backend can be specified globally or locally:
 ```python
 from imops import imops_backend, set_backend, zoom
 
-set_backend('Numba')  # sets Numba as default backend
+set_backend('Scipy')  # sets Scipy as default backend
 with imops_backend('Cython'):  # sets Cython backend via context manager
     zoom(x, 2)
 ```
-Note that for `Numba` backend setting `num_threads` argument has no effect for now and you should use `NUMBA_NUM_THREADS` environment variable.
 Available backends:
-|         function / backend            | Scipy   | Cython  | Numba   |
-|:-------------------:|:---------:|:---------:|:---------:|
-| `zoom`            | ✓ | ✓ | ✓ |
-| `interp1d`        | ✓ | ✓ | ✓ |
-| `radon`           | ✗ | ✓ | ✗ |
-| `inverse_radon`   | ✗ | ✓ | ✗ |
-| `binary_dilation` | ✓ | ✓ | ✗ |
-| `binary_erosion`  | ✓ | ✓ | ✗ |
-| `binary_closing`  | ✓ | ✓ | ✗ |
-| `binary_opening`  | ✓ | ✓ | ✗ |
-| `center_of_mass`  | ✓ | ✓ | ✗ |
+|         function / backend            | Scipy   | Cython  |
+|:-------------------:|:---------:|:---------:|
+| `zoom`            | ✓ | ✓ |
+| `interp1d`        | ✓ | ✓ |
+| `radon`           | ✗ | ✓ |
+| `inverse_radon`   | ✗ | ✓ |
+| `binary_dilation` | ✓ | ✓ |
+| `binary_erosion`  | ✓ | ✓ |
+| `binary_closing`  | ✓ | ✓ |
+| `binary_opening`  | ✓ | ✓ |
+| `center_of_mass`  | ✓ | ✓ |
 
 # Acknowledgements
 

asv.conf.json

@@ -15,14 +15,12 @@
             "Cython": ["3.0.10"],
             "scipy": [],
             "scikit-image": [],
-            "numba": [],
             "pip+connected-components-3d": [],
             "pip+fastremap": [],
             "pybind11": []
         },
         "env_nobuild": {
-            "OMP_NUM_THREADS": "8",
-            "NUMBA_NUM_THREADS": "8"
+            "OMP_NUM_THREADS": "8"
         }
     },
     "env_dir": ".asv/env",