Adding Python 3.13 and numpy>2 support

.github/workflows/build_test_deploy_all_wheels.yml

@@ -13,26 +13,26 @@ jobs:
           - os: macOS-ARM
             runner: [self-hosted, macOS, ARM64]
             archs: arm64
-            cibw_build: cp39-macosx_arm64 cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64
+            cibw_build: cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64 cp313-macosx_arm64
           - os: manylinux
             runner: [self-hosted, Ubuntu, Native]
             archs: auto
-            cibw_build: cp39-manylinux_x86_64 cp310-manylinux_x86_64 cp311-manylinux_x86_64 cp312-manylinux_x86_64
+            cibw_build: cp310-manylinux_x86_64 cp311-manylinux_x86_64 cp312-manylinux_x86_64 cp313-manylinux_x86_64
           - os: windows
             runner: [self-hosted, Windows]
             archs: auto
-            cibw_build: cp39-win_amd64 cp310-win_amd64 cp311-win_amd64 cp312-win_amd64
+            cibw_build: cp310-win_amd64 cp311-win_amd64 cp312-win_amd64 cp313-win_amd64
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
           python-version: |
-            3.9
             3.10
             3.11
-            3.12 
+            3.12
+            3.13
 
       - name: Install cibuildwheel and nox
         run: |
@@ -52,6 +52,7 @@ jobs:
         env:
           CIBW_BUILD: ${{ matrix.cibw_build }}
           CIBW_ARCHS: ${{ matrix.archs }}
+          MACOSX_DEPLOYMENT_TARGET: "14.0"
           CIBW_BEFORE_ALL_LINUX: >
             sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*.repo &&
             sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*.repo &&

.github/workflows/build_wheels.yml

@@ -13,27 +13,27 @@ jobs:
           - os: macOS-ARM
             runner: [self-hosted, macOS, ARM64]
             archs: arm64
-            cibw_build: cp39-macosx_arm64 cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64
+            cibw_build: cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64 cp313-macosx_arm64
           - os: manylinux
             runner: [self-hosted, Ubuntu, Native]
             archs: auto
-            cibw_build: cp39-manylinux_x86_64 cp310-manylinux_x86_64 cp311-manylinux_x86_64 cp312-manylinux_x86_64
+            cibw_build: cp310-manylinux_x86_64 cp311-manylinux_x86_64 cp312-manylinux_x86_64 cp313-manylinux_x86_64
           - os: windows
             runner: [self-hosted, Windows]
             archs: auto
-            cibw_build: cp39-win_amd64 cp310-win_amd64 cp311-win_amd64 cp312-win_amd64
+            cibw_build: cp310-win_amd64 cp311-win_amd64 cp312-win_amd64 cp313-win_amd64
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9  # Works as bootstrap for cibuildwheel
+          python-version: 3.10  # Works as bootstrap for cibuildwheel
 
       - name: Install cibuildwheel and nox
         run: |
           python -m pip install --upgrade pip
-          python -m pip install cibuildwheel==2.16.2
+          python -m pip install cibuildwheel==2.21.3
           python -m pip install nox
 
       - name: Build sdist (only on Windows)
@@ -45,6 +45,7 @@ jobs:
         env:
           CIBW_BUILD: ${{ matrix.cibw_build }}
           CIBW_ARCHS: ${{ matrix.archs }}
+          MACOSX_DEPLOYMENT_TARGET: "14.0"
 
       - name: Test wheels (only on macOS ARM64)
         if: matrix.os == 'macOS-ARM'

.github/workflows/buildtest_mac_arm_wheels.yml

@@ -7,24 +7,33 @@ jobs:
     runs-on: [self-hosted, macOS, ARM64]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
-
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
-
+          python-version: |
+            3.10
+            3.11
+            3.12
+            3.13
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade nox
-          python -m pip install cibuildwheel==2.16.2
+          python -m pip install cibuildwheel==2.21.3
+          python -m pip install setuptools==73.0.1
+      - name: Run Nox Quick-Tests
+        run: |
+          python -m nox --sessions test_source clear_wheelhouse
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
           # to supply options, put them in 'env', like:
         env:
-          CIBW_BUILD: cp39-macosx_arm64 cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64 cp313-macosx_arm64
+          CIBW_BUILD: cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64 cp313-macosx_arm64
           CIBW_ARCHS: arm64
+          MACOSX_DEPLOYMENT_TARGET: "14.0"
 
       - name: Test wheels
         run: python -m nox --sessions test_wheel

.github/workflows/buildtest_manylinux_wheels.yml

@@ -13,15 +13,15 @@ jobs:
         # Used to host cibuildwheel
         - uses: actions/setup-python@v5
           with:
-            python-version: 3.9
+            python-version: 3.10
 
         - name: Install cibuildwheel
           run: python -m pip install cibuildwheel==2.16.2
 
         - name: Build wheels
           run: python -m cibuildwheel --output-dir wheelhouse
           env:
-            CIBW_BUILD: cp39-manylinux_x86_64 cp310-manylinux_x86_64 cp311-manylinux_x86_64 cp312-manylinux_x86_64 cp313-manylinux_x86_64
+            CIBW_BUILD: cp310-manylinux_x86_64 cp311-manylinux_x86_64 cp312-manylinux_x86_64 cp313-manylinux_x86_64
           # to supply options, put them in 'env', like:
           # env:
           #   CIBW_SOME_OPTION: value

.github/workflows/buildtest_windows_x86.yml

@@ -11,7 +11,7 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.10
       - name: Build sdist
         run: |
           python -m pip install --upgrade pip
@@ -33,18 +33,18 @@ jobs:
         - uses: actions/setup-python@v5
           with:
             python-version: |
-              3.9
               3.10
               3.11
               3.12
+              3.13
 
         - name: Install cibuildwheel
           run: python -m pip install cibuildwheel==2.16.2
 
         - name: Build wheels
           run: python -m cibuildwheel --output-dir wheelhouse
           env:
-            CIBW_BUILD: cp39-win_amd64 cp310-win_amd64 cp311-win_amd64 cp312-win_amd64 cp313-win_amd64
+            CIBW_BUILD: cp310-win_amd64 cp311-win_amd64 cp312-win_amd64 cp313-win_amd64
           # to supply options, put them in 'env', like:
           # env:
           #   CIBW_SOME_OPTION: value

.github/workflows/nanopyx_night_mechanic.yml

@@ -29,15 +29,15 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
       - name: Run Nox Quick-Tests
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade nox
-          python -m pip install cibuildwheel==2.16.2
+          python -m pip install cibuildwheel==2.21.3
           python -m nox --sessions test_source clear_wheelhouse build_wheel build_sdist test_wheel
         env:
           LOG_LEVEL: ${{ github.event.inputs.logLevel }}
@@ -58,15 +58,15 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
       - name: Run Nox Quick-Tests
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade nox
-          python -m pip install cibuildwheel==2.16.2
+          python -m pip install cibuildwheel==2.21.3
           python -m pip install setuptools==73.0.1
           python -m nox --sessions test_source clear_wheelhouse build_wheel build_sdist test_wheel
         env:
@@ -92,11 +92,12 @@ jobs:
             3.10
             3.11
             3.12
+            3.13
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade nox
-          python -m pip install cibuildwheel==2.16.2
+          python -m pip install cibuildwheel==2.21.3
           python -m pip install setuptools==73.0.1
       - name: Run Nox Quick-Tests
         run: |
@@ -107,8 +108,9 @@ jobs:
         run: python -m cibuildwheel --output-dir wheelhouse
           # to supply options, put them in 'env', like:
         env:
-          CIBW_BUILD: cp39-macosx_arm64 cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64
+          CIBW_BUILD: cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64 cp313-macosx_arm64
           CIBW_ARCHS: arm64
+          MACOSX_DEPLOYMENT_TARGET: "14.0"
 
       - name: Test wheels
         run: python -m nox --sessions test_wheel

.github/workflows/nanopyx_oncall_all_os.yml

@@ -25,10 +25,10 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
       - name: Run Nox Quick-Tests
         run: |
           python -m pip install --upgrade pip
@@ -53,10 +53,10 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
       - name: Run Nox Quick-Tests
         run: |
           python -m pip install --upgrade pip
@@ -81,15 +81,15 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade nox
-          python -m pip install cibuildwheel==2.16.2
+          python -m pip install cibuildwheel==2.21.3
       - name: Test Source
         run: python -m nox --sessions test_source
         env:

.github/workflows/nanopyx_oncall_mechanic.yml

@@ -38,10 +38,10 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
       - name: Run Nox Quick-Tests
         run: |
           python -m pip install --upgrade pip

CONTRIBUTING.md

@@ -65,7 +65,7 @@ Ready to contribute? Here's how to set up **nanopyx** for local development.
 Before you submit a pull request, check that it meets these guidelines:
 
 - The pull request should pass every existing test.
-- The pull request should work for Python 3.8, 3.9 and 3.10
+- The pull request should work for Python 3.10, 3.11, 3.12, and 3.13
 - If the pull request adds functionality, new automated tests should be included in the pull request covering the new functionality
 - Please ensure pytest coverage at least stays the same before you submit a pull request.
 - The core development team reserves the right to reject pull requests, particularly if these only entail cosmetic changes to the code such as orthographic correction or the addition of type hint to variables.

README.md

@@ -16,7 +16,7 @@
 
 Nanoscopy Python library (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging
 
-WARNING: Currently stable and working for Python 3.9 to 3.12. For Python 3.13, it is possible to use it if you build numpy<2 from source but it is not officially supported (Yet!)
+⚠️ **Python 3.10+ Required**: NanoPyx v2.0+ supports Python 3.10-3.13 with NumPy 2.x compatibility.
 
 ---
 
@@ -87,7 +87,7 @@ pip install napari-nanopyx
 
 ## Installation
 
-`NanoPyx` is compatible and tested with Python 3.9, 3.10, 3.11 and 3.12 in MacOS, Windows and Linux. Installation time depends on your hardware and internet connection, but should take around 5 minutes.
+`NanoPyx` is compatible and tested with Python 3.10, 3.11, 3.12, and 3.13 in macOS, Windows and Linux. Installation time depends on your hardware and internet connection, but should take around 5 minutes.
 
 You can install `NanoPyx` via [pip]: