diff --git a/.github/workflows/build_test_deploy_all_wheels.yml b/.github/workflows/build_test_deploy_all_wheels.yml
index 383b459a..e8c5dba2 100644
--- a/.github/workflows/build_test_deploy_all_wheels.yml
+++ b/.github/workflows/build_test_deploy_all_wheels.yml
@@ -13,15 +13,15 @@ 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
@@ -29,10 +29,10 @@ jobs:
- 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 &&
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 6476c9a3..9ab8ea28 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.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'
diff --git a/.github/workflows/buildtest_mac_arm_wheels.yml b/.github/workflows/buildtest_mac_arm_wheels.yml
index 4be1da32..7431d8a9 100644
--- a/.github/workflows/buildtest_mac_arm_wheels.yml
+++ b/.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
diff --git a/.github/workflows/buildtest_manylinux_wheels.yml b/.github/workflows/buildtest_manylinux_wheels.yml
index b3984f50..c55afe7d 100644
--- a/.github/workflows/buildtest_manylinux_wheels.yml
+++ b/.github/workflows/buildtest_manylinux_wheels.yml
@@ -13,7 +13,7 @@ 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
@@ -21,7 +21,7 @@ jobs:
- 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
diff --git a/.github/workflows/buildtest_windows_x86.yml b/.github/workflows/buildtest_windows_x86.yml
index fae66bf9..40842dd8 100644
--- a/.github/workflows/buildtest_windows_x86.yml
+++ b/.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
@@ -33,10 +33,10 @@ 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
@@ -44,7 +44,7 @@ jobs:
- 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
diff --git a/.github/workflows/nanopyx_night_mechanic.yml b/.github/workflows/nanopyx_night_mechanic.yml
index ba2f7fe5..25717815 100644
--- a/.github/workflows/nanopyx_night_mechanic.yml
+++ b/.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
\ No newline at end of file
diff --git a/.github/workflows/nanopyx_oncall_all_os.yml b/.github/workflows/nanopyx_oncall_all_os.yml
index 2eb74443..e5c3ca61 100644
--- a/.github/workflows/nanopyx_oncall_all_os.yml
+++ b/.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:
diff --git a/.github/workflows/nanopyx_oncall_mechanic.yml b/.github/workflows/nanopyx_oncall_mechanic.yml
index ad81563e..ba7a29b1 100644
--- a/.github/workflows/nanopyx_oncall_mechanic.yml
+++ b/.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
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index ff9c08c6..dfccac4f 100644
--- a/CONTRIBUTING.md
+++ b/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.
diff --git a/README.md b/README.md
index eb870d2e..bde3f961 100644
--- a/README.md
+++ b/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]:
diff --git a/notebooks/eSRRFandQC.ipynb b/notebooks/eSRRFandQC.ipynb
index 3f00df8e..5e2ac7bf 100644
--- a/notebooks/eSRRFandQC.ipynb
+++ b/notebooks/eSRRFandQC.ipynb
@@ -50,12 +50,20 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 2,
"id": "cdd9b61d",
"metadata": {
"cellView": "form"
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Cupy implementation is not available. Make sure you have the right version of Cupy and CUDA installed.\n"
+ ]
+ }
+ ],
"source": [
"#@title Install NanoPyx, import necessary libraries and connect to Google Drive\n",
"import sys\n",
@@ -113,7 +121,22 @@
"metadata": {
"cellView": "form"
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "bfb9d1b8649e421d97415f0b91544fe6",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "VBox(children=(Button(description='Use Own data', layout=Layout(width='50%'), style=ButtonStyle()), Button(des…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"#@title Load image stack\n",
"# Create a GUI\n",
@@ -209,12 +232,27 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 4,
"id": "322720a0",
"metadata": {
"cellView": "form"
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "9ef4e6c84f7f41468a928a3849bc09b8",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "VBox(children=(FloatSlider(value=1.5, description='Ring Radius:', layout=Layout(width='50%'), max=3.0, min=0.1…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"# @title Create eSRRF GUI\n",
"gui_esrrf = EasyGui(\"esrrf\")\n",
@@ -348,12 +386,98 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 5,
"id": "a93a23e6",
"metadata": {
"cellView": "form"
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "3c9d73a06084425080dc8f2f54b8856f",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "VBox(children=(Checkbox(value=True, description='Save output', layout=Layout(width='50%'), style=CheckboxStyle…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
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+ " \n",
+ " \n",
+ " | \n",
+ " Slice | \n",
+ " RSE | \n",
+ " RSP | \n",
+ "
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+ " \n",
+ " \n",
+ " \n",
+ " | 0 | \n",
+ " 0 | \n",
+ " 51.197170 | \n",
+ " 0.915127 | \n",
+ "
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+ " \n",
+ " | 1 | \n",
+ " 1 | \n",
+ " 48.797817 | \n",
+ " 0.922706 | \n",
+ "
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+ " \n",
+ "
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+ "