merge for v1.2.0

.coveragerc

@@ -0,0 +1,6 @@
+[run]
+omit =
+    */convolution.py
+    */_transonic.py
+    */_le_template_simple_.py
+    */benchmark.py

.github/workflows/build_test_deploy_all_wheels.yml

@@ -74,4 +74,4 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.BMS_DEPLOY_PYPI_TOKEN }}
-          packages-dir: ./final_dist/
+          packages-dir: ./final_dist/

.github/workflows/build_wheels.yml

@@ -0,0 +1,56 @@
+name: (self-hosted) Build and Publish Wheels
+
+on: workflow_dispatch
+
+jobs:
+  build:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.runner }}
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - os: macOS-ARM
+            runner: [self-hosted, macOS, ARM64]
+            archs: arm64
+            cibw_build: cp39-macosx_arm64 cp310-macosx_arm64 cp311-macosx_arm64 cp312-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
+          - os: windows
+            runner: [self-hosted, Windows]
+            archs: auto
+            cibw_build: cp39-win_amd64 cp310-win_amd64 cp311-win_amd64 cp312-win_amd64
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.9  # 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 nox
+
+      - name: Build sdist (only on Windows)
+        if: matrix.os == 'windows'
+        run: python -m nox --sessions build_sdist
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BUILD: ${{ matrix.cibw_build }}
+          CIBW_ARCHS: ${{ matrix.archs }}
+
+      - name: Test wheels (only on macOS ARM64)
+        if: matrix.os == 'macOS-ARM'
+        run: python -m nox --sessions test_wheel
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*

.github/workflows/buildtest_mac_arm_wheels.yml

@@ -23,7 +23,7 @@ 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: cp39-macosx_arm64 cp310-macosx_arm64 cp311-macosx_arm64 cp312-macosx_arm64 cp313-macosx_arm64
           CIBW_ARCHS: arm64
 
       - name: Test wheels

.github/workflows/buildtest_manylinux_wheels.yml

@@ -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
+            CIBW_BUILD: cp39-manylinux_x86_64 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

@@ -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
+            CIBW_BUILD: cp39-win_amd64 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

notebooks/ChannelRegistration.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "313252b6",
+   "id": "21d1e58b",
    "metadata": {},
    "source": [
     "# NanoPyx \"Codeless\" Jupyter Notebook\n",
@@ -22,7 +22,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a7fd8e2a",
+   "id": "b3c2a12b",
    "metadata": {
     "cellView": "form"
    },
@@ -54,7 +54,10 @@
     "from IPython.display import display, clear_output\n",
     "from matplotlib import pyplot as plt\n",
     "\n",
-    "from nanopyx.core.utils.easy_gui import EasyGui\n",
+    "try:\n",
+    "    from ezinput import EZInput as EasyGui\n",
+    "except ImportError:\n",
+    "    from nanopyx.core.utils.easy_gui import EasyGui\n",
     "from nanopyx.core.utils.find_files import find_files\n",
     "from nanopyx.data.download import ExampleDataManager\n",
     "\n",
@@ -77,7 +80,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "321413ab",
+   "id": "a5c09b00",
    "metadata": {
     "cellView": "form"
    },
@@ -91,7 +94,7 @@
     "\n",
     "def on_button_select_own(b):\n",
     "    clear_output()\n",
-    "    gui_data.add_label(\"Select data to use:\")\n",
+    "    gui_data.add_label(value=\"Select data to use:\")\n",
     "    gui_data.add_file_upload(\"upload\")\n",
     "    gui_data.add_dropdown(\"cmaps\", description=\"Colormap:\",\n",
     "                          options=sorted(list(mpl.colormaps)),\n",
@@ -102,7 +105,7 @@
     "\n",
     "def on_button_select_example(b):\n",
     "    clear_output()\n",
-    "    gui_data.add_label(\"Select data to use:\")\n",
+    "    gui_data.add_label(value=\"Select data to use:\")\n",
     "    gui_data.add_dropdown(\"data_source\", options=image_files,\n",
     "                    value=\"Example dataset: \"+example_datasets[4], remember_value=True)\n",
     "    gui_data.add_dropdown(\"cmaps\", description=\"Colormap:\",\n",
@@ -161,7 +164,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a84604a2",
+   "id": "535b3d44",
    "metadata": {},
    "source": [
     "# Channel Registration Parameters:  \n",
@@ -179,7 +182,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7a99907f",
+   "id": "5c4e28f4",
    "metadata": {
     "cellView": "form"
    },
@@ -229,7 +232,7 @@
     "    gui_reg._main_display.children = gui_reg._main_display.children + (stackview.slice(dataset_registered, colormap=gui_reg[\"cmaps\"].value, continuous_update=True),)\n",
     "\n",
     "\n",
-    "gui_reg.add_label(\"Channel Registration parameters:\")\n",
+    "gui_reg.add_label(value=\"Channel Registration parameters:\")\n",
     "gui_reg.add_int_slider(\"ref\", description=\"Reference channel\", min=0, max=dataset_original.shape[0]-1, value=0)\n",
     "gui_reg.add_int_slider(\"max\", description=\"Max expected drift\", min=0, max=1000, value=10)\n",
     "gui_reg.add_int_slider(\"blocks\", description=\"Blocks per axis\", min=1, max=10, value=5)\n",
@@ -247,7 +250,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "eefc7618",
+   "id": "ae281b8a",
    "metadata": {},
    "source": [
     "## Use the following cell only if you have a previously calculated translation mask\n",
@@ -257,7 +260,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "55cdcf4f",
+   "id": "c0e91c8c",
    "metadata": {
     "cellView": "form"
    },
@@ -312,9 +315,9 @@
     "    gui_reg_apply[\"Register Image\"].description = \"Align\"\n",
     "    gui_reg_apply._main_display.children = gui_reg_apply._main_display.children + (stackview.slice(aligned_image, colormap=gui_reg_apply[\"cmaps\"].value, continuous_update=True),)\n",
     "\n",
-    "gui_reg_apply.add_label(\"Load translation mask:\")\n",
+    "gui_reg_apply.add_label(value=\"Load translation mask:\")\n",
     "gui_reg_apply.add_file_upload(\"upload\")\n",
-    "gui_reg_apply.add_label(\"Load image to register:\")\n",
+    "gui_reg_apply.add_label(value=\"Load image to register:\")\n",
     "gui_reg_apply.add_file_upload(\"upload image\")\n",
     "gui_reg_apply.add_dropdown(\"cmaps\", description=\"Colormap:\",\n",
     "                      options=sorted(list(mpl.colormaps)),\n",

notebooks/DriftCorrection.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "065b6c17",
+   "id": "4a8ab58f",
    "metadata": {},
    "source": [
     "# NanoPyx \"Codeless\" Jupyter Notebook\n",
@@ -22,7 +22,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7f4d7a86",
+   "id": "80886110",
    "metadata": {
     "cellView": "form"
    },
@@ -54,7 +54,10 @@
     "from IPython.display import display, clear_output\n",
     "from matplotlib import pyplot as plt\n",
     "\n",
-    "from nanopyx.core.utils.easy_gui import EasyGui\n",
+    "try:\n",
+    "    from ezinput import EZInput as EasyGui\n",
+    "except ImportError:\n",
+    "    from nanopyx.core.utils.easy_gui import EasyGui\n",
     "from nanopyx.core.utils.find_files import find_files\n",
     "from nanopyx.data.download import ExampleDataManager\n",
     "\n",
@@ -77,7 +80,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7e22c6f0",
+   "id": "7d8288ff",
    "metadata": {
     "cellView": "form"
    },
@@ -91,7 +94,7 @@
     "\n",
     "def on_button_select_own(b):\n",
     "    clear_output()\n",
-    "    gui_data.add_label(\"Select data to use:\")\n",
+    "    gui_data.add_label(value=\"Select data to use:\")\n",
     "    gui_data.add_file_upload(\"upload\")\n",
     "    gui_data.add_dropdown(\"cmaps\", description=\"Colormap:\",\n",
     "                          options=sorted(list(mpl.colormaps)),\n",
@@ -102,7 +105,7 @@
     "\n",
     "def on_button_select_example(b):\n",
     "    clear_output()\n",
-    "    gui_data.add_label(\"Select data to use:\")\n",
+    "    gui_data.add_label(value=\"Select data to use:\")\n",
     "    gui_data.add_dropdown(\"data_source\", options=image_files,\n",
     "                    value=\"Example dataset: \"+example_datasets[4], remember_value=True)\n",
     "    gui_data.add_dropdown(\"cmaps\", description=\"Colormap:\",\n",
@@ -161,7 +164,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9b2595dc",
+   "id": "c800a0e9",
    "metadata": {},
    "source": [
     "# Drift Correction Parameters:  \n",
@@ -178,7 +181,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4aeea0dc",
+   "id": "e2d6671a",
    "metadata": {
     "cellView": "form"
    },
@@ -254,30 +257,13 @@
     "    )\n",
     "\n",
     "\n",
-    "gui_drift.add_label(\"Drift Correction parameters:\")\n",
-    "gui_drift.add_dropdown(\n",
-    "    \"ref\",\n",
-    "    description=\"Reference frame\",\n",
-    "    options=[\"First frame\", \"Previous frame\"],\n",
-    "    value=\"First frame\",\n",
-    ")\n",
-    "gui_drift.add_int_slider(\n",
-    "    \"max\", description=\"Max expected drift\", min=0, max=1000, value=10\n",
-    ")\n",
-    "gui_drift.add_int_slider(\n",
-    "    \"time_averaging\",\n",
-    "    description=\"Time averaging\",\n",
-    "    min=1,\n",
-    "    max=dataset_original.shape[0],\n",
-    "    value=1,\n",
-    ")\n",
-    "gui_drift.add_dropdown(\n",
-    "    \"cmaps\",\n",
-    "    description=\"Colormap:\",\n",
-    "    options=sorted(list(mpl.colormaps)),\n",
-    "    value=\"viridis\",\n",
-    "    remember_value=True,\n",
-    ")\n",
+    "gui_drift.add_label(value=\"Drift Correction parameters:\")\n",
+    "gui_drift.add_dropdown(\"ref\", description=\"Reference frame\", options=[\"First frame\", \"Previous frame\"], value=\"First frame\")\n",
+    "gui_drift.add_int_slider(\"max\", description=\"Max expected drift\", min=0, max=1000, value=10)\n",
+    "gui_drift.add_int_slider(\"time_averaging\", description=\"Time averaging\", min=1, max=dataset_original.shape[0], value=1)\n",
+    "gui_drift.add_dropdown(\"cmaps\", description=\"Colormap:\",\n",
+    "                      options=sorted(list(mpl.colormaps)),\n",
+    "                      value=\"viridis\", remember_value=True)\n",
     "gui_drift.add_checkbox(\"save\", description=\"Save Output\", value=True)\n",
     "gui_drift.add_button(\"align\", description=\"Align\")\n",
     "gui_drift[\"align\"].on_click(on_button_align)\n",
@@ -288,7 +274,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5678e56d",
+   "id": "60fc5a28",
    "metadata": {},
    "source": [
     "## Use the following cell only if you have a previously calculated drift table\n",
@@ -298,7 +284,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3bdca2b8",
+   "id": "45dc3ea1",
    "metadata": {
     "cellView": "form"
    },
@@ -355,9 +341,9 @@
     "    gui_drift_apply[\"Align image\"].description = \"Align\"\n",
     "    gui_drift_apply._main_display.children = gui_drift_apply._main_display.children + (stackview.slice(aligned_image, colormap=gui_drift_apply[\"cmaps\"].value, continuous_update=True),)\n",
     "\n",
-    "gui_drift_apply.add_label(\"Load drift table:\")\n",
+    "gui_drift_apply.add_label(value=\"Load drift table:\")\n",
     "gui_drift_apply.add_file_upload(\"upload\")\n",
-    "gui_drift_apply.add_label(\"Load image to align:\")\n",
+    "gui_drift_apply.add_label(value=\"Load image to align:\")\n",
     "gui_drift_apply.add_file_upload(\"upload image\")\n",
     "gui_drift_apply.add_dropdown(\"cmaps\", description=\"Colormap:\",\n",
     "                      options=sorted(list(mpl.colormaps)),\n",