Merge pull request #150 from TimMonko/main_container

Add nDev app

.github/workflows/test_and_deploy.yml

@@ -59,7 +59,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install setuptools tox tox-gh-actions
+          python -m pip install setuptools tox tox-gh-actions codecov
 
       # this runs the platform-specific tests declared in tox.ini
       - name: Test with tox

README.md

@@ -7,7 +7,7 @@
 [![codecov](https://codecov.io/gh/TimMonko/napari-ndev/branch/main/graph/badge.svg)](https://codecov.io/gh/TimMonko/napari-ndev)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ndev)](https://napari-hub.org/plugins/napari-ndev)
 
-<img src="docs/resources/images/neuralDev-logo.svg" alt="logo" width="300">
+<img src="resources/nDev-logo-large.png" alt="logo" width="400" style="display: block; margin: auto;">
 
 A collection of widgets intended to serve any person seeking to process microscopy images from start to finish, *with no coding necessary*. `napari-ndev` was designed to address the **gap between the napari viewer and batch python scripting**.
 

docs/index.md

@@ -8,7 +8,7 @@
 [![codecov](https://codecov.io/gh/TimMonko/napari-ndev/branch/main/graph/badge.svg)](https://codecov.io/gh/TimMonko/napari-ndev)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ndev)](https://napari-hub.org/plugins/napari-ndev)
 
-<img src="resources/images/neuralDev-logo.svg" alt="neuralDev logo" width="300">
+<img src="resources/images/nDev-logo-large.png" alt="nDev logo" width="400" style="display: block; margin: auto;">
 
 A collection of widgets intended to serve any person seeking to process microscopy images from start to finish, *with no coding necessary*. `napari-ndev` was designed to address the **gap between the napari viewer and batch python scripting**.
 

docs/installation.md

@@ -4,20 +4,26 @@ If you are unfamiliar with python or the command line, instead use the bundled a
 
 ## Install with uv
 
-uv is the newest and fastest way to manage python libraries. It is very easy to install, and simplifies environment manage, but requires minimal input to the command line.  [Install uv from here](https://docs.astral.sh/uv/getting-started/installation/#__tabbed_1_1).  Then, the simplest way to install `napari-ndev`:
+uv is the newest and fastest way to manage python libraries. It is very easy to install, and simplifies environment manage, but requires some minimal input to the command line.  [Install uv from here](https://docs.astral.sh/uv/getting-started/installation/#__tabbed_1_1). Then, the simplest way to install `napari-ndev`:
 
 ```bash
 uv tool install napari-ndev
-napari-ndev
 ```
 
-With this method, plugins installed via the plugin menu persist between each call to `napari-ndev`
 Alternatively, download the full opinionated package, which includes non-BSD3 licensed libraries with:
 
 ```bash
 uv tool install napari-ndev[all]
 ```
 
+Then, you can easily open napari with the command line every time by just typing:
+
+```bash
+napari-ndev
+```
+
+The tool version of `napari-ndev` effectively runs as an alias for `napari -w napari-ndev` and opens the `nDev App` upon launch. With this method, additional plugins installed via the plugin menu persist between each call to `napari-ndev`
+
 To update a tool with uv:
 
 ```bash
@@ -26,7 +32,7 @@ uv tool upgrade napari-ndev
 
 ## Install with pip
 
-**napari-ndev** is a pure Python package, and can be installed with [pip]:
+**napari-ndev** is a pure Python package, and can be installed with [pip] (and it is recommended to do so in a [managed environment](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html)):
 
 ```bash
 pip install napari-ndev
@@ -38,6 +44,8 @@ The easiest way to get started with **napari-ndev** is to install all the option
 pip install napari-ndev[all]
 ```
 
+Afterwards, you can call from the command line (in the same environment) `napari-ndev` to open napari with the `nDev App` open on launch.
+
 ### Optional Libraries
 
 **napari-ndev** is most useful when interacting with some other napari plugins (e.g. napari-assistant) and can read additional filetypes. A few extra BSD3 compatible napari-plugins may be installed with [pip]:
@@ -85,7 +93,7 @@ You may also test the tool version of uv during development with:
 uv install tool .
 ```
 
-You may also test with tox in parallel ([via tox-uv](https://github.com/tox-dev/tox-uv)) with:
+You can also test with tox in parallel ([via tox-uv](https://github.com/tox-dev/tox-uv)) with:
 
 ```bash
 tox - p auto

pyproject.toml

@@ -72,7 +72,7 @@ dynamic = ["version"]
 napari-ndev = "napari_ndev:napari.yaml"
 
 [project.scripts]
-napari-ndev = "napari.__main__:main"
+napari-ndev = "napari_ndev.__main__:main"
 
 [project.optional-dependencies]
 testing = [

src/napari_ndev/__init__.py

@@ -13,6 +13,7 @@
     MeasureContainer,
     UtilitiesContainer,
     WorkflowContainer,
+    nDevContainer,
 )
 
 __all__ = [
@@ -28,5 +29,6 @@
     'image_overview',
     'measure',
     'morphology',
+    'nDevContainer',
     'nImage',
 ]

src/napari_ndev/__main__.py

@@ -0,0 +1,8 @@
+"""Open napari with the napari_ndev plugin using command line."""
+
+import subprocess
+
+
+def main():
+    """Run napari with the napari_ndev plugin."""
+    subprocess.run(["napari", "-w", "napari-ndev"])

src/napari_ndev/_tests/test_main.py

@@ -0,0 +1,12 @@
+from unittest.mock import patch
+
+from napari_ndev import __main__
+
+
+@patch('subprocess.run')
+def test_main(mock_run):
+    __main__.main()
+    # Check if subprocess.run was called, indicating an attempt to open napari
+    assert mock_run.called
+    # Optionally, you can check the arguments to ensure it was called correctly
+    mock_run.assert_called_with(["napari", "-w", "napari-ndev"])

src/napari_ndev/_tests/widgets/test_ndev_container.py

@@ -0,0 +1,58 @@
+from pathlib import Path
+from unittest.mock import patch
+
+import pytest
+
+from napari_ndev import nImage
+from napari_ndev.widgets._ndev_container import nDevContainer
+
+
+def test_ndev_container_init_no_viewer():
+    ndev = nDevContainer()
+
+    assert ndev._viewer is None
+    assert ndev._apoc_container is not None
+    assert ndev._measure_container is not None
+    assert ndev._utilities_container is not None
+    assert ndev._workflow_container is not None
+
+    with patch('webbrowser.open') as mock_open:
+        ndev._open_docs_link()
+        mock_open.assert_called_once_with('https://timmonko.github.io/napari-ndev')
+
+    with patch('webbrowser.open') as mock_open:
+        ndev._open_bug_report_link()
+        mock_open.assert_called_once_with('https://github.com/TimMonko/napari-ndev/issues')
+
+@pytest.fixture
+def test_cells3d2ch_image(resources_dir: Path):
+    path = resources_dir / 'cells3d2ch.tiff'
+    img = nImage(path)
+    return path, img
+
+def test_ndev_container_viewer(make_napari_viewer, test_cells3d2ch_image, tmp_path: Path):
+    viewer = make_napari_viewer()
+
+    ndev = nDevContainer(viewer=viewer)
+    assert ndev._viewer is viewer
+
+    path, img = test_cells3d2ch_image
+    ndev._utilities_container._files.value = path
+    ndev._utilities_container.open_images()
+
+    # make sure images opened and there are callbacks to the widgets
+    assert viewer.layers[0] is not None
+
+    # check interacting with alyers in utilities container works
+    ndev._utilities_container._save_directory.value = tmp_path
+    ndev._utilities_container._save_name.value = 'test'
+    layer_data = ndev._utilities_container.save_layers_as_ome_tiff()
+
+    expected_save_loc = tmp_path / 'Image' / 'test.tiff'
+    assert layer_data.shape.__len__() == 5
+    assert expected_save_loc.exists()
+
+    # check interacting with apoc container works
+    assert ndev._apoc_container._image_layers.choices == (
+        viewer.layers[0], viewer.layers[1]
+    )

src/napari_ndev/napari.yaml

@@ -6,6 +6,9 @@ contributions:
     - id: napari-ndev.get_reader
       python_name: napari_ndev._napari_reader:napari_get_reader
       title: Get BioIO Reader
+    - id: napari-ndev.make_ndev_container
+      python_name: napari_ndev.widgets._ndev_container:nDevContainer
+      title: Make nDev App
     - id: napari-ndev.make_utilities_container
       python_name: napari_ndev.widgets._utilities_container:UtilitiesContainer
       title: Make Image Utilities
@@ -23,6 +26,8 @@ contributions:
       title: Make Measure Container
 
   widgets:
+    - command: napari-ndev.make_ndev_container
+      display_name: nDev App
     - command: napari-ndev.make_utilities_container
       display_name: Image Utilities
     - command: napari-ndev.make_workflow_container

src/napari_ndev/widgets/__init__.py

@@ -12,6 +12,7 @@
 from napari_ndev.widgets._apoc_container import ApocContainer
 from napari_ndev.widgets._apoc_feature_stack import ApocFeatureStack
 from napari_ndev.widgets._measure_container import MeasureContainer
+from napari_ndev.widgets._ndev_container import nDevContainer
 from napari_ndev.widgets._utilities_container import UtilitiesContainer
 from napari_ndev.widgets._workflow_container import WorkflowContainer
 
@@ -21,4 +22,5 @@
     'MeasureContainer',
     'UtilitiesContainer',
     'WorkflowContainer',
+    'nDevContainer',
 ]

src/napari_ndev/widgets/_ndev_container.py

@@ -0,0 +1,121 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from magicclass.widgets import (
+    ScrollableContainer,
+    TabbedContainer,
+)
+from magicgui.widgets import (
+    Container,
+    Label,
+    PushButton,
+)
+
+if TYPE_CHECKING:
+    import napari
+
+class nDevContainer(ScrollableContainer):
+    """
+    A widget container to container the primary ndev widgets.
+
+    Parameters
+    ----------
+    viewer: napari.viewer.Viewer, optional
+        The napari viewer instance.
+
+    """
+
+    def __init__(self, viewer: napari.viewer.Viewer = None):
+        """
+        Initialize the MainContainer.
+
+        Parameters
+        ----------
+        viewer: napari.viewer.Viewer, optional
+            The napari viewer instance.
+
+        """
+        super().__init__(labels=False)
+
+        self.min_width = 700 # TODO: remove this hardcoded value
+        self._viewer = viewer if viewer is not None else None
+
+        _logo_path = r'resources\nDev-logo-small.png'
+        self._logo_label = Label(
+            value='<h1 style="text-align: center;">'
+            f'<img src="{_logo_path}"/>'
+            '</h1>'
+        )
+
+
+        self._docs_link_button = PushButton(
+            text='Docs',
+            icon='ic:round-menu-book'
+        )
+        self._bug_report_link_button = PushButton(
+            text='Bug Report',
+            icon='ic:outline-bug-report',
+        )
+        self._link_container = Container(
+            widgets=[self._docs_link_button, self._bug_report_link_button],
+            layout='vertical',
+        )
+        self._header_container = Container(
+            widgets=[self._logo_label, self._link_container],
+            layout='horizontal',
+        )
+
+        self._init_widget_containers()
+        self._init_layout()
+        self._init_callbacks()
+
+    def _init_widget_containers(self):
+        from napari_ndev import (
+            ApocContainer,
+            MeasureContainer,
+            UtilitiesContainer,
+            WorkflowContainer,
+        )
+        """Initialize the widget containers."""
+        self._apoc_container = ApocContainer(viewer=self._viewer)
+        self._apoc_container.label = "APOC"
+        self._measure_container = MeasureContainer(viewer=self._viewer)
+        self._measure_container.label = "Measure"
+        self._utilities_container = UtilitiesContainer(viewer=self._viewer)
+        self._utilities_container.label = "Utilities"
+        self._workflow_container = WorkflowContainer(viewer=self._viewer)
+        self._workflow_container.label = "Workflow"
+
+        self._tabbed_container = TabbedContainer(
+            # labels=["Apoc", "Measure", "Utilities", "Workflow"],
+            labels = False,
+            layout="horizontal",
+            widgets=[
+                self._utilities_container,
+                self._apoc_container,
+                self._workflow_container,
+                self._measure_container,
+            ],
+        )
+
+    def _init_layout(self):
+        """Initialize the layout."""
+        self.append(self._header_container)
+        self.append(self._tabbed_container)
+        # self.stretch(self._tabbed_container)
+
+    def _init_callbacks(self):
+        """Initialize the widget callbacks."""
+        self._docs_link_button.clicked.connect(self._open_docs_link)
+        self._bug_report_link_button.clicked.connect(self._open_bug_report_link)
+
+    def _open_docs_link(self):
+        """Open the documentation link."""
+        import webbrowser
+        webbrowser.open('https://timmonko.github.io/napari-ndev')
+
+    def _open_bug_report_link(self):
+        """Open the bug report link."""
+        import webbrowser
+        webbrowser.open('https://github.com/TimMonko/napari-ndev/issues')