adds napari screenshot to quickstart

Makefile

@@ -80,8 +80,8 @@ help-docs:
 
 ### REQUIREMENTS #############################################
 #
-GENERATED_REQUIREMENT_FILES=starfish/REQUIREMENTS-STRICT.txt requirements/REQUIREMENTS-CI.txt requirements/REQUIREMENTS-NAPARI-CI.txt
-SOURCE_REQUIREMENT_FILES=REQUIREMENTS.txt requirements/REQUIREMENTS-CI.txt.in requirements/REQUIREMENTS-NAPARI-CI.txt.in
+GENERATED_REQUIREMENT_FILES=starfish/REQUIREMENTS-STRICT.txt requirements/REQUIREMENTS-CI.txt requirements/REQUIREMENTS-NAPARI-CI.txt requirements/REQUIREMENTS-DOCS.txt
+SOURCE_REQUIREMENT_FILES=REQUIREMENTS.txt requirements/REQUIREMENTS-CI.txt.in requirements/REQUIREMENTS-NAPARI-CI.txt.in requirements/REQUIREMENTS-DOCS.txt.in
 
 # This rule pins the requirements with the minimal set of changes required to satisfy the
 # requirements.  This is typically run when a new requirement is added, and we want to

docs/source/conf.py

@@ -130,6 +130,10 @@
     'download_section_examples': False,
     'default_thumb_file': f'{dir_}/_static/design/logo-solo.png',
     'min_reported_time': 10,
+    'first_notebook_cell': ("# This cell is added by sphinx-gallery\n"
+                            "# It can be customized to whatever you like\n"
+                            "%matplotlib inline\n"
+                            "%gui qt"),
 
 }
 
@@ -157,7 +161,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 def setup(app):
-    app.add_stylesheet("my-styles.css")
+    app.add_css_file("my-styles.css")
 
 html_theme_options = {
     'navbar_title': " ",

examples/data_loading/plot_loading_data.py

@@ -68,10 +68,14 @@
 # can optionally specify a set of cropping parameters. To demonstrate how those work, we'll slice
 # out a 100 pixel square from the :code:`(200, 140)` pixel :py:class:`.FieldOfView`:
 
+from starfish import display
+
 image = fov.get_image("primary", x=slice(0, 100), y=slice(0, 100))
 image
 
+display(stack=image)
+
 ###################################################################################################
 # Calling :py:meth:`.FieldOfView.get_image` localizes the data and produces an
 # :py:class:`.ImageStack`, a 5-d tensor and *starfish*'s main in-memory image storage and
-# processing class.
+# processing class.

examples/quick_start/plot_quick_start.py

@@ -66,13 +66,11 @@
 # the dimension slider to compare channels 1 and 3 of round 1 (zero-based indexing),
 # you can already see which cells express mouse ACTB and which cells express human ACTB.
 #
-# .. code-block:: python
-#
-#   from starfish import display
-#
-#   %gui qt
-#   viewer = display(imgs)
-#   viewer.layers[0].name = "raw stack" # rename the layer
+from starfish import display
+
+viewer = display(imgs)
+viewer.layers[0].name = "raw stack" # rename the layer
+viewer
 
 ####################################################################################################
 # **View codebook**
@@ -260,9 +258,8 @@ def make_expression_matrix(masks, decoded):
 # and segmented cells (:py:class:`.BinaryMaskCollection`) as layers in napari to verify the
 # results.
 #
-# .. code-block:: python
-#
-#   display(stack=registered_imgs, spots=decoded, masks=masks, viewer=viewer)
+
+display(stack=registered_imgs, spots=decoded, masks=masks, viewer=viewer)
 
 ####################################################################################################
 # **View decoded spots as a table**

readthedocs.yml

@@ -5,6 +5,6 @@ build:
 python:
     version: 3.6
     install:
-        - requirements: requirements/REQUIREMENTS-CI.txt
+        - requirements: requirements/REQUIREMENTS-DOCS.txt
         - method: pip
           path: .

requirements/REQUIREMENTS-DOCS.txt

@@ -0,0 +1,141 @@
+# You should not edit this file directly.  Instead, you should edit one of the following files (requirements/REQUIREMENTS-DOCS.txt.in) and run make requirements/REQUIREMENTS-DOCS.txt
+alabaster==0.7.12
+appdirs==1.4.4
+appnope==0.1.2
+argon2-cffi==20.1.0
+async-generator==1.10
+attrs==20.3.0
+Babel==2.9.0
+backcall==0.2.0
+bleach==3.3.0
+boto3==1.17.10
+botocore==1.20.10
+cached-property==1.5.2
+cachey==0.2.1
+certifi==2020.12.5
+cffi==1.14.5
+chardet==4.0.0
+click==7.1.2
+cycler==0.10.0
+dask==2021.2.0
+dataclasses==0.6
+decorator==4.4.2
+defusedxml==0.6.0
+diskcache==5.2.1
+docutils==0.16
+entrypoints==0.3
+freetype-py==2.2.0
+h5py==3.1.0
+HeapDict==1.0.1
+idna==2.10
+imageio==2.9.0
+imagesize==1.2.0
+importlib-metadata==3.4.0
+iniconfig==1.1.1
+ipykernel==5.4.3
+ipython==7.16.1
+ipython-genutils==0.2.0
+ipywidgets==7.6.3
+jedi==0.18.0
+Jinja2==2.11.3
+jmespath==0.10.0
+joblib==1.0.1
+jsonschema==3.2.0
+jupyter-client==6.1.11
+jupyter-core==4.7.1
+jupyterlab-pygments==0.1.2
+jupyterlab-widgets==1.0.0
+kiwisolver==1.3.1
+m2r2==0.2.7
+MarkupSafe==1.1.1
+matplotlib==3.3.4
+mistune==0.8.4
+mpmath==1.2.1
+napari==0.3.8
+napari-plugin-engine==0.1.9
+napari-svg==0.1.4
+nbclient==0.5.2
+nbconvert==6.0.7
+nbformat==5.1.2
+nest-asyncio==1.5.1
+networkx==2.5
+notebook==6.2.0
+numpy==1.19.5
+numpydoc==1.1.0
+packaging==20.9
+pandas==1.1.5
+pandocfilters==1.4.3
+parso==0.8.1
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==8.1.0
+pluggy==0.13.1
+prometheus-client==0.9.0
+prompt-toolkit==3.0.16
+psutil==5.8.0
+ptyprocess==0.7.0
+py==1.10.0
+pycparser==2.20
+Pygments==2.8.0
+PyOpenGL==3.1.5
+pyparsing==2.4.7
+PyQt5==5.14.2
+PyQt5-sip==12.8.1
+pyrsistent==0.17.3
+pytest==6.2.2
+pytest-qt==3.3.0
+python-dateutil==2.8.0
+pytz==2021.1
+PyWavelets==1.1.1
+PyYAML==5.4.1
+pyzmq==22.0.3
+qtconsole==5.0.2
+QtPy==1.9.0
+read-roi==1.6.0
+regional==1.1.2
+requests==2.25.1
+s3transfer==0.3.4
+scikit-image==0.15.0
+scikit-learn==0.24.1
+scipy==1.5.4
+seaborn==0.11.1
+semantic-version==2.8.5
+Send2Trash==1.5.0
+setuptools==40.6.2
+showit==1.1.4
+six==1.15.0
+slicedimage==4.1.1
+snowballstemmer==2.1.0
+Sphinx==3.5.1
+sphinx-autodoc-typehints==1.11.1
+sphinx-bootstrap-theme==0.7.1
+sphinx-gallery==0.8.2
+sphinx-rtd-theme==0.5.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==1.0.3
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-programoutput==0.16
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.4
+sympy==1.5.1
+terminado==0.9.2
+testpath==0.4.4
+threadpoolctl==2.1.0
+tifffile==2020.9.3
+toml==0.10.2
+toolz==0.11.1
+tornado==6.1
+tqdm==4.56.2
+trackpy==0.4.2
+traitlets==4.3.3
+typing-extensions==3.7.4.3
+urllib3==1.26.3
+validators==0.18.2
+vispy==0.6.6
+wcwidth==0.2.5
+webencodings==0.5.1
+widgetsnbextension==3.5.1
+wrapt==1.12.1
+xarray==0.16.2
+zipp==3.4.0

requirements/REQUIREMENTS-DOCS.txt.in

@@ -0,0 +1,11 @@
+napari >= 0.3.4
+PyQt5==5.14.2
+pytest-qt
+sphinx
+sphinx_autodoc_typehints
+sphinx_bootstrap_theme
+sphinxcontrib-programoutput
+sphinx-gallery
+sphinx_rtd_theme
+m2r2
+seaborn

starfish/core/_display.py

@@ -1,6 +1,8 @@
 import __main__
+import base64
 import warnings
 from collections import OrderedDict
+from io import BytesIO
 from typing import Iterable, List, Optional, Set, Tuple, Union
 
 import numpy as np
@@ -13,9 +15,33 @@
 from starfish.core.types import Axes, Features
 
 try:
-    from napari import Viewer
+    from napari import Viewer as NapariViewer
+
+    class Viewer(NapariViewer):
+
+        def _get_png(self):
+            from imageio import imsave
+
+            image = self.screenshot(canvas_only=False)
+            with BytesIO() as file_obj:
+                imsave(file_obj, image, format='png')
+                file_obj.seek(0)
+                png = file_obj.read()
+            return png
+
+        def _repr_html_(self):
+
+            png = self._get_png()
+            data = base64.b64encode(png).decode('utf-8')
+
+            return (
+                "<div>"
+                f"<img class='screenshot' src='data:image/png;base64, {data}' />"
+                "</div>"
+            )
+
 except ImportError:
-    Viewer = None
+    Viewer = None  # type: ignore
 
 
 NAPARI_VERSION = "0.3.4"  # when changing this, update docs in display