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Home Page: https://napari.org/
napari.github.io's Issues
Dask Image transformation - Napari Development
Hi,
Currently I am working with images with size (25600, 49152, 3) px and I am trying to slice the image in smaller sizes to accelerate the computation. I am using napari for visualization, but after reading the documentation from dask I haven't come up with an acquire solution to slice the image in smaller dask arrays. What would be your suggestions?
Also, is it possible to use napari as the base for the image analysis tool that I am currently developing? I would like to include buttons and other user interface to facilitate the search and processing of the images.
Thanks in advance for your help,
confusion on napari console functionality
In trying the tutorial, it was not clear to me that the console was only available if napari is launched from bash. More clear documentation would be an okay choice on addressing this, but it would be fantastic if the console button is greyed out or removed when napari is started in ipython or a jupyter notebook - or a pop-up telling the user that the console is only available when napari is launched from bash.
signing up with en invalid email sometimes causes page to jump
from October 2021 pre-launch bug bash
Created by: Kira Evans
Description
how to reproduce (on iPad):
- load https://staging.napari-hub.org/plugins/napari-btrack-reader or any other plugin page
- click "Installation" to navigate to that header (link should be https://staging.napari-hub.org/plugins/napari-btrack-reader#installation)
- click subscribe on the signup form with an invalid email
- your page will scroll back to the Installation header
this does not occur with valid emails and I cannot reproduce on Desktop
Info
Bug source: unknown
Browser: Safari, Firefox, Edge, Chrome
PR: none
Attachments
Links to hosted docs
We need to put in links to our hosted docs / api reference.
We also need to put in doc string snippets into our layer tutorials
404 error volume tutorial
This link is broken
https://napari.org/tutorials/volume.md
found at the bottom of this page https://napari.org/gallery/gallery.html
Refining of functional breakpoints needed
from October 2021 pre-launch bug bash
Created by: Lia
Description
Since the breakpoints that exist exclusively for the home page are based on the width that things are rendered, they need a little refining since the rendering of some elements in HTML is not exactly the same as the design (i.e. spacing between bullet disc and bullet text, etc). This is fine, but slightly affects the point at which the breakpoint itself should occur.
Work with Lia to refine. Dependent on #66 being completed first
Info
Bug source: <875px
Browser: unknown
PR: none
Attachments
radio button off-center
from October 2021 pre-launch bug bash
Created by: Kira Evans
Description
on iPad landscape and portrait the center dot in the radio button is off-center
Info
Bug source: 1366px x 908px
Browser: Chrome, Safari, Firefox, Edge
PR: none
Attachments
idea: napari.org link in footer
from October 2021 pre-launch bug bash
Created by: Nathan Clack
Description
I had a moment of confusion seeing "napari hub" in the footer. I expected "napari.org" to be there. Adding a "napari.org" link back to the root page in the footer might be expected by some users and might help further distinguish napari.org from the hub.
Info
Bug source: unknown
Browser: ipad chrome. appears in other browsers
PR: none
Attachments
napari + imageJ integration how-to-guide
It would be great to adapt the demos on napari + imageJ integration here and here by @ctrueden into a how-to-guide, similar to the dask + napari how to guide
Hyperlink doesn't work
So, I was browsing through your website napari.org/tutorials and I saw the urls for getting started section do not work. It is not a major issue and the links at the bottom of the page under fundamentals work but I just wanted to let you know.
search param isn't added to URL for empty string searches
from October 2021 pre-launch bug bash
Created by: Allen
Description
When searching for the empty string, "", the search parameter is not added to the URL. I consider this a design issue rather than a functionality issue.
Info
Bug source: unknown
Browser: unknown
PR: none
Attachments
Link to videos of napari talks and tutorials available on the web
I think it would be good to have a page to put the links to videos of napari talks elsewhere. There's starting to be quite the list. Here is a (very incomplete) list of napari talks & tutorials previously given.
In reverse chronological order...
TALKS
- Nick Sofroniew — napari: a fast, interactive, multi-dimensional image viewer — BIDS ImageXD 2021 https://www.youtube.com/watch?v=66m8qtOQehs
- Talley Lambert | napari | Life science lightning talk | Dask Summit 2021 https://www.youtube.com/watch?v=YrQzAMdLU6c&list=PLJ0vO2F_f6OBAY6hjRHM_mIQ9yh32mWr0&index=4
- napari: an n-dimensional image viewer in Python (Vis2021) Juan Nunez-Iglesias https://www.youtube.com/watch?v=VXdFOcBCto4
- napari, a fast n dimensional array viewer for scientifc Python | Juan Nunez-Iglesias | SciPy JP 2020 https://www.youtube.com/watch?v=9_Zo2sR75To
- Kira Evans — ImageXD 2019: Napari: multi-dimensional image visualization in Python https://www.youtube.com/watch?v=L6flM3PYI0Q
TUTORIALS
- The I2K napari tutorial (I don't think the recording is up online, maybe we could follow up with the organisers?)
- Multi-dimensional image visualization in Python using napari [NEUBIAS Academy@Home] webinar 2020 https://www.youtube.com/watch?v=VgvDSq5aCDQ
"Close" button within install window is too tall + wrong font weight compared to design
from October 2021 pre-launch bug bash
Created by: Lia
Description
Should be 50px tall, inspector says it is 60px tall; should be semi-bold, inspector says it is normal
Info
Bug source: unknown
Browser: Safari
PR: none
Attachments
images on dask post broken
The images are no longer showing up on the dask post: https://napari.org/tutorials/applications/dask.html
embedded calendar on napari.org not showing in local time
🐛 Bug
the embedded calendar at https://napari.org/community/team.html#meeting-schedule used to show me the meeting in my local timezone but it's now showing up in pacific
When I originally put the link on I removed time zone info, will check whether someone mistakely left it on when updating the site
Error messages at https://napari.org/tutorials/
Getting to the tutorial landing page https://napari.org/tutorials/, one currently sees:
I guess there is a bug somewhere.
And just some ideas:
I don't know what framework you use for rendering the docs, but I have made wonderful experiences with readthedocs where users can see different doc versions from different releases:
One can even see docs from pull requests that are build at readthedocs servers with sphinx.
And with the plugin nbsphinx, one only has to write and commit some Jupyter notebooks, that are then automatically rendered to web-page tutorials.
Probably you are using other tools that are not compatible with that workflow, but maybe it might be useful.
Link Checker Report
Errors were reported while checking the availability of links.
📝 Summary
---------------------
🔍 Total.........1100
✅ Successful.....960
⏳ Timeouts.........0
🔀 Redirected.......0
👻 Excluded.........0
⚠ Unknown..........0
🚫 Errors.........140
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✗ file:///github/workspace/tutorials/fundamentals/installation (Cannot find file file:///github/workspace/tutorials/fundamentals/installation)
✗ https://forum.image.sc/tags/napari (HTTP status client error (403 Forbidden) for url (https://forum.image.sc/tags/napari))
✗ file:///github/workspace/tutorials/gallery (Cannot find file file:///github/workspace/tutorials/gallery)
✗ file:///github/workspace/tutorials/fundamentals/getting_started (Cannot find file file:///github/workspace/tutorials/fundamentals/getting_started)
Errors in guides/stable/magicgui.md
✗ file:///github/workspace/guides/plugins/index.md (Cannot find file file:///github/workspace/guides/plugins/index.md)
Errors in tutorials/fundamentals/image.md
✗ file:///github/workspace/tutorials/fundamentals/viewer (Cannot find file file:///github/workspace/tutorials/fundamentals/viewer)
✗ file:///github/workspace/tutorials/fundamentals/installation (Cannot find file file:///github/workspace/tutorials/fundamentals/installation)
✗ file:///github/workspace/tutorials/fundamentals/getting_started (Cannot find file file:///github/workspace/tutorials/fundamentals/getting_started)
✗ http://vispy.org/color.html#vispy.color.Colormap (HTTP status client error (404 Not Found) for url (https://vispy.org/color.html))
✗ file:///github/workspace/tutorials/fundamentals/labels (Cannot find file file:///github/workspace/tutorials/fundamentals/labels)
Errors in tutorials/fundamentals/getting_started.md
✗ file:///github/workspace/tutorials/fundamentals/viewer (Cannot find file file:///github/workspace/tutorials/fundamentals/viewer)
✗ file:///github/workspace/tutorials/fundamentals/installation (Cannot find file file:///github/workspace/tutorials/fundamentals/installation)
Errors in community/team.md
✗ https://github.com/jni (HTTP status client error (429 Too Many Requests) for url (https://github.com/jni))
✗ https://github.com/ziyangczi (HTTP status client error (429 Too Many Requests) for url (https://github.com/ziyangczi))
✗ https://github.com/justinelarsen (HTTP status client error (429 Too Many Requests) for url (https://github.com/justinelarsen))
✗ https://github.com/kne42 (HTTP status client error (429 Too Many Requests) for url (https://github.com/kne42))
✗ https://github.com/AhmetCanSolak (HTTP status client error (429 Too Many Requests) for url (https://github.com/AhmetCanSolak))
✗ https://github.com/royerloic (HTTP status client error (429 Too Many Requests) for url (https://github.com/royerloic))
✗ https://github.com/sofroniewn (HTTP status client error (429 Too Many Requests) for url (https://github.com/sofroniewn))
✗ https://github.com/GenevieveBuckley (HTTP status client error (429 Too Many Requests) for url (https://github.com/GenevieveBuckley))
✗ https://github.com/kevinyamauchi (HTTP status client error (429 Too Many Requests) for url (https://github.com/kevinyamauchi))
✗ https://github.com/tlambert03 (HTTP status client error (429 Too Many Requests) for url (https://github.com/tlambert03))
✗ https://github.com/alisterburt (HTTP status client error (429 Too Many Requests) for url (https://github.com/alisterburt))
Errors in release/release_0_4_3.md
✗ https://napari.org/docs/dev/developers/ROADMAP_0_4.html (HTTP status client error (404 Not Found) for url (https://napari.org/docs/dev/developers/ROADMAP_0_4.html))
✗ https://napari.org/docs/dev/events/rendering.html (HTTP status client error (404 Not Found) for url (https://napari.org/docs/dev/events/rendering.html))
✗ https://napari.org/docs/dev/developers/ROADMAP_0_3_retrospective.html (HTTP status client error (404 Not Found) for url (https://napari.org/docs/dev/developers/ROADMAP_0_3_retrospective.html))
Installation tutorial - add info on how to choose pyside/pyqt backends
It would be good to include information in the installation tutorial about choosing different backends for napari (pyside2/pyqt5).
There is an open issue at napari/napari#704 which discusses how we should use pip extras for this. The leading current suggestion is this napari/napari#704 (comment):
pip install napari-> get PySide2
pip install napari[pyqt]orpip install napari[pyqt5]-> get PyQt5
pip install napari[pyside]orpip install napari[pyside2]-> get PySide2
When this is settled in the main napari repository, I'd suggest adding a short section on choosing different backends, maybe just before the section on troubleshooting in napari-tutorials/tutorials/installation.md.
add "back to search results" button
from October 2021 pre-launch bug bash
Created by: unknown
Description
No description
Info
Bug source: unknown
Browser: unknown
PR: none
Attachments
Downloadable code snippets
It might be nice if some of our longer, self contained examples were downloadable as code snippets that people could run as scripts to reproduce the examples.
Remove notebook error caused by comment following ipython magic
We want to remove this notebook error.
I think it's caused by the comment immediately following ipython magic. We could try to either:
- Put the comment on a line by itself, before the
%gui qtmagic, OR - Put text of the commend into a markdown cell (I do think we need to explain why this magic is there)
right nav highlighting jumps to end
from October 2021 pre-launch bug bash
Created by: justin
Description
when I click the next-to-last item on the right nav, if the last two sections are short, the last item gets highlighted. this happens on the about page as well as plugin pages
Info
Bug source: wide
Browser: chrome
PR: none
Attachments
https://dl.airtable.com/.attachments/f1adb5121031e79c3bdb51bfc8e8d8b7/c9fe1aa4/image.png
Radio button vertical spacing too tall
from October 2021 pre-launch bug bash
Created by: Lia
Description
The vertical spacing between the radio buttons + their labels is to tall compared to design
Info
Bug source: on wider than mobile sizes
Browser: Chrome
PR: none
Attachments
python versions out of order in filters
from October 2021 pre-launch bug bash
Created by: justin
Description
I expected the filters to be in order.... 3.7, 3.8, 3.9
Info
Bug source: wide
Browser: chrome
PR: chanzuckerberg/napari-hub#86
Attachments
https://dl.airtable.com/.attachments/0921d80bc1ddfbe2882bb28c843c6b63/85b2ecc9/image.png
Partial SCSS updates not picked up by dev server
Background
Currently the dev server doesn't pick up changes made to partial SCSS files like _app-bar.scss. This is because:
- Gulp is only watching for non-partial SCSS files:
Line 17 in a99aa85
Line 50 in a99aa85
- Gulp rebuilds files iteratively using
since:
Line 24 in a99aa85
- Gulp doesn't detect changes to import dependencies like a bundler would
Possible Solutions
- Remove the
sinceand watch for non-partial SCSS files - Switch to a bundler
- Implement some custom logic for watching partials
I think (1) will be the quickest solution, but (2) would be the most efficient since bundlers were designed for handling dependencies between assets.
Workaround
- Save the partial SCSS file (i.e.
_app-bar.scss) - Save the non-partial SCSS file importing the partial you updated (i.e.
main.scss)
Failing CI
Our continuous integration checks are failing (noticed on a recent PR that made no code changes, just updated the user instructions #128).
The logs seem to suggest that a flaky X11 connection is to blame:
WARNING: The X11 connection broke: I/O error (code 1)
XIO: fatal IO error 0 (Success) on X server ":0"
after 3379 requests (3356 known processed) with 0 events remaining.
Error: Process completed with exit code 1.
Someone else also suggested that maybe the test failures could be due to deprecation of other packages like pytest.
Multiple images
Great work, thanks for your effots! I'm not sure if it fits within your plans for napari but it would be great to display multiple images at specified x-y-z points utilizing the gpu.
It would be great to customize -like visualizations.
Markdown images not rendered correctly in installation.md
The screenshot images for the bundle installation guide in installation.md are not rendering correctly.
We see this type of text, instead of the actual image:
An empty napari viewer should appear as follows
Tornado error & Qt warning visible in tutorials documentation
Currently, there is:
- A Qt warning, and
- A tornado error
... in the first page of the napari tutorials website (so, it's probably on every other page too)
See:
- Rendered website: https://napari.org/tutorials/
- Jupytext docs used to generate the website: https://github.com/napari/napari.github.io/blob/main/tutorials/index.md
Details:
WARNING: QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-runner'
ERROR:tornado.general:Uncaught exception in ZMQStream callback
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/site-packages/zmq/eventloop/zmqstream.py", line 431, in _run_callback
callback(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/site-packages/jupyter_client/threaded.py", line 121, in _handle_recv
msg_list = self.ioloop._asyncio_event_loop.run_until_complete(get_msg(future_msg))
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/asyncio/base_events.py", line 592, in run_until_complete
self._check_running()
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/asyncio/base_events.py", line 554, in _check_running
raise RuntimeError(
RuntimeError: Cannot run the event loop while another loop is running
ERROR:tornado.general:Uncaught exception in zmqstream callback
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/site-packages/zmq/eventloop/zmqstream.py", line 448, in _handle_events
self._handle_recv()
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/site-packages/zmq/eventloop/zmqstream.py", line 477, in _handle_recv
self._run_callback(callback, msg)
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/site-packages/zmq/eventloop/zmqstream.py", line 431, in _run_callback
callback(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/site-packages/jupyter_client/threaded.py", line 121, in _handle_recv
msg_list = self.ioloop._asyncio_event_loop.run_until_complete(get_msg(future_msg))
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/asyncio/base_events.py", line 592, in run_until_complete
self._check_running()
File "/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/asyncio/base_events.py", line 554, in _check_running
raise RuntimeError(
RuntimeError: Cannot run the event loop while another loop is running
/opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/site-packages/napari/utils/events/event.py:444: RuntimeWarning: coroutine 'get_msg' was never awaited
for ri, criteria in enumerate((before, after)):
RuntimeWarning: Enable tracemalloc to get the object allocation traceback
purge git history
Right now the git is taking around 600M to track history, checking out the code is quite slow, we should try to clean up some of the histories to speed it up
Chips don't quite match design
from October 2021 pre-launch bug bash
Created by: Lia
Description
A little too tall
Not right color grey (too dark)
Not enough space between end of “x” and end of chip
Info
Bug source: All
Browser: Chrome
PR: none
Attachments
Documentation: review and fix typos/broken links
Hi folks,
At the last Documentation working group meeting we talked about checking a few documents for typos, inconsistencies and broken links. A few pages will need changing due to the Docs reorganization work (see #176), but the following are likely to stay the same, and so can be worked on.
- napari viewer tutorial
- Annotating segmentation with text and bounding boxes
- Annotating videos with napari
- Using Dask and napari to process & view large datasets
- Single cell tracking with napari
- An introduction to the event loop in napari
- Asynchronous rendering
- Rendering in napari
- Creating a napari plugin
- napari hook specification reference
- Finding and installing a napari plugin
- napari ImageJ how-to guide
Jupytext instead of ipynb?
How do people feel about using jupytext frontmatter and markdown format instead of checking in ipynb files? It makes version control much easier to parse, and it's easier to look at files on github (I know that ipynb eventually renders on github ... but it's slow and buggy).
many examples of jupytext usage can be found in the jupyter-book docs, and the recent magicgui doc in napari uses it too
Get rid of XDG_RUNTIME_DIR warning in notebook output
There are warnings included as the output from our executed notebooks: XDG_RUNTIME_DIR not set, defaulting to /tmp/runtime-runner'
We do not want to see this in the published docs.
License filter options for the common licenses
from October 2021 pre-launch bug bash
Created by: Allen
Description
License filter options for the common licenses people want to exclusively use (e.g. GNU General Public License)
Info
Bug source: unknown
Browser: unknown
PR: none
Attachments
Remove `%gui qt` from tutorials and installation guide
Given napari/napari#2406 will be available from napari version 0.4.7 we can probably get rid of all the %gui qt stuff here.
Vertical spacing between radio + label is too large on wide screens
from October 2021 pre-launch bug bash
Created by: Jeremy
Description
One tiny thing I am adding now, but can be done for bug bash (or later, if not triaged for bug bash time):The vertical spacing between the radio buttons + their labels (on wider than mobile sizes) is a little too tall.
Info
Bug source: >875
Browser: All Browsers
PR: none
Attachments
https://dl.airtable.com/.attachments/f4afb407ff0428cc149d7c87e90fff82/fbca0571/image.png
"Install" button text should be semi-bold
from October 2021 pre-launch bug bash
Created by: Lia
Description
Currently regular weight; applies to Install button at top / right margin and at bottom
Info
Bug source: All
Browser: Chrome + Safari
PR: none
Attachments
Semantic line breaks in docs
I was looking through the tutorial files after running codespell in the main repo.
I think it could be easier to maintain/view the markdown files if semantic line breaks were used (new lines after period or comma etc). Currently each "paragraph" is on a single line. The output would be the same.
This will make it easier to identify the changes in a given commit since the lines are much shorter.
Ex:
The input data to the vectors layer must either be a Nx2xD numpy array representing N vectors with start position and projection values in D dimensions, or it must be an N1xN2 ... xNDxD, array where each of the first D dimensions corresponds to the voxel of the location of the vector, and the last dimension contains the D values of the projection of that vector. The former representation is useful when you have vectors that can start in arbitrary positions in the canvas. The latter representation is useful when your vectors are defined on a grid, say corresponding to the voxels of an image, and you have one vector per grid.
could be
The input data to the vectors layer must either be a Nx2xD numpy array representing N vectors with start position and projection values in D dimensions,
or it must be an N1xN2 ... xNDxD, array where each of the first D dimensions corresponds to the voxel of the location of the vector,
and the last dimension contains the D values of the projection of that vector.
The former representation is useful when you have vectors that can start in arbitrary positions in the canvas.
The latter representation is useful when your vectors are defined on a grid,
say corresponding to the voxels of an image, and you have one vector per grid.
which still renders the same.
There's room for debate for some of the linebreaks, but it could overall be helpful
Does anyone care about "First released?"
from October 2021 pre-launch bug bash
Created by: Allen
Description
Does anyone care about "First released?" Why?
Info
Bug source: unknown
Browser: unknown
PR: none
Attachments
Spacing between email input and subscribe button is too narrow (at small screen widths)
from October 2021 pre-launch bug bash
Created by: Lia
Description
Sorry if this was not clear in the design, but the spacing should start at 15px (at our smallest supported screen size: 300px)
Info
Bug source: 300px - 495px
Browser: unknown
PR: none
Attachments
low contrast CZI logo
cc @sofroniewn - is there a version of the logo which looks better on dark backgrounds?
docs test failing
just wanted to note from napari/napari#2473 that the doc tests were failing so I've made them able to continue on error so it will still be built. we'll see if this resolves itself or if further investigation is required
filter checkbox hover state off-center
from October 2021 pre-launch bug bash
Created by: Kira Evans
Description
the gray circle indicating that you are hovering over the checkbox is misaligned with the checkbox itself
Info
Bug source: unknown
Browser: unknown
PR: none
Attachments
Wish for a conda package
It would be nice to have a conda package for this tool.
clearing chip tags "hovers" over next plugin on iPad
from October 2021 pre-launch bug bash
Created by: Kira Evans
Description
steps to reproduce (on iPad):
- apply a filter
- clear the filter by clicking on the X on the tag chip
Info
Bug source: unknown
Browser: Firefox, Safari, Edge, Chrome
PR: none
Attachments
https://dl.airtable.com/.attachments/5b1c1f58a54c165c107c2125ee9b06b8/b52837a4/2750B669-64FF-4296-A716-949AAF45797A.png https://dl.airtable.com/.attachments/27f16db378a761d6afb62394db0668e8/6f1d0453/B1AF92AA-4073-4351-AC77-FC3C7265A1C3.png
Some screenshots not being rendered
I noticed that some of the screenshots from the code examples are no longer rendering during deployment. Here's an example from https://napari.org/tutorials/fundamentals/viewer.html:
And here's the same page when built locally:
Tests failing on ubuntu-latest python 3.9 CI - Shader compilation error in GL_VERTEX_SHADER:
The CI tests failing on ubuntu-latest python 3.9: https://github.com/napari/napari.github.io/pull/125/checks?check_run_id=2413215369
It looks like there's some kind of compilation error causing the failure in test_docs.py::test_doc_code_cells[guides/stable/magicgui.md]
Here's the log:
test_docs.py::test_doc_code_cells[guides/stable/magicgui.md] FAILED [100%]
=================================== FAILURES ===================================
________________ test_doc_code_cells[guides/stable/magicgui.md] ________________
CALL ERROR: Exceptions caught in Qt event loop:
________________________________________________________________________________
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/app/backends/_qt.py", line 825, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/util/event.py", line 473, in _invoke_callback
_handle_exception(self.ignore_callback_errors,
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/canvas.py", line 217, in on_draw
self._draw_scene()
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/canvas.py", line 266, in _draw_scene
self.draw_visual(self.scene)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/canvas.py", line 304, in draw_visual
node.draw()
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/visuals/visual.py", line 595, in draw
v.draw()
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/visuals/visual.py", line 442, in draw
self._program.draw(self._vshare.draw_mode,
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/visuals/shaders/program.py", line 101, in draw
Program.draw(self, *args, **kwargs)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/program.py", line 533, in draw
canvas.context.flush_commands()
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/context.py", line 176, in flush_commands
self.glir.flush(self.shared.parser)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 572, in flush
self._shared.flush(parser)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 494, in flush
parser.parse(self._filter(self.clear(), parser))
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 819, in parse
self._parse(command)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 787, in _parse
ob.set_data(*args)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 929, in set_data
raise RuntimeError("Shader compilation error in %s:\n%s" %
RuntimeError: Shader compilation error in GL_VERTEX_SHADER:
________________________________________________________________________________
----------------------------- Captured Qt messages -----------------------------
QtWarningMsg: QMainWindow::saveState(): 'objectName' not set for QDockWidget 0x56521db4fc60 ';
QtWarningMsg: QMainWindow::saveState(): 'objectName' not set for QDockWidget 0x56521644a160 ';
----------------------------- Captured stderr call -----------------------------
WARNING: Error drawing visual <Text at 0x7f3d2b651a90>
Exceptions caught in Qt event loop:
________________________________________________________________________________
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/app/backends/_qt.py", line 825, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/util/event.py", line 473, in _invoke_callback
_handle_exception(self.ignore_callback_errors,
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/canvas.py", line 217, in on_draw
self._draw_scene()
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/canvas.py", line 266, in _draw_scene
self.draw_visual(self.scene)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/canvas.py", line 304, in draw_visual
node.draw()
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/visuals/visual.py", line 595, in draw
v.draw()
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/visuals/visual.py", line 442, in draw
self._program.draw(self._vshare.draw_mode,
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/visuals/shaders/program.py", line 101, in draw
Program.draw(self, *args, **kwargs)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/program.py", line 533, in draw
canvas.context.flush_commands()
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/context.py", line 176, in flush_commands
self.glir.flush(self.shared.parser)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 572, in flush
self._shared.flush(parser)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 494, in flush
parser.parse(self._filter(self.clear(), parser))
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 819, in parse
self._parse(command)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 787, in _parse
ob.set_data(*args)
File "/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/vispy/gloo/glir.py", line 929, in set_data
raise RuntimeError("Shader compilation error in %s:\n%s" %
RuntimeError: Shader compilation error in GL_VERTEX_SHADER:
________________________________________________________________________________
------------------------------ Captured log call -------------------------------
WARNING vispy:visual.py:445 Error drawing visual <Text at 0x7f3d2b651a90>
=============================== warnings summary ===============================
test_docs.py::test_doc_code_cells[tutorials/index.md]
/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/ipykernel/zmqshell.py:57: DeprecationWarning: ipykernel.datapub is deprecated. It has moved to ipyparallel.datapub
from ipykernel.datapub import ZMQDataPublisher
test_docs.py::test_doc_code_cells[tutorials/index.md]
/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/ipykernel/datapub.py:21: DeprecationWarning: ipykernel.serialize is deprecated. It has moved to ipyparallel.serialize
from ipykernel.serialize import serialize_object
test_docs.py::test_doc_code_cells[tutorials/index.md]
/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/ipykernel/serialize.py:25: DeprecationWarning: ipykernel.pickleutil is deprecated. It has moved to ipyparallel.
from ipykernel.pickleutil import (
test_docs.py::test_doc_code_cells[tutorials/index.md]
/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/ipykernel/pickleutil.py:26: DeprecationWarning: ipykernel.codeutil is deprecated since IPykernel 4.3.1. It has moved to ipyparallel.serialize
from ipykernel import codeutil
test_docs.py::test_doc_code_cells[tutorials/index.md]
/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/ipykernel/iostream.py:9: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
from imp import lock_held as import_lock_held
test_docs.py::test_doc_code_cells[guides/stable/magicgui.md]
/opt/hostedtoolcache/Python/3.9.4/x64/lib/python3.9/site-packages/magicgui/widgets/_bases/ranged_widget.py:28: FutureWarning: The 'maximum' keyword arguments has been changed to 'max'. In the future this will raise an exception
warn(
-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
FAILED test_docs.py::test_doc_code_cells[guides/stable/magicgui.md]
=================== 1 failed, 8 passed, 6 warnings in 14.88s ===================
Enhancement proposal: use jupyter notebooks for all tutorial examples
I'd like to propose that we change the napari tutorials repository to hold example notebooks, instead of example markdown files, which get rendered in html on the tutorial website.
Since we're adding functionality for displaying screenshots in-line in notebooks, this seems like it could be the perfect time (especially since there's relatively few examples in here now).
This would have several advantages:
- It makes our tutorial docs more robust to API changes. We can add CI to check notebooks run without errors (and compare notebook outputs to some benchmark, if need be). This prevents tutorials drifting out of sync with the main napari repo.
- It entirely solves the problem of downloadable scripts, raised by Nick here: #19
- It would make things easier for people running napari workshops. I'm pretty sure every time Juan has given a talk or workshop on napari he has put together his own notebooks with examples. It'd be great if people could upload and share those here, then when someone else gives a talk there's a wider pool of resources available.
Some other projects using notebooks to generate docs:
- dask uses notebooks in their examples respository, and has CI to run all notebooks & check for errors. Here's a link to the website.
- fastai uses notebooks for documentation and code alike, and it all renders pretty nicely on their website.
project link text not aligned
from October 2021 pre-launch bug bash
Created by: unknown
Description
"Documentation" seems to be to the left compared to other text
Info
Bug source: unknown
Browser: unknown
PR: none
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