UI issues with pydata 0.13.3

Describe the bug
Some of the UI issues I noticed are :

next, prev button floating up

bibliography affecting the UI

sidebar not getting hidden

have a min-width for content

Reproduce the bug

install pydata 0.13.3 , with the latest sbt (1.0.1 about to be released)

List your environment
No response

@AakashGfude some of these might be due to docutils>0.17.1 causing issues with breaking pages when including a bibliography due to https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/322

Same problem

This should now be fixed

Hi, I am still getting the same issue for the 2nd screenshot above. The bibliography will push the article footer to the right side.

I think this is fixed in the release candidate that's out now, it should be released soon in full!

thanks for replying, just re-clarifying on this - in other words, this issue will be fixed at v0.14.5?

@jackshiwl no, the RC is 1.1.0rc1, so the next version should be 1.1.0:
https://pypi.org/project/sphinx-book-theme/1.1.0rc1/
That RC is already downloadable, and should fix the problem. We're stuck on making a proper release right now because a build-time dependency is broken on one of our release platforms, and we want a working sdist.

@choldgraf it seems the issue is coming from pydata-sphinx-theme, could you point me to the PR/commit that fixed the issue so I can propagate the fix you found here ?

any updates on this?

For issues relating to sphinxcontrib-bibtex interaction, see https://github.com/pydata/pydata-sphinx-theme/issues/1581#issuecomment-1856907745


SyntaxError: invalid syntax

$ retmux -v
retmux 1.0.2
$ retmux -b
backing up the current tmux sessions
0:=:(,):=:1
Traceback (most recent call last):
File "/usr/bin/retmux", line 92, in
func(sys.argv[2])
File "/usr/lib/python2.7/site-packages/tmuxbk/controller.py", line 116, in do_backup
backup.backup_tmux(name)
File "/usr/lib/python2.7/site-packages/tmuxbk/backup.py", line 23, in backup_tmux
tmux.sessions = load_sessions()
File "/usr/lib/python2.7/site-packages/tmuxbk/backup.py", line 50, in load_sessions
session.size = eval(s_l[1])
File "", line 1
(,)
^
SyntaxError: invalid syntax

thanks @1o1o1
Tmux 2.9 has removed some options:

The force-width and force-height options and the session_width and session_height formats have been removed.

The old backed up can still be restored, however, backup fails due to the usage of the removed options. I'll take a closer look at the problem and fix it.

@1o1o1 pushed a fix (v.1.0.3) in the master branch. You can give it a try.

Working ok)  but when restore backup, programs not running automatically :(

If you meant the “programs “ is tmux, then it is fine. Because retmux restores sessions in detached mode.  If you want to attach after the  restore, you can try retmux -r xxx && tmux attach @1o1o1

i meant apps running in windows of terminals tmux!

@1o1o1 I don't get you. sorry.
If you restore a back inside an active tmux session, it should work too. You can use the list-session or prefix-s to see the restored sessions.
If it was not what you meant, can you please tell me what did you do in each step?
Or give this a try:

first backup sessions from the current tmux using retmux -b with or without name
if the backup is well done, run tmux kill-server (kill the tmux)
run retmux -r && tmux attach
Can you see your backup sessions get restored?
I tested once yesterday, it works. Of course, probably, I could miss something.


How to define alert in page class?

Hi
I want to test the following application: https://romashov.tech/chat
This is code of my MainPage:
using Atata;
using _ = Chat.Tests.Model.MainPage;

namespace Chat.Tests.Model
{
    [Url("")]
    public class MainPage : Page<_>
    {
        [FindById("send")]
        public Button<_> Send { get; private set; }
    }
}

When I run my test I have the following exception:
OpenQA.Selenium.UnhandledAlertException : unexpected alert open: {Alert text : Your name:}   (Session info: chrome=75.0.3770.100)
How I can define it in page class?
How I can put nickname in this allert?

Hi,
You can add a method (EnterAs or somehow else) to your page object which will handle prompt alert using WebDriver API:
using Atata;
using OpenQA.Selenium;

namespace Chat.UITests
{
    using _ = MainPage;

    public class MainPage : Page<_>
    {
        [FindFirst]
        public TextInput<_> Message { get; private set; }

        [FindByClass("send-button")]
        public Button<_> Send { get; private set; }

        public _ EnterAs(string name)
        {
            IAlert alert = Driver.SwitchTo().Alert();
            alert.SendKeys(name); // Note that SendKeys doesn't work in Chrome for a long time. Works in Firefox for example.
            alert.Accept();

            Driver.SwitchTo().DefaultContent();

            return Owner;
        }
    }
}

Then use it in the test this way:
Go.To<MainPage>().
    EnterAs("SomeUser").
    Message.Set("test message").
    Send.Click();

@YevgeniyShunevych seems, that alert.SendKeys works on Chrome)

This is cool then. It was not working for me in Chrome. On what version of ChromeDriver and Chrome it worked for you?


Changed terminology from whitelist to allowlist

Changed instances of whitelist to allowlist everywhere in the docs except for instances that refer to UI elements (CloudFormation UI, Kafka, and Jekyll builds)

This change is

Online preview: http://cockroach-docs-review.s3-website-us-east-1.amazonaws.com/d057c5e1a662e068c927cd40ff2792cea1fec2ef/
Edited pages:

v19.1/change-data-capture.md
v19.1/create-changefeed.md
v19.1/gssapi_authentication.md
v19.2/change-data-capture.md
v19.2/create-changefeed.md
v19.2/gssapi_authentication.md
v2.1/change-data-capture.md
v2.1/create-changefeed.md
v20.1/change-data-capture.md
v20.1/cockroachcloud-authorization.md
v20.1/cockroachcloud-connect-to-your-cluster.md
v20.1/cockroachcloud-frequently-asked-questions.md
v20.1/create-changefeed.md
v20.1/deploy-a-python-to-do-app-with-flask-kubernetes-and-cockroachcloud.md
v20.1/gssapi_authentication.md


yf.pdr_override() warning message

Using the code:
from pandas_datareader import data as pdr
import yfinance as yf
yf.pdr_override() # <== that's all it takes :-)
download dataframe
data = pdr.get_data_yahoo("SPY", start="2017-01-01", end="2017-04-30")
generates this warning:
/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/pandas_datareader/compat/init.py:7: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
pandas_datareader is using the latest version running python3.8.2 on a Mac

Found a fix at stack overflow (YMMV, I made a copy of the file before changing it but it does work without error now)
For mac OS open /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/pandas_datareader/compat/init.py
change: from pandas.util.testing import assert_frame_equal
to: from pandas.testing import assert_frame_equal
(source: https://stackoverflow.com/questions/60039161/getting-a-future-warning-when-importing-for-yahoo-with-pandas-datareader)


Error installing OpenBLAS on ubuntu 12.04 precise.

I am trying to install OpenBLAS using the instructions and the download file given here:
http://xianyi.github.io/OpenBLAS/
I get the following error:
../common.h:579:27: fatal error: cblas_noconst.h: No such file or directory
compilation terminated.
make[1]: *** [cblas_isamax.o] Error 1
make[1]: Leaving directory `/home/admin/downloads/xianyi-OpenBLAS-9c51cdf/interface'
make: *** [libs] Error 1
I was having trouble installing Julia and then thought I will install OpenBLAS first but am having the same trouble. Can someone please help?
Thanks.

Same problem .
My CPU is CORE i5 6300HQ, which TARGET should I Select?

TARGET=HASWELL should work - which version of OpenBLAS are you trying to build ? ("SkyLake" type CPUs should be autodetected since about version 0.2.15, released more than a year ago)


(Bug) Undesired (((NEW LINE))) added to generated localization

What is the current behavior?
When generating localization, some lines/options are having a (((NEW LINE))) text added to the end of the locale and I have no idea what prompts this. In this example, the option does not show any new line character and does not continue onto the next line.

In the loc however a (((NEW LINE))) is present.

Please provide the steps to reproduce, and if possible a minimal demo of the problem:
Example Raw Yarn Script
title: Start
tags:
colorID: 0
position: -182,-977
---
Hey there #line:028faf4
I see The Rescue sent you a care package! #line:069ef91
You should make use of that #line:014fdc5
[[I’ve only been back for like 24 hours|Node_2]] #line:0afef88
===
title: Node_2
tags:
colorID: 0
position: -182,-709
---
Hi, this is text on Node_2 #line:060a8fe

[[Node_3]]
===
title: Node_3
tags:
colorID: 0
position: -180,-460
---
Hi, this is text on Node_3 #line:005e60b
===

These files are:

Being edited in the latest version of the local Yarn Editor.
Saved as Yarn files to Unity.
Line Tags generated
Localization generated.

Expected
Localization generated includes only player-visible text from Yarn Script.
Expected localization
id,text,file,node,lineNumber
line:028faf4,Hey there,MultipleNode,Start,6
line:069ef91,I see The Rescue sent you a care package!,MultipleNode,Start,7
line:014fdc5,You should make use of that,MultipleNode,Start,8
line:0afef88,I’ve only been back for like 24 hours,MultipleNode,Start,9
line:060a8fe,"Hi, this is text on Node_2",MultipleNode,Node_2,16
line:005e60b,"Hi, this is text on Node_3",MultipleNode,Node_3,25

Actual
Localization generated includes player-visible text from Yarn Script and a (((NEW LINE)))  appended to some lines.
Actual Localization
id,text,file,node,lineNumber
line:028faf4,Hey there,MultipleNode,Start,6
line:069ef91,I see The Rescue sent you a care package!,MultipleNode,Start,7
line:014fdc5,You should make use of that,MultipleNode,Start,8
line:0afef88,I’ve only been back for like 24 hours (((NEW LINE))),MultipleNode,Start,9
line:060a8fe,"Hi, this is text on Node_2",MultipleNode,Node_2,16
line:005e60b,"Hi, this is text on Node_3",MultipleNode,Node_3,25

Please tell us about your environment:
Unity: 2020.3.20f1
Yarn: 1.2.0 (based on included package.json).
Other information

Can't reproduce this across a few different versions of Yarn Spinner or Unity.
Does this go away if you use YS from the head of main instead of the version of YS you used?

Hi @McJones, I apologize for the delayed response. We're in the final days to a significant milestone so it may take a week or so to be able to attempt a repro/further investigation.

There's been no movement on these for a while now, closing them.
Feel free to reopen if the issue persists.


Align API with SVG where possible

Hi,
I'm converting a somewhat complex SVG component to work with ReactART.  It's a huge thrill to see it rendering to canvas without rewriting the codebase, but the experience of learning the API has been a pretty painful groking of source. That's part lack of documentation but also that the prop names are sometimes consistent with SVG and other times not.
React has, except in cases of naming confict, maintained attribute similarity with HTML with an easy-enough camelCase translation. I think it would be a good approach for ReactART too. It would reduce cognitive load for developers by using an already familiar API, and it would make code reuse from SVG to ReactART all the easier.
I recognise that it could only ever be a subset of the ginormous SVG API, but a clearly defined subset could still be a lot easier to get up to speed with.  At present, the API sometimes aligns with SVG, other times not, with no clear pattern for mental translation.
Examples that spring to mind...

opacity = opacity (same, i.e. not blend as in ART)
stroke-dasharray(string) = strokeDash(array)
stroke-linecap(string) = strokeCap(string)
text-anchor(start/middle/end) = alignment(left/center/right)
d for path property, mimicking SVG
<rect> = <Rectangle>

What do you think?

It is interesting because several people have actually asked that we unify more with the CSS model (e.g. background/border instead of fill/stroke) since people that are familiar with SVG is a very small subset compared to those who know CSS.
IMO, SVG made a few mistakes due to the DOM centric API. The string based data model won even though the DOM properties are rich data structures. The rich data structures are, however, very verbose and difficult to work with - and nobody really knows how to use them.
That's why I designed transforms, paths and gradients as rich objects but with a convenient API instead of strings and ids.
The ART <Rectangle /> is different than the SVG <rect /> because the rounded corner API is completely different. The ART one is closer to the CSS API. It was originally designed by Valerio Proietti but I think the rationale was that you often control different radius on different corners in modern designs. However, you rarely have different x/y radius which is what the SVG API opts for.
React at some point chose the camel-case PROPERTY names (className/htmlFor) rather than the equivalent ATTRIBUTE names (class/for). It seemed to make sense to use that for React ART as well. Hence strokeWidth etc. which has corresponding CSSOM properties in SVG. That's also much more convenient when you're working with objects in JS since you don't have to fallback to the bracket syntax.
The strokeCap/strokeDash APIs where added later on. We could rename them to strokeLinecap/strokeDasharray for consistency I suppose.
However, another consideration is that since the main target is Canvas and the Canvas API is seeing nicer API development and unification with newer SVG APIs maybe we should be trying to unify with the Canvas API rather than SVG. In that case, maybe lineCap and lineDash makes more sense.
Similarly Canvas calls it textAlign instead of textAnchor. I think at some point I had some rationale for why alignment made more sense when right-to-left isn't fully properly supported in some environment. That's a pretty weak argument. A better one would be that when people read alignment they'll know what it means. When people read textAnchor they'll only understand it if it they're already familiar with SVG which is, sadly, a very small set.
I suppose it is difficult to strike a fine balance between consistency amongst several competing standards, what people are most familiar with and what would be a nicer API if you had a chance to rethink assumptions.
I think the end goal is to create a nice ideal API to code dynamic content. It is not a primary goal to be a target for copy/pasting existing static SVG content. There is an automated SVG -> ART converter although sadly there is no React ART version. I'd love for someone to update it to support React ART output though.
Even though the JSX may make it seem strange, I think I'd rather error on the side of Canvas/CSS than SVG for consistency.
Given this context, what do you think? What changes would you suggest?

There is an automated SVG -> ART converter although sadly there is no React ART version. I'd love for someone to update it to support React ART output though.

Can you point me to that?
In principle it's the same to me whether the API aligns closer to SVG or CSS or Canvas. Whatever provides the cleanest declarative API should be appropriate. SVG seemed to me the more logical, since it's already a declarative drawing API much like react-art, but I take your point regarding the limitations of string based transformations.
I do think there is a strong argument to be made for an easy transition from SVG. Being able to export a design to SVG and, with minimal changes, have the option to render via Canvas is a big deal. This use case could be covered by a SVG > ReactART convertor, of course.
Another big deal would be to not need an SVG renderer, since the source is a subset of SVG to begin with. ReactART could, with minimal tweaks to allow for programatic Transformations, output the SVG with very little changes.
Do you have any thoughts on that? Is that an avenue already pursued and rejected?
Regarding rect and rectangle, and as a general notion to the idea of a subset of SVG as an API, I would argue that there is no problem to providing additional API where is doesn't conflict with SVG.  E.g. rx and ry behave as defined by the SVG spec, r could act as a shortcut property to assign the value to rx and ry and the topRightRadius etc properties can be additional also.
On the same note, the API could allow transformations to be set with a string or a Transform instance, providing consistency with the SVG API while also enriching it.
By using a subset of SVG, a fallback also comes for free. Accessibility becomes a solved problem too, a fallback to the original SVG for screen readers could be implemented easily.
I'm not sure on the numbers of people familiar with SVG so I'll defer to your experience, but I do think SVG represents a well established standard for declarative drawing, albeit with some clumsy bits.  textAnchor, for example.
I'm curious to know how an API aligned more closely with Canvas would look. SVG and Canvas already share a path description language. Beyond that would it just be property names? Or are there some areas where you would move away from the declarative?
Another question is, how is this library most used and approached? I'm coming at all this from the approach of someone working with SVG who needs to target canvas on mobile for performance. My browser compatibility targets on desktop already have great SVG support so for me SVG is the base from which I'd like to sometimes render to Canvas.
For that use, a library aligned with SVG makes a lot of sense.
It'd be great to hear your thoughts and experiences on other approaches to the library.

svgconverter here, I think: http://sebmarkbage.github.io/art/. Though it looks broken. It's possible that it works locally and is just broken on GitHub pages right now?


Fix pagination when paginate_link points to a directory

permalink can point to a directory, and Pretzel knows it must create an index.html in that directory.
This patch add support for this behavior when pagination is used.
Modified custom pagination link tests to test this case.
fixes #254

Sorry for the silence, I was out of town for a few weeks.
Thanks a lot for your PR, I haven't the time to check all pagination :smiley:
Could you just merge your PR with the updated master?
Thanks in advance.

Sure. Probably I'll do it in the weekend.

Updated branch with upstream changes. (btw is any notification generated by updating the branch in the PR?)

Thanks!
I didn't receive mail for each commits if that's what your mean.

Yes that is what I meant.


Change dependencies to peerDependencies

If I some plugin include leaflet to dependencies and I have local version leaflet, then I have two version - leaflet from plugin and my.

I am confused now - so this was a wrong thing to do? https://github.com/Leaflet/Leaflet/issues/4534

Plus one on the confusion

I would suggest the same thing as @hyperknot in https://github.com/Leaflet/Leaflet/issues/4534
If Leaflet is required for building a plugin, it should be specified in devDependencies, not peer.


processed image is neither in T1 nor in MNI space

Hi Matt,
I have noticed the following few issues while preprocessing our multi-shell DWI data. Could you please help me in resolving these issues!

The preprocessed data (sub-10003_ses-V1_space-T1w_desc-preproc_dwi.nii.gz) is neither in T1 space nor in MNI space. Please see the attached images (one is overlayed with T1 and the other is overlayed with standard image). I had specifically used the --ouput-space T1w to make sure that the outputs are saved in T1w space.  I want to preserve the same orientation as the original image.  Please see the attachment
The output images like carpet plot, brain segmentation, etc. are not embedded in the HTML report. For e.g. the reportlets directory contains a file sub-10003_summary.html which only has information about data but the results of the T1 processing is not embedded in the file.
The outputs are weirdly organized. i.e. there are 2 anat directories; one inside the ses-v1 and one outside the ses-v1. The one outside ses-v1 contains the outputs but the other anat has only  txt file

qsiprep
│   ├── dataset_description.json
│   ├── dwiqc.json
│   ├── logs
│   │   ├── CITATION.html
│   │   ├── CITATION.md
│   │   └── CITATION.tex
│   ├── sub-10003
│   │   ├── anat
│   │   │   ├── sub-10003_desc-brain_mask.nii.gz
│   │   │   ├── sub-10003_desc-preproc_T1w.nii.gz
│   │   │   ├── sub-10003_dseg.nii.gz
│   │   │   ├── sub-10003_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│   │   │   ├── sub-10003_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│   │   │   ├── sub-10003_label-CSF_probseg.nii.gz
│   │   │   ├── sub-10003_label-GM_probseg.nii.gz
│   │   │   ├── sub-10003_label-WM_probseg.nii.gz
│   │   │   ├── sub-10003_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│   │   │   ├── sub-10003_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
│   │   │   ├── sub-10003_space-MNI152NLin2009cAsym_dseg.nii.gz
│   │   │   ├── sub-10003_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
│   │   │   ├── sub-10003_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
│   │   │   └── sub-10003_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
│   │   ├── figures
│   │   │   ├── sub-10003_seg_brainmask.svg
│   │   │   ├── sub-10003_ses-V1_carpetplot.svg
│   │   │   ├── sub-10003_ses-V1_coreg.svg
│   │   │   ├── sub-10003_ses-V1_desc-resampled_b0ref.svg
│   │   │   ├── sub-10003_ses-V1_desc-sdc_b0.svg
│   │   │   ├── sub-10003_ses-V1_dwi_denoise_ses_V1_dwi_wf_biascorr.svg
│   │   │   ├── sub-10003_ses-V1_dwi_denoise_ses_V1_dwi_wf_denoising.svg
│   │   │   ├── sub-10003_ses-V1_dwi_denoise_ses_V1_dwi_wf_unringing.svg
│   │   │   ├── sub-10003_ses-V1_sampling_scheme.gif
│   │   │   └── sub-10003_t1_2_mni.svg
│   │   └── ses-V1
│   │       ├── anat
│   │       │   └── sub-10003_ses-V1_from-orig_to-T1w_mode-image_xfm.txt
│   │       └── dwi
│   │           ├── sub-10003_ses-V1_confounds.tsv
│   │           ├── sub-10003_ses-V1_desc-ImageQC_dwi.csv
│   │           ├── sub-10003_ses-V1_desc-SliceQC_dwi.json
│   │           ├── sub-10003_ses-V1_dwiqc.json
│   │           ├── sub-10003_ses-V1_space-T1w_desc-brain_mask.nii.gz
│   │           ├── sub-10003_ses-V1_space-T1w_desc-eddy_cnr.nii.gz
│   │           ├── sub-10003_ses-V1_space-T1w_desc-preproc_dwi.b
│   │           ├── sub-10003_ses-V1_space-T1w_desc-preproc_dwi.bval
│   │           ├── sub-10003_ses-V1_space-T1w_desc-preproc_dwi.bvec
│   │           ├── sub-10003_ses-V1_space-T1w_desc-preproc_dwi.nii.gz
│   │           └── sub-10003_ses-V1_space-T1w_dwiref.nii.gz

If we run the processing with --only-dwi option, QSIprep does not create any figures i.e. no carpet plots etc.

Overlayed over MNI

Overlayed over T1

Here is the processed image

This is the original image (just increased the brightness)

Thanks

Are you overlaying the preprocessed DWI on the original T1? Unless you use the longitudinal option, QSIPrep will make a T1 template aligned to ACPC using all T1s available for that subject. The DWI is also aligned to ACPC. The individual session anatomical text files show the transform each T1 takes to get to ACPC.

Yes, I am using the original T1 image mainly because the T1 reference aligned to ACPC is not present if I use the --dwi-only  option. Also, can you please also comment on the other issues?
Thanks!

It makes sense then that the preprocessed DWI will not be aligned to your original T1. The output-space flag is deprecated. All outputs are in ACPC space. If you want to get DWI back to original T1, you can try doing a rigid transform between the T1 and the FA image, which you can create after fitting the DTI tensor on the preprocessed image. Or use the "from_orig_to_t1" transform files created when you did not use dwi_only
In regards to the multiple anat folders per session, those are the transforms between those individual T1s and the ACPC aligned T1 reference. If you would prefer to have individual T1 files (that is, treat keep session separate), you can use the --longitudinal flag.
I'm not a dev, but I can say that I have also replicated the no carpet plot when running dwi_only, but there was another error the happened during the creation of the reports, so I don't know what it would be like in a error-less run. Can you check the subject-specific HTML and see if any errors were reported?

Thanks, good to know that the output-space is deprecated. Also, is that the reason that the orientation of all the pre-processed DWI images is flipped to LPS?

I could be wrong, but I think that is because LPS is the standard FSL orientation, and FSL is used for the later stages of processing (EDDY, TOPUP, etc).

Thanks for your help/suggestions :)

@bwinsto2 Sure, that would be helpful. Thanks :)