Bokeh_class #1899
Bokeh_class #1899
Conversation
hamogu
added
general:visualization
note:needs SDS testing
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This PR looks a lot more intimidating than it is, because it is build on top of #1382. Only the last commit (at the time of writing) is actually new. Locally, this passes almost all ploting tests we have, but I've not activated them in this PR, because it only passes "almost" all plotting tests - see #1887. When we get close to merging, I csn simply add bokeh as a new requirement on CI and special case those few tests that fail; but that's not a priority here. It's more important that @DougBurke and @anetasie take a look at the current functionality. |
Codecov Report
@@ Coverage Diff @@
## main #1899 +/- ##
===========================================
- Coverage 81.41% 67.72% -13.69%
===========================================
Files 75 78 +3
Lines 27227 27861 +634
Branches 4130 4010 -120
===========================================
- Hits 22166 18870 -3296
- Misses 4871 8871 +4000
+ Partials 190 120 -70
... and 37 files with indirect coverage changes Continue to review full report in Codecov by Sentry.
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EDIT This comment was posted here erroneously and it does not apply to this PR. I added the test and rebased to pick up the uo-to-date RTD configuration file (to fix the RTD failure in the previous run) |
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I've got this far before I've run out of TUITs today: |
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I did just try the example-plots backend and added a call to but then the |
That comment is in the wrong PR... it was meant for the link-parameters PR. I ahve too many tabs open that tool almost, but not quite identical. Sorry for the confusion. |
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@DougBurke Are you running in the notebook or on a traditional command line? See https://sherpa--1899.org.readthedocs.build/en/1899/plots/bokeh_backend.html#module-sherpa.plot.bokeh_backend for display help. But yes, it should be |
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So, I start with "jupyter lab" [*] and then have import numpy as np
from sherpa import data
from sherpa.astro import data as astrodata
from sherpa import plot
from sherpa.astro import plot as astroplot
x1 = [100, 200, 600, 1200]
y1 = [2000, 2100, 1400, 3050]
d1 = data.Data1D('oned', x1, y1)
plot1 = plot.DataPlot()
plot1.prepare(d1)
plot1.plot()
show(plot.backend.current_fig['all_axes'])and a new tab opens up with a file-not-found error (in my case looking for file:///tmp/tmpg6_1hr2n.html but it's obviously a randomly-generated file. Actually, the file exists but for some reason trying to display it fails. At first I thought it was a permissions error from jupyter lab, but trying "gio open /tmp/...html" failed in the same way. It's too late and wet for me to diagnose. Is firefox being protective of my /tmp/ directory (or something equally annoying to diagnose)? I think so, because if I "firefox /tmp/..." or "gio open /tmp/..." you get a file-not-found error, but if I manually open the file via file/open file it displays. Gah.... <!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Bokeh Plot</title>
<style>
html, body {
box-sizing: border-box;
display: flow-root;
height: 100%;
margin: 0;
padding: 0;
}
</style>
<script type="text/javascript" src="https://cdn.bokeh.org/bokeh/release/bokeh-3.2.2.min.js"></script>
<script type="text/javascript">
Bokeh.set_log_level("info");
</script>
</head>
<body>
<div id="e0448a2b-9e27-4fb9-a01d-57a21641536b" data-root-id="p1063" style="display: contents;"></div>
<script type="application/json" id="p1076">
{"21276715-a5ae-4bcf-b18f-09fa6758ce03":{"version":"3.2.2","title":"Bokeh Application","roots":[{"type":"object","name":"GridPlot","id":"p1063","attributes":{"rows":null,"cols":null,"toolbar":{"type":"object","name":"Toolbar","id":"p1062","attributes":{"tools":[{"type":"object","name":"PanTool","id":"p1054"},{"type":"object","name":"WheelZoomTool","id":"p1055"},{"type":"object","name":"BoxZoomTool","id":"p1056","attributes":{"overlay":{"type":"object","name":"BoxAnnotation","id":"p1057","attributes":{"syncable":false,"level":"overlay","visible":false,"left_units":"canvas","right_units":"canvas","bottom_units":"canvas","top_units":"canvas","line_color":"black","line_alpha":1.0,"line_width":2,"line_dash":[4,4],"fill_color":"lightgrey","fill_alpha":0.5}}}},{"type":"object","name":"SaveTool","id":"p1061"},{"type":"object","name":"ResetTool","id":"p1059"},{"type":"object","name":"HelpTool","id":"p1060"}]}},"children":[[{"type":"object","name":"Figure","id":"p1033","attributes":{"x_range":{"type":"object","name":"DataRange1d","id":"p1034"},"y_range":{"type":"object","name":"DataRange1d","id":"p1035"},"x_scale":{"type":"object","name":"LinearScale","id":"p1065"},"y_scale":{"type":"object","name":"LinearScale","id":"p1066"},"title":{"type":"object","name":"Title","id":"p1040","attributes":{"text":"oned"}},"renderers":[{"type":"object","name":"GlyphRenderer","id":"p1071","attributes":{"data_source":{"type":"object","name":"ColumnDataSource","id":"p1067","attributes":{"selected":{"type":"object","name":"Selection","id":"p1068","attributes":{"indices":[],"line_indices":[]}},"selection_policy":{"type":"object","name":"UnionRenderers","id":"p1069"},"data":{"type":"map","entries":[["x",{"type":"ndarray","array":{"type":"bytes","data":"ZAAAAMgAAABYAgAAsAQAAA=="},"shape":[4],"dtype":"int32","order":"little"}],["y",{"type":"ndarray","array":{"type":"bytes","data":"0AcAADQIAAB4BQAA6gsAAA=="},"shape":[4],"dtype":"int32","order":"little"}]]}}},"view":{"type":"object","name":"CDSView","id":"p1072","attributes":{"filter":{"type":"object","name":"AllIndices","id":"p1073"}}},"glyph":{"type":"object","name":"Scatter","id":"p1070","attributes":{"size":{"type":"value","value":5},"fill_color":{"type":"value","value":"black"}}}}}],"toolbar":{"type":"object","name":"Toolbar","id":"p1041","attributes":{"tools":[{"id":"p1054"},{"id":"p1055"},{"id":"p1056"},{"type":"object","name":"SaveTool","id":"p1058"},{"id":"p1059"},{"id":"p1060"}]}},"toolbar_location":null,"left":[{"type":"object","name":"LinearAxis","id":"p1049","attributes":{"ticker":{"type":"object","name":"BasicTicker","id":"p1050","attributes":{"mantissas":[1,2,5]}},"formatter":{"type":"object","name":"BasicTickFormatter","id":"p1051"},"axis_label":"y","major_label_policy":{"type":"object","name":"AllLabels","id":"p1052"}}}],"below":[{"type":"object","name":"LinearAxis","id":"p1044","attributes":{"ticker":{"type":"object","name":"BasicTicker","id":"p1045","attributes":{"mantissas":[1,2,5]}},"formatter":{"type":"object","name":"BasicTickFormatter","id":"p1046"},"axis_label":"x","major_label_policy":{"type":"object","name":"AllLabels","id":"p1047"}}}],"center":[{"type":"object","name":"Grid","id":"p1048","attributes":{"axis":{"id":"p1044"}}},{"type":"object","name":"Grid","id":"p1053","attributes":{"dimension":1,"axis":{"id":"p1049"}}}]}},0,0]]}}]}}
</script>
<script type="text/javascript">
(function() {
const fn = function() {
Bokeh.safely(function() {
(function(root) {
function embed_document(root) {
const docs_json = document.getElementById('p1076').textContent;
const render_items = [{"docid":"21276715-a5ae-4bcf-b18f-09fa6758ce03","roots":{"p1063":"e0448a2b-9e27-4fb9-a01d-57a21641536b"},"root_ids":["p1063"]}];
root.Bokeh.embed.embed_items(docs_json, render_items);
}
if (root.Bokeh !== undefined) {
embed_document(root);
} else {
let attempts = 0;
const timer = setInterval(function(root) {
if (root.Bokeh !== undefined) {
clearInterval(timer);
embed_document(root);
} else {
attempts++;
if (attempts > 100) {
clearInterval(timer);
console.log("Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing");
}
}
}, 10, root)
}
})(window);
});
};
if (document.readyState != "loading") fn();
else document.addEventListener("DOMContentLoaded", fn);
})();
</script>
</body>
</html>[*] EDITED TO ADD this is version 4.0.6 of jupyterlab (although there's a bunch of other related components), in case it's a jupyter permissions issue [but I don't think it is, at least not completely] |
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Plotting and displaying in my browser (chrome on macOS 13) with the Bokeh back end works. Accessing help on the plot object shows a possible discrepancy:
Note that the help example has the marker is set to a space (ascii char 0x20). However, using that marker setting results in the following error message (plot displays):
Setting the marker to the empty string generates a plot without markers and does not generate the warning. |
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Where is the temp file cleanup handled? Deleting the objects doesn't appear to clean up the tmp files and after exiting out of the python and closing the bokeh plot tabs, I can still view the plot image by accessing the /tmp/*.html file. |
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I don't actually know where clean-up is handled - I consider that out of scope for Sherpa. Sherpa does not specify where to put any file (or to have any file at all), that's in the bokeh layer. https://docs.bokeh.org/en/latest/docs/first_steps/first_steps_7.html In that case, it'll keep overwriting that one specific file name for every new plot you make. |
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@DougBurke Can you try a plain bokeh plot (no sherpa involved) and see if that works. If not, then we can fairly confidently say that it's jupyterlab. From: https://docs.bokeh.org/en/latest/docs/first_steps/first_steps_1.html (see there for more details). It might also be specific to jupyerlab, as opposed to the classic Jupyter notebook that I use (though I thought Project Jupyter has merged both projects now that the notebook today is just a specific UI on top of jupyterlab) - you might try https://github.com/bokeh/jupyter_bokeh |
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FYI I'm not sure how much time I have today for bokeh. |
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Now that #1382 has been merged can we have this rebased, to make it easier to review? [not that I'm likely to do it today] |
I believe this comes from line 1276 of sherpa/plot/init.py in Class DataPlot. Since both existing backends (bokeh and pylab) take the empty string for no markers, perhaps the space should be omitted. |
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I'm re-running the jobs because the error was a bizarre conda issue unrelated to this code. |
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I'm activating most of the tests for bokeh, but because of #1902 at least three of them fail (and since we parameterize, the actual number of failures is larger). |
hamogu
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In reference to #1899 (comment) - it's probably because I'm using ubuntu, and hence firefox via a snap (so would be similar possibilities about flatpak version) which probably can't see /tmp/ ... This is what clued me in to the problem, https://askubuntu.com/questions/1389798/how-to-correctly-configure-snapd-firefox-to-open-local-html-file-generated-by but it's not realy helped me with a solution. This is much older, and so may be wrong now, but it's basically saying I have to bind mount the /tmp directory which is just insane (I can understand the snap restriction, and that this problem is not bokeh or snap's "fault", but it is a UX fail... Now I just need to know what I can point and then and the bokeh-only code created a plot. |
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So is the idea that we get #1906 merged, so this can then be merged into this (or rebased,or whatever) and everything will be copaceptic ;-) |
This is a fully working implementation, that could be merged as is. However, there are a few UI improvements that might be worthwile, e.g. there is no color cycline and the bokeh.plot.show could do with a nice wrapper in sherpa. fixes sherpa#499
Note that some tests that produce images fail due to sherpa#1902.
DougBurke
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the
note:needs SDS testing
hamogu
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Also includes some unrelated typos
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Removing that spare print line will also restart the tests... |
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Again the test failure is not related to this code (*).
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Note that the test that fails here is "Pip CI/Linux Build (w/o XSPEC, Python 3.11) (https://github.com/sherpa/sherpa/actions/runs/6341413247/job/17224999177?pr=1899). That's the only one that I've added bokeh, to (I think) because I did not want to drive up our testing times for something that's still a little experimental. Also, bokeh is pretty independent of Sherpa, in the sense that we don't build C code are binaries that have anything to do with bokeh. So, it seemed like a reasonable compromise for the time being. I have a solution to that failure in hamogu#6, where "Pip CI/Linux Build (w/o XSPEC, Python 3.11)" passes: https://github.com/hamogu/sherpa/actions/runs/6385025927/job/17328888999?pr=6 I will move that code into this PR in the next few minutes, but we will now get a different failure in some other build that has noting to do with this PR, but that @DougBurke reported this morning and that probably has something to do with some dependency being upgraded on conda-forge. (We might have to find with one and pin it for the time being). |
This is a fully working implementation, that could be merged as is.
However, there are a few UI improvements that might be worthwile, e.g. there is no color cycline and the bokeh.plot.show could do with a nice wrapper in sherpa.