Replace fastprogress progress bars with rich #7233

fonnesbeck · 2024-03-30T13:01:24Z

Description

This PR aims to improve the robustness of PyMC's progress bars by implementing them with the rich library in place of fastprogress

Checklist

Checked that the pre-commit linting/style checks pass
Included tests that prove the fix is effective or that the new feature works
Added necessary documentation (docstrings and/or example notebooks)
If you are a pro: each commit corresponds to a relevant logical change

Type of change

📚 Documentation preview 📚: https://pymc--7233.org.readthedocs.build/en/7233/

fonnesbeck · 2024-03-30T13:21:30Z

Still some testing to do, but they appear to play nicely with Jupyter.

fonnesbeck · 2024-04-01T16:20:37Z

I'm sure someone like @zaxtax could be fancier with the progress bar styling. Feel free to embellish!

fonnesbeck · 2024-04-01T16:48:08Z

Also, making the progress bars work involved changing how parallel processing works in SMC sampling. Please have a close look.

codecov · 2024-04-01T16:51:36Z

Codecov Report

Attention: Patch coverage is 93.56436% with 13 lines in your changes are missing coverage. Please review.

Project coverage is 92.29%. Comparing base (4f6831e) to head (3f107e9).
Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #7233      +/-   ##
==========================================
- Coverage   92.30%   92.29%   -0.02%     
==========================================
  Files         100      101       +1     
  Lines       16895    16891       -4     
==========================================
- Hits        15595    15589       -6     
- Misses       1300     1302       +2

Files	Coverage Δ
pymc/sampling/mcmc.py	`87.71% <100.00%> (ø)`
pymc/sampling/parallel.py	`88.38% <100.00%> (-0.05%)`	⬇️
pymc/smc/sampling.py	`99.20% <100.00%> (-0.10%)`	⬇️
pymc/stats/log_density.py	`98.33% <100.00%> (+0.02%)`	⬆️
pymc/util.py	`81.09% <100.00%> (+0.16%)`	⬆️
pymc/sampling/forward.py	`95.94% <94.11%> (+0.03%)`	⬆️
pymc/sampling/population.py	`73.88% <94.73%> (+0.02%)`	⬆️
pymc/tuning/starting.py	`91.30% <77.27%> (-0.44%)`	⬇️
pymc/variational/inference.py	`87.93% <91.42%> (+1.93%)`	⬆️

... and 7 files with indirect coverage changes

ColCarroll · 2024-04-01T18:29:30Z

Can we haz screenshot plz?

fonnesbeck · 2024-04-01T23:09:31Z

pm.sample is quite simple:

fonnesbeck · 2024-04-01T23:11:49Z

pm.fit is similar:

fonnesbeck · 2024-04-01T23:15:35Z

For SMC, since the number of iterations is not fixed I use a spinner for each chain:

zaxtax · 2024-04-01T23:18:34Z

I love so much of this! Looking forward to reviewing

…

On Tue, 2 Apr 2024, 01:16 Chris Fonnesbeck, ***@***.***> wrote: For SMC, since the number of iterations is not fixed I use a spinner for each chain: image.png (view on web) <https://github.com/pymc-devs/pymc/assets/81476/8a7e49fa-5784-4bcb-b624-475df12d4a9a> — Reply to this email directly, view it on GitHub <#7233 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAACCUOSNG7AR2VGWAIJAPDY3HTCZAVCNFSM6AAAAABFPRMAVKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZQG43TCMBWGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

zaxtax · 2024-04-01T23:35:15Z

Would having a way for people to theme their progress bars be in scope? If so I can offer some suggestions.

…

On Tue, 2 Apr 2024, 01:18 Rob Zinkov, ***@***.***> wrote: I love so much of this! Looking forward to reviewing On Tue, 2 Apr 2024, 01:16 Chris Fonnesbeck, ***@***.***> wrote: > For SMC, since the number of iterations is not fixed I use a spinner for > each chain: > > image.png (view on web) > <https://github.com/pymc-devs/pymc/assets/81476/8a7e49fa-5784-4bcb-b624-475df12d4a9a> > > — > Reply to this email directly, view it on GitHub > <#7233 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAACCUOSNG7AR2VGWAIJAPDY3HTCZAVCNFSM6AAAAABFPRMAVKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZQG43TCMBWGA> > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> >

fonnesbeck · 2024-04-01T23:50:15Z

Yes! Feel free to point me toward relevant examples/resources.

zaxtax · 2024-04-02T07:36:10Z

Yes! Feel free to point me toward relevant examples/resources.

So there are two ways to style. For simple stuff, you can just pass in a styles to track:

import time
from rich.progress import track

for i in track(range(20), description="Processing...", complete_style="rgb(83,145,210)"):
    time.sleep(1)

But for theming it's probably easiest to take a theme or console object and pass it to Progress

from rich.theme import Theme
custom_theme = Theme({
    "bar.complete": "rgb(83,145,210)",
})

from rich.progress import Progress
from rich.console import Console
import time

with Progress(console=Console(theme=custom_theme)) as progress:
    task1 = progress.add_task("[red]Downloading...", total=100)
    task2 = progress.add_task("[green]Processing...", total=100)
    task3 = progress.add_task("[cyan]Cooking...", total=100)

    while not progress.finished:
        progress.update(task1, advance=0.5)
        progress.update(task2, advance=0.3)
        progress.update(task3, advance=0.9)
        time.sleep(0.02)

The style page (https://rich.readthedocs.io/en/latest/style.html) is the best resource for styling.

zaxtax · 2024-04-02T07:38:46Z

Stylistically, I associate red with error. I prefer blue to indicate normal operation, green for completion, and red for some error state.

fonnesbeck · 2024-04-02T14:44:22Z

Running:

fonnesbeck · 2024-04-02T14:44:31Z

Complete:

fonnesbeck · 2024-04-02T18:29:00Z

Can now pass custom progressbar themes to samplers!

zaxtax

I don't feel confident in reviewing the sampling.parallel code, but otherwise looks good!

pymc/stats/log_density.py

pymc/sampling/parallel.py

pymc/sampling/forward.py

ricardoV94 · 2024-04-03T13:11:41Z

PR looks good to me. Was there any open / known issue with the old library?

zaxtax · 2024-04-03T14:22:22Z

Bad at displaying more than one progress bar AnswerDotAI/fastprogress#39

…

On Wed, 3 Apr 2024, 15:12 Ricardo Vieira, ***@***.***> wrote: PR looks good to me. Was there any open / known issue with the old library? — Reply to this email directly, view it on GitHub <#7233 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAACCUO3EHEQE56EALF7Y6LY3P52JAVCNFSM6AAAAABFPRMAVKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZUGU3DSMRRGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

fonnesbeck · 2024-04-03T15:39:13Z

These should be more robust progress bars by virtue of being rich text-based. Also the rich project itself appears to be much better-maintained right now.

ricardoV94 · 2024-04-03T16:04:11Z

mypy is not happy

Armavica · 2024-04-03T16:48:01Z

It looks great on terminal too!

fonnesbeck · 2024-04-03T16:55:54Z

mypy seems to be complaining about things that have nothing to do with this PR

Armavica · 2024-04-03T16:58:53Z

mypy seems to be complaining about things that have nothing to do with this PR

It looks like mcmc.py is the file that causes the error with

pymc/sampling/mcmc.py:1195: error: Argument "progressbar_theme" to "ParallelSampler" has incompatible type "Optional[Theme]"; expected "Theme"

juanitorduz · 2024-04-04T12:41:05Z

I just say this is a fantastic addition 🙌 ! Thanks!

jucor · 2024-07-06T21:11:58Z

Adding my thanks here!! 👏 👏 👏 🙌

fonnesbeck · 2024-07-06T21:53:16Z

Thanks! I'm sure they can be improved, so feel free to suggest additional changes.

jucor · 2024-07-06T22:27:10Z

I've spotted a bug with the progressbar when PyMC is called from R via Reticulate, and have opened a bug report at both Reticulate and Rich. Mentioned them below in case you want to follow what resolution there might be:

Thanks for the extra option progressbar=False that you have in PyMC, which allows to override, but those progress bars are so useful due to long computations, that I really still need them :)

jucor · 2024-07-08T15:57:08Z

I have found the root cause for this problem with progress bars! Rstudio Console does not support cursor motion ANSI control sequences. I have opened a feature request upstream in rstudio/rstudio#14942 , as well as an associated bug report rstudio/rstudio#14941 .

Meanwhile, is there a way to have some basic SMC progress bars working without cursor motion control sequences, even if in a much simpler capacity? Basically just printing out the current version of Beta and a timestamp?

fonnesbeck added 2 commits March 30, 2024 07:57

Replace fastprogress with rich

d3df08f

Bugfixes for ADVI progress bars

0a7b02c

fonnesbeck added 3 commits March 30, 2024 08:37

Bugfixes for MAP progress bars

7634baa

Fixed final update to progress bar

9d1702d

SMC progress bar working

32c9c11

fonnesbeck marked this pull request as ready for review April 1, 2024 16:18

fonnesbeck requested review from zaxtax and ricardoV94 April 1, 2024 16:19

Fixes to MAP progress bar

58c2b17

fonnesbeck added 2 commits April 2, 2024 09:52

Customize progress bar theme

41603c3

Added progressbar_theme argument

c4e8fca

zaxtax approved these changes Apr 2, 2024

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pymc/stats/log_density.py Outdated Show resolved Hide resolved

ricardoV94 reviewed Apr 3, 2024

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pymc/sampling/parallel.py Outdated Show resolved Hide resolved

ricardoV94 reviewed Apr 3, 2024

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pymc/sampling/forward.py Outdated Show resolved Hide resolved

fonnesbeck added 2 commits April 3, 2024 07:55

Moved default progressbar theme to util

eefa29d

Convert compute_log_density to use Progress instead of track

3f107e9

fonnesbeck requested a review from ricardoV94 April 3, 2024 13:08

Getting rid of mypy complaint

f490b79

fonnesbeck merged commit 22e8f0b into pymc-devs:main Apr 3, 2024

fonnesbeck deleted the rich_progress branch April 3, 2024 18:15

jucor mentioned this pull request Jul 6, 2024

Reticulate does not play nice with Rich progressbars rstudio/reticulate#1632

Open

jucor mentioned this pull request Jul 8, 2024

Support cursor motion ANSI control sequences in Console rstudio/rstudio#14942

Closed

jucor mentioned this pull request Jul 10, 2024

Log SMC progress via Python logger when progress bar deactivated #7410

Open

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Replace fastprogress progress bars with rich #7233

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