Remove commented-out function definitions and delete files with no executable code #452

rileyjmurray · 2024-06-07T12:16:29Z

This PR aims to resolve #428.

At time of opening this PR, the changes might be over-zealous, so I'm happy to roll some changes back. That said, I suggest we be aggressive in removing this kind of unused text. Here's a proposal for how to decide what to actually keep and what to remove:

We can/should keep simple reference implementations of functions that are important but very complicated.
- Example: there's an implementation of Levenberg-Marquardt from Wikipedia that I've kept. I think this is valuable because our actual LM code is very complicated, so having a reference is helpful for maintainability.
We could keep text that's related to memory profiling.
- Rationale: The question of whether or not to bother trying to profile memory usage in a certain location requires a fair amount of expertise, so I think keeping this kind of text could serve as a flag for suspected hot code paths.
Commented-out pyx code should be removed unless we have a very good reason for keeping it.

Another source of criteria for figuring out what to keep is to look for a short note at the beginning of some commented-out code block. Often there are notes that say "FUTURE," "Removed," "unused," "REMOVE," "Debugging," etc...

Other, miscellaneous changes

Removed some unused imports.

…itions. Likely over-zealous.

These changes address unexpected behavior that can occur when manually adding an operation without then manually rebuilding the parameter vector. When this happens it is possible for the Model's internal attributes to fall out of sync with those of it's child objects. Now we check for the need to rebuild the parameter vector every time.

This is relevant when attempting to use Dask outside of pyGSTi, where signals cannot be set in the workers. Setting the PYGSTI_NO_CUSTOMLM_SIGINT env variable now skips this behavior.

A bug in the parameter label handling code was causing parameter labels to explode exponentially in size when _rebuild_paramvec was caused, leading to major memory issues. This now makes it so that the value of _paramlbls is fixed to that of the underlying operations and adds a new version of the parameter_labels property that goes through the interposer (making the interposer labels something generated on demand). Also add a threshold for coefficients printing in the LinearInterposer to avoid obnoxious labels.

The creation of COPA layouts relies on a number of specialized circuit structures which require non-trivial time to construct. In the context of iterative GST estimation with nested circuit lists (i.e. the default) this results in unnecessarily repeat construction of these objects. This is an initial implementation of a caching scheme allowing for more efficient re-use of these circuit structures across iterations.

Cache the expanded SPAM-free circuits to reduce recomputing things unnecessarily.

Adds a new method to OpModel that allows for doing instrument expansion and povm expansion in bulk, speeding things up be avoiding recomputation of shared quantities. Also adds a pipeline for re-using completed or split circuits (as produced by the related OpModel methods) for more efficient re-use of done work.

Some minor performance oriented tweaks to the init for COPA layouts.

Refactor some of the ordered dictionaries in matrix layout creation into regular ones.

Start adding infrastructure for caching things used in MDC store creation and for plumbing in stuff from layout creation.

Performance optimization for the method for adding omitted frequencies to incorporate caching of the number of outcomes per circuit (which is somewhat expensive since it goes through the instrument/povm expansion code). Additionally refactor some other parts of this code for improved efficiency. Also makes a few minor tweaks to the method for adding counts to speed that up as well. Can probably make this a bit faster still by merging the two calls to reduce redundancy, but that is a future us problem. Additionally make a few microoptimizations to the dataset code for grabbing counts, and to slicetools adding a function for directly giving a numpy array for a slice (instead of needing to cast from a list). Miscellaneous cleanup of old commented out code that doesn't appear needed any longer.

Fix a bug I introduced in dataset indexing into something that could be None.

Another minor bug caught by testing.

Improve the performance of __getitem__ when indexing into static circuits by making use of the _copy_init code path.

Implement caching of circuit structures tailored to the map forward simulator's requirements.

This finishes the process of refactoring expand_instruments_and_separate_povm from a circuit method to a method of OpModel.

Refactor expand_instruments_and_separate_povm to use the multi-circuit version under the hood to reduce code duplication.

rileyjmurray · 2024-09-30T15:19:24Z

Hi @pcwysoc, @kmrudin, @kevincyoung, @adhumu, and @sserita. This pull request is a big spring-cleaning for commented-out code. You're all designated as code-owners for files that are affected by this pull request. Please review the changes for files you "own" and let me know if you object to removing specific blocks of commented-out code.

Things to keep in mind:

TODOs can be moved to GitHub issues. You can paste code in the GitHub issue as a starting point, for later reference.

You can replace massive comment-out code blocks with a short comment, like the following

# NOTE: The FancyClass is admittedly very complicated. We used to have an equivalent SimpleClass, but
# for maintainability reasons we removed it. The old SimpleClass can be found at
# https://github.com/sandialabs/pyGSTi/blob/d27e4e688a64914a0b7aaec1de91aa56f7ce70c2/pygsti/drivers/longsequence.py#L153

-- I've used a dummy link for reference.

If you really want to keep a commented-out code block, please at least add your name and date so it's obvious who made the call to keep it and when. (There's semi-automated tools for this, but they aren't as reliable as old-fashioned comments.)
Use triple-ticks or triple-quotes for gigantic comments, rather than hundreds of lines that start with the single-line comment character #. Using the former styles makes it possible to collapse irrelevant text in most code editors.

pcwysoc

I have no objection to the removed comments on the files for which I'm a code owner. Someone may wish to put the code for the old RB plot somewhere however if it still has utility. I defer to @jordanh6 or @tjproct on this.

adhumu

Ditto what Piper said. Stefan and I were working on changing parts of ForwardSims in a different branch and on my local computer. This part of the code is still in development. I'm happy to approve these changes, thanks Riley!

pygsti/algorithms/germselection.py

pygsti/baseobjs/errorgenbasis.py

pygsti/baseobjs/polynomial.py

pygsti/evotypes/densitymx/opreps.pyx

pygsti/modelmembers/povms/denseeffect.py

pygsti/models/model.py

pygsti/tools/fogitools.py

test/unit/objects/test_prefixtable.py

coreyostrove · 2024-10-23T22:39:05Z

Whoops, forgot to add the top-level comment for my review.

TLDR: Good work @rileyjmurray. It will be a while till most of us can vie for the crown of most lines written, but at this pace you’re definitely in the running for most lines of pyGSTi deleted! I’ll defer judgement to other code owners for stuff they manage (i.e. a lack of comment may just mean I am waiting for one of them to decide whether to chime in rather than explicit approval), but have added a few comments regarding code I would like to keep, as well as a few minor suggestion for additional deletion related clean-up.

pygsti/extras/interpygate/process_tomography.py

sserita

2/3 of the way check-in

pygsti/algorithms/mirroring.py

pygsti/algorithms/randomcircuit.py

pygsti/algorithms/rbfit.py

pygsti/baseobjs/polynomial.py

sserita · 2024-11-12T17:19:05Z

pygsti/evotypes/chp/statereps.py

-#            + self.op_rep.chp_ops(seed_or_state=seed_or_state)
-
-# TODO: Untested, only support computational and composed for now
-#class StateRepTensorProduct(StateRep):


For Stefan to check out

@sserita did you look into this? If not, could you open a GitHub issue articulating the question that needs investigation?

It is fine to remove this without further action. I have a personal vested interest in the CHP code so wanted to look into it a bit further, but there's no specific actionable issues to articulate based on the code you are removing here.

pygsti/modelmembers/povms/denseeffect.py

pygsti/modelmembers/povms/marginalizedpovm.py

pygsti/modelmembers/term.py

pygsti/modelpacks/stdtarget.py

pygsti/models/memberdict.py

tjproct · 2024-11-12T18:05:55Z

I’m guessing I’m meant to be doing something? My main reaction to this pull request is/was “argh I’m pretty sure some of that commented out code should be revived, but I have no time to even think about this”. That’s probably very unhelpful, but that’s how it is right now. -T From: Stefan Seritan ***@***.***> Date: Tuesday, November 12, 2024 at 11:53 AM To: sandialabs/pyGSTi ***@***.***> Cc: Proctor, Timothy James ***@***.***>, Mention ***@***.***> Subject: [EXTERNAL] Re: [sandialabs/pyGSTi] Remove commented-out function definitions and delete files with no executable code (PR #452) <<< Insert lots of content here >>> — Reply to this email directly, view it on GitHub<#452 (review)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AFQEBIBJDOEXVBODCBD527L2AI5VXAVCNFSM6AAAAABI6RXALOVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDIMZQGIZDSOBYGI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

rileyjmurray · 2024-11-12T22:19:15Z

Nah, you're good, Tim. No action items for you!

sserita

The majority of my comments are just personal notes for things we should highlight/bookmark in the PR in case we want to come back and revive them later.
Some of my comments are things I would like to be left in, and at least one is an item I need to dig further into to decide.

Thanks for your hard work in help clean up the code, it is super appreciated!

pygsti/optimize/optimize.py

pygsti/protocols/vb.py

pygsti/report/workspaceplots.py

pygsti/tools/rbtheory.py

test/unit/objects/test_prefixtable.py

…e old commented-out SLOWPolynomial class and move it into test/objects/test_polynomial.py

rileyjmurray · 2024-12-10T19:08:28Z

I've made some changes based on comments above. Some questions remain. The ball is now simultaneously in Corey's and Stefan's courts.

…Tio/pyGSTi into remove-unused-function-defs

coreyostrove

Approved! Thanks for managing this slog!

sserita

I looked through all the unresolved conversations that needed my input. None of them have actions required on this PR, so I'm approving. Thanks for your hard work on this Riley.

As we complete/merge this in, I'll probably go through and put together a list of things that we removed that we might want to revisit in the future (either to fill out the feature or to turn it into tests). I'll include that as a comment on the finalized PR, and probably also summarize it in the 0.9.13 release notes.

pygsti/models/memberdict.py

sserita · 2025-01-13T20:53:34Z

pygsti/forwardsims/termforwardsim.py

@@ -416,105 +406,6 @@ def _bulk_fill_hprobs_atom(self, array_to_fill, dest_param_slice1, dest_param_sl
                hpolys[0], hpolys[1], self.model.to_vector(), (nEls, len(wrtInds1), len(wrtInds2)))
        _fas(array_to_fill, [slice(0, array_to_fill.shape[0]), dest_param_slice1, dest_param_slice2], hprobs)

-    #DIRECT FNS - keep these around, but they need to be updated (as do routines in fastreplib.pyx)


What I mean is that we update the code so that it works with modern pyGSTi, and then turn it into a unit test. No action item on this PR, I'll make a note of this in the summary of what is removed here.

sserita · 2025-01-13T20:54:05Z

pygsti/forwardsims/termforwardsim_calc_statevec.pyx

@@ -1531,654 +1531,3 @@ def circuit_achieved_and_max_sopm(fwdsim, rholabel, elabels, circuit, repcache,
        max_sopm[i] = max_sum_of_pathmags[i]

    return achieved_sopm, max_sopm
-
-


Yes you can keep this course of action.

sserita · 2025-01-13T20:54:37Z

pygsti/extras/interpygate/core.py

@@ -241,15 +241,6 @@ def create_object(self, args=None, sslbls=None):
        return InterpolatedDenseOp(target_op, self.base_interpolator, self.aux_interpolator, self.to_vector(),
                                   _np.array(args), self._argument_indices)

-    #def write(self, dirname):


You can keep this removed.

sserita · 2025-01-13T20:56:32Z

pygsti/evotypes/densitymx_slow/effectreps.py

@@ -105,11 +105,6 @@ def __init__(self, povm_factors, effect_labels, state_space):
        super(EffectRepTensorProduct, self).__init__(state_space)
        self.factor_effects_have_changed()

-    #TODO: fix this:
-    #def __reduce__(self):


I think this is being tracked by #505 now, and I've added a test that will catch those bug failures once we fix it. All that to say, I don't think there is any more action items left for this on this particular PR.

sserita · 2025-01-13T21:02:45Z

pygsti/evotypes/chp/statereps.py

-#            + self.op_rep.chp_ops(seed_or_state=seed_or_state)
-
-# TODO: Untested, only support computational and composed for now
-#class StateRepTensorProduct(StateRep):


It is fine to remove this without further action. I have a personal vested interest in the CHP code so wanted to look into it a bit further, but there's no specific actionable issues to articulate based on the code you are removing here.

rileyjmurray mentioned this pull request Jun 7, 2024

legacyio.py contains no executable code. #424

Closed

rileyjmurray marked this pull request as ready for review September 24, 2024 18:11

rileyjmurray requested review from a team, pcwysoc, kmrudin, kevincyoung and adhumu as code owners September 24, 2024 18:11

rileyjmurray requested a review from sserita September 24, 2024 18:11

rileyjmurray and others added 20 commits September 30, 2024 10:37

initial attempt at removing out unneeded commented-out function defin…

10ba164

…itions. Likely over-zealous.

Allow SIGINT set to be skipped via env variable.

0a1b0ca

This is relevant when attempting to use Dask outside of pyGSTi, where signals cannot be set in the workers. Setting the PYGSTI_NO_CUSTOMLM_SIGINT env variable now skips this behavior.

Logic bugfix

dd7bfe2

Add caching for spam-free circuit expansion

6383cc3

Cache the expanded SPAM-free circuits to reduce recomputing things unnecessarily.

Minor COPA Layout __init__ tweaks

9d57884

Some minor performance oriented tweaks to the init for COPA layouts.

Refactor some OrderedDicts into regular ones

aa9519d

Refactor some of the ordered dictionaries in matrix layout creation into regular ones.

Start the process of adding caching to MDC store creation

957facd

Start adding infrastructure for caching things used in MDC store creation and for plumbing in stuff from layout creation.

Fix dataset bug

8d5cfc7

Fix a bug I introduced in dataset indexing into something that could be None.

Another minor bugfix caught by testing

cd653b3

Another minor bug caught by testing.

Another minor bugfix caught by testing

fd1e8d1

Faster implementation of __getitem__

1ee6112

Improve the performance of __getitem__ when indexing into static circuits by making use of the _copy_init code path.

Implement caching for map layout creation

1c83f9b

Implement caching of circuit structures tailored to the map forward simulator's requirements.

Fix bugs in new extract_labels implementation

7a38689

Finish refactoring expand_instruments_and_separate_povm

070c2f4

This finishes the process of refactoring expand_instruments_and_separate_povm from a circuit method to a method of OpModel.

Refactor expand_instruments_and_separate_povm

8f80e31

Refactor expand_instruments_and_separate_povm to use the multi-circuit version under the hood to reduce code duplication.

found lots of other commented-out function definitions

024d553

pcwysoc approved these changes Sep 30, 2024

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adhumu approved these changes Oct 2, 2024

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coreyostrove requested changes Oct 23, 2024

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add back commented-out function per request from Corey

5aa5cb7

rileyjmurray commented Oct 24, 2024

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pygsti/extras/interpygate/process_tomography.py Outdated Show resolved Hide resolved

rileyjmurray added 2 commits October 24, 2024 09:25

revert out-of-scope and unnecessary change

344670d

restore fogitools to state on develop

00982b2

sserita reviewed Nov 12, 2024

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rileyjmurray mentioned this pull request Nov 19, 2024

test coverage for slow evotype classes #505

Open

sserita requested changes Nov 21, 2024

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pygsti/optimize/optimize.py Show resolved Hide resolved

pygsti/protocols/vb.py Show resolved Hide resolved

pygsti/report/workspaceplots.py Show resolved Hide resolved

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test/unit/objects/test_prefixtable.py Outdated Show resolved Hide resolved

rename FASTPolynomial to Polynomial, create FASTPolynomial alias, tak…

0585fd6

…e old commented-out SLOWPolynomial class and move it into test/objects/test_polynomial.py

rileyjmurray added 3 commits December 10, 2024 11:09

restore some content I had removed, per comments on the GitHub PR.

04581ae

restore commented-out class definition in opreps.pyx

c9db90d

move comment

57ebdee

rileyjmurray mentioned this pull request Dec 10, 2024

Missing implementation for the density_mx evotype's "identity plus error gen" OpRep #513

Open

rileyjmurray and others added 4 commits December 12, 2024 15:29

obliterate extras/rb per Tim's comment: #452 (comment)

375ddef

Merge branch 'develop' into remove-unused-function-defs

8e5bde8

account for removed extras/rb.py

c19a9f4

Merge branch 'remove-unused-function-defs' of https://github.com/pyGS…

bf50f6e

…Tio/pyGSTi into remove-unused-function-defs

coreyostrove approved these changes Jan 7, 2025

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sserita approved these changes Jan 13, 2025

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sserita merged commit 6905edf into develop Jan 13, 2025
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sserita deleted the remove-unused-function-defs branch January 13, 2025 21:08

sserita added this to the 0.9.13 milestone Jan 13, 2025

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Remove commented-out function definitions and delete files with no executable code #452

Remove commented-out function definitions and delete files with no executable code #452

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		@@ -1531,654 +1531,3 @@ def circuit_achieved_and_max_sopm(fwdsim, rholabel, elabels, circuit, repcache,
		max_sopm[i] = max_sum_of_pathmags[i]

		return achieved_sopm, max_sopm

Remove commented-out function definitions and delete files with no executable code #452

Remove commented-out function definitions and delete files with no executable code #452

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