ENH: Added CLI command to update skops files #343

EdAbati · 2023-04-10T18:03:19Z

Reference Issues/PRs

Closes #333

What does this implement/fix? Explain your changes.

Taking inspiration from the implementation from skops convert, this adds the update command to the CLI.
It allows to update a skops file by simply 'loading' it and 'dumping' it again.

I have also added MacOS files in the gitignore.

BenjaminBossan

Thanks a lot for working on this.

Before going further, we need a few more things: tests and documentation (see docs/persistence.rst).

IMO it would also be nice to have a feature to check the protocol of the loaded file and if it's the same as the current protocol, to skip the conversion. If it's too complicated, we can also leave this open for a future PR, though.

EdAbati · 2023-04-19T16:04:01Z

Hi @BenjaminBossan

I finally moved this PR from "Draft" to "ready for review". 🙂

You can see that, for now, I have not implemented any extra checks that we discussed here and in the issue. I wanted to make sure I’m on the right track before adding anything else.

The interfaces of the functions are now slightly different from the ones in _convert. I am passing a logger argument to make testing easier.

BenjaminBossan · 2023-04-20T10:15:23Z

I did a quick pass and it looks good to me overall. @adrinjalali would you be fine with this PR as is, i.e. no extra checks etc.?

adrinjalali · 2023-04-20T13:24:13Z

I'm happy as is, without the checks, but we should figure out the checks separately, we've needed them in a few places now.

BenjaminBossan

Thanks a lot, this is a very clean implementation, well done.

There are only a few minor code comments from my side, please take a look.

Regarding the more general points, I have two suggestions (not must haves):

How about making it possible to call the command without -o to just overwrite the existing file? I.e. skops update my_model.skops would write the new, updated skops file to my_model.skops.
There is no test for the actual work that is being done. So e.g. if the _update_file function would just create a copy, the tests would still pass fine. I know that creating a file in an old skops format to test the updating feature is not trivial. Maybe you could come up with something clever? Say, create the skops file, manually set the protocol to an older version, then checking after the update that the protocol is the current version now. WDYT?

skops/cli/_update.py

skops/cli/tests/test_entrypoint.py

Co-authored-by: Benjamin Bossan <BenjaminBossan@users.noreply.github.com>

EdAbati · 2023-04-23T16:03:07Z

Thank you very much for your review!

How about making it possible to call the command without -o' to just overwrite the existing file? I.e. skops update my_model.skopswould write the new, updated skops file tomy_model.skops`.

I actually did that initially, but then I thought that if we did that by default, it could be a negative surprise for certain users that want to keep the original file. Another idea was to attach a prefix or a suffix to the file name provided as input if no output-file is provided. For example: my-model.skops could be updated by default to my-model-updated.skops. In the end, this is a design decision; I'm happy to do what you think is best :)

There is no test for the actual work that is being done. So e.g. if the _update_file function would just create a copy, the tests would still pass fine. I know that creating a file in an old skops format to test the updating feature is not trivial. Maybe you could come up with something clever? Say, create the skops file, manually set the protocol to an older version, then checking after the update that the protocol is the current version now. WDYT?

You are right! I added the protocol check inside the update function so that we can also test it :) Let me know if it's what you had in mind

BenjaminBossan

Thanks for implementing the feedback. Clever way of patching the protocol.

I think there is a bug with one of the log messages, please take a look at my comment. Otherwise, I just left some comments on how to potentially tighten the tests.

I actually did that initially, but then I thought that if we did that by default, it could be a negative surprise for certain users that want to keep the original file. Another idea was to attach a prefix or a suffix to the file name provided as input if no output-file is provided. For example: my-model.skops could be updated by default to my-model-updated.skops. In the end, this is a design decision; I'm happy to do what you think is best :)

Good points. My intuition for being okay with allowing to overwrite the existing file is that other terminal commands also allow to just overwrite existing files without warning (say, mv). Adding a prefix/suffix would be a way to prevent accidents but has its own complications (what if my-model-updated.skops already exists?). @adrinjalali wanna break the tie?

skops/cli/_update.py

skops/cli/tests/test_update.py

adrinjalali · 2023-04-24T16:01:18Z

re: overwriting the existing file

I think kinda what black does would be my ideal:

only print info about the diffs by default, no change in any file, no new files created

-i would change file in place

-o creates a new file

WDYT?

BenjaminBossan · 2023-04-25T09:40:05Z

only print info about the diffs by default, no change in any file, no new files created

Hmm, how exactly would that diff look like for a skops file?

-i would change file in place

-o creates a new file

I can get behind the idea to allow inplace but requiring an extra argument. Not sure about -i, as it is often used to mark the input (especially when -o is used for the output). If there is some precedence for a given argument name, we should probably use that. Maybe -f or --force to force overwriting but IMO it doesn't quite fit here. cp has -n (no clobber) to prevent overwriting an existing file, making overwriting the default, but I don't like that too much. If nothing else comes up, we could require the full --inplace.

adrinjalali · 2023-04-25T12:34:11Z

Hmm, how exactly would that diff look like for a skops file?

we can start by reporting if there'd be any change at all or not, we can improve the diff maybe later if needed. It could be something like the diff of the json schema, and reporting any other saved file (like numpy files) if they're changed.

I can get behind the idea to allow inplace but requiring an extra argument. Not sure about -i, as it is often used to mark the input (especially when -o is used for the output). If there is some precedence for a given argument name, we should probably use that. Maybe -f or --force to force overwriting but IMO it doesn't quite fit here. cp has -n (no clobber) to prevent overwriting an existing file, making overwriting the default, but I don't like that too much. If nothing else comes up, we could require the full --inplace.

Input is usually just an argument, w/o a parameter. grep uses -i for case insensitive for instance. But I don't really mind, I'm also happy with --inplace.

BenjaminBossan

Thanks for the fixes. I missed the test for the error, my bad. There is a merge conflict, apart from that, the PR is ready to be merged.

adrinjalali · 2023-05-23T16:17:44Z

I'm gonna wait for this one before pushing out a release :)

EdAbati · 2023-05-23T20:32:46Z

Hi both so sorry for the delay, I have been very busy lately. 🥲

I checked all the remaining comments and fixed the conflicts. Let me know if anything else should be updated.

BenjaminBossan

This looks good, thanks a lot for all your work. I don't have any blockers for merging, just two comments, please take a look. If the general thought is that they don't require changes, I'm fine with you merging @adrinjalali

BenjaminBossan · 2023-05-24T09:14:43Z

skops/cli/_update.py

+        )
+        return None
+
+    dump(input_model, output_file)


This is an extreme edge case, but I wanted to bring it up: If the user cancels the process during the dumping operation, could they end up with a broken file? Since we write to the zip archive progressively, I think it could happen. Sometimes, I would start a command and see I did a mistake and would cancel it, so it's not impossible.

Now when the user uses inplace, they could even bust their original file, ending up with no working version. It is an extreme edge case for this to happen, not sure if we want to take measures against it. @adrinjalali WDYT?

To prevent this behavior, we could write the output to a temp file and then move it to output_file.

I think is quite major, and you're right. We should simply create a temp file beside the existing file, and then replace the existing file with what's created if conversion is successful.

Hi both :) is this what you had in mind? 3a30721

BenjaminBossan · 2023-05-24T09:20:35Z

skops/cli/_update.py

+    parser_subgroup.add_argument(
+        "--inplace",
+        help="Update and overwrite the input file in place.",
+        action="store_true",


That behavior would be fine. It would also be acceptable IMO to update inplace by default, since it would only be done if the current version is higher, but leaving it like this is also good.

Just one question: Right now, if using the defaults (no change to log level), a user would typically not get feedback at all, right? Do we want the default behavior to be not do anything, nor message anything?

adrinjalali · 2023-06-20T15:32:37Z

skops/cli/_update.py

+    tmp_output_file = f"{output_file}.tmp"
+    logger.debug(f"Writing updated skops file to temporary path: {tmp_output_file}")
+    dump(input_model, tmp_output_file)
+    logger.debug(f"Moving updated skops file to output path: {output_file}")
+    os.replace(tmp_output_file, output_file)
+    logger.info(f"Updated skops file written to {output_file}")


we probably don't need so much debug logging.

This should use a temp file from (https://docs.python.org/3/library/tempfile.html), and in a context manager to protect from random OS failures. Otherwise LGTM.

Changed it now. I used tempfile.TemporaryDirectory because I understood that tempfile.NamedTemporaryFile cannot be moved when opened on Windows ("Whether the name can be used to open the file a second time, while the named temporary file is still open, varies across platforms (it can be so used on Unix; it cannot on Windows).").

Am I overcomplicating this? 🤔

adrinjalali · 2023-06-21T12:49:37Z

The issues on the CI are numpy / persistence related. Merging.

adrinjalali · 2023-06-21T12:51:00Z

@BenjaminBossan somehow here it shows you've requested changes

BenjaminBossan

Thanks for all the changes, this LGTM now.

BenjaminBossan · 2023-06-26T10:10:26Z

@EdAbati Could you please rebase on/merge with main to ensure the tests pass (#373 should have fixed the issues)? It's probably fine now, I just want to be sure.

EdAbati · 2023-06-26T11:08:32Z

Done now! 🤞
Thank you for the feedback and apologies for taking a bit long to update the PR :)

EdAbati · 2023-06-26T11:43:21Z

There is still a small issue with SciPy, that it shouldn't be caused by this PR

EdAbati · 2023-06-26T14:55:40Z

Made a separate PR in an attempt to fix the issues with the test_persist.py #374

adrinjalali · 2023-06-27T13:04:25Z

The failing tests are unrelated to this PR, so I'll merge.

EdAbati added 3 commits April 10, 2023 12:33

added update entrypoint

c0238de

minimal working cli without optionals

c23b4d0

added macos file to gitignore

f0923c1

EdAbati mentioned this pull request Apr 10, 2023

CLI: Command to update a skops file #333

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BenjaminBossan requested changes Apr 11, 2023

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EdAbati added 2 commits April 15, 2023 18:16

added update cli documentation

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added unittests for update entrypoint

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EdAbati marked this pull request as ready for review April 19, 2023 16:03

EdAbati mentioned this pull request Apr 19, 2023

FIX: fixed get_log_level when level = 3 #346

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EdAbati and others added 7 commits April 23, 2023 14:36

adjusted logging message

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Co-authored-by: Benjamin Bossan <BenjaminBossan@users.noreply.github.com>

removed redundant space

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Co-authored-by: Benjamin Bossan <BenjaminBossan@users.noreply.github.com>

adjusted narrow docstring in test

5c382da

added check for protocol number before update

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removed load_schema

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Merge remote-tracking branch 'origin/main' into cli-uupdate-skops-file

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added change description to changelog

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EdAbati added 5 commits April 29, 2023 11:04

updated logging message when file not updated

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testing all logging messages

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updated test_no_update based on feedback

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added inplace arg and only diff as default

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Merge remote-tracking branch 'origin/main' into cli-uupdate-skops-file

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changed name of test

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EdAbati added 5 commits May 23, 2023 21:46

updated docstring with inplace

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refactored _update_file

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added edge case for newer protocol

734ed43

updated the docs to explain when skops updates a file

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Merge remote-tracking branch 'upstream/main' into cli-uupdate-skops-file

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EdAbati added 3 commits May 26, 2023 15:15

changed level of certain log messages

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saving update skops to tmp file before saving to output

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Merge remote-tracking branch 'upstream/main' into cli-uupdate-skops-file

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adrinjalali reviewed Jun 20, 2023

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EdAbati added 2 commits June 20, 2023 22:58

using tempfile to create the temporary updated file

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fixed types

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adrinjalali enabled auto-merge (squash) June 21, 2023 12:50

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BenjaminBossan approved these changes Jun 26, 2023

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Merge remote-tracking branch 'upstream/main' into cli-uupdate-skops-file

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Merge remote-tracking branch 'upstream/main' into cli-uupdate-skops-file

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adrinjalali merged commit 70185a9 into skops-dev:main Jun 27, 2023

EdAbati deleted the cli-uupdate-skops-file branch June 27, 2023 13:23

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ENH: Added CLI command to update skops files #343

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ENH: Added CLI command to update skops files #343

ENH: Added CLI command to update skops files #343

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EdAbati commented Apr 10, 2023

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What does this implement/fix? Explain your changes.

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