Added parameters and exception behaviour to pqdm #792

Sherwin-14 · 2024-08-24T17:42:28Z

I did all the steps outlined in the issue #581, we can now build upon this.

📚 Documentation preview 📚: https://earthaccess--792.org.readthedocs.build/en/792/

chuckwondo

Thanks for your work on this PR @Sherwin-14!

There are still several places where you have to expose the new fail_fast parameter. So far, you have added it only to "protected" methods, so it is not yet exposed to the user in the "public" function and methods. You need to keep following the call chains up to the top (public) API so that users can use the parameter, if they want to choose False instead of the default True.

For example, you added fail_fast to Store._open_files, but you have not added it to all places that call Store._open_files. You did add it to Store._open_urls, which calls _open_files, but you did not yet add it to Store._open_granules, which also calls _open_files.

Further, both _open_files and _open_granules are dispatched when Store._open is called, so you must find all places where Store._open is called. In this case, it is called from Store.open, which is a public method, so you must add fail_fast to Store.open so the user can override the default, if they wish.

Further still, Store.open is called by the open top-level function in the api module, so you must add fail_fast there as well.

You must follow all such call chains from all points where pqdm is called, all the way up to the top of the call chains (up to the public functions and methods), adding fail_fast to each function and method along all such call chains.

chuckwondo · 2024-08-26T13:51:32Z

@mfisher87, I see lots of Ruff error messages regarding a number of files that @Sherwin-14 has not touched in this PR. Is there something already on main to address these errors, such that Sherwin simply needs to merge main into his own branch to silence them?

mfisher87 · 2024-08-26T16:19:25Z

Not yet, but that should be an easy fix. I'll take care of it now :) #788

mfisher87 · 2024-08-26T16:24:12Z

#793

chuckwondo · 2024-08-26T16:41:57Z

Not yet, but that should be an easy fix. I'll take care of it now :) #788
#793

Excellent! Thank you for the quick fix.

@Sherwin-14, Matt's fix is now merged into main, so please update your branch with the fix from main, which will eliminate the ruff errors in your build.

chuckwondo · 2024-09-03T10:08:56Z

@Sherwin-14, do you have enough information to proceed with the changes I requested?

Sherwin-14 · 2024-09-03T11:21:34Z

@Sherwin-14, do you have enough information to proceed with the changes I requested?

Yeah I have the info I needed, I had put this on hold since I was preoccupied with some other things for the last couple of days. I'll resume my work on this asap.

betolink · 2024-09-03T15:53:44Z

Would it be possible and in scope of this PR to use **kwargs and pass them to pqdm for both open() and download() with sane defaults? Users could be in control of the failing behavior but also the number of threads to use and the verbosity (don't display the progress bar). I'm not sure about the style, in Xarray they use **kwargs and an equivalent backend_kwargs={} that in our case could be something like pqdm_opts={}

# code in api.py and something similar in store.py
# in this example we leave threads out to ensure backwards compatibility and will use it in the store class if present
def open(granules, threads, provider, pqdm_opts):
    default_pqdm_opts = {
      n_jobs=threads,
      exception_behaviour='immediate'
      colour="green",
      disable=False # True means no output including the progress bar.
    }

    if not pqdm_opts;
        pqdm_opts = default_pqdm_opts
    earthaccess.__store__.open(granules, treads, pqdm_opts)

and actually we should do the same with fsspec so we let users tune their caching behavior when opening the files, aka a "smart_open". What do you all think?

mfisher87 · 2024-09-03T16:46:19Z

I had put this on hold since I was preoccupied with some other things for the last couple of days. I'll resume my work on this asap.

@Sherwin-14 No rush! We really appreciate any time you can spare, and don't want to ask for more than that :)

mfisher87 · 2024-09-03T16:48:31Z

@betolink I really like that idea. Basically "Allow customizing all pqdm behaviors" (and separately, "Allow customizing all fsspec behaviors")?

I'm not sure how I feel about including that as part of this PR. I lean towards separate out of respect for @Sherwin-14 's time, but I don't want to speak for you, Sherwin!

mfisher87 · 2024-09-03T17:58:40Z

We decided during hack day today that we want to allow users to customize pqdm behaviors like so:

def open(something, threads=16, *, pqdm_kwargs={...}, ...):
    pqdm_kwargs_defaults = {"exception_behavior": "immediate", "threads": threads}
    pqdm_kwargs = pqdm_kwargs_defaults.update(pqdm_kwargs)
    ...

We considered the threads argument as fundamental to the function of earthaccess, so we think it should remain a top-level parameter. We'll use threads whether we use pqdm or not in 5 years.

Sherwin-14 · 2024-09-05T10:45:36Z

We decided during hack day today that we want to allow users to customize pqdm behaviors like so:
def open(something, threads=16, *, pqdm_kwargs={...}, ...):
    pqdm_kwargs_defaults = {"exception_behavior": "immediate", "threads": threads}
    pqdm_kwargs = pqdm_kwargs_defaults.update(pqdm_kwargs)
    ...
We considered the threads argument as fundamental to the function of earthaccess, so we think it should remain a top-level parameter. We'll use threads whether we use pqdm or not in 5 years.

How should we now proceed with the changes we discussed during the hackday?

chuckwondo · 2024-09-05T13:35:46Z

We decided during hack day today that we want to allow users to customize pqdm behaviors like so:
def open(something, threads=16, *, pqdm_kwargs={...}, ...):
    pqdm_kwargs_defaults = {"exception_behavior": "immediate", "threads": threads}
    pqdm_kwargs = pqdm_kwargs_defaults.update(pqdm_kwargs)
    ...
We considered the threads argument as fundamental to the function of earthaccess, so we think it should remain a top-level parameter. We'll use threads whether we use pqdm or not in 5 years.
How should we now proceed with the changes we discussed during the hackday?

Do the same thing you did in the PR you already started for this, but instead of fail_fast (which is what you pretty much completed) change it to pqdm_kwargs and adjust your code changes similar to what is shown above, although the code above won't work because pqdm has an n_jobs arg, not a threads arg, so I suggest something like so, instead, within the functions/methods that invoke pqdm:

pqdm_kwargs = {
    "exception_behavior": "immediate",
    "n_jobs": threads,
    **pqdm_kwargs,
}

...

pqdm(<other args>, **pqdm_kwargs)

mfisher87 · 2024-09-05T23:10:04Z

Great point! Much clearer with the double splat too ;)

chuckwondo · 2024-09-14T12:20:06Z

@Sherwin-14, do you need some help with this?

Sherwin-14 · 2024-09-14T16:11:06Z

@Sherwin-14, do you need some help with this?

I will try to accomodate the change asap, I was caught up in something else up untill now

chuckwondo · 2024-09-14T16:30:07Z

@Sherwin-14, do you need some help with this?

I will try to accomodate the change asap, I was caught up in something else up untill now

No rush. I just wanted to check in to see if you need any help or if something else was requiring you to postpone your continuation.

Sherwin-14 · 2024-09-28T10:38:11Z

@chuckwondo

def download(
    granules: Union[DataGranule, List[DataGranule], str, List[str]],
    local_path: Optional[str],
    provider: Optional[str] = None,
    threads: int = 8,
    pqdm_kwargs: dict = {}
) -> List[str]:
    """Retrieves data granules from a remote storage system.

       * If we run this in the cloud, we will be using S3 to move data to `local_path`.
       * If we run it outside AWS (us-west-2 region) and the dataset is cloud hosted,
            we'll use HTTP links.

    Parameters:
        granules: a granule, list of granules, a granule link (HTTP), or a list of granule links (HTTP)
        local_path: local directory to store the remote data granules
        provider: if we download a list of URLs, we need to specify the provider.
        threads: parallel number of threads to use to download the files, adjust as necessary, default = 8

    Returns:
        List of downloaded files

    Raises:
        Exception: A file download failed.
    """
    provider = _normalize_location(provider)
    pqdm_kwargs = {
        "exception_behavior": "immediate",
        "n_jobs": threads,
        **pqdm_kwargs,
    }
    if isinstance(granules, DataGranule):
        granules = [granules]
    elif isinstance(granules, str):
        granules = [granules]
    try:
        results = earthaccess.__store__.get(
            granules, local_path, provider, threads, pqdm_kwargs
        )    
    except AttributeError as err:
        logger.error(
            f"{err}: You must call earthaccess.login() before you can download data"
        )
        return []
    return results

Just for clarification, the public API function download would look something like this. The pqdm_kwargs would be taken in at the user interface and then passed on to the lower level functions in the entire call chain isn't it? or am I missing something?

chuckwondo · 2024-09-28T13:41:09Z

Correct, but you almost never want to use mutable values for default values, and this is one of those cases (among other references, see https://docs.python-guide.org/writing/gotchas/#mutable-default-arguments).

So, do NOT do this:

def download(
    granules: Union[DataGranule, List[DataGranule], str, List[str]],
    local_path: Optional[str],
    provider: Optional[str] = None,
    threads: int = 8,
    pqdm_kwargs: dict = {}
) -> List[str]:
    pqdm_kwargs = {
        "exception_behavior": "immediate",
        "n_jobs": threads,
        **pqdm_kwargs,
    }

Instead, DO THIS:

def download(
    granules: Union[DataGranule, List[DataGranule], str, List[str]],
    local_path: Optional[str],
    provider: Optional[str] = None,
    threads: int = 8,
    pqdm_kwargs: Optional[Mapping[str, Any]] = None,
) -> List[str]:
    pqdm_kwargs = {
        "exception_behavior": "immediate",
        "n_jobs": threads,
        **(pqdm_kwargs or {}),
    }

codecov-commenter · 2024-09-29T14:15:54Z

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Attention: Patch coverage is 50.00000% with 27 lines in your changes missing coverage. Please review.

Project coverage is 68.78%. Comparing base (2f49c08) to head (1061743).
Report is 69 commits behind head on main.

Files with missing lines	Patch %	Lines
earthaccess/store.py	0.00%	22 Missing ⚠️
earthaccess/api.py	37.50%	5 Missing ⚠️

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@@            Coverage Diff             @@
##             main     #792      +/-   ##
==========================================
- Coverage   73.88%   68.78%   -5.11%     
==========================================
  Files          31       32       +1     
  Lines        2003     2153     +150     
==========================================
+ Hits         1480     1481       +1     
- Misses        523      672     +149

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chuckwondo

Thanks @Sherwin-14. In addition to my other comments, please add at least 1 unit test. I don't think you need to test passing all possible pqdm kwargs, but perhaps just test that you can produce an error for downloading and have it raise an error (now that the default exception behavior is "immediate") instead of returning with a list containing errors.

earthaccess/api.py

earthaccess/store.py

CHANGELOG.md

chuckwondo · 2024-09-30T22:25:09Z

earthaccess/store.py

+                access = "direct"
+                provider = granules[0]["meta"]["provider-id"]
+                # if the data has its own S3 credentials endpoint, we will use it
+                endpoint = self._own_s3_credentials(granules[0]["umm"]["RelatedUrls"])
+                if endpoint is not None:
+                    logger.info(f"using endpoint: {endpoint}")
+                    s3_fs = self.get_s3_filesystem(endpoint=endpoint)
+                else:
+                    logger.info(f"using provider: {provider}")
+                    s3_fs = self.get_s3_filesystem(provider=provider)


Where did this come from?

@Sherwin-14, it seems you've marked many suggestions as resolved, but I don't see the changes. Perhaps I'm not looking in the right spot in the GitHub UI, but are you sure you pushed your changes?

earthaccess/api.py

earthaccess/store.py

chuckwondo

@Sherwin-14, I suspect you marked many suggestions as "resolved," but forgot to push the changes that resolve the suggestions.

Also, please remember to go back to the Conversations tab of your PR and, in the upper-right area of the tab, click the circular double-arrows next to a reviewer's name to request a re-review after the reviewer has requested changes. Otherwise, the reviewer doesn't know when you're finished making changes and ready for a follow-up review.

Clicking that icon will send another email indicating that you want another review.

earthaccess/store.py

CHANGELOG.md

earthaccess/api.py

chuckwondo · 2024-10-06T13:56:45Z

earthaccess/store.py

+                access = "direct"
+                provider = granules[0]["meta"]["provider-id"]
+                # if the data has its own S3 credentials endpoint, we will use it
+                endpoint = self._own_s3_credentials(granules[0]["umm"]["RelatedUrls"])
+                if endpoint is not None:
+                    logger.info(f"using endpoint: {endpoint}")
+                    s3_fs = self.get_s3_filesystem(endpoint=endpoint)
+                else:
+                    logger.info(f"using provider: {provider}")
+                    s3_fs = self.get_s3_filesystem(provider=provider)


@Sherwin-14, it seems you've marked many suggestions as resolved, but I don't see the changes. Perhaps I'm not looking in the right spot in the GitHub UI, but are you sure you pushed your changes?

chuckwondo · 2024-10-06T13:57:31Z

earthaccess/store.py

+            fail_fast: if set to True, the download process will stop immediately
+            upon encountering the first error. If set to False, errors will be
+            deferred, allowing the download of remaining files to continue.


I don't see a change. Unresolving.

chuckwondo · 2024-10-06T14:16:20Z

@Sherwin-14, several other PRs have landed on main, so please also be sure to merge the changes from main and resolve conflicts.

Sherwin-14 · 2024-10-06T14:56:50Z

@chuckwondo Hey Chuck, I have made the appropriate changes but I haven't pushed the code yet since I was writing unittest for this one which you suggested earlier. I will re-request for a review once I feel this is ready to be reviewed

chuckwondo · 2024-10-06T15:07:42Z

@chuckwondo Hey Chuck, I have made the appropriate changes but I haven't pushed the code yet since I was writing unittest for this one which you suggested earlier. I will re-request for a review once I feel this is ready to be reviewed

Sounds good, but please wait to mark any suggestions as resolved until you push the corresponding code changes, otherwise it is confusing to others.

Sherwin-14 · 2024-10-27T07:15:48Z

class TestEarthAccessDownload(unittest.TestCase):
    def test_download(self):

        earthaccess.login()

        results = earthaccess.search_data(
            short_name='ATL06',  # ATLAS/ICESat-2 L3A Land Ice Height
            bounding_box=(-10, 20, 10, 50),  # Only include files in area of interest...
            temporal=("1999-02", "2019-03"),  # ...and time period of interest.
            count=10
        )


        with patch.object(earthaccess, '__store__', return_value= Mock()) as mock_store:
            with patch.object(mock_store, 'get') as mock_get:
    
                mock_get.side_effect = Exception('Download failed')
    
     
                files = earthaccess.download(results, "/home/download-folder")
    
                self.assertEqual(files, [])

if __name__ == '__main__':
    unittest.main()

This is the test function I came up with and this is giving me an error log that looks something like this. Is this the thing we want to achieve at this point? Also if the test is correct then where should I place it should I make a completely new file for this like test_api.py?

chuckwondo · 2024-10-27T14:47:38Z

Hi @Sherwin-14. Thanks for working on the unit tests for this PR.

The first thing I suggest you do is merge the latest from main into your branch, so you're working with the latest code.

Regarding the test you've written, it looks like you're generally heading in the right direction.

I have some suggestions:

Sure, if you want to put your new tests in a new tests/unit/test_api.py file, that sounds good to me.
Do not use the unittest library. There's no need for the additional "overhead". Simply use top-level test functions and built-in assert statements. We have almost completely moved away from unittest in our integration tests, and we have a mix in our unit tests, but we should continue moving away from unittest (although I suspect this may be up for debate).
Regarding your test shown above, that looks good, but since the new behavior is for the call to download to fail immediately upon any single download failure (i.e., pqdm exception_behavior="immediate"), then you will want to put your call to download in a context manager, as by default we expect an exception to be raised (as shown in your linked test failure output), thus we do not expect to be able to assert that we get back an empty list of results:

        with patch.object(earthaccess, '__store__', return_value= Mock()) as mock_store:
            with patch.object(mock_store, 'get') as mock_get:
                mock_get.side_effect = Exception('Download failed')

                with pytest.raises(Exception, match="Download failed"):
                    earthaccess.download(results, "/home/download-folder")

Sherwin-14 · 2024-10-28T13:52:19Z

I have taken out unittest but it seems that it is necessary to use unittest for importing the likes of Mock. Another option here would be to use the pytest mock library but that means we will need to add an additional dependency.

chuckwondo · 2024-10-28T14:04:23Z

I have taken out unittest but it seems that it is necessary to use unittest for importing the likes of Mock. Another option here would be to use the pytest mock library but that means we will need to add an additional dependency.

You can still use unittest Mocks, but there's no need for creating a subclass of unittest.TestCase.

github-actions · 2024-10-28T14:20:25Z

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chuckwondo

In addition to my comments, please also make corrections to fix the pre-commit issues: https://results.pre-commit.ci/run/github/399867529/1730125212.zyU74SY_QNaQKq_PZmUrIQ

It looks like you perhaps have not installed pre-commit hooks locally, otherwise your attempt to commit your changes should have produced those same pre-commit issues locally, thus preventing your commit from completing.

Please install pre-commit, if you haven't already done so, an then run the following from your forked/cloned repo to install the hooks configured in the repo: pre-commit install --install-hooks. Then run pre-commit run -a to run the pre-commit checks against all the files, which should then help you fix the pre-commit errors.

earthaccess/api.py

CHANGELOG.md

chuckwondo · 2024-10-28T16:34:38Z

tests/unit/test_api.py

+from earthaccess import api,download
+from unittest.mock import Mock
+
+def test_download(monkeypatch):


Suggested change

def test_download(monkeypatch):

def test_download_immediate_failure(monkeypatch):

tests/unit/test_api.py

Co-authored-by: Chuck Daniels <[email protected]>

chuckwondo

It looks like you have not correctly merged/rebased from main. I see changes that I should not see. For example, in CHANGELOG.md, I see a new Fixed section, which is not new. It is already on main, so should not show up as something new on your branch.

I think there are some other spots that seem out of sync too, such as in the earthacces/store.py method _open_files, where the type of the threads parameter seems to have been clobbered. It should be threads: int = 8 (a recent change), instead of threads: Optional[int] = 8.

chuckwondo

Thanks @Sherwin-14.

I'm approving, but do @mfisher87, @betolink, or @jhkennedy want to take a pass over this before it gets merged?

mfisher87

Looks amazing, @Sherwin-14 ! Thank you! A little nitpick, and let's merge this!

tests/unit/test_api.py

…diate_failure Co-authored-by: Matt Fisher <[email protected]>

github-actions · 2024-11-05T00:26:45Z

User pre-commit-ci[bot] does not have permission to run integration tests. A maintainer must perform a security review of the code changes in this pull request and re-run the failed integration tests jobs, if the code is deemed safe.

Sherwin-14 force-pushed the download branch from 66edbea to 980469a Compare August 24, 2024 17:44

chuckwondo requested review from chuckwondo and mfisher87 August 26, 2024 13:29

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Sherwin-14 force-pushed the download branch from 980469a to 2afc65b Compare September 3, 2024 11:41

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Sherwin-14 added 5 commits October 23, 2024 17:55

Made changes like adding excpetion_behaviour and fail_fast parameter

1e3d523

Changes made to public functions

42f97ce

Added pqdm_kwargs to the functions

0e76a23

Fixed some glarring issues

fc59282

Removed threads from open

87cd8fc

chuckwondo mentioned this pull request Oct 23, 2024

Action to automatically create hack day discussion threads #801

Open

Sherwin-14 force-pushed the download branch from 77efee9 to d22f2ac Compare October 28, 2024 14:20

Sherwin-14 requested a review from chuckwondo October 28, 2024 14:22

chuckwondo requested changes Oct 28, 2024

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Replaced fast_fail with pqdm_kwargs the code and added a test

374f303

Sherwin-14 force-pushed the download branch from d22f2ac to 374f303 Compare October 28, 2024 17:22

Sherwin-14 and others added 2 commits October 28, 2024 22:53

remove an unnecessary line

de8df1c

Co-authored-by: Chuck Daniels <[email protected]>

Update CHANGELOG.md

767e119

Co-authored-by: Chuck Daniels <[email protected]>

chuckwondo requested changes Oct 28, 2024

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Added a second test for download

2d485b3

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chuckwondo previously approved these changes Oct 29, 2024

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tests/unit/test_api.py Outdated Show resolved Hide resolved

Update tests/unit/test_api.py changed test name to test_download_imme…

1061743

…diate_failure Co-authored-by: Matt Fisher <[email protected]>

Sherwin-14 dismissed chuckwondo’s stale review via 1061743 November 4, 2024 06:48

Sherwin-14 requested a review from mfisher87 November 4, 2024 06:49

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chuckwondo merged commit 84be54e into nsidc:main Nov 4, 2024
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chuckwondo mentioned this pull request Nov 5, 2024

Fix failing integration tests #869

Merged

9 tasks

	def test_download(monkeypatch):
	def test_download_immediate_failure(monkeypatch):

Added parameters and exception behaviour to pqdm #792

Added parameters and exception behaviour to pqdm #792

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