[JOSS review] Improve documentation #1

Sbozzolo · 2023-05-09T02:03:48Z

(Main review for JOSS happening here)

The current documentation is very very minimal and needs to be expanded to describe capabilities and usage.

More specifically, here are some of the issues I've seen:

This list is not comprehensive and I would recommend designing the documentation from scratch.

Here is a good resource for a possible way to write effective documentation: https://documentation.divio.com/

a-renzini · 2023-05-13T00:26:43Z

Thank you! We are hard at work addressing this issue. Could this be turned into a checklist by any chance?

cmbiwer · 2023-05-19T16:48:19Z

I went through before looking at @Sbozzolo review. I wrote down basically the same issues and agree with @Sbozzolo . There is a lot missing from the documentation/tutorial and things currently point to URLs that require LIGO credentials.

I'll add a few more things though.

Test suite seems to fail.

I installed pytest myself (see the comments above, its not there) and tried the test suite. I see two test fail; TestInterferometer.test_set_timeseries_from_channel_name and TestInterferometer.test_from_parameters. The message (truncated):

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

fobj = '/var/folders/7b/9dh6yr6n6d9dvwlc33g1_3rw0000gp/T/astropy-download-92331-u335cim9', args = (), kwargs = {'end': LIGOTimeGPS(1247644588, 0), 'start': LIGOTimeGPS(1247644169, 0), 'tag': 'C00'}
h5f = <Closed HDF5 file>

    @wraps(func)
    def decorated_func(fobj, *args, **kwargs):
        # pylint: disable=missing-docstring
        if not isinstance(fobj, h5py.HLObject):
            if isinstance(fobj, FILE_LIKE):
                fobj = fobj.name
            with h5py.File(fobj, 'r') as h5f:
>               return func(h5f, *args, **kwargs)
E               TypeError: Failed to read GWOSC data from 'https://gwosc.org/archive/data/O3a_16KHZ_R1/1246756864/H-H1_GWOSC_O3a_16KHZ_R1-1247641600-4096.hdf5': read_gwosc_hdf5() got an unexpected keyword argument 'tag'

../../../opt/anaconda3/envs/pygwb/lib/python3.8/site-packages/gwpy/io/hdf5.py:59: TypeError

Installation instructions seem incomplete.

Aside from the issues already mentioned. It says to do:

conda install .

From the dir above the repo.

That didn't work either there. And even cd into in the repo, it didn't work. Conda couldn't find the package; eg.:

$ conda install .
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - .

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

I ended up using python -m pip install . to try using the package.

It may just be my Anaconda version. But its not stated anywhere what version is required.

cmbiwer · 2023-05-19T16:55:08Z

State of the field in the JOSS paper submission.

One more with the paper itself. The state of the field is a requirement in the paper. But there wasn't really any mention of the state of the field (eg. LALStochastic) and other packages, and what separates pygwb from those packages.

a-renzini · 2023-05-23T00:09:52Z

@Sbozzolo and @cmbiwer : thanks for your feedback! Several of the issues you point out are easy to resolve and we will update the documentation accordingly; there are a couple though that I am unsure how to address so let me post questions here.

a-renzini · 2023-05-23T00:12:36Z

I went through before looking at @Sbozzolo review. I wrote down basically the same issues and agree with @Sbozzolo . There is a lot missing from the documentation/tutorial and things currently point to URLs that require LIGO credentials.

I'll add a few more things though.

Test suite seems to fail.

I installed pytest myself (see the comments above, its not there) and tried the test suite. I see two test fail; TestInterferometer.test_set_timeseries_from_channel_name and TestInterferometer.test_from_parameters. The message (truncated):
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

fobj = '/var/folders/7b/9dh6yr6n6d9dvwlc33g1_3rw0000gp/T/astropy-download-92331-u335cim9', args = (), kwargs = {'end': LIGOTimeGPS(1247644588, 0), 'start': LIGOTimeGPS(1247644169, 0), 'tag': 'C00'}
h5f = <Closed HDF5 file>

    @wraps(func)
    def decorated_func(fobj, *args, **kwargs):
        # pylint: disable=missing-docstring
        if not isinstance(fobj, h5py.HLObject):
            if isinstance(fobj, FILE_LIKE):
                fobj = fobj.name
            with h5py.File(fobj, 'r') as h5f:
>               return func(h5f, *args, **kwargs)
E               TypeError: Failed to read GWOSC data from 'https://gwosc.org/archive/data/O3a_16KHZ_R1/1246756864/H-H1_GWOSC_O3a_16KHZ_R1-1247641600-4096.hdf5': read_gwosc_hdf5() got an unexpected keyword argument 'tag'

../../../opt/anaconda3/envs/pygwb/lib/python3.8/site-packages/gwpy/io/hdf5.py:59: TypeError
Installation instructions seem incomplete.

Aside from the issues already mentioned. It says to do:
conda install .
From the dir above the repo.

That didn't work either there. And even cd into in the repo, it didn't work. Conda couldn't find the package; eg.:
$ conda install .
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - .

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org
I ended up using python -m pip install . to try using the package.

It may just be my Anaconda version. But its not stated anywhere what version is required.

The failure of the test suite here seems to be due to a gwpy issue which (at least to my knowledge) was solved a while ago. Could you upload the full logs so I know what version you are running, etc?

Also, we run the testing suite in the pygwb gitlab repo, so that is why the CI badges are broken in the github version. Should I duplicate the testing also in github? It seems like a bit of a waste of computational resources. The gitlab repo is now public so you can see the test coverage here: https://git.ligo.org/pygwb/pygwb

a-renzini · 2023-05-23T00:49:15Z

@Sbozzolo the reason there are pickle files as a part of the repository is because some of our tests depend on them; they are not part of the codebase itself (when packaging the code for distribution the test suite is omitted). Our objects are designed as data containers, at different stages of a GWB analysis, and the test suite is based on pre-compiled pickled versions of these objects. We have found this an effective way of keeping track of changes in the modules and objects, without having the test suite re-run the analysis every time.

a-renzini · 2023-05-23T00:53:03Z

The readme does not say what the package is about

Now addressed here: 07926e3

a-renzini · 2023-05-23T00:56:49Z

The "about" page in the documentation consist of a single diagram (the meaning of which is unclear to me)

Now addressed here: 7ea65ea

a-renzini · 2023-05-23T02:16:17Z

@cmbiwer re:

Test suite seems to fail.

I tracked this issue back and it is due to a backwards-incompatible change in the gwosc package; this was fixed in pygwb v.1.1, but the version you see here is the one associated to the ApJ paper, and thus does not have this change. I have gone ahead and updated (and cleaned up) the code here, removing the tag argument which was deprecated by gwosc. We will merge these changes into pygwb once the review is over. The documentation should now run.

See 213fa0c

(I could also have fixed the version of gwosc to an older one, to make the old v1.0.0 work; however, as I expect the changes we make here will eventually be merged with the current version of the code, I thought it would be more useful to update the code this way. I am also happy to go the other way.)

cmbiwer · 2023-05-23T15:16:43Z

The failure of the test suite here seems to be due to a gwpy issue which (at least to my knowledge) was solved a while ago. Could you upload the full logs so I know what version you are running, etc?

This is the version it installed for me:

(pygwb) pn1618376:pygwb cmbiwer$ python
Python 3.8.16 | packaged by conda-forge | (default, Feb  1 2023, 16:05:36) 
[Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pygwb
>>> pygwb.__version__
'1.0.1.dev4'

a-renzini · 2023-05-23T15:47:01Z

The failure of the test suite here seems to be due to a gwpy issue which (at least to my knowledge) was solved a while ago. Could you upload the full logs so I know what version you are running, etc?

This is the version it installed for me:
(pygwb) pn1618376:pygwb cmbiwer$ python
Python 3.8.16 | packaged by conda-forge | (default, Feb  1 2023, 16:05:36) 
[Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pygwb
>>> pygwb.__version__
'1.0.1.dev4'

sorry - I meant gwpy version; in any case, I addressed this issue now in 213fa0c as mentioned above - please let me know whether the test suite now works with these changes :)

(note that the issue was coming from the fact that gwpy depends on gwosc, and although the version of gwpy installed by pygwb v1.0.0 is correct, gwpy doesn't fix the version of gwosc it needs and the break was coming from updates in gwosc)

Sbozzolo · 2023-05-28T16:58:54Z

Thank you! We are hard at work addressing this issue. Could this be turned into a checklist by any chance?

Sorry for the delay. I changed the list into a checklist. In this, let me remark again that this list summarizes my first impressions, so I'd encourage you to also think about the documentation beyond these points.

@Sbozzolo the reason there are pickle files as a part of the repository is because some of our tests depend on them; they are not part of the codebase itself (when packaging the code for distribution the test suite is omitted). Our objects are designed as data containers, at different stages of a GWB analysis, and the test suite is based on pre-compiled pickled versions of these objects. We have found this an effective way of keeping track of changes in the modules and objects, without having the test suite re-run the analysis every time.

I was under the impression that pickle files were not portable across versions/OSs, but it turns out that they are, as long as the same protocol is being used. Nonetheless, I think that sharing pickles is not the best idea. As the documentation clearly remarks, pickles are not safe. Moreover, they are opaque and can only be read by Python. Finally, if you change the object in your code in a future version (or if an upstream package changes its code), the pickle might stop working.
If it is possible and not too difficult, I'd suggest moving to something like JSON. Also, if used only for tests, the file should not be at the root level of your repository.

Now addressed here: 07926e3

What branch should I look at when reviewing the code/documentation?

a-renzini · 2023-05-28T17:34:33Z

Sorry for the delay. I changed the list into a checklist. In this, let me remark again that this list summarizes my first impressions, so I'd encourage you to also think about the documentation beyond these points.

Thank you - yes I understand the documentation is very lacking, we are working hard on it. Apologies it is taking quite some time, we will keep updating here as we go along!

I was under the impression that pickle files were not portable across versions/OSs, but it turns out that they are, as long as the same protocol is being used. Nonetheless, I think that sharing pickles is not the best idea. As the documentation clearly remarks, pickles are not safe. Moreover, they are opaque and can only be read by Python. Finally, if you change the object in your code in a future version (or if an upstream package changes its code), the pickle might stop working. If it is possible and not too difficult, I'd suggest moving to something like JSON. Also, if used only for tests, the file should not be at the root level of your repository.

Apologies - I don't quite understand what you mean by "the file should not be at the root level of your repository". Should these be in a separate branch? Every time we update a part of the code, indeed the pickles "stop working", and we update them accordingly. We've found this to be a useful check of the structure of the code. I'm afraid moving to JSON, while surely possible, would remove a layer of the checks we do, so I would be slightly against that.

What branch should I look at when reviewing the code/documentation?

Please refer to the joss_submission branch.

Sbozzolo · 2023-05-28T17:50:02Z

Sorry for the delay. I changed the list into a checklist. In this, let me remark again that this list summarizes my first impressions, so I'd encourage you to also think about the documentation beyond these points.

Thank you - yes I understand the documentation is very lacking, we are working hard on it. Apologies it is taking quite some time, we will keep updating here as we go along!

Thank you! There's no hurry, the goal of this review is to help you built and publish an awesome package :)

Apologies - I don't quite understand what you mean by "the file should not be at the root level of your repository". Should these be in a separate branch?

The file is at the same level as the directories "docs", "pygwb", ....

However, this file is very technical and is used only for tests (as I understand). Wouldn't it more appropriate to put it in the "test" folder? This would immediately give users a sense of what the file is about.

Every time we update a part of the code, indeed the pickles "stop working", and we update them accordingly. We've found this to be a useful check of the structure of the code. I'm afraid moving to JSON, while surely possible, would remove a layer of the checks we do, so I would be slightly against that.

In the interest of maintainability of the package, I think it would be best to have readers/writers to standard formats, and unit tests over those readers and writers to restore the layer of checks. This would be a more robust solution for two reasons: (1) you use a stable and clear format, as opposed to an opaque pickle, (2) new developers would see the reader/writer functions with their unit tests, and they would be able to more easily understand what is going on and extend the package (suppose a test fails with a pickle error, how would the developer know what to do? If you have reader/writers with tests, the failing test would immediately point the developer to the right direction).

Of course, this is my suggestion, and you are free to pick your preferred implementation. In any case, make sure to document everything.

Sbozzolo · 2023-05-28T17:52:09Z

Addendum: I realized that there are more pickle files in the tests folder. I had "checkpoint.pkl" in mind when writing the message.

a-renzini · 2023-05-28T17:53:31Z

Addendum: I realized that there are more pickle files in the tests folder. I had "checkpoint.pkl" in mind when writing the message.

oops - that file is NOT meant to be there. All the pickles used for checks should be in test/test_data! We must have forgotten to gitignore it...

a-renzini · 2023-05-28T17:59:38Z

Sorry for the delay. I changed the list into a checklist. In this, let me remark again that this list summarizes my first impressions, so I'd encourage you to also think about the documentation beyond these points.

Thank you - yes I understand the documentation is very lacking, we are working hard on it. Apologies it is taking quite some time, we will keep updating here as we go along!

Thank you! There's no hurry, the goal of this review is to help you built and publish an awesome package :)

Apologies - I don't quite understand what you mean by "the file should not be at the root level of your repository". Should these be in a separate branch?

The file is at the same level as the directories "docs", "pygwb", ....

However, this file is very technical and is used only for tests (as I understand). Wouldn't it more appropriate to put it in the "test" folder? This would immediately give users a sense of what the file is about.

Every time we update a part of the code, indeed the pickles "stop working", and we update them accordingly. We've found this to be a useful check of the structure of the code. I'm afraid moving to JSON, while surely possible, would remove a layer of the checks we do, so I would be slightly against that.

In the interest of maintainability of the package, I think it would be best to have readers/writers to standard formats, and unit tests over those readers and writers to restore the layer of checks. This would be a more robust solution for two reasons: (1) you use a stable and clear format, as opposed to an opaque pickle, (2) new developers would see the reader/writer functions with their unit tests, and they would be able to more easily understand what is going on and extend the package (suppose a test fails with a pickle error, how would the developer know what to do? If you have reader/writers with tests, the failing test would immediately point the developer to the right direction).

Of course, this is my suggestion, and you are free to pick your preferred implementation. In any case, make sure to document everything.

I like this suggestion. Our data writer functions can write to multiple formats, pickle is just one of them. So as I said, storing/checking JSONs (or other) is no problem. However, what I was originally thinking of adding is a test which runs our pipeline and writes the object pickle file, which then can be used by other tests to check its content. This would avoid storing static pickle files, but would maintain the test of the object structure. What are your thoughts on this?

Sbozzolo · 2023-05-31T22:19:28Z

I like this suggestion. Our data writer functions can write to multiple formats, pickle is just one of them. So as I said, storing/checking JSONs (or other) is no problem. However, what I was originally thinking of adding is a test which runs our pipeline and writes the object pickle file, which then can be used by other tests to check its content. This would avoid storing static pickle files, but would maintain the test of the object structure. What are your thoughts on this?

That's excellent!

a-renzini · 2023-07-17T23:32:23Z

Hello @Sbozzolo and @cmbiwer - apologies on the delay. I'm making a list here of the things we have addressed which you can take a look at, as we continue working on documentation+. I remember I had a few things to improve in the unit tests as well, I'm working on it!

READY (ish)

About page
Installation page
All the API pages

We're working on restructuring the docs, essentially turning some of the tutorials into actual pages and leaving some remaining tutorials as "extras". The idea is that the API pages present each module/object, but we will add pages that describe how these are then used for analysis, and clarify the objectives/deliverables of the package, as well as how to obtain them. We will probably add about one page per script present in the pygwb_pipe folder (these are the scripts used in our day to day analyses)

kevinturbang · 2023-08-17T08:13:34Z

Hello @Sbozzolo and @cmbiwer,

We have made significant progress in updating and refining our code and the documentation. Concretely,

All module API pages have been updated, ensuring that all class methods contain a description, and that the style used across module API pages is consistent throughout. Each of the API “landing pages" contains a brief description of the module itself, often with a few lines of code to illustrate the basic functionalities of the module.
The about, contribution and installation pages have been updated.
A few additional pages were created as well, and will be added moving forward. This to highlight some of the key scripts and functionalities of the pygwb package. The addition of those pages goes together with the removal of some tutorials. The idea behind these changes is to group all general information in these pages, whereas tutorials should contain more details or anything that deviates from the default usage.

At this point of the review process, it would be most useful if you could provide feedback on the work that has been done so far, while we finalize the documentation. This will allow us to incorporate any proposed changes as we are making these final modifications to the documentation.

Sbozzolo · 2023-08-17T14:40:32Z

Hi @kevinturbang.

Thank you for your hard work. I'll review the new documentation over the weekend and provide my feedback.

Sbozzolo · 2023-08-18T00:28:00Z

Should I still be looking at the joss_submission branch even if the last commit was on Jun 21?

a-renzini · 2023-08-18T23:52:38Z

@Sbozzolo no - we are now working directly in the gitlab as suggested: https://pygwb.docs.ligo.org/pygwb/ (I have updated the README in the repo to reflect this)

Sbozzolo · 2023-08-21T00:53:13Z

Thanks, @a-renzini. I went through the documentation and here are some comments.

The diagram in the about page feels too technical detail for an "about" page. I'd suggest moving it somewhere else because it is not useful to readers that are not already familiar with pyGWB.
I don't see where you specify what versions of python are supported (or recommended).
There is no clear progression on how users should approach the documentation. Right now, if you follow the "next" buttons in the docs you get: About, Installation, Contributing guide, Using pygwb_pipe: a quickstart manual, ... It would be nice to have a general quickstart. It's unclear how I should use the package. If pygwb_pipe is a central piece, it should be explained.
Following on the previous point, given that I am unfamiliar with pygwb_pipe, I do not understand what it means to be a pipeline, or what a dag file is, or why I should care about this. Similar to pygwb_pe.
The tutorials look good. I would recommend backlinking all the various functions/objects you name in the notebooks, so that one can click on the link and learn more about the object/function from the API manual.
I'd recommend running the tutorials in a sandbox while you generate your documentation instead of uploading an evaluated notebook. Right now, the tutorials come with warnings generated on Keving Turbang's machine. If you run in a sandbox, you can do some additional quality control on your docs/package, and be closer to the environment a new user might have. (Also, it is not great to see unexplanined warnings in tutorials)
There's a typo "choise -> choice" in the inject a power spectrum tutorial, "cto -> to" in inject SGWB. If you care about it, there's also a mix of British (e.g., initialise) and American (e.g., visualize) spelling of words. There are also extra new lines.
Some acronyms are never defined. Most people in the field know what PSD or H1 are, but you can make your package even more accessible to outsiders (or new students!) by defining all the acronyms at least once.
What is a notch list/notches?
I'd also recommend ensuring that your plots are readable (e.g., with a large font size, with different line styles for visually impaired people)

I haven't gone through the APIs carefully yet, but they seem fairly comprehensive.

To sum up my current assessment of your documentation: you wrote good pages/API/tutorials, but there is no underlying thread that joins them. As a new user, I still feel lost and I couldn't explain what pyGWB does exactly. I would recommend holding your users's hands a little bit more (e.g., providing a learning progression). I can give you examples of packages with good documentation if you want some inspiration on how to structure yours. One that might be close is LEGWORK.

kevinturbang · 2023-09-14T17:57:31Z

Dear @Sbozzolo,

First of all, thank you very much for all the useful feedback. This has been very valuable to get the documentation to its current status. We have implemented the comments above, and tried to add a more logical structure within the documentation itself. Could you please have a look and let us know if any further improvements are necessary? Thank you!

Sbozzolo · 2023-09-16T23:07:16Z

Dear PyGWB team,

Thank you for your efforts. The user documentation is looking great (I like the "tips" to direct the reader to other pages).

I only have two remaining comments, one trivial, and the other less so:

I think it is uncommon to have external links in the main menu (the one of the side, e.g., "pyGWB paper"), so I was surprised when I clicked on some items and left the documentation. There's nothing wrong about it, but I think it's always good to follow the principle of least surprise.
It would be great if you could describe in more detail the input/outputs of the various scripts, and maybe provide some examples and comments. You are already kind of doing that, but you fall short from actually showing and discussing the output. Instead of telling the user "load the file and print the keys", I'd recommend being very explicit. Users that might be interested in your package would want to know what it produces. Moreover, plots are a great way for visual learners to get a sense of what pyGWB is about.

Sbozzolo · 2023-09-16T23:32:21Z

Also, the CONTRIBUTING.MD file and the contributing page in the docs are not perfectly in agreement.

By the way, can non-LIGO users contribute using LIGO's gitlab?

kevinturbang · 2023-11-17T09:21:13Z

Dear reviewers,

Apologies for the delay on our end. We have added the following to address the points above:

Additional explanation on how to contribute for non-LIGO members.
Additional information about the output of the various scripts in the documentation.
We decided to keep the external links in the documentation, as we thought these are an added value for the users. Furthermore, the example of the LEGWORK documentation that you previously shared with us also has some external links.

Hopefully this addresses all your remaining comments. Please let us know if anything else needs modification.

a-renzini · 2023-11-20T11:38:23Z

Dear @Sbozzolo and team, can we mark this issue as closed? Thanks!

a-renzini · 2023-11-20T11:39:01Z

(sorry accidentally hit the purple button)

Sbozzolo · 2023-11-20T15:02:22Z

Documentation is a never ending process, and I invite you to keep working on it as you expand PyGWB. For JOSS, feel free to close this issue.

cmbiwer mentioned this issue May 19, 2023

[REVIEW]: pygwb: a Python-based library for gravitational-wave background searches openjournals/joss-reviews#5454

Closed

a-renzini closed this as completed Nov 20, 2023

a-renzini reopened this Nov 20, 2023

a-renzini closed this as completed Nov 20, 2023

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a-renzini commented Nov 20, 2023

a-renzini commented Nov 20, 2023

Sbozzolo commented Nov 20, 2023

[JOSS review] Improve documentation #1

[JOSS review] Improve documentation #1

Comments

Sbozzolo commented May 9, 2023 • edited Loading

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Sbozzolo commented May 28, 2023 • edited Loading

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Sbozzolo commented May 9, 2023 •

edited

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a-renzini commented May 23, 2023 •

edited

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Sbozzolo commented May 28, 2023 •

edited

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