1st_version of the github_auto_add #235

SeverusYixin · 2024-10-10T14:00:33Z

Hi @haesleinhuepf, would you mind helping me review it?

This PR relates to #185
This PR closes #185

SeverusYixin · 2024-10-10T14:07:45Z

I changed it according to auto-add-zenodo-entry.py, in theory it should work, I can't test it locally. So there is a problem, for example, when I give it this URL 'https://github.com/guiwitz/Python_image_processing', which should be the name 'Python_image_processing' or 'Image processing with Python'.

haesleinhuepf · 2024-10-10T14:08:12Z

scripts/auto-add-github-resources.py

+    - issue (int): Issue number containing the GitHub link.
+
+    Example:
+    python auto_add_github_entry.py "username/repo" 123


Suggested change

python auto_add_github_entry.py "username/repo" 123

python scripts/auto-add-github-resources.py username/repo 123

I presume this is correct?

I have deleted it. I wanted to test it locally or on my github, but it seems I'm not allowed to.

SeverusYixin · 2024-10-10T14:13:20Z

Why can I not write this link like you did "

training/scripts/auto-add-zenodo-entry.py

Line 1 in 2f17431

# This script is executed when a new issue is created on our github repository.

"?

haesleinhuepf

Hi @SeverusYixin ,

awesome, thanks for this! Two things:

Before sending a PR, please check if the tool works as you describe it in the documentation.
I just tested it and received an error message. That's the command I ran:

python scripts/auto-add-github-resources.py nfdi4bioimage/training 236

And that's the error:

-> get_conversation_on_issue(nfdi4bioimage/training, 236)
Request GET /repos/rmassei/ymia_python_event_series_material/collaborators?per_page=1 failed with 403: Forbidden
Traceback (most recent call last):
  File "C:\structure\code\training\scripts\auto-add-github-resources.py", line 139, in <module>
    main()
  File "C:\structure\code\training\scripts\auto-add-github-resources.py", line 34, in main
    github_data_dict = complete_github_data(github_repo_url)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\structure\code\training\scripts\auto-add-github-resources.py", line 97, in complete_github_data
    if collaborators.totalCount > 0:
       ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\PaginatedList.py", line 192, in totalCount
    headers, data = self.__requester.requestJsonAndCheck(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 550, in requestJsonAndCheck
    return self.__check(*self.requestJson(verb, url, parameters, headers, input, self.__customConnection(url)))
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 715, in requestJson
    return self.__requestEncode(cnx, verb, url, parameters, headers, input, encode)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 812, in __requestEncode
    status, responseHeaders, output = self.__requestRaw(cnx, verb, url, requestHeaders, encoded_input)
                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 846, in __requestRaw
    response = cnx.getresponse()
               ^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 198, in getresponse
    r = verb(
        ^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\requests\sessions.py", line 602, in get
    return self.request("GET", url, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\requests\sessions.py", line 589, in request
    resp = self.send(prep, **send_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\requests\sessions.py", line 703, in send
    r = adapter.send(request, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\requests\adapters.py", line 667, in send
    resp = conn.urlopen(
           ^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\urllib3\connectionpool.py", line 934, in urlopen
    retries = retries.increment(method, url, response=response, _pool=self)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\GithubRetry.py", line 187, in increment
    raise Requester.createException(response.status, response.headers, content)  # type: ignore
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
github.GithubException.GithubException: 403 {"message": "Must have push access to view repository collaborators.", "documentation_url": "https://docs.github.com/rest/collaborators/collaborators#list-repository-collaborators", "status": "403"}

Let me know if I should try again!

And thanks again for working on this. This will be cool to have!

Best,
Robert

SeverusYixin · 2024-10-10T14:18:22Z

Hi @SeverusYixin ,

awesome, thanks for this! Two things:

Before sending a PR, please check if the tool works as you describe it in the documentation.
I just tested it and received an error message. That's the command I ran:

python scripts/auto-add-github-resources.py nfdi4bioimage/training 236

And that's the error:

-> get_conversation_on_issue(nfdi4bioimage/training, 236)
Request GET /repos/rmassei/ymia_python_event_series_material/collaborators?per_page=1 failed with 403: Forbidden
Traceback (most recent call last):
  File "C:\structure\code\training\scripts\auto-add-github-resources.py", line 139, in <module>
    main()
  File "C:\structure\code\training\scripts\auto-add-github-resources.py", line 34, in main
    github_data_dict = complete_github_data(github_repo_url)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\structure\code\training\scripts\auto-add-github-resources.py", line 97, in complete_github_data
    if collaborators.totalCount > 0:
       ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\PaginatedList.py", line 192, in totalCount
    headers, data = self.__requester.requestJsonAndCheck(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 550, in requestJsonAndCheck
    return self.__check(*self.requestJson(verb, url, parameters, headers, input, self.__customConnection(url)))
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 715, in requestJson
    return self.__requestEncode(cnx, verb, url, parameters, headers, input, encode)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 812, in __requestEncode
    status, responseHeaders, output = self.__requestRaw(cnx, verb, url, requestHeaders, encoded_input)
                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 846, in __requestRaw
    response = cnx.getresponse()
               ^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\Requester.py", line 198, in getresponse
    r = verb(
        ^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\requests\sessions.py", line 602, in get
    return self.request("GET", url, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\requests\sessions.py", line 589, in request
    resp = self.send(prep, **send_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\requests\sessions.py", line 703, in send
    r = adapter.send(request, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\requests\adapters.py", line 667, in send
    resp = conn.urlopen(
           ^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\urllib3\connectionpool.py", line 934, in urlopen
    retries = retries.increment(method, url, response=response, _pool=self)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rober\miniforge3\envs\devbio-napari-env\Lib\site-packages\github\GithubRetry.py", line 187, in increment
    raise Requester.createException(response.status, response.headers, content)  # type: ignore
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
github.GithubException.GithubException: 403 {"message": "Must have push access to view repository collaborators.", "documentation_url": "https://docs.github.com/rest/collaborators/collaborators#list-repository-collaborators", "status": "403"}

Let me know if I should try again!

And thanks again for working on this. This will be cool to have!

Best, Robert

The problem is that I can not test it, it told me the scads.ai clould refuse me XD

haesleinhuepf · 2024-10-10T15:02:38Z

What is "scads.ai clould" in this context? What was the exact error message?

SeverusYixin · 2024-10-10T15:07:39Z

I have found another way to test. The "scads.ai cloud" problem is if I use my own github to test, I think my own github can not edit the thing on our repositories, e.g. create a PR.

haesleinhuepf · 2024-10-10T20:11:53Z

The error above is not about our repository:

Request GET /repos/rmassei/ymia_python_event_series_material/collaborators?per_page=1 failed with 403: Forbidden
...
Must have push access to view repository collaborators.

The error happens when accessing the other repository. I'd say we will not be able to read out collaborators from remote repositories.

SeverusYixin · 2024-10-11T07:21:06Z

The error above is not about our repository:

Request GET /repos/rmassei/ymia_python_event_series_material/collaborators?per_page=1 failed with 403: Forbidden
...
Must have push access to view repository collaborators.

The error happens when accessing the other repository. I'd say we will not be able to read out collaborators from remote repositories.

Yes, I used the code snippet to check locally that the link to our repository is no problem, it show me as PS C:\Users\huang\Documents\GitHub\training\scripts> & 'c:\Users\huang\AppData\Local\Programs\ Python\Python312\python. exe' 'c:\Users\huang.vscode\extensions\ms-python.debugpy-2024.10.0-win32-x64\bundled\libs\debugpy\adapter/ ... /... \debugpy\launcher' "51870" "--" "C:\Users\huang\Documents\GitHub\training\scripts\test.py"
Token found: githu
Repository successfully accessed: NFDI4BIOIMAGE/training
PS C:\Users\huang\Documents\GitHub\training\scripts>

I'm trying to see if this can be avoided, but nothing I've seen so far seems to work! Or maybe not with github token, I'm not sure

haesleinhuepf · 2024-10-11T07:22:41Z

nothing I've seen so far seems to work!

Yes, it is possible that this will not work. Do you have an overview about which meta data we can access and which not?

SeverusYixin · 2024-10-11T08:02:24Z

nothing I've seen so far seems to work!

Yes, it is possible that this will not work. Do you have an overview about which meta data we can access and which not?

At the moment, it looks like the request will be denied when you try to access it with github token.

haesleinhuepf · 2024-10-11T08:07:45Z

Can you please try "repo.get_contributors()" instead of "repo.get_collaborators()"?

SeverusYixin · 2024-10-11T08:08:50Z

Can you please try "repo.get_contributors()" instead of "repo.get_collaborators()"?

Let me try

haesleinhuepf · 2024-10-11T09:00:49Z

Did it work?

SeverusYixin · 2024-10-11T09:13:37Z

Did it work?

no

SeverusYixin · 2024-10-11T09:36:15Z

Please do not merge. There are still some details to discuss :)

Currently it looks like Add https://github.com/rmassei/ymia_python_event_series_material #238, so again, what should the name be, "ymia_python_event_series_material" or "YMIA - Python-Based Event Series Training Material"?
and for tags, do we need this "tags: No tags available"? or this "tags: "

haesleinhuepf · 2024-10-11T09:46:20Z

"ymia_python_event_series_material" or "YMIA - Python-Based Event Series Training Material"?

I would use whatever the github returns as repo.name

2. and for tags, do we need this "tags: No tags available"? or this "tags: "

If there are no tags, we should not have a "tag:" in our yaml.

haesleinhuepf · 2024-10-11T09:47:29Z

no

Consider posting an error message, in case you wish that I assist you.

SeverusYixin · 2024-10-11T09:57:47Z

Consider posting an error message, in case you wish that I assist you.

Already solved, thank you if I need that I will post a error message. Thank you again :)

This reverts commit 6e41ca0.

…IOIMAGE/training into auto_add_github_resources

1st_version of the github_auto_add

881106e

haesleinhuepf reviewed Oct 10, 2024

View reviewed changes

Remove the test example from the local page

fe84604

haesleinhuepf requested changes Oct 10, 2024

View reviewed changes

error 403, still not be solve

2bac904

1.1 version, it works

499050b

SeverusYixin and others added 3 commits October 11, 2024 16:23

1.2version,Updating the output sequence

49ccc5e

1.3 version, update to return full name if available

f0a5956

update git-bob config

6e41ca0

haesleinhuepf force-pushed the auto_add_github_resources branch from 4cbfbbb to 6e41ca0 Compare October 12, 2024 16:20

haesleinhuepf and others added 3 commits October 12, 2024 18:21

Revert "update git-bob config"

eb36950

This reverts commit 6e41ca0.

No updates, clean code redundancy

27242ed

Merge branch 'auto_add_github_resources' of https://github.com/NFDI4B…

b4d9577

…IOIMAGE/training into auto_add_github_resources

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1st_version of the github_auto_add #235

1st_version of the github_auto_add #235

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	python auto_add_github_entry.py "username/repo" 123
	python scripts/auto-add-github-resources.py username/repo 123

1st_version of the github_auto_add #235

Are you sure you want to change the base?

1st_version of the github_auto_add #235

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