Talip7/scikit-learn-issues-multilabel huggingface dataset:
DOC Outdated note at top of `build_tools/circle/push_doc.sh`

### Describe the issue linked to the documentation

The top of [`build_tools/circle/push_doc.sh`](https://github.com/scikit-learn/scikit-learn/blob/main/build_tools/circle/push_doc.sh) says:

```
# The behavior of the script is controlled by environment variable defined
# in the circle.yml in the top level folder of the project.
```

I think `circle.yml` has changed to `.circleci/config.yml` although the deloy step doesn't seem to use the `environment` key, so potentially this note could be removed altogether?

Ref: https://github.com/scikit-learn/scikit-learn/issues/26598#issuecomment-1596152204

### Suggest a potential alternative/fix

Amend  `circle.yml`  to `.circleci/config.yml` or remove this part altogether.

COMMENT:
Yeah maybe that could be what it is referring to the path maybe the wording needs to be changed, let's see if some core dev can clarify.

Labels: Documentation, Needs Triage
DOC Outdated note at top of `build_tools/circle/push_doc.sh`

### Describe the issue linked to the documentation

The top of [`build_tools/circle/push_doc.sh`](https://github.com/scikit-learn/scikit-learn/blob/main/build_tools/circle/push_doc.sh) says:

```
# The behavior of the script is controlled by environment variable defined
# in the circle.yml in the top level folder of the project.
```

I think `circle.yml` has changed to `.circleci/config.yml` although the deloy step doesn't seem to use the `environment` key, so potentially this note could be removed altogether?

Ref: https://github.com/scikit-learn/scikit-learn/issues/26598#issuecomment-1596152204

### Suggest a potential alternative/fix

Amend  `circle.yml`  to `.circleci/config.yml` or remove this part altogether.

COMMENT:
Had another look and maybe they do just mean circle ci built in env variables like $CIRCLE_BRANCH?

Labels: Documentation, Needs Triage
DOC Outdated note at top of `build_tools/circle/push_doc.sh`

### Describe the issue linked to the documentation

The top of [`build_tools/circle/push_doc.sh`](https://github.com/scikit-learn/scikit-learn/blob/main/build_tools/circle/push_doc.sh) says:

```
# The behavior of the script is controlled by environment variable defined
# in the circle.yml in the top level folder of the project.
```

I think `circle.yml` has changed to `.circleci/config.yml` although the deloy step doesn't seem to use the `environment` key, so potentially this note could be removed altogether?

Ref: https://github.com/scikit-learn/scikit-learn/issues/26598#issuecomment-1596152204

### Suggest a potential alternative/fix

Amend  `circle.yml`  to `.circleci/config.yml` or remove this part altogether.

COMMENT:
Yes as confirmed by core dev in my PR

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
Hi @lucyleeow ,

I would love to fix the issue. I am new to open source and looking for contributions. Kindly guide me so I can resolve this.

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
I was checking the script:

[https://github.com/scikit-learn/scikit-learn/blob/20be4dfb50e015ca62c11bc3f4c73ffe4d74c36f/build_tools/update_environments_and_lock_files.py](url)

Which says "Environments are conda environment.yml", also in 

[https://github.com/scikit-learn/scikit-learn/blob/20be4dfb50e015ca62c11bc3f4c73ffe4d74c36f/build_tools/circle/push_doc.sh](url)

Says
```
#!/bin/bash
# This script is meant to be called in the "deploy" step defined in
# circle.yml. See https://circleci.com/docs/ for more details.
# The behavior of the script is controlled by environment variable defined
# in the circle.yml in the top level folder of the project.

```
"circle.yml", Which also does not exist

So this could have been changed to the whole new file update_environments_and_lock_files.py

In that case both documentation should be changed.

Thoughts @glemaitre @adrinjalali

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
> Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

From what I've seen, `SPHINX_VERSION` is `"min"`, so that we should look up in `sklearn/_min_dependencies.py`. I suppose that the search can be like [this](https://github.com/search?q=%5C%22sphinx%5C%22+repo%3Ascikit-learn%2Fscikit-learn+path%3Asklearn%2F_min_dependencies.py&type=code), which gives

![image](https://github.com/scikit-learn/scikit-learn/assets/108576690/c0f90220-7712-461e-868a-21afc260cf7d)

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
Thanks for all the interest.

@Charlie-XIAO the warning reads:

> While we do our best to have the documentation build under as many versions of Sphinx as possible, the different versions tend to behave slightly differently. To get the best results, you should use the same version as the one we used on CircleCI. Look at this [github search](https://github.com/search?utf8=%E2%9C%93&q=sphinx+repo%3Ascikit-learn%2Fscikit-learn+extension%3Ash+path%3Abuild_tools%2Fcircle&type=Code) to know the exact version.

We do not want the min dependency version of Sphinx, we want the version of Sphinx used by CircleCI to build the documentation for scikit-learn (this is also the documentation that can be viewed in doc PRs, see: https://scikit-learn.org/dev/developers/contributing.html#generated-documentation-on-github-actions and for more info on CI see: https://scikit-learn.org/dev/developers/contributing.html#continuous-integration-ci) 

It's probably best to wait for a core-dev to suggest the best alternative link.

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
@lucyleeow My bad, thanks for reminding me. I was looking back a few commits when the CircleCI build was still using `get_dep sphinx min` which looks for the min version specified in `_min_dependencies.py`. For the current version, I think we should look up in [this GitHub search link](https://github.com/search?q=repo%3Ascikit-learn%2Fscikit-learn+path%3Abuild_tools%2Fcircle%2F*.yml+sphinx&type=code), which shows

![image](https://github.com/scikit-learn/scikit-learn/assets/108576690/d069e04c-ab99-47d3-b512-7b28f7c90f8b)

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
This search can be confusing because it shows both the min dependency (not what we want) and the version of sphinx that is used to build docs.

I would suggest either:

> Could this link just be to the file build_tools/circle/doc_environment.yml ? Or link to github search for 'sphinx' within this file?

Making it a link directly to the file seems cleaner but the search gives you what you are looking for quicker.

Again, probably best to wait for a core-dev to chime in, thank you for your patience.

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
Sorry about that @lucyleeow, I didn't see that you have already found that file. I will close my PR in favor of your earlier investigation.

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
I think the issue @rand0wn raised is different from this one, and they did not open a PR. I will open another issue about this.

I think you can keep your PR open and just amend when we know the best alternative link.

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
@lucyleeow I @ the wrong person previously 😂 (now fixed), it should be in favor of *your* earlier investigation. Sorry for the confusion.

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
No problem, happy for you to take this issue.

Labels: Documentation, Needs Triage
DOC Link in warning about doc build with Sphinx versions outdated

### Describe the issue linked to the documentation

The link in the warning about sphinx versions at the end of ['Building the documentation'](https://scikit-learn.org/dev/developers/contributing.html#building-the-documentation) is to a Github search that uses a now unrecognised qualifier. Also I think there has been a change in how dependencies in CI are dealt with now (original PR, #10685, adding this section is 6 years old) and even when the qualifier syntax is updated, that search no longer shows the circle CI sphinx version.


### Suggest a potential alternative/fix

Could this link just be to the file `build_tools/circle/doc_environment.yml` ? Or link to github search for 'sphinx' within this file?

COMMENT:
Thanks for spotting this!

I like the suggestion of using https://github.com/search?q=repo%3Ascikit-learn%2Fscikit-learn+sphinx+path%3Abuild_tools%2Fcircle%2Fdoc_environment.yml&type=code (a search for "sphinx" inside the specific file).

Labels: Documentation, Needs Triage
calibrated classifier cv estimator is not fitted

### Describe the bug

fitted estimator behaves as if it is unfitted if under CalibatedClassifier CV


### Steps/Code to Reproduce

```
from sklearn.calibration import CalibratedClassifierCV
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.datasets import make_classification
from sklearn.pipeline import make_pipeline
pipeline = CalibratedClassifierCV(estimator=GradientBoostingClassifier())
pipeline.fit(x,y)
m=pipeline.estimator
m.feature_importances_m.feature_importances_
```

### Expected Results

feature importance

### Actual Results

> NotFittedError: This GradientBoostingClassifier instance is not fitted yet. Call 'fit' with appropriate arguments before using this estimator.

### Versions

```shell
System:
    python: 3.10.12 (main, Jun  7 2023, 12:45:35) [GCC 9.4.0]
executable: /usr/bin/python3
   machine: Linux-5.15.107+-x86_64-with-glibc2.31

Python dependencies:
      sklearn: 1.2.2
          pip: 23.1.2
   setuptools: 67.7.2
        numpy: 1.22.4
        scipy: 1.10.1
       Cython: 0.29.34
       pandas: 1.5.3
   matplotlib: 3.7.1
       joblib: 1.2.0
threadpoolctl: 3.1.0

Built with OpenMP: True

threadpoolctl info:
       user_api: blas
   internal_api: openblas
         prefix: libopenblas
       filepath: /usr/local/lib/python3.10/dist-packages/numpy.libs/libopenblas64_p-r0-2f7c42d4.3.18.so
        version: 0.3.18
threading_layer: pthreads
   architecture: Haswell
    num_threads: 2

       user_api: openmp
   internal_api: openmp
         prefix: libgomp
       filepath: /usr/local/lib/python3.10/dist-packages/scikit_learn.libs/libgomp-a34b3233.so.1.0.0
        version: None
    num_threads: 2

       user_api: blas
   internal_api: openblas
         prefix: libopenblas
       filepath: /usr/local/lib/python3.10/dist-packages/scipy.libs/libopenblasp-r0-41284840.3.18.so
        version: 0.3.18
threading_layer: pthreads
   architecture: Haswell
    num_threads: 2
```

COMMENT:
You are accessing the unfitted estimator. You should use instead the fitted attribute `calibrated_classifiers_`.

```python
pipeline.calibrated_classifiers_[0].estimator.feature_importances_
```

Labels: Bug, Needs Triage
calibrated classifier cv estimator is not fitted

### Describe the bug

fitted estimator behaves as if it is unfitted if under CalibatedClassifier CV


### Steps/Code to Reproduce

```
from sklearn.calibration import CalibratedClassifierCV
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.datasets import make_classification
from sklearn.pipeline import make_pipeline
pipeline = CalibratedClassifierCV(estimator=GradientBoostingClassifier())
pipeline.fit(x,y)
m=pipeline.estimator
m.feature_importances_m.feature_importances_
```

### Expected Results

feature importance

### Actual Results

> NotFittedError: This GradientBoostingClassifier instance is not fitted yet. Call 'fit' with appropriate arguments before using this estimator.

### Versions

```shell
System:
    python: 3.10.12 (main, Jun  7 2023, 12:45:35) [GCC 9.4.0]
executable: /usr/bin/python3
   machine: Linux-5.15.107+-x86_64-with-glibc2.31

Python dependencies:
      sklearn: 1.2.2
          pip: 23.1.2
   setuptools: 67.7.2
        numpy: 1.22.4
        scipy: 1.10.1
       Cython: 0.29.34
       pandas: 1.5.3
   matplotlib: 3.7.1
       joblib: 1.2.0
threadpoolctl: 3.1.0

Built with OpenMP: True

threadpoolctl info:
       user_api: blas
   internal_api: openblas
         prefix: libopenblas
       filepath: /usr/local/lib/python3.10/dist-packages/numpy.libs/libopenblas64_p-r0-2f7c42d4.3.18.so
        version: 0.3.18
threading_layer: pthreads
   architecture: Haswell
    num_threads: 2

       user_api: openmp
   internal_api: openmp
         prefix: libgomp
       filepath: /usr/local/lib/python3.10/dist-packages/scikit_learn.libs/libgomp-a34b3233.so.1.0.0
        version: None
    num_threads: 2

       user_api: blas
   internal_api: openblas
         prefix: libopenblas
       filepath: /usr/local/lib/python3.10/dist-packages/scipy.libs/libopenblasp-r0-41284840.3.18.so
        version: 0.3.18
threading_layer: pthreads
   architecture: Haswell
    num_threads: 2
```

COMMENT:
It would make sense to make estimator be trained on all the data.

Get Outlook for Android<https://aka.ms/AAb9ysg>
________________________________
From: Guillaume Lemaitre ***@***.***>
Sent: Friday, June 16, 2023 5:40:26 PM
To: scikit-learn/scikit-learn ***@***.***>
Cc: Dr. Hanan Shteingart ***@***.***>; Author ***@***.***>
Subject: Re: [scikit-learn/scikit-learn] calibrated classifier cv estimator is not fitted (Issue #26596)


You are accessing the unfitted estimator. You should use instead the fitted attribute calibrated_classifiers_.

pipeline.calibrated_classifiers_[0].estimator.feature_importances_


—
Reply to this email directly, view it on GitHub<https://github.com/scikit-learn/scikit-learn/issues/26596#issuecomment-1594806599>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABNULTAAXEWF7F62T6YSZ63XLRV5VANCNFSM6AAAAAAZJI5R3A>.
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Labels: Bug, Needs Triage
calibrated classifier cv estimator is not fitted

### Describe the bug

fitted estimator behaves as if it is unfitted if under CalibatedClassifier CV


### Steps/Code to Reproduce

```
from sklearn.calibration import CalibratedClassifierCV
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.datasets import make_classification
from sklearn.pipeline import make_pipeline
pipeline = CalibratedClassifierCV(estimator=GradientBoostingClassifier())
pipeline.fit(x,y)
m=pipeline.estimator
m.feature_importances_m.feature_importances_
```

### Expected Results

feature importance

### Actual Results

> NotFittedError: This GradientBoostingClassifier instance is not fitted yet. Call 'fit' with appropriate arguments before using this estimator.

### Versions

```shell
System:
    python: 3.10.12 (main, Jun  7 2023, 12:45:35) [GCC 9.4.0]
executable: /usr/bin/python3
   machine: Linux-5.15.107+-x86_64-with-glibc2.31

Python dependencies:
      sklearn: 1.2.2
          pip: 23.1.2
   setuptools: 67.7.2
        numpy: 1.22.4
        scipy: 1.10.1
       Cython: 0.29.34
       pandas: 1.5.3
   matplotlib: 3.7.1
       joblib: 1.2.0
threadpoolctl: 3.1.0

Built with OpenMP: True

threadpoolctl info:
       user_api: blas
   internal_api: openblas
         prefix: libopenblas
       filepath: /usr/local/lib/python3.10/dist-packages/numpy.libs/libopenblas64_p-r0-2f7c42d4.3.18.so
        version: 0.3.18
threading_layer: pthreads
   architecture: Haswell
    num_threads: 2

       user_api: openmp
   internal_api: openmp
         prefix: libgomp
       filepath: /usr/local/lib/python3.10/dist-packages/scikit_learn.libs/libgomp-a34b3233.so.1.0.0
        version: None
    num_threads: 2

       user_api: blas
   internal_api: openblas
         prefix: libopenblas
       filepath: /usr/local/lib/python3.10/dist-packages/scipy.libs/libopenblasp-r0-41284840.3.18.so
        version: 0.3.18
threading_layer: pthreads
   architecture: Haswell
    num_threads: 2
```

COMMENT:
You can control this behavior with the parameter `ensemble`.

Labels: Bug, Needs Triage