Minimartzz/github-issues huggingface dataset:
Fixes to pubmed dataset download function
State: closed

Pubmed has updated its settings for 2022 and thus existing download script does not work. 

Comments:
Hi ! I think we can simply add a new configuration for the 2022 data instead of replacing them.
You can add the new configuration here:
```python
    BUILDER_CONFIGS = [
        datasets.BuilderConfig(name="2021", description="The 2021 annual record", version=datasets.Version("1.0.0")),
        datasets.BuilderConfig(name="2022", description="The 2022 annual record", version=datasets.Version("1.0.0")),
    ]
```

And we can have the URLs for these two versions this way:
```python
_URLs = {
    "2021": f"ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed21n{i:04d}.xml.gz" for i in range(1, 1063)],
    "2022": f"ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed22n{i:04d}.xml.gz" for i in range(1, 1114)]
}
```
and depending on the configuration name (you can get it with `self.config.name`) we can pick the URLs of 2021 or the ones of 2022 and pass them to the `dl_manager` in `_split_generators`

Feel free to ping me if you have questions or if I can help !

Hi @spacemanidol, thanks for your contribution.

The update of the PubMed dataset URL (besides the update of the corresponding metadata and the dummy data) was already merged to master branch in this other PR:
- #3692 

I'm closing this PR then.

@lhoestq please take into account that 2021 data is no longer accessible: every year PubMed releases the baseline data (containing all previous data until that year) and from that on, they release daily updates.  

> @lhoestq please take into account that 2021 data is no longer accessible: every year PubMed releases the baseline data (containing all previous data until that year) and from that on, they release daily updates.

Oh ok I didn't know, thanks
Add support for continuous metrics (RMSE, MAE)
State: closed
Labels: description: New feature or request
name: enhancement

description: Good for newcomers
name: good first issue

**Is your feature request related to a problem? Please describe.**

I am uploading our dataset and models for the "Constructing interval measures" method we've developed, which uses item response theory to convert multiple discrete labels into a continuous spectrum for hate speech. Once we have this outcome our NLP models conduct regression rather than classification, so binary metrics are not relevant. The only continuous metrics available at https://huggingface.co/metrics are pearson & spearman correlation, which don't ensure that the prediction is on the same scale as the outcome.

**Describe the solution you'd like**
I would like to be able to tag our models on the Hub with the following metrics:
- RMSE
- MAE

**Describe alternatives you've considered**

I don't know if there are any alternatives.

**Additional context**
Our preprint is available here: https://arxiv.org/abs/2009.10277 . We are making it available for use in Jigsaw's Toxic Severity Rating Kaggle competition: https://www.kaggle.com/c/jigsaw-toxic-severity-rating/overview . I have our first model uploaded to the Hub at https://huggingface.co/ucberkeley-dlab/hate-measure-roberta-large

Thanks,
Chris


Comments:
Hey @ck37 

You can always use a custom metric as explained [in this guide from HF](https://huggingface.co/docs/datasets/master/loading_metrics.html#using-a-custom-metric-script).

If this issue needs to be contributed to (for enhancing the metric API) I think [this link](https://scikit-learn.org/stable/modules/generated/sklearn.metrics.mean_absolute_error.html) would be helpful for the `MAE` metric.

You can use a local metric script just by providing its path instead of the usual shortcut name 

#self-assign I have starting working on this issue to enhance the metric API.
Adding Turkic X-WMT evaluation set for machine translation
State: closed

This dataset is a human-translated evaluation set for MT crowdsourced and provided by the [Turkic Interlingua ](turkic-interlingua.org) community. It contains eval sets for 8 Turkic languages covering 88 language directions. Languages being covered are:

Azerbaijani (az)
Bashkir (ba)
English (en)
Karakalpak (kaa)
Kazakh (kk)
Kirghiz (ky)
Russian (ru)
Turkish (tr)
Sakha (sah)
Uzbek (uz)

More info about the corpus is here: [https://github.com/turkic-interlingua/til-mt/tree/master/xwmt](https://github.com/turkic-interlingua/til-mt/tree/master/xwmt)

A paper describing the test set is here: [https://arxiv.org/abs/2109.04593](https://arxiv.org/abs/2109.04593)


Comments:
hi! Thank you for all the comments! I believe I addressed them all. Let me know if there is anything else

Hi there! I was wondering if there is anything else to change before this can be merged

@lhoestq Hi! Just a gentle reminder about the steps to merge this one! 

Thanks for the heads up ! I think I fixed the last issue with the YAML tags

The CI failure is unrelated to this PR and fixed on master, let's merge :)

Thanks a lot !
Dataset Viewer not showing Previews for Private Datasets
State: closed
Labels: description: New feature or request
name: enhancement

description: Related to the dataset viewer on huggingface.co
name: dataset-viewer

## Dataset viewer issue for 'abidlabs/test-audio-13'

It seems that the dataset viewer does not show previews for `private` datasets, even for the user who's private dataset it is. See [1] for example. If I change the visibility to public, then it does show, but it would be useful to have the viewer even for private datasets.

![image](https://user-images.githubusercontent.com/1778297/150200515-93ff1545-11fd-4793-be64-6bed3cd895e2.png)

**Link:** 

[1] https://huggingface.co/datasets/abidlabs/test-audio-13

**Am I the one who added this dataset?** 

Yes


Comments:
Sure, it's on the roadmap.

Closing in favor of https://github.com/huggingface/datasets-server/issues/39.
Add British Library books dataset
State: closed

This pull request adds a dataset of text from digitised (primarily 19th Century) books from the British Library. This collection has previously been used for training language models, e.g. https://github.com/dbmdz/clef-hipe/blob/main/hlms.md. It would be nice to make this dataset more accessible for others to use through datasets. 

This is still a WIP but I wanted to get some initial feedback in particular; I wanted to check:
- I am handling the use of `iter_archive` correctly - I intend to ensure that `dl_manager.download` gets the complete list of URLs to download upfront, so the progress bar knows how much is left to download and then to pass through the `gen_kwargs` a list of downloaded zip archives wrapped in `iter_archive`. I am unsure if there is a more elegant approach for this?
- the number of configs: I have aimed to keep this limited - there are a lot of URLs covering the entire dataset, but I have tried to base the configs on what I believe the majority of people will want to they are not presented with too many options - I am happy to hear suggestions for changing this

If there are other glaring omissions or mistakes, I'd be happy to hear them. If this approach seems sensible in general, I will finish all the remaining TODOs, generate dummy_data, etc. 
 

Comments:
Thanks for all the help and suggestions

> Since the dataset has a very specific structure it might not be that easy so feel free to ping me if you have questions or if I can help !

I did get a little stuck here! So far I have created directories for each config i.e:

`datasets/datasets/blbooks/dummy/1700_1799/1.0.2/dummy_data.zip` 

I have then added two examples of the `jsonl.gz` files that are in the underlying dataset to each dummy_data directory.This fails the test using local files. 

Since 

```python
def _generate_examples(self, data_dirs):
```

takes as input `data_dirs` which is a list of `iter_dirs` do I need to put the dummy files inside another directory? i.e. 

`datasets/datasets/blbooks/dummy/1700_1799/1.0.2/dummy_data/1700/00.jsonl.gz` 


 

I think I managed to create the dummy data :)

I think everything is good now, if you don't have other changes to do, please mark your PR as "ready for review" and ping me!

> I think I managed to create the dummy data :)

Thanks so much for that!

> I think everything is good now, if you don't have other changes to do, please mark your PR as "ready for review" and ping me!

Think it is ready to merge from my end @lhoestq. 

The CI failure on windows is unrelated to your PR and fixed on `master`, we can ignore it
Update url for conll2003
State: closed

Following https://github.com/huggingface/datasets/issues/3582 I'm changing the download URL of the conll2003 data files, since the previous host doesn't have the authorization to redistribute the data

Comments:
Hi. lhoestq 

![image](https://user-images.githubusercontent.com/21982975/150345097-154f2b1a-bb12-47af-bddf-40eec0a0dadb.png)
What is the solution for it?
you can see it is still doesn't work here.
https://colab.research.google.com/drive/1l52FGWuSaOaGYchit4CbmtUSuzNDx_Ok?usp=sharing
Thank you.


For now you can specify `load_dataset(..., revision="master")` to use the fix on `master`.

We'll also do a new release of `datasets` tomorrow I think
Readme info not being parsed to show on Dataset card page
State: closed
Labels: description: Something isn't working
name: bug

## Describe the bug
The info contained in the README.md file is not being shown in the dataset main page. Basic info and table of contents are properly formatted in the README.

## Steps to reproduce the bug

# Sample code to reproduce the bug
The README file is this one: https://huggingface.co/datasets/softcatala/Tilde-MODEL-Catalan/blob/main/README.md

## Expected results
README info should appear in the Dataset card page.

## Actual results
Nothing is shown. However, labels are parsed and shown successfully.


Comments:
i suspect a markdown parsing error, @severo do you want to take a quick look at it when you have some time?

# Problem
The issue seems to coming from the front matter of the README
```---
annotations_creators:
- no-annotation
language_creators:
- machine-generated
languages:
- 'ca'
- 'de'
licenses:
- cc-by-4.0
multilinguality:
- translation
pretty_name: Catalan-German aligned corpora to train NMT systems.
size_categories:
- "1M<n<10M"            
source_datasets:
- extended|tilde_model
task_categories:
- machine-translation
task_ids:
- machine-translation
---
``` 
# Solution
The fix is to correctly style the README as explained [here](https://huggingface.co/docs/datasets/v1.12.0/dataset_card.html). I have also correctly parsed the font matter as shown below:
```
---
annotations_creators: []
language_creators: [machine-generated]
languages: ['ca', 'de']
licenses: []
multilinguality:
- multilingual
pretty_name: 'Catalan-German aligned corpora to train NMT systems.'
size_categories: 
- 1M<n<10M
source_datasets: ['extended|tilde_model']
task_categories: ['machine-translation']
task_ids: ['machine-translation']
---
```
You can find the README for a sample dataset [here](https://huggingface.co/datasets/ritwikraha/Test)

Thank you. It finally worked implementing your changes and leaving a white line between title and text in the description.

Thanks, if this solves your issue, can you please close it?
ERROR: File "setup.py" or "setup.cfg" not found. Directory cannot be installed in editable mode: /content
State: closed
Labels: description: Something isn't working
name: bug

## Bug
The install of streaming dataset is giving following error.

## Steps to reproduce the bug
```python
! git clone https://github.com/huggingface/datasets.git
! cd datasets
! pip install -e ".[streaming]"
```

## Actual results
Cloning into 'datasets'...
remote: Enumerating objects: 50816, done.
remote: Counting objects: 100% (2356/2356), done.
remote: Compressing objects: 100% (1606/1606), done.
remote: Total 50816 (delta 834), reused 1741 (delta 525), pack-reused 48460
Receiving objects: 100% (50816/50816), 72.47 MiB | 27.68 MiB/s, done.
Resolving deltas: 100% (22541/22541), done.
Checking out files: 100% (6722/6722), done.
ERROR: File "setup.py" or "setup.cfg" not found. Directory cannot be installed in editable mode: /content



Comments:
Hi! The `cd` command in Jupyer/Colab needs to start with `%`, so this should work:
```
!git clone https://github.com/huggingface/datasets.git
%cd datasets
!pip install -e ".[streaming]"
```

thanks @mariosasko i had the same mistake and your solution is what was needed
Add ImageNet toy datasets from fastai
State: closed
Labels: description: Contribution to a dataset script
name: dataset contribution

Adds the ImageNet toy datasets from FastAI: Imagenette, Imagewoof and Imagewang.

TODOs:
* [ ] add dummy data
* [ ] add dataset card
* [ ] generate `dataset_info.json`

Comments:
Thanks for your contribution, @mariosasko. Are you still interested in adding this dataset?

We are removing the dataset scripts from this GitHub repo and moving them to the Hugging Face Hub: https://huggingface.co/datasets

We would suggest you create this dataset there. Please, feel free to tell us if you need some help.
fix multiple language downloading in mC4
State: closed

If we try to access multiple languages of the [mC4 dataset](https://github.com/huggingface/datasets/tree/master/datasets/mc4), it will throw an error. For example, if we do 
```python
mc4_subset_two_langs = load_dataset("mc4", languages=["st", "su"])
```
we got
```
FileNotFoundError: Couldn't find file at https://huggingface.co/datasets/allenai/c4/resolve/1ddc917116b730e1859edef32896ec5c16be51d0/multilingual/c4-st+su.tfrecord-00000-of-00002.json.gz
```
Now it should work. Check it (from the root dir of a project): 
```python
mc4_subset_two_langs = load_dataset("./datasets/mc4/", languages=["st", "su"])
```

Comments:
The CI failure is unrelated to your PR and fixed on master, merging :)
Add support for time, date, duration, and decimal dtypes
State: closed

Add support for the pyarrow time (maps to `datetime.time` in python), date (maps to `datetime.time` in python), duration (maps to `datetime.timedelta` in python), and decimal (maps to `decimal.decimal` in python) dtypes. This should be helpful when writing scripts for time-series datasets. 

Comments:
Is there a dataset which uses these four datatypes for tests purposes?


@severo Not yet. I'll let you know if that changes.
Pin torchmetrics to fix the COMET test
State: closed

Torchmetrics 0.7.0 got released and has issues with `transformers` (see https://github.com/PyTorchLightning/metrics/issues/770)

I'm pinning it to 0.6.0 in the CI, since 0.7.0 makes the COMET metric test fail. COMET requires torchmetrics==0.6.0 anyway.

Comments:
No module named 'fsspec.archive'
State: closed
Labels: description: Something isn't working
name: bug

## Describe the bug
Cannot import datasets after installation.

## Steps to reproduce the bug
```shell
$ python
Python 3.9.7 (default, Sep 16 2021, 13:09:58)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import datasets
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/shuchen/miniconda3/envs/hf/lib/python3.9/site-packages/datasets/__init__.py", line 34, in <module>
    from .arrow_dataset import Dataset, concatenate_datasets
  File "/home/shuchen/miniconda3/envs/hf/lib/python3.9/site-packages/datasets/arrow_dataset.py", line 61, in <module>
    from .arrow_writer import ArrowWriter, OptimizedTypedSequence
  File "/home/shuchen/miniconda3/envs/hf/lib/python3.9/site-packages/datasets/arrow_writer.py", line 28, in <module>
    from .features import (
  File "/home/shuchen/miniconda3/envs/hf/lib/python3.9/site-packages/datasets/features/__init__.py", line 2, in <module>
    from .audio import Audio
  File "/home/shuchen/miniconda3/envs/hf/lib/python3.9/site-packages/datasets/features/audio.py", line 7, in <module>
    from ..utils.streaming_download_manager import xopen
  File "/home/shuchen/miniconda3/envs/hf/lib/python3.9/site-packages/datasets/utils/streaming_download_manager.py", line 18, in <module>
    from ..filesystems import COMPRESSION_FILESYSTEMS
  File "/home/shuchen/miniconda3/envs/hf/lib/python3.9/site-packages/datasets/filesystems/__init__.py", line 6, in <module>
    from . import compression
  File "/home/shuchen/miniconda3/envs/hf/lib/python3.9/site-packages/datasets/filesystems/compression.py", line 5, in <module>
    from fsspec.archive import AbstractArchiveFileSystem
ModuleNotFoundError: No module named 'fsspec.archive'
```


Comments:
Revisit `enable/disable_` toggle function prefix
State: closed
Labels: description: New feature or request
name: enhancement

As discussed in https://github.com/huggingface/transformers/pull/15167, we should revisit the `enable/disable_` toggle function prefix, potentially in favor of `set_enabled_`. Concretely, this translates to

- De-deprecating `disable_progress_bar()`
- Adding `enable_progress_bar()`
- On the caching side, adding `enable_caching` and `disable_caching`

Additional decisions have to be made with regards to the existing `set_enabled_X` functions; that is, whether to keep them as is or deprecate them in favor of the aforementioned functions. 

cc @mariosasko @lhoestq 

Comments:
Datasets streaming + map doesn't work for `Audio`
State: closed
Labels: description: Something isn't working
name: bug

description: This issue or pull request already exists
name: duplicate

## Describe the bug
When using audio datasets in streaming mode, applying a `map(...)` before iterating leads to an error as the key `array` does not exist anymore.

## Steps to reproduce the bug

```python
from datasets import load_dataset

ds = load_dataset("common_voice", "en", streaming=True, split="train")


def map_fn(batch):
    print("audio keys", batch["audio"].keys())
    batch["audio"] = batch["audio"]["array"][:100]
    return batch


ds = ds.map(map_fn) 

sample = next(iter(ds))
```

I think the audio is somehow decoded before `.map(...)` is actually called.

## Expected results

IMO, the above code snippet should work.

## Actual results

```bash
audio keys dict_keys(['path', 'bytes'])
Traceback (most recent call last):
  File "./run_audio.py", line 15, in <module>
    sample = next(iter(ds))
  File "/home/patrick/python_bin/datasets/iterable_dataset.py", line 341, in __iter__
    for key, example in self._iter():
  File "/home/patrick/python_bin/datasets/iterable_dataset.py", line 338, in _iter
    yield from ex_iterable
  File "/home/patrick/python_bin/datasets/iterable_dataset.py", line 192, in __iter__
    yield key, self.function(example)
  File "./run_audio.py", line 9, in map_fn
    batch["input"] = batch["audio"]["array"][:100]
KeyError: 'array'
```

## Environment info
<!-- You can run the command `datasets-cli env` and copy-and-paste its output below. -->
- `datasets` version: 1.17.1.dev0
- Platform: Linux-5.3.0-64-generic-x86_64-with-glibc2.17
- Python version: 3.8.12
- PyArrow version: 6.0.1


Comments:
This seems related to https://github.com/huggingface/datasets/issues/3505.
https://huggingface.co/datasets/huggingface/transformers-metadata
State: closed
Labels: description: This will not be worked on
name: wontfix

description: Related to the dataset viewer on huggingface.co
name: dataset-viewer

## Dataset viewer issue for '*name of the dataset*'

**Link:** *link to the dataset viewer page*

*short description of the issue*

Am I the one who added this dataset ? Yes-No


Comments:
Add The Medical Segmentation Decathlon Dataset
State: open
Labels: description: Requesting to add a new dataset
name: dataset request

description: Vision datasets
name: vision

## Adding a Dataset
- **Name:** *The Medical Segmentation Decathlon Dataset*
- **Description:** The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data, and small objects. 
- **Paper:** [link to the dataset paper if available](https://arxiv.org/abs/2106.05735)
- **Data:** http://medicaldecathlon.com/
- **Motivation:** Hugging Face seeks to democratize ML for society. One of the growing niches within ML is the ML + Medicine community. Key data sets will help increase the supply of HF resources for starting an initial community.

(cc @osanseviero @abidlabs )

Instructions to add a new dataset can be found [here](https://github.com/huggingface/datasets/blob/master/ADD_NEW_DATASET.md).


Comments:
Hello! I have recently been involved with a medical image segmentation project myself and was going through the `The Medical Segmentation Decathlon Dataset` as well. 
I haven't yet had experience adding datasets to this repository yet but would love to get started. Should I take this issue?
If yes, I've got two questions -
1. There are 10 different datasets available, so are all datasets to be added in a single PR, or one at a time? 
2. Since it's a competition, masks for the test-set are not available. How is that to be tackled? Sorry if it's a silly question, I have recently started exploring `datasets`.

Hi! Sure, feel free to take this issue. You can self-assign the issue by commenting `#self-assign`.

To answer your questions:
1. It makes the most sense to add each one as a separate config, so one dataset script with 10 configs in a single PR.
2. Just set masks in the test set to `None`.

Note that the images/masks in this dataset are in NIfTI format, which our `Image` feature currently doesn't support, so I think it's best to yield the paths to the images/masks in the script and add a preprocessing section to the card where we explain how to load/process the images/masks with `nibabel` (I can help with that).   



> Note that the images/masks in this dataset are in NIfTI format, which our `Image` feature currently doesn't support, so I think it's best to yield the paths to the images/masks in the script and add a preprocessing section to the card where we explain how to load/process the images/masks with `nibabel` (I can help with that).

Gotcha, thanks. Will start working on the issue and let you know in case of any doubt.

#self-assign

This is great! There is a first model on the HUb that uses this dataset! https://huggingface.co/MONAI/example_spleen_segmentation