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Fix HfFileSystem docstring
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Expose method and fix param
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A fix + expose a new method, following https://github.com/huggingface/datasets/pull/3670
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Fix head_qa data URL
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Fix #3758.
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Update URL for tagging app
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[ "Oh, this URL shouldn't be updated to the tagging app as it's actually used for creating the README - closing this." ]
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This PR updates the URL for the tagging app to be the one on Spaces.
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!
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## 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
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It's not possible download `20200501.pt` dataset
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[ "Hi @jvanz, thanks for reporting.\r\n\r\nPlease note that Wikimedia website does not longer host Wikipedia dumps for so old dates.\r\n\r\nFor a list of accessible dump dates of `pt` Wikipedia, please see: https://dumps.wikimedia.org/ptwiki/\r\n\r\nYou can load for example `20220220` `pt` Wikipedia:\r\n```python\r\ndataset = load_dataset(\"wikipedia\", language=\"pt\", date=\"20220220\", beam_runner=\"DirectRunner\")\r\n```", "> ```python\r\n> dataset = load_dataset(\"wikipedia\", language=\"pt\", date=\"20220220\", beam_runner=\"DirectRunner\")\r\n> ```\r\n\r\nThank you! I did not know that I can do this. I was following the example in the error message when I do not define which language dataset I'm trying to download.\r\n\r\nI've tried something similar changing the date in the `load_dataset` call that I've shared in the bug description. Obviously, it did not work. I need to read the docs more carefully next time. My bad!\r\n\r\nThanks again and sorry for the noise.\r\n\r\n" ]
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## Describe the bug The dataset `20200501.pt` is broken. The available datasets: https://dumps.wikimedia.org/ptwiki/ ## Steps to reproduce the bug ```python from datasets import load_dataset dataset = load_dataset("wikipedia", "20200501.pt", beam_runner='DirectRunner') ``` ## Expected results I expect to download the dataset locally. ## Actual results ``` >>> from datasets import load_dataset >>> dataset = load_dataset("wikipedia", "20200501.pt", beam_runner='DirectRunner') Downloading and preparing dataset wikipedia/20200501.pt to /home/jvanz/.cache/huggingface/datasets/wikipedia/20200501.pt/1.0.0/009f923d9b6dd00c00c8cdc7f408f2b47f45dd4f5fb7982a21f9448f4afbe475... /home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/apache_beam/__init__.py:79: UserWarning: This version of Apache Beam has not been sufficiently tested on Python 3.9. You may encounter bugs or missing features. warnings.warn( 0%| | 0/1 [00:00<?, ?it/s] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/load.py", line 1702, in load_dataset builder_instance.download_and_prepare( File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/builder.py", line 594, in download_and_prepare self._download_and_prepare( File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/builder.py", line 1245, in _download_and_prepare super()._download_and_prepare( File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/builder.py", line 661, in _download_and_prepare split_generators = self._split_generators(dl_manager, **split_generators_kwargs) File "/home/jvanz/.cache/huggingface/modules/datasets_modules/datasets/wikipedia/009f923d9b6dd00c00c8cdc7f408f2b47f45dd4f5fb7982a21f9448f4afbe475/wikipedia.py", line 420, in _split_generators downloaded_files = dl_manager.download_and_extract({"info": info_url}) File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/utils/download_manager.py", line 307, in download_and_extract return self.extract(self.download(url_or_urls)) File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/utils/download_manager.py", line 195, in download downloaded_path_or_paths = map_nested( File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/utils/py_utils.py", line 260, in map_nested mapped = [ File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/utils/py_utils.py", line 261, in <listcomp> _single_map_nested((function, obj, types, None, True)) File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/utils/py_utils.py", line 196, in _single_map_nested return function(data_struct) File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/utils/download_manager.py", line 216, in _download return cached_path(url_or_filename, download_config=download_config) File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/utils/file_utils.py", line 298, in cached_path output_path = get_from_cache( File "/home/jvanz/anaconda3/envs/tf-gpu/lib/python3.9/site-packages/datasets/utils/file_utils.py", line 612, in get_from_cache raise FileNotFoundError(f"Couldn't find file at {url}") FileNotFoundError: Couldn't find file at https://dumps.wikimedia.org/ptwiki/20200501/dumpstatus.json ``` ## Environment info ``` - `datasets` version: 1.18.3 - Platform: Linux-5.3.18-150300.59.49-default-x86_64-with-glibc2.31 - Python version: 3.9.7 - PyArrow version: 6.0.1 ```
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3,762
`Dataset.class_encode` should support custom class names
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[ "Hi @Dref360, thanks a lot for your proposal.\r\n\r\nIt totally makes sense to have more flexibility when class encoding, I agree.\r\n\r\nYou could even further customize the class encoding by passing an instance of `ClassLabel` itself (instead of replicating `ClassLabel` instantiation arguments as `Dataset.class_encode_column` arguments).\r\n\r\nAnd the latter made me think of `Dataset.cast_column`...\r\n\r\nMaybe better to have some others' opinions @lhoestq @mariosasko ", "Hi @Dref360! You can use [`Dataset.align_labels_with_mapping`](https://huggingface.co/docs/datasets/master/package_reference/main_classes.html#datasets.Dataset.align_labels_with_mapping) after `Dataset.class_encode_column` to assign a different mapping of labels to ids.\r\n\r\n@albertvillanova I'd like to avoid adding more complexity to the API where it's not (absolutely) needed, so I don't think introducing a new param in `Dataset.class_encode_column` is a good idea.\r\n\r\n", "I wasn't aware that it existed thank you for the link.\n\nClosing then! " ]
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I can make a PR, just wanted approval before starting. **Is your feature request related to a problem? Please describe.** It is often the case that classes are not ordered in alphabetical order. Current `class_encode_column` sort the classes before indexing. https://github.com/huggingface/datasets/blob/master/src/datasets/arrow_dataset.py#L1235 **Describe the solution you'd like** I would like to add a **optional** parameter `class_names` to `class_encode_column` that would be used for the mapping instead of sorting the unique values. **Describe alternatives you've considered** One can use map instead. I find it harder to read. ```python CLASS_NAMES = ['apple', 'orange', 'potato'] ds = ds.map(lambda item: CLASS_NAMES.index(item[label_column])) # Proposition ds = ds.class_encode_column(label_column, CLASS_NAMES) ``` **Additional context** I can make the PR if this feature is accepted.
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3,761
Know your data for HF hub
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[ "Hi @Muhtasham you should take a look at https://huggingface.co/blog/data-measurements-tool and accompanying demo app at https://huggingface.co/spaces/huggingface/data-measurements-tool\r\n\r\nWe would be interested in your feedback. cc @meg-huggingface @sashavor @yjernite " ]
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**Is your feature request related to a problem? Please describe.** Would be great to see be able to understand datasets with the goal of improving data quality, and helping mitigate fairness and bias issues. **Describe the solution you'd like** Something like https://knowyourdata.withgoogle.com/ for HF hub
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Unable to view the Gradio flagged call back dataset
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[ "Hi @kingabzpro.\r\n\r\nI think you need to create a loading script that creates the dataset from the CSV file and the image paths.\r\n\r\nAs example, you could have a look at the Food-101 dataset: https://huggingface.co/datasets/food101\r\n- Loading script: https://huggingface.co/datasets/food101/blob/main/food101.py\r\n\r\nOnce the loading script is created, the viewer will show a previsualization of your dataset. ", "@albertvillanova I don't think this is the issue. I have created another dataset with similar files and format and it works. https://huggingface.co/datasets/kingabzpro/savtadepth-flags-V2", "Yes, you are right, that was not the issue.\r\n\r\nJust take into account that sometimes the viewer can take some time until it shows the preview of the dataset.\r\nAfter some time, yours is finally properly shown: https://huggingface.co/datasets/kingabzpro/savtadepth-flags", "The problem was resolved by deleted the dataset and creating new one with similar name and then clicking on flag button.", "I think if you make manual changes to dataset the whole system breaks. " ]
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## Dataset viewer issue for '*savtadepth-flags*' **Link:** *[savtadepth-flags](https://huggingface.co/datasets/kingabzpro/savtadepth-flags)* *with the Gradio 2.8.1 the dataset viers stopped working. I tried to add values manually but its not working. The dataset is also not showing the link with the app https://huggingface.co/spaces/kingabzpro/savtadepth.* Am I the one who added this dataset ? Yes
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Rename GenerateMode to DownloadMode
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This PR: - Renames `GenerateMode` to `DownloadMode` - Implements `DeprecatedEnum` - Deprecates `GenerateMode` Close #769.
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head_qa file missing
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[ "We usually find issues with files hosted at Google Drive...\r\n\r\nIn this case we download the Google Drive Virus scan warning instead of the data file." ]
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## Describe the bug A file for the `head_qa` dataset is missing (https://drive.google.com/u/0/uc?export=download&id=1a_95N5zQQoUCq8IBNVZgziHbeM-QxG2t/HEAD_EN/train_HEAD_EN.json) ## Steps to reproduce the bug ```python >>> from datasets import load_dataset >>> load_dataset("head_qa", name="en") ``` ## Expected results The dataset should be loaded ## Actual results ``` Downloading and preparing dataset head_qa/en (download: 75.69 MiB, generated: 2.69 MiB, post-processed: Unknown size, total: 78.38 MiB) to /home/slesage/.cache/huggingface/datasets/head_qa/en/1.1.0/583ab408e8baf54aab378c93715fadc4d8aa51b393e27c3484a877e2ac0278e9... Downloading data: 2.21kB [00:00, 2.05MB/s] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/slesage/hf/datasets-preview-backend/.venv/lib/python3.9/site-packages/datasets/load.py", line 1729, in load_dataset builder_instance.download_and_prepare( File "/home/slesage/hf/datasets-preview-backend/.venv/lib/python3.9/site-packages/datasets/builder.py", line 594, in download_and_prepare self._download_and_prepare( File "/home/slesage/hf/datasets-preview-backend/.venv/lib/python3.9/site-packages/datasets/builder.py", line 665, in _download_and_prepare verify_checksums( File "/home/slesage/hf/datasets-preview-backend/.venv/lib/python3.9/site-packages/datasets/utils/info_utils.py", line 40, in verify_checksums raise NonMatchingChecksumError(error_msg + str(bad_urls)) datasets.utils.info_utils.NonMatchingChecksumError: Checksums didn't match for dataset source files: ['https://drive.google.com/u/0/uc?export=download&id=1a_95N5zQQoUCq8IBNVZgziHbeM-QxG2t'] ``` ## Environment info - `datasets` version: 1.18.4.dev0 - Platform: Linux-5.11.0-1028-aws-x86_64-with-glibc2.31 - Python version: 3.9.6 - PyArrow version: 6.0.1
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Add perplexity to metrics
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[ "Awesome thank you ! The implementation of the parent `Metric` class was assuming that all metrics were supposed to have references/predictions pairs - I just changed that so you don't have to override `compute()`. I took the liberty of doing the changes directly inside this PR to make sure it works as expected with perplexity.\r\n\r\nOther than that it looks in pretty good shape :) I just did minor changes like remove a remaining `print` as well as fixing the `Features` defined in `_info()`. I also renamed `input_text` to `input_texts` since it makes it more obvious that it's a list of strings - let me know if it sounds good to you.\r\n\r\nLet me know if you'd like to make other changes or if it's all good for you !" ]
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Adding perplexity metric This code differs from the code in [this](https://huggingface.co/docs/transformers/perplexity) HF blog post because the blogpost code fails in at least the following circumstances: - returns nans whenever the stride = 1 - hits a runtime error when the stride is significantly larger than the max model length (e.g. if max_model_length = 512 and stride = 1024) Note that: - As it is, it only works for causal models. Pseudoperplexity can be added later as another metric to work with masked language models. - It takes in a list of strings so that it can be dataset independent. This does mean that it doesn't currently batch inputs, and is therefore relatively slow. - It overwrites the metrics compute() function for a specific perplexity compute() function. This is because the current general metrics compute() function requires model-generated predictions, which doesn't make sense in the context of perplexity
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Images get decoded when using `map()` with `input_columns` argument on a dataset
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[ "Hi! If I'm not mistaken, this behavior is intentional, but I agree it could be more intuitive.\r\n\r\n@albertvillanova Do you remember why you decided not to decode columns in the `Audio` feature PR when `input_columns` is not `None`? IMO we should decode those columns, and we don't even have to use lazy structures here because the user explicitly requires them in the map transform. \r\n\r\ncc @lhoestq for visibility", "I think I excluded to decorate the function when `input_columns` were passed as a quick fix for some non-passing tests: \r\n- https://github.com/huggingface/datasets/pull/2324/commits/9d7c3e8fa53e23ec636859b4407eeec904b1b3f9\r\n\r\nThat PR was quite complex and I decided to focus on the main feature requests, leaving refinements for subsequent PRs.\r\n\r\nNote that when `input_columns` are passed, the signature of the function is effectively changed, while the decorated function expects an item (whether an example or a batch) as first arg (which is not the case when passing `input_columns`.\r\n\r\nI agree we should consider supporting the case when `input_columns` are passed." ]
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## Describe the bug The `datasets.features.Image` feature class decodes image data by default. Expectedly, when indexing a dataset or using the `map()` method, images are returned as PIL Image instances. However, when calling `map()` and setting a specific data column with the `input_columns` argument, the image data is passed as raw byte representation to the mapping function. ## Steps to reproduce the bug ```python from datasets import load_dataset from torchvision import transforms from PIL.Image import Image dataset = load_dataset('mnist', split='train') def transform_all_columns(example): # example['image'] is encoded as PIL Image assert isinstance(example['image'], Image) return example def transform_image_column(image): # image is decoded here and represented as raw bytes assert isinstance(image, Image) return image # single-sample dataset for debugging purposes dev = dataset.select([0]) dev.map(transform_all_columns) dev.map(transform_image_column, input_columns='image') ``` ## Expected results Image data should be passed in decoded form, i.e. as PIL Image objects to the mapping function unless the `decode` attribute on the image feature is set to `False`. ## Actual results The mapping function receives images as raw byte data. ## Environment info - `datasets` version: 1.18.3 - Platform: Linux-5.11.0-49-generic-x86_64-with-glibc2.32 - Python version: 3.8.0b4 - PyArrow version: 7.0.0
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[ "Thanks for reporting. The dataset viewer depends on some backend treatments, and for now, they might take some hours to get processed. We're working on improving it.", "It has finally been processed. Thanks for the patience.", "Thanks for the info @severo !" ]
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## Dataset viewer issue for '*rubrix/news*' **Link:https://huggingface.co/datasets/rubrix/news** *link to the dataset viewer page* Cannot see the dataset preview: ``` Status code: 400 Exception: Status400Error Message: Not found. Cache is waiting to be refreshed. ``` Am I the one who added this dataset ? No
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Overflowing indices in `select`
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[ "Fixed on master (see https://github.com/huggingface/datasets/pull/3719).", "Awesome, I did not find that one! Thanks." ]
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## Describe the bug The `Dataset.select` function seems to accept indices that are larger than the dataset size and seems to effectively use `index %len(ds)`. ## Steps to reproduce the bug ```python from datasets import Dataset ds = Dataset.from_dict({"test": [1,2,3]}) ds = ds.select(range(5)) print(ds) print() print(ds["test"]) ``` Result: ```python Dataset({ features: ['test'], num_rows: 5 }) [1, 2, 3, 1, 2] ``` This behaviour is not documented and can lead to unexpected behaviour when for example taking a sample larger than the dataset and thus creating a lot of duplicates. ## Expected results It think this should throw an error or at least a very big warning: ```python IndexError: Invalid key: 5 is out of bounds for size 3 ``` ## Environment info - `datasets` version: 1.18.3 - Platform: macOS-12.0.1-x86_64-i386-64bit - Python version: 3.9.10 - PyArrow version: 7.0.0
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Expanding streaming capabilities
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[ "Related to: https://github.com/huggingface/datasets/issues/3444", "Cool ! `filter` will be very useful. There can be a filter that you can apply on a streaming dataset:\r\n```python\r\nload_dataset(..., streaming=True).filter(lambda x: x[\"lang\"] == \"sw\")\r\n```\r\n\r\nOtherwise if you want to apply a filter on the source files that are going to be used for streaming, the logic has to be impIemented directly in the dataset script, or if there's no dataset script this can be done with pattern matching\r\n```python\r\nload_dataset(..., lang=\"sw\") # if the dataset script supports this parameter\r\nload_dataset(..., data_files=\"data/lang=sw/*\") # if there's no dataset script, but only data files\r\n```\r\n\r\n--------------\r\n\r\nHere are also some additional ideas of API to convert from iterable to map-style dataset:\r\n```python\r\non_disk_dataset = streaming_dataset.to_disk()\r\non_disk_dataset = streaming_dataset.to_disk(path=\"path/to/my/dataset/dir\")\r\n\r\nin_memory_dataset = streaming_dataset.take(100).to_memory() # to experiment without having to write files\r\n```\r\n--------------\r\n\r\nFinally regarding `push_to_hub`, we can replace `batch_size` by `shard_size` (same API as for on-disk datasets). The default is 500MB per file\r\n\r\nLet me know what you think !" ]
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Some ideas for a few features that could be useful when working with large datasets in streaming mode. ## `filter` for `IterableDataset` Adding filtering to streaming datasets would be useful in several scenarios: - filter a dataset with many languages for a subset of languages - filter a dataset for specific licenses - other custom logic to get a subset The only way to achieve this at the moment is I think through writing a custom loading script and implementing filters there. ## `IterableDataset` to `Dataset` conversion In combination with the above filter a functionality to "play" the whole stream would be useful. The motivation is that often one might filter the dataset to get a manageable size for experimentation. In that case streaming mode is no longer necessary as the filtered dataset is small enough and it would be useful to be able to play through the whole stream to create a normal `Dataset` with all its benefits. ```python ds = load_dataset("some_large_dataset", streaming=True) ds_filter = ds.filter(lambda x: x["lang"]="fr") ds_filter = ds_filter.stream() # here the `IterableDataset` is converted to a `Dataset` ``` Naturally, this could be expanded with `stream(n=1000)` which creates a `Dataset` with the first `n` elements similar to `take`. ## Stream to the Hub While streaming allows to use a dataset as is without saving the whole dataset on the local machine it is currently not possible to process a dataset and add it to the hub. The only way to do this is by downloading the full dataset and saving the processed dataset again before pushing them to the hub. The API could looks something like: ```python ds = load_dataset("some_large_dataset", streaming=True) ds_filter = ds.filter(some_filter_func) ds_processed = ds_filter.map(some_processing_func) ds_processed.push_to_hub("new_better_dataset", batch_size=100_000) ``` Under the hood this could be done by processing and aggregating `batch_size` elements and then pushing that batch as a single file to the hub. With this functionality one could process and create TB scale datasets while only requiring size of `batch_size` local disk space. cc @lhoestq @albertvillanova
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Update metadata JSON for cats_vs_dogs dataset
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Note that the number of examples in the train split was already fixed in the dataset card. Fix #3750.
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Fix typo in train split name
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In the README guide (and consequently in many datasets) there was a typo in the train split name: ``` | Tain | Valid | Test | ``` This PR: - fixes the typo in the train split name - fixes the column alignment of the split tables in the README guide and in all datasets.
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`NonMatchingSplitsSizesError` for cats_vs_dogs dataset
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[ "Thnaks for reporting @jaketae. We are fixing it. " ]
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## Describe the bug Cannot download cats_vs_dogs dataset due to `NonMatchingSplitsSizesError`. ## Steps to reproduce the bug ```python from datasets import load_dataset dataset = load_dataset("cats_vs_dogs") ``` ## Expected results Loading is successful. ## Actual results ``` NonMatchingSplitsSizesError: [{'expected': SplitInfo(name='train', num_bytes=7503250, num_examples=23422, dataset_name='cats_vs_dogs'), 'recorded': SplitInfo(name='train', num_bytes=7262410, num_examples=23410, dataset_name='cats_vs_dogs')}] ``` ## Environment info Reproduced on a fresh [Colab notebook](https://colab.research.google.com/drive/13GTvrSJbBGvL2ybDdXCBZwATd6FOkMub?usp=sharing). ## Additional Context Originally reported in https://github.com/huggingface/transformers/issues/15698. cc @mariosasko
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Add tqdm arguments
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In this PR, tqdm arguments can be passed to the map() function and such, in order to be more flexible.
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Add tqdm arguments
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In this PR, there are two changes. 1. It is able to show the progress bar by adding the length of the iterator. 2. Pass in tqdm_kwargs so that can enable more feasibility for the control of tqdm library.
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Passing invalid subset should throw an error
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## Describe the bug Only some datasets have a subset (as in `load_dataset(name, subset)`). If you pass an invalid subset, an error should be thrown. ## Steps to reproduce the bug ```python import datasets datasets.load_dataset('rotten_tomatoes', 'asdfasdfa') ``` ## Expected results This should break, since `'asdfasdfa'` isn't a subset of the `rotten_tomatoes` dataset. ## Actual results This API call silently succeeds.
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Use the same seed to shuffle shards and metadata in streaming mode
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When shuffling in streaming mode, those two entangled lists are shuffled independently. In this PR I changed this to shuffle the lists of same length with the exact same seed, in order for the files and metadata to still be aligned. ```python gen_kwargs = { "files": [os.path.join(data_dir, filename) for filename in all_files], "metadata_files": [all_metadata[filename] for filename in all_files], } ``` IMO this is important to avoid big but silent issues. Fix https://github.com/huggingface/datasets/issues/3744
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Add mIoU metric
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This PR adds the mean Intersection-over-Union metric to the library, useful for tasks like semantic segmentation. It is entirely based on mmseg's [implementation](https://github.com/open-mmlab/mmsegmentation/blob/master/mmseg/core/evaluation/metrics.py). I've removed any PyTorch dependency, and rely on Numpy only.
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Better shards shuffling in streaming mode
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Sometimes a dataset script has a `_split_generators` that returns several files as well as the corresponding metadata of each file. It often happens that they end up in two separate lists in the `gen_kwargs`: ```python gen_kwargs = { "files": [os.path.join(data_dir, filename) for filename in all_files], "metadata_files": [all_metadata[filename] for filename in all_files], } ``` It happened for Multilingual Spoken Words for example in #3666 However currently **the two lists are shuffled independently** when shuffling the shards in streaming mode. This leads to `_generate_examples` not having the right metadata for each file. To prevent this issue I suggest that we always shuffle lists of the same length the exact same way to avoid such a big but silent issue. cc @polinaeterna
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Fix ValueError message formatting in int2str
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Hi! I bumped into this particular `ValueError` during my work (because an instance of `np.int64` was passed instead of regular Python `int`), and so I had to `print(type(values))` myself. Apparently, it's just the missing `f` to make message an f-string. It ain't much for a contribution, but it's honest work. Hope it spares someone else a few seconds in the future 😃
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Rm sphinx doc
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Checklist - [x] Update circle ci yaml - [x] Delete sphinx static & python files in docs dir - [x] Update readme in docs dir - [ ] Update docs config in setup.py
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Support streaming for pubmed
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[ "@albertvillanova just FYI, since you were so helpful with the previous pubmed issue :) ", "IIRC streaming from FTP is not fully tested yet, so I'm fine with switching to HTTPS for now, as long as the download speed/availability is great", "@albertvillanova Thanks for pointing me to the `ET` module replacement. It should look a lot cleaner now.\r\n\r\nUnfortunately I tried keeping the `ftp://` protocol but was seeing timeout errors? in streaming mode (below). I think the `https://` performance is not an issue, when I was profiling the `open(..) -> f.read() -> etree.fromstring(xml_str)` codepath, most of the time was spent in the XML parsing rather than the data download.\r\n\r\n\r\nError when using `ftp://`:\r\n\r\n```\r\nTraceback (most recent call last):\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/venv/lib/python3.8/site-packages/fsspec/implementations/ftp.py\", line 301, in _fetch_range\r\n self.fs.ftp.retrbinary(\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/ftplib.py\", line 430, in retrbinary\r\n callback(data)\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/venv/lib/python3.8/site-packages/fsspec/implementations/ftp.py\", line 293, in callback\r\n raise TransferDone\r\nfsspec.implementations.ftp.TransferDone\r\n\r\nDuring handling of the above exception, another exception occurred:\r\n\r\nTraceback (most recent call last):\r\n File \"test_pubmed_streaming.py\", line 9, in <module>\r\n print (next(iter(pubmed_train_streaming)))\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/abhi-datasets/src/datasets/iterable_dataset.py\", line 365, in __iter__\r\n for key, example in self._iter():\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/abhi-datasets/src/datasets/iterable_dataset.py\", line 362, in _iter\r\n yield from ex_iterable\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/abhi-datasets/src/datasets/iterable_dataset.py\", line 79, in __iter__\r\n yield from self.generate_examples_fn(**self.kwargs)\r\n File \"/Users/abhinav/.cache/huggingface/modules/datasets_modules/datasets/pubmed/af552ed918e2841e8427203530e3cfed3a8bc3213041d7853bea1ca67eec683d/pubmed.py\", line 362, in _generate_examples\r\n tree = ET.parse(filename)\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/abhi-datasets/src/datasets/streaming.py\", line 65, in wrapper\r\n return function(*args, use_auth_token=use_auth_token, **kwargs)\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/abhi-datasets/src/datasets/utils/streaming_download_manager.py\", line 636, in xet_parse\r\n return ET.parse(f, parser=parser)\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/xml/etree/ElementTree.py\", line 1202, in parse\r\n tree.parse(source, parser)\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/xml/etree/ElementTree.py\", line 595, in parse\r\n self._root = parser._parse_whole(source)\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/abhi-datasets/src/datasets/utils/streaming_download_manager.py\", line 293, in read_with_retries\r\n out = read(*args, **kwargs)\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/gzip.py\", line 292, in read\r\n return self._buffer.read(size)\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/_compression.py\", line 68, in readinto\r\n data = self.read(len(byte_view))\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/gzip.py\", line 479, in read\r\n if not self._read_gzip_header():\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/gzip.py\", line 422, in _read_gzip_header\r\n magic = self._fp.read(2)\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/gzip.py\", line 96, in read\r\n self.file.read(size-self._length+read)\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/venv/lib/python3.8/site-packages/fsspec/spec.py\", line 1485, in read\r\n out = self.cache._fetch(self.loc, self.loc + length)\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/venv/lib/python3.8/site-packages/fsspec/caching.py\", line 153, in _fetch\r\n self.cache = self.fetcher(start, end) # new block replaces old\r\n File \"/Users/abhinav/Documents/mosaicml/hf_datasets/venv/lib/python3.8/site-packages/fsspec/implementations/ftp.py\", line 311, in _fetch_range\r\n self.fs.ftp.getmultiline()\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/ftplib.py\", line 224, in getmultiline\r\n line = self.getline()\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/ftplib.py\", line 206, in getline\r\n line = self.file.readline(self.maxline + 1)\r\n File \"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/socket.py\", line 669, in readinto\r\n return self._sock.recv_into(b)\r\nsocket.timeout: timed out\r\n```" ]
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This PR makes some minor changes to the `pubmed` dataset to allow for `streaming=True`. Fixes #3739. Basically, I followed the C4 dataset which works in streaming mode as an example, and made the following changes: * Change URL prefix from `ftp://` to `https://` * Explicilty `open` the filename and pass the XML contents to `etree.fromstring(xml_str)` The Github diff tool makes it look like the changes are larger than they are, sorry about that. I tested locally and the `pubmed` dataset now works in both normal and streaming modes. There is some overhead at the start of each shard in streaming mode as building the XML tree online is quite slow (each pubmed .xml.gz file is ~20MB), but the overhead gets amortized over all the samples in the shard. On my laptop with a single CPU worker I am able to stream at about ~600 samples/s.
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Pubmed dataset does not work in streaming mode
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[ "Thanks for reporting, @abhi-mosaic (related to #3655).\r\n\r\nPlease note that `xml.etree.ElementTree.parse` already supports streaming:\r\n- #3476\r\n\r\nNo need to refactor to use `open`/`xopen`. Is is enough with importing the package `as ET` (instead of `as etree`)." ]
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## Describe the bug Trying to use the `pubmed` dataset with `streaming=True` fails. ## Steps to reproduce the bug ```python import datasets pubmed_train = datasets.load_dataset('pubmed', split='train', streaming=True) print (next(iter(pubmed_train))) ``` ## Expected results I would expect to see the first training sample from the pubmed dataset. ## Actual results ``` Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/abhinav/Documents/mosaicml/mosaicml_venv/lib/python3.8/site-packages/datasets/iterable_dataset.py", line 367, in __iter__ for key, example in self._iter(): File "/Users/abhinav/Documents/mosaicml/mosaicml_venv/lib/python3.8/site-packages/datasets/iterable_dataset.py", line 364, in _iter yield from ex_iterable File "/Users/abhinav/Documents/mosaicml/mosaicml_venv/lib/python3.8/site-packages/datasets/iterable_dataset.py", line 79, in __iter__ for key, example in self.generate_examples_fn(**self.kwargs): File "/Users/abhinav/.cache/huggingface/modules/datasets_modules/datasets/pubmed/9715addf10c42a7877a2149ae0c5f2fddabefc775cd1bd9b03ac3f012b86ce46/pubmed.py", line 373, in _generate_examples tree = etree.parse(filename) File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/xml/etree/ElementTree.py", line 1202, in parse tree.parse(source, parser) File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/xml/etree/ElementTree.py", line 584, in parse source = open(source, "rb") FileNotFoundError: [Errno 2] No such file or directory: 'gzip://pubmed21n0001.xml::ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed21n0001.xml.gz' ``` ## Environment info <!-- You can run the command `datasets-cli env` and copy-and-paste its output below. --> - `datasets` version: 1.18.2 - Platform: macOS-11.4-x86_64-i386-64bit - Python version: 3.8.2 - PyArrow version: 6.0.0 ## Comments The error looks like an issue with `open` vs. `xopen` inside the `xml` package. It looks like it's trying to open the remote source URL, which has been edited with prefix `gzip://...`. Maybe there can be an explicit `xopen` before passing the raw data to `etree`, something like: ```python # Before tree = etree.parse(filename) root = tree.getroot() # After with xopen(filename) as f: data_str = f.read() root = etree.fromstring(data_str) ```
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For data-only datasets, streaming and non-streaming don't behave the same
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[ "Note that we might change the heuristic and create a different config per file, at least in that case.", "Hi @severo, thanks for reporting.\r\n\r\nYes, this happens because when non-streaming, a cast of all data is done in order to \"concatenate\" it all into a single dataset (thus the error), while this casting is not done while yielding item by item in streaming mode.\r\n\r\nMaybe in streaming mode we should keep the schema (inferred from the first item) and throw an exception if a subsequent item does not conform to the inferred schema?", "Why do we want to concatenate the files? Is it the expected behavior for most datasets that lack a script and dataset info?", "These files are two different dataset configurations since they don't share the same schema.\r\n\r\nIMO the streaming mode should fail in this case, as @albertvillanova said.\r\n\r\nThere is one challenge though: inferring the schema from the first example is not robust enough in the general case - especially if some fields are nullable. I guess we can at least make sure that no new columns are added", "OK. So, if we make the streaming also fail, the dataset https://huggingface.co/datasets/huggingface/transformers-metadata will never be [viewable](https://github.com/huggingface/datasets-preview-backend/issues/144) (be it using streaming or fallback to downloading the files), right?\r\n", "Yes, until we have a way for the user to specify explicitly that those two files are different configurations.\r\n\r\nWe can maybe have some rule to detect this automatically, maybe checking the first line of each file ? That would mean that for dataset of 10,000+ files we would have to verify every single one of them just to know if there is one ore more configurations, so I'm not sure if this is a good idea", "i think requiring the user to specify that those two files are different configurations is in that case perfectly reasonable.\r\n\r\n(Maybe at some point we could however detect this type of case and prompt them to define a config mapping etc)", "OK, so, before closing the issue, what do you think should be done?\r\n\r\n> Maybe in streaming mode we should keep the schema (inferred from the first item) and throw an exception if a subsequent item does not conform to the inferred schema?\r\n\r\nor nothing?", "We should at least raise an error if a new sample has column names that are missing, or if it has extra columns. No need to check for the type for now.\r\n\r\nI'm in favor of having an error especially because we want to avoid silent issues as much as possible - i.e. when something goes wrong (when schemas don't match or some data are missing) and no errors/warnings are raised.\r\n\r\nConsistency between streaming and non-streaming is also important." ]
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See https://huggingface.co/datasets/huggingface/transformers-metadata: it only contains two JSON files. In streaming mode, the files are concatenated, and thus the rows might be dictionaries with different keys: ```python import datasets as ds iterable_dataset = ds.load_dataset("huggingface/transformers-metadata", split="train", streaming=True); rows = list(iterable_dataset.take(100)) rows[0] # {'model_type': 'albert', 'pytorch': True, 'tensorflow': True, 'flax': True, 'processor': 'AutoTokenizer'} rows[99] # {'model_class': 'BartModel', 'pipeline_tag': 'feature-extraction', 'auto_class': 'AutoModel'} ``` In normal mode, an exception is thrown: ```python import datasets as ds dataset = ds.load_dataset("huggingface/transformers-metadata", split="train"); ``` ``` ValueError: Couldn't cast model_class: string pipeline_tag: string auto_class: string to {'model_type': Value(dtype='string', id=None), 'pytorch': Value(dtype='bool', id=None), 'tensorflow': Value(dtype='bool', id=None), 'flax': Value(dtype='bool', id=None), 'processor': Value(dtype='string', id=None)} because column names don't match ```
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Make RedCaps streamable
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Make RedCaps streamable. @lhoestq Using `data/redcaps_v1.0_annotations.zip` as a download URL gives an error locally when running `datasets-cli test` (will investigate this another time)
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Local paths in common voice
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[ "I just changed to `dl_manager.is_streaming` rather than an additional parameter `streaming` that has to be handled by the DatasetBuilder class - this way the streaming logic doesn't interfere with the base builder's code.\r\n\r\nI think it's better this way, but let me know if you preferred the previous way and I can revert\r\n\r\n> But on the other hand, IMHO, I think this specific solution adds complexity to handling streaming/non-streaming, and moves this complexity to the loading script and thus to the contributors/users who want to create the loading script for their canonical/community datasets (instead of keeping it hidden form the end users).\r\n\r\nI'm down to discuss this more in the future !" ]
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Continuation of https://github.com/huggingface/datasets/pull/3664: - pass the `streaming` parameter to _split_generator - update @anton-l's code to use this parameter for `common_voice` - add a comment to explain why we use `download_and_extract` in non-streaming and `iter_archive` in streaming Now the `common_voice` dataset has a local path back in `ds["path"]`, and this field is `None` in streaming mode. cc @patrickvonplaten @anton-l @albertvillanova
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Performance of `datasets` at scale
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[ "> using command line git-lfs - [...] 300MB/s!\r\n\r\nwhich server location did you upload from?", "From GCP region `us-central1-a`.", "The most surprising part to me is the saving time. Wondering if it could be due to compression (`ParquetWriter` uses SNAPPY compression by default; it can be turned off with `to_parquet(..., compression=None)`). " ]
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# Performance of `datasets` at 1TB scale ## What is this? During the processing of a large dataset I monitored the performance of the `datasets` library to see if there are any bottlenecks. The insights of this analysis could guide the decision making to improve the performance of the library. ## Dataset The dataset is a 1.1TB extract from GitHub with 120M code files and is stored as 5000 `.json.gz` files. The goal of the preprocessing is to remove duplicates and filter files based on their stats. While the calculating of the hashes for deduplication and stats for filtering can be parallelized the filtering itself is run with a single process. After processing the files are pushed to the hub. ## Machine The experiment was run on a `m1` machine on GCP with 96 CPU cores and 1.3TB RAM. ## Performance breakdown - Loading the data **3.5h** (_30sec_ from cache) - **1h57min** single core loading (not sure what is going on here, corresponds to second progress bar) - **1h10min** multi core json reading - **20min** remaining time before and after the two main processes mentioned above - Process the data **2h** (_20min_ from cache) - **20min** Getting reading for processing - **40min** Hashing and files stats (96 workers) - **58min** Deduplication filtering (single worker) - Save parquet files **5h** - Saving 1000 parquet files (16 workers) - Push to hub **37min** - **34min** git add - **3min** git push (several hours with `Repository.git_push()`) ## Conclusion It appears that loading and saving the data is the main bottleneck at that scale (**8.5h**) whereas processing (**2h**) and pushing the data to the hub (**0.5h**) is relatively fast. To optimize the performance at this scale it would make sense to consider such an end-to-end example and target the bottlenecks which seem to be loading from and saving to disk. The processing itself seems to run relatively fast. ## Notes - map operation on a 1TB dataset with 96 workers requires >1TB RAM - map operation does not maintain 100% CPU utilization with 96 workers - sometimes when the script crashes all the data files have a corresponding `*.lock` file in the data folder (or multiple e.g. `*.lock.lock` when it happened a several times). This causes the cache **not** to be triggered (which is significant at that scale) - i guess because there are new data files - parallelizing `to_parquet` decreased the saving time from 17h to 5h, however adding more workers at this point had almost no effect. not sure if this is: a) a bug in my parallelization logic, b) i/o limit to load data form disk to memory or c) i/o limit to write from memory to disk. - Using `Repository.git_push()` was much slower than using command line `git-lfs` - 10-20MB/s vs. 300MB/s! The `Dataset.push_to_hub()` function is even slower as it only uploads one file at a time with only a few MB/s, whereas `Repository.git_push()` pushes files in parallel (each at a similar speed). cc @lhoestq @julien-c @LysandreJik @SBrandeis
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Fix bugs in NewsQA dataset
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Fix #3733.
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Bugs in NewsQA dataset
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## Describe the bug NewsQA dataset has the following bugs: - the field `validated_answers` is an exact copy of the field `answers` but with the addition of `'count': [0]` to each dict - the field `badQuestion` does not appear in `answers` nor `validated_answers` ## Steps to reproduce the bug By inspecting the dataset script we can see that: - the parsing of `validated_answers` is a copy-paste of the one for `answers` - the `badQuestion` field is ignored in the parsing of both `answers` and `validated_answers`
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Support streaming in size estimation function in `push_to_hub`
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[ "would this allow to include the size in the dataset info without downloading the files? related to https://github.com/huggingface/datasets/pull/3670", "@severo I don't think so. We could use this to get `info.download_checksums[\"num_bytes\"]`, but we must process the files to get the rest of the size info. " ]
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This PR adds the streamable version of `os.path.getsize` (`fsspec` can return `None`, so we fall back to `fs.open` to make it more robust) to account for possible streamable paths in the nested `extra_nbytes_visitor` function inside `push_to_hub`.
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Fix Multi-News dataset metadata and card
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Fix #3730.
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Checksum Error when loading multi-news dataset
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[ "Thanks for reporting @byw2.\r\nWe are fixing it.\r\nIn the meantime, you can load the dataset by passing `ignore_verifications=True`:\r\n ```python\r\ndataset = load_dataset(\"multi_news\", ignore_verifications=True)" ]
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## Describe the bug When using the load_dataset function from datasets module to load the Multi-News dataset, does not load the dataset but throws Checksum Error instead. ## Steps to reproduce the bug ```python from datasets import load_dataset dataset = load_dataset("multi_news") ``` ## Expected results Should download and load Multi-News dataset. ## Actual results Throws the following error and cannot load data successfully: ``` NonMatchingChecksumError: Checksums didn't match for dataset source files: ['https://drive.google.com/uc?export=download&id=1vRY2wM6rlOZrf9exGTm5pXj5ExlVwJ0C'] ``` Could this issue please be looked at? Thanks!
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## Describe the bug when I use load_dataset to read a txt file I find that the number of the samples is incorrect ## Steps to reproduce the bug ``` fr = open('train.txt','r',encoding='utf-8').readlines() print(len(fr)) # 1199637 datasets = load_dataset('text', data_files={'train': ['train.txt']}, streaming=False) print(len(datasets['train'])) # 1199649 ``` I also use command line operation to verify it ``` $ wc -l train.txt 1199637 train.txt ``` ## Expected results please fix that issue ## Environment info <!-- You can run the command `datasets-cli env` and copy-and-paste its output below. --> - `datasets` version: 1.8.3 - Platform:windows&linux - Python version:3.7 - PyArrow version:6.0.1
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## Adding a Dataset - **Name:** VoxPopuli - **Description:** A Large-Scale Multilingual Speech Corpus - **Paper:** https://arxiv.org/pdf/2101.00390.pdf - **Data:** https://github.com/facebookresearch/voxpopuli - **Motivation:** one of the largest (if not the largest) multilingual speech corpus: 400K hours of multilingual unlabeled speech + 17k hours of labeled speech Instructions to add a new dataset can be found [here](https://github.com/huggingface/datasets/blob/master/ADD_NEW_DATASET.md). 👀 @kahne @Molugan
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Patch all module attributes in its namespace
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When patching module attributes, only those defined in its `__all__` variable were considered by default (only falling back to `__dict__` if `__all__` was None). However those are only a subset of all the module attributes in its namespace (`__dict__` variable). This PR fixes the problem of modules that have non-None `__all__` variable, but try to access an attribute present in `__dict__` (and not in `__all__`). For example, `pandas` has attribute `__version__` only present in `__dict__`. - Before version 1.4, pandas `__all__` was None, thus all attributes in `__dict__` were patched - From version 1.4, pandas `__all__` is not None, thus attributes in `__dict__` not present in `__all__` are ignored Fix #3724. CC: @severo @lvwerra
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