AniketTec/github-issues huggingface dataset:
Title: [Tests] Clean tests
State: closed

the abseil testing library (https://abseil.io/docs/python/quickstart.html) is better than the one I had before, so I decided to switch to that and changed the `setup.py` config file. 
Abseil has more support and a cleaner API for parametrized testing I think. 

I added a list of all dataset scripts that are currently on AWS, but will replace that once the 
API is integrated into this lib. 

One can now easily test for just a single function for a single dataset with:
`tests/test_dataset_common.py::DatasetTest::test_load_dataset_wikipedia` 

NOTE: This PR is rebased on PR #29 so should be merged after.

Comments:
Title: Add script csv datasets
State: closed

This is a PR allowing to create datasets from local CSV files. A usage might be:

```python
import nlp
ds = nlp.load(
    path="csv",
    name="bbc",
    dataset_files={
        nlp.Split.TRAIN: ["datasets/dummy_data/csv/train.csv"],
        nlp.Split.TEST: [""datasets/dummy_data/csv/test.csv""]
    },
    csv_kwargs={
        "skip_rows": 0,
        "delimiter": ",",
        "quote_char": "\"",
        "header_as_column_names": True
    }
)
```

```
Downloading and preparing dataset bbc/1.0.0 (download: Unknown size, generated: Unknown size, total: Unknown size) to /home/jplu/.cache/huggingface/datasets/bbc/1.0.0...
Dataset bbc downloaded and prepared to /home/jplu/.cache/huggingface/datasets/bbc/1.0.0. Subsequent calls will reuse this data.
{'test': Dataset(schema: {'category': 'string', 'text': 'string'}, num_rows: 49), 'train': Dataset(schema: {'category': 'string', 'text': 'string'}, num_rows: 99), 'validation': Dataset(schema: {'category': 'string', 'text': 'string'}, num_rows: 0)}
```

How it is read:

- `path`: the `csv` word means "I want to create a CSV dataset"
- `name`: the name of this dataset is `bbc`
- `dataset_files`: this is a dictionary where each key is the list of files corresponding to the key split.
- `csv_kwargs`: this is the keywords arguments to "explain" how to read the CSV files
  * `skip_rows`: number of rows have to be skipped, starting from the beginning of the file
  * `delimiter`: which delimiter is used to separate the columns
  * `quote_char`: which quote char is used to represent a column where the delimiter appears in one of them
  * `header_as_column_names`: will use the first row (header) of the file as name for the features. Otherwise the names will be automatically generated as `f1`, `f2`, etc... Will be applied after the `skip_rows` parameter.

**TODO**:  for now the `csv.py` is copied each time we create a new dataset as `ds_name.py`, this behavior will be modified to have only the `csv.py` script copied only once and not for all the CSV datasets.

Comments:
Title: Add checksums
State: closed

### Checksums files

They are stored next to the dataset script in urls_checksums/checksums.txt.
They are used to check the integrity of the datasets downloaded files.
I kept the same format as tensorflow-datasets.
There is one checksums file for all configs.

### Load a dataset

When you do `load("squad")`, it will also download the checksums file and put it next to the script in nlp/datasets/hash/urls_checksums/checksums.txt.
It also verifies that the downloaded files checksums match the expected ones.

You can ignore checksum tests with `load("squad", ignore_checksums=True)` (under the hood it just adds `ignore_checksums=True` in the `DownloadConfig`)

### Test a dataset

There is a new command `nlp-cli test squad` that runs `download_and_prepare` to see if it runs ok, and that verifies that all the checksums match. Allowed arguments are `--name`, `--all_configs`, `--ignore_checksums` and `--register_checksums`.

### Register checksums

1. If the dataset has external dataset files

The command `nlp-cli test squad --register_checksums --all_configs` runs `download_and_prepare` on all configs to see if it runs ok, and it creates the checksums file.
You can also register one config at a time using `--name` instead ; the checksums file will be completed and not overwritten.

If the script is a local script, the checksum file is moved to urls_checksums/checksums.txt next to the local script, to enable the user to upload both the script and the checksums file afterwards with `nlp-cli upload squad`.

2. If the dataset files are all inside the directory of the dataset script

The user can directly do `nlp-cli upload squad --register_checksums`, as there is no need to download anything.
In this case however, all the dataset must be uploaded at once.

--

PS : it doesn't allow to register checksums for canonical datasets, the file has to be added manually on S3 for now (I guess ?)

Also I feel like we must be sure that this processes would not constrain too much any user from uploading its dataset.
Let me know what you think :)

Comments:
Title: Add metrics
State: closed

This PR is a draft for adding metrics (sacrebleu and seqeval are added)

use case examples:
`import nlp`
**sacrebleu:**
```
refs = [['The dog bit the man.', 'It was not unexpected.', 'The man bit him first.'],
        ['The dog had bit the man.', 'No one was surprised.', 'The man had bitten the dog.']]
sys = ['The dog bit the man.', "It wasn't surprising.", 'The man had just bitten him.']
sacrebleu = nlp.load_metrics('sacrebleu')
print(sacrebleu.score)
```

**seqeval:**
```
y_true = [['O', 'O', 'O', 'B-MISC', 'I-MISC', 'I-MISC', 'O'], ['B-PER', 'I-PER', 'O']]
y_pred = [['O', 'O', 'B-MISC', 'I-MISC', 'I-MISC', 'I-MISC', 'O'], ['B-PER', 'I-PER', 'O']]
seqeval = nlp.load_metrics('seqeval')
print(seqeval.accuracy_score(y_true, y_pred)
print(seqeval.f1_score(y_true, y_pred)
```
_examples are taken from the corresponding web page_

your comments and suggestions are more than welcomed





Comments:
Title: adding bleu score code
State: closed

this PR add the BLEU score metric to the lib. It can be tested by running the following code.

` from nlp.metrics import bleu

hyp1 = "It is a guide to action which ensures that the military always obeys the commands of the party"
ref1a = "It is a guide to action that ensures that the military  forces always being under the commands of the party "
 ref1b = "It is the guiding principle which guarantees the military force always being under the command of the Party"
ref1c = "It is the practical guide for the army always to heed the directions of the party"
    
list_of_references = [[ref1a, ref1b, ref1c]]
hypotheses = [hyp1]
bleu = bleu.bleu_score(list_of_references, hypotheses,4, smooth=True)
print(bleu) `

Comments:
Title: Cleanup Features - Updating convert command - Fix Download manager
State: closed

This PR makes a number of changes:

# Updating `Features`

Features are a complex mechanism provided in `tfds` to be able to modify a dataset on-the-fly when serializing to disk and when loading from disk.

We don't really need this because (1) it hides too much from the user and (2) our datatype can be directly mapped to Arrow tables on drive so we usually don't need to change the format before/after serialization.

This PR extracts and refactors these features in a single `features.py` files. It still keep a number of features classes for easy compatibility with tfds, namely the `Sequence`, `Tensor`, `ClassLabel` and `Translation` features.

Some more complex features involving a pre-processing on-the-fly during serialization are kept:
- `ClassLabel` which are able to convert from label strings to integers,
- `Translation`which does some check on the languages.

# Updating the `convert` command

We do a few updates here
- following the simplification of the `features` (cf above), conversion are updated
- we also makes it simpler to convert a single file
- some code need to be fixed manually after conversion (e.g. to remove some encoding processing in former tfds `Text` features. We highlight this code with a "git merge conflict" style syntax for easy manual fixing.

# Fix download manager iterator

You kept me up quite late on Tuesday night with this `os.scandir` change @lhoestq ;-)


Comments:
Title: Replace tf.constant for TF
State: closed

Replace simple tf.constant type of Tensor to tf.ragged.constant which allows to have examples of different size in a tf.data.Dataset.

Now the training works with TF. Here the same example than for the PT in collab:

```python
import tensorflow as tf
import nlp
from transformers import BertTokenizerFast, TFBertForQuestionAnswering

# Load our training dataset and tokenizer
train_dataset = nlp.load('squad', split="train[:1%]")
tokenizer = BertTokenizerFast.from_pretrained('bert-base-cased')

def get_correct_alignement(context, answer):
    start_idx = answer['answer_start'][0]
    text = answer['text'][0]
    end_idx = start_idx + len(text)
    if context[start_idx:end_idx] == text:
        return start_idx, end_idx       # When the gold label position is good
    elif context[start_idx-1:end_idx-1] == text:
        return start_idx-1, end_idx-1   # When the gold label is off by one character
    elif context[start_idx-2:end_idx-2] == text:
        return start_idx-2, end_idx-2   # When the gold label is off by two character
    else:
        raise ValueError()

# Tokenize our training dataset
def convert_to_features(example_batch):
    # Tokenize contexts and questions (as pairs of inputs)
    input_pairs = list(zip(example_batch['context'], example_batch['question']))
    encodings = tokenizer.batch_encode_plus(input_pairs, pad_to_max_length=True)

    # Compute start and end tokens for labels using Transformers's fast tokenizers alignement methods.
    start_positions, end_positions = [], []
    for i, (context, answer) in enumerate(zip(example_batch['context'], example_batch['answers'])):
        start_idx, end_idx = get_correct_alignement(context, answer)
        start_positions.append([encodings.char_to_token(i, start_idx)])
        end_positions.append([encodings.char_to_token(i, end_idx-1)])
    
    if start_positions and end_positions:
      encodings.update({'start_positions': start_positions,
                        'end_positions': end_positions})
    return encodings

train_dataset = train_dataset.map(convert_to_features, batched=True)

columns = ['input_ids', 'token_type_ids', 'attention_mask', 'start_positions', 'end_positions']
train_dataset.set_format(type='tensorflow', columns=columns)
features = {x: train_dataset[x] for x in columns[:3]} 
labels = {"output_1": train_dataset["start_positions"]}
labels["output_2"] = train_dataset["end_positions"]
tfdataset = tf.data.Dataset.from_tensor_slices((features, labels)).batch(8)
model = TFBertForQuestionAnswering.from_pretrained("bert-base-cased")
loss_fn = tf.keras.losses.SparseCategoricalCrossentropy(reduction=tf.keras.losses.Reduction.NONE, from_logits=True)
opt = tf.keras.optimizers.Adam(learning_rate=3e-5)
model.compile(optimizer=opt,
              loss={'output_1': loss_fn, 'output_2': loss_fn},
              loss_weights={'output_1': 1., 'output_2': 1.},
              metrics=['accuracy'])
model.fit(tfdataset, epochs=1, steps_per_epoch=3)
```

Comments:
Title: Updating caching mechanism - Allow dependency in dataset processing scripts - Fix style and quality in the repo
State: closed

This PR has a lot of content (might be hard to review, sorry, in particular because I fixed the style in the repo at the same time).

# Style & quality:
You can now install the style and quality tools with `pip install -e .[quality]`. This will install black, the compatible version of sort and flake8.
You can then clean the style and check the quality before merging your PR with:
```bash
make style
make quality
```

# Allow dependencies in dataset processing scripts
We can now allow (some level) of imports in dataset processing scripts (in addition to PyPi imports).
Namely, you can do the two following things:

Import from a relative path to a file in the same folder as the dataset processing script:
```python
import .c4_utils 
``` 

Or import from a relative path to a file in a folder/archive/github repo to which you provide an URL after the import state with `# From: [URL]`:
```python
import .clicr.dataset_code.build_json_dataset  # From: https://github.com/clips/clicr
```

In both these cases, after downloading the main dataset processing script, we will identify the location of these dependencies, download them and copy them in the dataset processing script folder.

Note that only direct import in the dataset processing script will be handled.
We don't recursively explore the additional import to download further files.
Also, when we download from an additional directory (in the second case above), we recursively add `__init__.py` to all the sub-folder so you can import from them.

This part is still tested for now. If you've seen datasets which required external utilities, tell me and I can test it.

# Update the cache to have a better local structure

The local structure in the `src/datasets` folder is now: `src/datasets/DATASET_NAME/DATASET_HASH/*`

The hash is computed from the full code of the dataset processing script as well as all the local and downloaded dependencies as mentioned above. This way if you change some code in a utility related to your dataset, a new hash should be computed.

Comments:
Title: create our own DownloadManager
State: closed

I tried to create our own - and way simpler - download manager, by replacing all the complicated stuff with our own `cached_path` solution.
With this implementation, I tried `dataset = nlp.load('squad')` and it seems to work fine.

For the implementation, what I did exactly:
- I copied the old download manager
- I removed all the dependences to the old `download` files
- I replaced all the download + extract calls by calls to `cached_path`
- I removed unused parameters (extract_dir, compute_stats) (maybe compute_stats could be re-added later if we want to compute stats...)
- I left some functions unimplemented for now. We will probably have to implement them because they are used by some datasets scripts (download_kaggle_data, iter_archive) or because we may need them at some point (download_checksums, _record_sizes_checksums)

Let me know if you think that this is going the right direction or if you have remarks.
Note: I didn't write any test yet as I wanted to read your remarks first

Comments:
Title: [Tests] General Test Design for all dataset scripts
State: closed

The general idea is similar to how testing is done in `transformers`. There is one general `test_dataset_common.py` file which has a `DatasetTesterMixin` class. This class implements all of the logic that can be used in a generic way for all dataset classes. The idea is to keep each individual dataset test file as minimal as possible. 

In order to test whether the specific data set class can download the data and generate the examples **without** downloading the actual data all the time, a MockDataLoaderManager class is used which receives a `mock_folder_structure_fn` function from each individual dataset test file that create "fake" data and which returns the same folder structure that would have been created when using the real data downloader. 

Comments:
Title: [Map Function] add assert statement if map function does not return dict or None
State: closed

IMO, if a function is provided that is not a print statement (-> returns variable of type `None`) or a function that updates the datasets (-> returns variable of type `dict`), then a `TypeError` should be raised. 

Not sure whether you had cases in mind where the user should do something else @thomwolf , but I think a lot of silent errors can be avoided with this assert statement.

Comments:
Title: [Clean up] Datasets
State: closed

Clean up `nlp/datasets` folder. 

As I understood, eventually the `nlp/datasets` shall not exist anymore at all. 

The folder `nlp/datasets/nlp` is kept for the moment, but won't be needed in the future, since it will live on S3 (actually it already does) at: `https://s3.console.aws.amazon.com/s3/buckets/datasets.huggingface.co/nlp/?region=us-east-1` and the different `dataset downloader scripts will be added to `nlp/src/nlp` when downloaded by the user. 

The folder `nlp/datasets/checksums` is kept for now, but won't be needed anymore in the future. 

The remaining folders/ files are leftovers from tensorflow-datasets and are not needed. The can be looked up in the private tensorflow-dataset repo.

Comments:
Title: Error when citation is not given in the DatasetInfo
State: closed

The following error is raised when the `citation` parameter is missing when we instantiate a `DatasetInfo`:
```
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/jplu/dev/jplu/datasets/src/nlp/info.py", line 338, in __repr__
    citation_pprint = _indent('"""{}"""'.format(self.citation.strip()))
AttributeError: 'NoneType' object has no attribute 'strip'
```

I propose to do the following change in the `info.py` file. The method:
```python
def __repr__(self):
        splits_pprint = _indent("\n".join(["{"] + [
                "    '{}': {},".format(k, split.num_examples)
                for k, split in sorted(self.splits.items())
        ] + ["}"]))
        features_pprint = _indent(repr(self.features))
        citation_pprint = _indent('"""{}"""'.format(self.citation.strip()))
        return INFO_STR.format(
                name=self.name,
                version=self.version,
                description=self.description,
                total_num_examples=self.splits.total_num_examples,
                features=features_pprint,
                splits=splits_pprint,
                citation=citation_pprint,
                homepage=self.homepage,
                supervised_keys=self.supervised_keys,
                # Proto add a \n that we strip.
                license=str(self.license).strip())
```
Becomes:
```python
def __repr__(self):
        splits_pprint = _indent("\n".join(["{"] + [
                "    '{}': {},".format(k, split.num_examples)
                for k, split in sorted(self.splits.items())
        ] + ["}"]))
        features_pprint = _indent(repr(self.features))
        ## the strip is done only is the citation is given
        citation_pprint = self.citation

        if self.citation:
            citation_pprint = _indent('"""{}"""'.format(self.citation.strip()))
        return INFO_STR.format(
                name=self.name,
                version=self.version,
                description=self.description,
                total_num_examples=self.splits.total_num_examples,
                features=features_pprint,
                splits=splits_pprint,
                citation=citation_pprint,
                homepage=self.homepage,
                supervised_keys=self.supervised_keys,
                # Proto add a \n that we strip.
                license=str(self.license).strip())
```
And now it is ok. @thomwolf are you ok with this fix?

Comments: