helmo/github-issues huggingface dataset:
Update to simplify some datasets conversion
State: closed | Author: thomwolf (MEMBER)

This PR updates the encoding of `Values` like `integers`, `boolean` and `float` to use python casting and avoid having to cast in the dataset scripts, as mentioned here: https://github.com/huggingface/nlp/pull/37#discussion_r420176626

We could also change (not included in this PR yet):
- `supervized_keys` to make them a NamedTuple instead of a dataclass, and
- handle specifically the `Translation` features.
as mentioned here: https://github.com/huggingface/nlp/pull/37#discussion_r421740236

@patrickvonplaten @mariamabarham tell me if you want these two last changes as well.

Comments: Awesome! 

Also we should convert `tf.io.gfile.exists` into `os.path.exists` , `tf.io.gfile.listdir`into `os.listdir` and `tf.io.gfile.glob`  into `glob.glob` (will need to add `import glob`)

> Also we should convert `tf.io.gfile.exists` into `os.path.exists` , `tf.io.gfile.listdir`into `os.listdir` and `tf.io.gfile.glob` into `glob.glob` (will need to add `import glob`)

We should probably open a new PR about this

I think it might be a good idea to both change the supervised keys to a named tuple and also handle the translation features specifically.

Just noticed that `pyarrow` apparently does not have a `is_boolean` function. Or do I have the wrong `pyarrow` version? 

Ah, it was a typo `pa.types.is_boolean` is the correct name. Will fix in: https://github.com/huggingface/nlp/pull/59
Better cached path
State: closed | Author: lhoestq (MEMBER)

### Changes:
- The `cached_path` no longer returns None if the file is missing/the url doesn't work. Instead, it can raise `FileNotFoundError` (missing file), `ConnectionError` (no cache and unreachable url) or `ValueError` (parsing error)
- Fix requests to firebase API that doesn't handle HEAD requests...
- Allow custom download in datasets script: it allows to use `tf.io.gfile.copy` for example, to download from google storage. I added an example: the `boolq` script

Comments: I should have read this PR before doing my own: https://github.com/huggingface/nlp/pull/62 :D 
will close mine. Looks great :-) 

> Awesome, this is really nice!
> 
> By the way, we should improve the `cached_path` method of the `transformers` repo similarly, don't you think (@patrickvonplaten in particular).

Yeah, we should do the same in `transformers` I think - will note it down.
[Testing] Improved testing structure
State: closed | Author: patrickvonplaten (CONTRIBUTOR)

This PR refactors the test design a bit and puts the mock download manager in the `utils` files as it is just a test helper class.

as @mariamabarham pointed out, creating a dummy folder structure can be quite hard to grasp.
This PR tries to change that to some extent.

It follows the following logic for the `dummy` folder structure now:
1.) The data bulider has no config -> the  `dummy` folder structure is:
`dummy/<version>/dummy_data.zip`
2) The data builder has >= 1 configs -> the `dummy` folder structure is: 
`dummy/<config_name_1>/<version>/dummy_data.zip`
`dummy/<config_name_2>/<version>/dummy_data.zip`

Now, the difficult part is how to create the `dummy_data.zip` file. There are two cases:
A) The `data_urs` parameter inserted into the `download_and_extract` fn is a **string**:
-> the `dummy_data.zip` file zips the folder: 
`dummy_data/<relative_path_of_folder_structure_of_url>`
B) The `data_urs` parameter inserted into the `download_and_extract` fn is a **dict**:
-> the `dummy_data.zip` file zips the folder: 
`dummy_data/<relative_path_of_folder_structure_of_url_behind _key_1>`
`dummy_data/<relative_path_of_folder_structure_of_url_behind _key_2>`

By relative folder structure I mean `url_path.split('./')[-1]`. As an example the dataset **xquad** by deepmind has the following url path behind the key `de`: `https://github.com/deepmind/xquad/blob/master/xquad.de.json` 
-> This means that the relative url path should be `xquad.de.json`.


@mariamabarham B) is a change from how is was before and I think is makes more sense. 
While before the `dummy_data.zip` file for xquad with config `de` looked like:
`dummy_data/de` it would now look like `dummy_data/xquad.de.json`. I think this is better and easier to understand. 

Therefore there are currently 6 tests that would have to have changed their dummy folder structure, but which can easily be done (30min). 

I also added a function: `print_dummy_data_folder_structure` that prints out the expected structures when testing which should be quite helpful.

Comments: Awesome!
Let's have this in the doc at the end :-)
[Checksums] If no configs exist prevent to run over empty list
State: closed | Author: patrickvonplaten (CONTRIBUTOR)

`movie_rationales` e.g. has no configs.

Comments: Whoops I fixed it directly on master before checking that you have done it in this PR. We may close it

Yeah, I saw :-) But I think we should add this as well since some datasets have an empty list of configs and then as the code is now it would fail. 

In this PR, I just make sure that the code jumps in the correct else if "there are no configs" as is the case for some datasets @mariamabarham 

Sorry, I thought you meant a different commit . Just saw this one: https://github.com/huggingface/nlp/commit/7c644f284e2303b57612a6e7c904fe13906d893f
.

All good then :-)
[Checksums] Error for some datasets
State: closed | Author: patrickvonplaten (CONTRIBUTOR)

The checksums command works very nicely for `squad`. But for `crime_and_punish` and `xnli`, 
the same bug happens:

When running: 
```
python nlp-cli nlp-cli test xnli --save_checksums
```

leads to:

```
  File "nlp-cli", line 33, in <module>
    service.run()
  File "/home/patrick/python_bin/nlp/commands/test.py", line 61, in run
    ignore_checksums=self._ignore_checksums,
  File "/home/patrick/python_bin/nlp/builder.py", line 383, in download_and_prepare
    self._download_and_prepare(dl_manager=dl_manager, download_config=download_config)
  File "/home/patrick/python_bin/nlp/builder.py", line 627, in _download_and_prepare
    dl_manager=dl_manager, max_examples_per_split=download_config.max_examples_per_split,
  File "/home/patrick/python_bin/nlp/builder.py", line 431, in _download_and_prepare
    split_generators = self._split_generators(dl_manager, **split_generators_kwargs)
  File "/home/patrick/python_bin/nlp/datasets/xnli/8bf4185a2da1ef2a523186dd660d9adcf0946189e7fa5942ea31c63c07b68a7f/xnli.py", line 95, in _split_generators
    dl_dir = dl_manager.download_and_extract(_DATA_URL)
  File "/home/patrick/python_bin/nlp/utils/download_manager.py", line 246, in download_and_extract
    return self.extract(self.download(url_or_urls))
  File "/home/patrick/python_bin/nlp/utils/download_manager.py", line 186, in download
    self._record_sizes_checksums(url_or_urls, downloaded_path_or_paths)
  File "/home/patrick/python_bin/nlp/utils/download_manager.py", line 166, in _record_sizes_checksums
    self._recorded_sizes_checksums[url] = get_size_checksum(path)
  File "/home/patrick/python_bin/nlp/utils/checksums_utils.py", line 81, in get_size_checksum
    with open(path, "rb") as f:
TypeError: expected str, bytes or os.PathLike object, not tuple
```


Comments: @lhoestq - could you take a look? It's not very urgent though!

Fixed with 06882b4

Now your command works :)
Note that you can also do
```
nlp-cli test datasets/nlp/xnli --save_checksums
```
So that it will save the checksums directly in the right directory.

Awesome!
[Tests] add slow tests
State: closed | Author: patrickvonplaten (CONTRIBUTOR)

This PR adds a slow test that downloads the "real" dataset. The test is decorated as "slow" so that it will not automatically run on circle ci.

Before uploading a dataset, one should test that this test passes, manually by running 

```
RUN_SLOW=1 pytest tests/test_dataset_common.py::DatasetTest::test_load_real_dataset_<your-dataset-script-name>
```

This PR should be merged after PR: #33
Fix map caching notebooks
State: closed | Author: lhoestq (MEMBER)

Previously, caching results with `.map()` didn't work in notebooks.
To reuse a result, `.map()` serializes the functions with `dill.dumps` and then it hashes it.

The problem is that when using `dill.dumps` to serialize a function, it also saves its origin (filename + line no.) and the origin of all the `globals` this function needs. However for notebooks and shells, the filename looks like \<ipython-input-13-9ed2afe61d25\> and the line no. changes often.

To fix the problem, I added a new dispatch function for code objects that ignore the origin of the code if it comes from a notebook or a python shell.

I tested these cases in a notebook:
- lambda functions
- named functions
- methods
- classmethods
- staticmethods
- classes that implement `__call__`

The caching now works as expected for all of them :)
I also tested the caching in the demo notebook and it works fine !
[Circle ci] Install a virtual env before running tests
State: closed | Author: patrickvonplaten (CONTRIBUTOR)

Install a virtual env before running tests to not running into sudo issues when dynamically downloading files. 

Same number of tests now pass / fail as on my local computer: 
![Screenshot from 2020-05-01 12-14-44](https://user-images.githubusercontent.com/23423619/80798814-8a0a0a80-8ba5-11ea-8db8-599d33bbfccd.png)
add metrics which require download files from github
State: closed | Author: mariamabarham (CONTRIBUTOR)

To download files from github, I copied the `load_dataset_module` and its dependencies (without the builder) in `load.py` to `metrics/metric_utils.py`. I made the following changes:

- copy the needed files in a folder`metric_name` 
- delete all other files that are not needed

For metrics that require an external import, I first create a `<metric_name>_imports.py` file which contains all external urls. Then I create a `<metric_name>.py` in which I will load the external files using `<metric_name>_imports.py`
[Tests] Clean tests
State: closed | Author: patrickvonplaten (CONTRIBUTOR)

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.
Add metrics
State: closed | Author: mariamabarham (CONTRIBUTOR)

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
adding bleu score code
State: closed | Author: mariamabarham (CONTRIBUTOR)

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) `
Cleanup Features - Updating convert command - Fix Download manager
State: closed | Author: thomwolf (MEMBER)

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: For conflicts, I think the mention hint "This should be modified because it mentions ..." is missing.

Looks great!
Replace tf.constant for TF
State: closed | Author: jplu (CONTRIBUTOR)

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: Awesome!
Updating caching mechanism - Allow dependency in dataset processing scripts - Fix style and quality in the repo
State: closed | Author: thomwolf (MEMBER)

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: LGTM
create our own DownloadManager
State: closed | Author: lhoestq (MEMBER)

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: Looks great to me! 

The new download manager is ready. I removed the old folder and I fixed a few remaining dependencies.
I tested it on squad and a few others from the dataset folder and it works fine.

The only impact of these changes is that it breaks the `download_and_prepare` script that was used to register the checksums when we create a dataset, as the checksum logic is not implemented.

Let me know if you have remarks

Ok merged it (a bit fast for you to update the copyright, now I see that. but it's ok, we'll do a pass on these doc/copyright before releasing anyway)

Actually two additional things here @lhoestq (I merged too fast sorry, let's make a new PR for additional developments):
- I think we can remove some dependencies now (e.g. `promises`) in setup.py, can you have a look?
- also, I think we can remove the boto3 dependency like here: https://github.com/huggingface/transformers/pull/3968
[Make style]
State: closed | Author: patrickvonplaten (CONTRIBUTOR)

Added Makefile and applied make style to all. 
make style runs the following code:

```
style:
          black --line-length 119 --target-version py35 src
          isort --recursive src
```

It's the same code that is run in `transformers`.

Comments: I think this can be quickly reproduced. 
I use `black, version 19.10b0`. 

When running: 
`black nlp/src/arrow_reader.py` 
it gives me: 

```
error: cannot format /home/patrick/hugging_face/nlp/src/nlp/arrow_reader.py: cannot use --safe with this file; failed to parse source file.  AST error message: invalid syntax (<unknown>, line 78)
Oh no! 💥 💔 💥
1 file failed to reformat.
```

The line in question is: 
https://github.com/huggingface/nlp/blob/6922a16705e61f9e31a365f2606090b84d49241f/src/nlp/arrow_reader.py#L78

What is weird is that the trainer file in `transformers` has more or less the same syntax and black does not fail there: 
https://github.com/huggingface/transformers/blob/cb3c2212c79d7ff0a4a4e84c3db48371ecc1c15d/src/transformers/trainer.py#L95

I googled quite a bit about black & typing hints yesterday and didn't find anything useful. 
Any ideas @thomwolf @julien-c @LysandreJik ?

> I think this can be quickly reproduced.
> I use `black, version 19.10b0`.
> 
> When running:
> `black nlp/src/arrow_reader.py`
> it gives me:
> 
> ```
> error: cannot format /home/patrick/hugging_face/nlp/src/nlp/arrow_reader.py: cannot use --safe with this file; failed to parse source file.  AST error message: invalid syntax (<unknown>, line 78)
> Oh no! 💥 💔 💥
> 1 file failed to reformat.
> ```
> 
> The line in question is:
> https://github.com/huggingface/nlp/blob/6922a16705e61f9e31a365f2606090b84d49241f/src/nlp/arrow_reader.py#L78
> 
> What is weird is that the trainer file in `transformers` has more or less the same syntax and black does not fail there:
> https://github.com/huggingface/transformers/blob/cb3c2212c79d7ff0a4a4e84c3db48371ecc1c15d/src/transformers/trainer.py#L95
> 
> I googled quite a bit about black & typing hints yesterday and didn't find anything useful.
> Any ideas @thomwolf @julien-c @LysandreJik ?

Ok I found the problem. It was the one Julien mentioned and has nothing to do with this line. Black's error message is a bit misleading here, I guess

Ok, just had to remove the python 2 syntax comments `# type`. 

Good to merge for me now @thomwolf