* patchtsmixer initial commit * x,y->context_values,target_values, unittest addded * cleanup code * minor * return hidden states * model tests, partial integration tests * ettm notebook temporary * minor * config mask bug fix, tests updated * final ETT notebooks * add selfattn * init * added docstrings * PatchTSMixerForPretraining -> PatchTSMixerForMaskPretraining * functionality tests added * add start and input docstrings * docstring edits * testcase edits * minor changes * docstring error fixed * ran make fixup * finalize integration tests and docs * minor * cleaned gitignore * added dataclass decorator, ran black formatter * ran ruff * formatting * add slow decorator * renamed in_Channel to input_size and default to 1 * shorten dataclass names * use smaller model for testing * moved the 3 heads to the modeling file * use scalers instead of revin * support forecast_channel_indices * fix regression scaling * undo reg. scaling * removed unneeded classes * forgot missing * add more layers * add copied positional_encoding * use patchmask from patchtst * removed dependency on layers directory * formatting * set seed * removed unused imports * fixed forward signature test * adding distributional head for PatchTSMixerForecasting * add generate to forecast * testcases for generate * add generate and distributional head for regression * raise Exception for negative values for neg binominal distribution * formatting changes * remove copied from patchtst and add TODO for test passing * make copies * doc edits * minor changes * format issues * minor changes * minor changes * format docstring * change some class names to PatchTSMixer + class name Transpose to PatchTSMixerTranspose GatedAttention to PatchTSMixerGatedAttention * change NormLayer to PatchTSMixerNormLayer * change MLP to PatchTSMixerMLP * change PatchMixer to PatchMixerBlock, FeatureMixer to FeatureMixerBlock * change ChannelFeatureMixer to ChannelFeatureMixerBlock * change PatchMasking to PatchTSMixerMasking * change Patchify to PatchTSMixerPatchify * list to `list` * fix docstrings * formatting * change bs to batch_size, edit forecast_masking * edit random_masking * change variable name and update docstring in PatchTSMixerMasking * change variable name and update docstring in InjectScalerStatistics4D * update forward call in PatchTSMixerTranspose * change variable name and update docstring in PatchTSMixerNormLayer * change variable name and update docstring in PatchTSMixerMLP * change variable name and update docstring in ChannelFeatureMixerBlock * formatting * formatting issues * docstring issue * fixed observed_mask type in docstrings * use FloatTensor type * formatting * fix rescaling issue in forecasting, fixed integration tests * add docstring from decorator * fix docstring * Update README.md Co-authored-by: NielsRogge <48327001+NielsRogge@users.noreply.github.com> * Update src/transformers/models/patchtsmixer/configuration_patchtsmixer.py Co-authored-by: NielsRogge <48327001+NielsRogge@users.noreply.github.com> * Update src/transformers/models/patchtsmixer/modeling_patchtsmixer.py Co-authored-by: NielsRogge <48327001+NielsRogge@users.noreply.github.com> * Update src/transformers/models/patchtsmixer/configuration_patchtsmixer.py Co-authored-by: NielsRogge <48327001+NielsRogge@users.noreply.github.com> * Update src/transformers/models/patchtsmixer/modeling_patchtsmixer.py Co-authored-by: NielsRogge <48327001+NielsRogge@users.noreply.github.com> * PatchTSMixerChannelFeatureMixerBlock * formatting * ForPretraining * use num_labels instead of n_classes * remove commented out code * docstring fixed * nn.functional used instead of one letter F * x_tmp renamed * one letter variable x removed from forward calls * one letter variable y removed * remove commented code * rename patch_size, in_channels, PatchTSMixerBackbone * add config to heads * add config to heads tests * code reafactoring to use config instead of passing individual params * Cdocstring fixes part 1 * docstring fixes part 2 * removed logger.debug * context_values -> past_values * formatting changes * pe -> positional_encoding * removed unused target variable * self.mode logic fixed * formatting change * edit docstring and var name * change n_targets to num_targets * rename input_size to num_input_channels * add head names with prefix PatchTSMixer * edit docstring in PatchTSMixerForRegression * fix var name change in testcases * add PatchTSMixerAttention * return dict for all exposed classes, test cases added * format * move loss function to forward call * make style * adding return dict/tuple * make repo-consistency * remove flatten mode * code refactoring * rename data * remove PatchTSMixer and keep only PatchTSMixerEncoder * docstring fixes * removed unused code * format * format * remove contiguous and formatting changes * remove model description from config * replace asserts with ValueError * remove nn.Sequential from PatchTSMixerNormLayer * replace if-else with map * remove all nn.Sequential * format * formatting * fix gradient_checkpointing error after merge, and formatting * make fix-copies * remove comments * reshape * doesnt support gradient checkpointing * corect Patchify * masking updates * batchnorm copy from * format checks * scaler edits * remove comments * format changes * remove self.config * correct class PatchTSMixerMLP(nn.Module): * makr fix * doc updates * fix-copies * scaler class correction * doc edits * scaler edits * update readme with links * injectstatistics add * fix-copies * add norm_eps option to LayerNorm * format changes * fix copies * correct make copies * use parametrize * fix doc string * add docs to toctree * make style * doc segmenting * docstring edit * change forecast to prediction * edit doc * doc edits * remove PatchTSMixerTranspose * add PatchTSMixerPositionalEncoding and init position_enc * remove positional_encoding * edit forecast_masking, remove forecast_mask_ratios * fix broken code * var rename target_values -> future_values * num_features -> d_model * fix broken code after master merge * repo consistency * use postional embedding * prediction_logits -> prediction_outputs, make fix-copies * uncommented @slow * minor changes * loss first in tuple * tuple and dict same ordering * style edits * minor changes * dict/tuple consistent enablement * Update src/transformers/models/patchtsmixer/modeling_patchtsmixer.py Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com> * Update tests/models/patchtsmixer/test_modeling_patchtsmixer.py Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com> * Update src/transformers/models/patchtsmixer/modeling_patchtsmixer.py Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com> * fix formatting * formatting * usage tip * test on cpu only * add sample usage * change PatchTSMixerForClassification to PatchTSMixerForTimeSeriesClassification * push changes * fix copies * std scaling set to default True case * minor changes * stylechanges --------- Co-authored-by: Arindam Jati <arindam.jati@ibm.com> Co-authored-by: vijaye12 <vijaye12@in.ibm.com> Co-authored-by: Kashif Rasul <kashif.rasul@gmail.com> Co-authored-by: nnguyen <nnguyen@us.ibm.com> Co-authored-by: vijaye12 <vijaykr.e@gmail.com> Co-authored-by: NielsRogge <48327001+NielsRogge@users.noreply.github.com> Co-authored-by: Nam Nguyen <namctin@gmail.com> Co-authored-by: Wesley Gifford <79663411+wgifford@users.noreply.github.com> Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com>
Generating the documentation
To generate the documentation, you first have to build it. Several packages are necessary to build the doc, you can install them with the following command, at the root of the code repository:
pip install -e ".[docs]"
Then you need to install our special tool that builds the documentation:
pip install git+https://github.com/huggingface/doc-builder
NOTE
You only need to generate the documentation to inspect it locally (if you're planning changes and want to check how they look before committing for instance). You don't have to commit the built documentation.
Building the documentation
Once you have setup the doc-builder and additional packages, you can generate the documentation by
typing the following command:
doc-builder build transformers docs/source/en/ --build_dir ~/tmp/test-build
You can adapt the --build_dir to set any temporary folder that you prefer. This command will create it and generate
the MDX files that will be rendered as the documentation on the main website. You can inspect them in your favorite
Markdown editor.
Previewing the documentation
To preview the docs, first install the watchdog module with:
pip install watchdog
Then run the following command:
doc-builder preview {package_name} {path_to_docs}
For example:
doc-builder preview transformers docs/source/en/
The docs will be viewable at http://localhost:3000. You can also preview the docs once you have opened a PR. You will see a bot add a comment to a link where the documentation with your changes lives.
NOTE
The preview command only works with existing doc files. When you add a completely new file, you need to update _toctree.yml & restart preview command (ctrl-c to stop it & call doc-builder preview ... again).
Adding a new element to the navigation bar
Accepted files are Markdown (.md).
Create a file with its extension and put it in the source directory. You can then link it to the toc-tree by putting
the filename without the extension in the _toctree.yml file.
Renaming section headers and moving sections
It helps to keep the old links working when renaming the section header and/or moving sections from one document to another. This is because the old links are likely to be used in Issues, Forums, and Social media and it'd make for a much more superior user experience if users reading those months later could still easily navigate to the originally intended information.
Therefore, we simply keep a little map of moved sections at the end of the document where the original section was. The key is to preserve the original anchor.
So if you renamed a section from: "Section A" to "Section B", then you can add at the end of the file:
Sections that were moved:
[ <a href="#section-b">Section A</a><a id="section-a"></a> ]
and of course, if you moved it to another file, then:
Sections that were moved:
[ <a href="../new-file#section-b">Section A</a><a id="section-a"></a> ]
Use the relative style to link to the new file so that the versioned docs continue to work.
For an example of a rich moved section set please see the very end of the Trainer doc.
Writing Documentation - Specification
The huggingface/transformers documentation follows the
Google documentation style for docstrings,
although we can write them directly in Markdown.
Adding a new tutorial
Adding a new tutorial or section is done in two steps:
- Add a new file under
./source. This file can either be ReStructuredText (.rst) or Markdown (.md). - Link that file in
./source/_toctree.ymlon the correct toc-tree.
Make sure to put your new file under the proper section. It's unlikely to go in the first section (Get Started), so depending on the intended targets (beginners, more advanced users, or researchers) it should go in sections two, three, or four.
Translating
When translating, refer to the guide at ./TRANSLATING.md.
Adding a new model
When adding a new model:
- Create a file
xxx.mdor under./source/model_doc(don't hesitate to copy an existing file as template). - Link that file in
./source/_toctree.yml. - Write a short overview of the model:
- Overview with paper & authors
- Paper abstract
- Tips and tricks and how to use it best
- Add the classes that should be linked in the model. This generally includes the configuration, the tokenizer, and
every model of that class (the base model, alongside models with additional heads), both in PyTorch and TensorFlow.
The order is generally:
- Configuration
- Tokenizer
- PyTorch base model
- PyTorch head models
- TensorFlow base model
- TensorFlow head models
- Flax base model
- Flax head models
These classes should be added using our Markdown syntax. Usually as follows:
## XXXConfig
[[autodoc]] XXXConfig
This will include every public method of the configuration that is documented. If for some reason you wish for a method not to be displayed in the documentation, you can do so by specifying which methods should be in the docs:
## XXXTokenizer
[[autodoc]] XXXTokenizer
- build_inputs_with_special_tokens
- get_special_tokens_mask
- create_token_type_ids_from_sequences
- save_vocabulary
If you just want to add a method that is not documented (for instance magic methods like __call__ are not documented
by default) you can put the list of methods to add in a list that contains all:
## XXXTokenizer
[[autodoc]] XXXTokenizer
- all
- __call__
Writing source documentation
Values that should be put in code should either be surrounded by backticks: `like so`. Note that argument names
and objects like True, None, or any strings should usually be put in code.
When mentioning a class, function, or method, it is recommended to use our syntax for internal links so that our tool adds a link to its documentation with this syntax: [`XXXClass`] or [`function`]. This requires the class or function to be in the main package.
If you want to create a link to some internal class or function, you need to
provide its path. For instance: [`utils.ModelOutput`]. This will be converted into a link with
utils.ModelOutput in the description. To get rid of the path and only keep the name of the object you are
linking to in the description, add a ~: [`~utils.ModelOutput`] will generate a link with ModelOutput in the description.
The same works for methods so you can either use [`XXXClass.method`] or [~`XXXClass.method`].
Defining arguments in a method
Arguments should be defined with the Args: (or Arguments: or Parameters:) prefix, followed by a line return and
an indentation. The argument should be followed by its type, with its shape if it is a tensor, a colon, and its
description:
Args:
n_layers (`int`): The number of layers of the model.
If the description is too long to fit in one line, another indentation is necessary before writing the description after the argument.
Here's an example showcasing everything so far:
Args:
input_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`):
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using [`AlbertTokenizer`]. See [`~PreTrainedTokenizer.encode`] and
[`~PreTrainedTokenizer.__call__`] for details.
[What are input IDs?](../glossary#input-ids)
For optional arguments or arguments with defaults we follow the following syntax: imagine we have a function with the following signature:
def my_function(x: str = None, a: float = 1):
then its documentation should look like this:
Args:
x (`str`, *optional*):
This argument controls ...
a (`float`, *optional*, defaults to 1):
This argument is used to ...
Note that we always omit the "defaults to `None`" when None is the default for any argument. Also note that even
if the first line describing your argument type and its default gets long, you can't break it on several lines. You can
however write as many lines as you want in the indented description (see the example above with input_ids).
Writing a multi-line code block
Multi-line code blocks can be useful for displaying examples. They are done between two lines of three backticks as usual in Markdown:
```
# first line of code
# second line
# etc
```
We follow the doctest syntax for the examples to automatically test the results to stay consistent with the library.
Writing a return block
The return block should be introduced with the Returns: prefix, followed by a line return and an indentation.
The first line should be the type of the return, followed by a line return. No need to indent further for the elements
building the return.
Here's an example of a single value return:
Returns:
`List[int]`: A list of integers in the range [0, 1] --- 1 for a special token, 0 for a sequence token.
Here's an example of a tuple return, comprising several objects:
Returns:
`tuple(torch.FloatTensor)` comprising various elements depending on the configuration ([`BertConfig`]) and inputs:
- ** loss** (*optional*, returned when `masked_lm_labels` is provided) `torch.FloatTensor` of shape `(1,)` --
Total loss is the sum of the masked language modeling loss and the next sequence prediction (classification) loss.
- **prediction_scores** (`torch.FloatTensor` of shape `(batch_size, sequence_length, config.vocab_size)`) --
Prediction scores of the language modeling head (scores for each vocabulary token before SoftMax).
Adding an image
Due to the rapidly growing repository, it is important to make sure that no files that would significantly weigh down the repository are added. This includes images, videos, and other non-text files. We prefer to leverage a hf.co hosted dataset like
the ones hosted on hf-internal-testing in which to place these files and reference
them by URL. We recommend putting them in the following dataset: huggingface/documentation-images.
If an external contribution, feel free to add the images to your PR and ask a Hugging Face member to migrate your images
to this dataset.
Styling the docstring
We have an automatic script running with the make style comment that will make sure that:
- the docstrings fully take advantage of the line width
- all code examples are formatted using black, like the code of the Transformers library
This script may have some weird failures if you made a syntax mistake or if you uncover a bug. Therefore, it's
recommended to commit your changes before running make style, so you can revert the changes done by that script
easily.
Testing documentation examples
Good documentation often comes with an example of how a specific function or class should be used. Each model class should contain at least one example showcasing how to use this model class in inference. E.g. the class Wav2Vec2ForCTC includes an example of how to transcribe speech to text in the docstring of its forward function.
Writing documentation examples
The syntax for Example docstrings can look as follows:
Example:
```python
>>> from transformers import Wav2Vec2Processor, Wav2Vec2ForCTC
>>> from datasets import load_dataset
>>> import torch
>>> dataset = load_dataset("hf-internal-testing/librispeech_asr_demo", "clean", split="validation")
>>> dataset = dataset.sort("id")
>>> sampling_rate = dataset.features["audio"].sampling_rate
>>> processor = Wav2Vec2Processor.from_pretrained("facebook/wav2vec2-base-960h")
>>> model = Wav2Vec2ForCTC.from_pretrained("facebook/wav2vec2-base-960h")
>>> # audio file is decoded on the fly
>>> inputs = processor(dataset[0]["audio"]["array"], sampling_rate=sampling_rate, return_tensors="pt")
>>> with torch.no_grad():
... logits = model(**inputs).logits
>>> predicted_ids = torch.argmax(logits, dim=-1)
>>> # transcribe speech
>>> transcription = processor.batch_decode(predicted_ids)
>>> transcription[0]
'MISTER QUILTER IS THE APOSTLE OF THE MIDDLE CLASSES AND WE ARE GLAD TO WELCOME HIS GOSPEL'
```
The docstring should give a minimal, clear example of how the respective model is to be used in inference and also include the expected (ideally sensible) output. Often, readers will try out the example before even going through the function or class definitions. Therefore, it is of utmost importance that the example works as expected.
Docstring testing
To do so each example should be included in the doctests. We use pytests' doctest integration to verify that all of our examples run correctly. For Transformers, the doctests are run on a daily basis via GitHub Actions as can be seen here.
For Python files
Run all the tests in the docstrings of a given file with the following command, here is how we test the modeling file of Wav2Vec2 for instance:
pytest --doctest-modules src/transformers/models/wav2vec2/modeling_wav2vec2.py -sv --doctest-continue-on-failure
If you want to isolate a specific docstring, just add :: after the file name then type the whole path of the function/class/method whose docstring you want to test. For instance, here is how to just test the forward method of Wav2Vec2ForCTC:
pytest --doctest-modules src/transformers/models/wav2vec2/modeling_wav2vec2.py::transformers.models.wav2vec2.modeling_wav2vec2.Wav2Vec2ForCTC.forward -sv --doctest-continue-on-failure
For Markdown files
You can test locally a given file with this command (here testing the quicktour):
pytest --doctest-modules docs/source/quicktour.md -sv --doctest-continue-on-failure --doctest-glob="*.md"
Writing doctests
Here are a few tips to help you debug the doctests and make them pass:
- The outputs of the code need to match the expected output exactly, so make sure you have the same outputs. In particular doctest will see a difference between single quotes and double quotes, or a missing parenthesis. The only exceptions to that rule are:
- whitespace: one give whitespace (space, tabulation, new line) is equivalent to any number of whitespace, so you can add new lines where there are spaces to make your output more readable.
- numerical values: you should never put more than 4 or 5 digits to expected results as different setups or library versions might get you slightly different results.
doctestis configured to ignore any difference lower than the precision to which you wrote (so 1e-4 if you write 4 digits).
- Don't leave a block of code that is very long to execute. If you can't make it fast, you can either not use the doctest syntax on it (so that it's ignored), or if you want to use the doctest syntax to show the results, you can add a comment
# doctest: +SKIPat the end of the lines of code too long to execute - Each line of code that produces a result needs to have that result written below. You can ignore an output if you don't want to show it in your code example by adding a comment
# doctest: +IGNORE_RESULTat the end of the line of code producing it.