bogdankostic 655d721371
Add Table Reader (#1446)
* first draft / notes on new primitives

* wip label / feedback refactor

* rename doc.text -> doc.content. add doc.content_type

* add datatype for content

* remove faq_question_field from ES and weaviate. rename text_field -> content_field in docstores. update tutorials for content field

* update converters for . Add warning for empty

* Add first draft of TableReader

* renam label.question -> label.query. Allow sorting of Answers.

* Add calculation of answer scores

* WIP primitives

* Adapt input and output to new primitives

* Add doc strings

* Add tests

* update ui/reader for new Answer format

* Improve Label. First refactoring of MultiLabel. Adjust eval code

* fixed workflow conflict with introducing new one (#1472)

* Add latest docstring and tutorial changes

* make add_eval_data() work again

* fix reader formats. WIP fix _extract_docs_and_labels_from_dict

* fix test reader

* Add latest docstring and tutorial changes

* fix another test case for reader

* fix mypy in farm reader.eval()

* fix mypy in farm reader.eval()

* WIP ORM refactor

* Add latest docstring and tutorial changes

* fix mypy weaviate

* make label and multilabel dataclasses

* bump mypy env in CI to python 3.8

* WIP refactor Label ORM

* WIP refactor Label ORM

* simplify tests for individual doc stores

* WIP refactoring markers of tests

* test alternative approach for tests with existing parametrization

* WIP refactor ORMs

* fix skip logic of already parametrized tests

* fix weaviate behaviour in tests - not parametrizing it in our general test cases.

* Add latest docstring and tutorial changes

* fix some tests

* remove sql from document_store_types

* fix markers for generator and pipeline test

* remove inmemory marker

* remove unneeded elasticsearch markers

* add dataclasses-json dependency. adjust ORM to just store JSON repr

* ignore type as dataclasses_json seems to miss functionality here

* update readme and contributing.md

* update contributing

* adjust example

* fix duplicate doc handling for custom index

* Add latest docstring and tutorial changes

* fix some ORM issues. fix get_all_labels_aggregated.

* update drop flags where get_all_labels_aggregated() was used before

* Add latest docstring and tutorial changes

* add to_json(). add + fix tests

* fix no_answer handling in label / multilabel

* fix duplicate docs in memory doc store. change primary key for sql doc table

* fix mypy issues

* fix mypy issues

* haystack/retriever/base.py

* fix test_write_document_meta[elastic]

* fix test_elasticsearch_custom_fields

* fix test_labels[elastic]

* fix crawler

* fix converter

* fix docx converter

* fix preprocessor

* fix test_utils

* fix tfidf retriever. fix selection of docstore in tests with multiple fixtures / parameterizations

* Add latest docstring and tutorial changes

* fix crawler test. fix ocrconverter attribute

* fix test_elasticsearch_custom_query

* fix generator pipeline

* fix ocr converter

* fix ragenerator

* Add latest docstring and tutorial changes

* fix test_load_and_save_yaml for elasticsearch

* fixes for pipeline tests

* fix faq pipeline

* fix pipeline tests

* Add latest docstring and tutorial changes

* fix weaviate

* Add latest docstring and tutorial changes

* trigger CI

* satisfy mypy

* Add latest docstring and tutorial changes

* satisfy mypy

* Add latest docstring and tutorial changes

* trigger CI

* fix question generation test

* fix ray. fix Q-generation

* fix translator test

* satisfy mypy

* wip refactor feedback rest api

* fix rest api feedback endpoint

* fix doc classifier

* remove relation of Labels -> Docs in SQL ORM

* fix faiss/milvus tests

* fix doc classifier test

* fix eval test

* fixing eval issues

* Add latest docstring and tutorial changes

* fix mypy

* WIP replace dataclasses-json with manual serialization

* Add latest docstring and tutorial changes

* revert to dataclass-json serialization for now. remove debug prints.

* update docstrings

* fix extractor. fix Answer Span init

* fix api test

* Adapt answer format

* Add latest docstring and tutorial changes

* keep meta data of answers in reader.run()

* Fix mypy

* fix meta handling

* adress review feedback

* Add latest docstring and tutorial changes

* Allow inference on GPU

* Remove automatic aggregation

* Add automatic aggregation

* Add latest docstring and tutorial changes

* Add torch-scatter dependency

* Add wheel to torch-scatter dependency

* Fix requirements

* Fix requirements

* Fix requirements

* Adapt setup.py to allow for wheels

* Fix requirements

* Fix requirements

* Add type hints and code snippet

* Add latest docstring and tutorial changes

Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
Co-authored-by: Markus Paff <markuspaff.mp@gmail.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-15 16:34:48 +02:00
..
2021-10-15 16:34:48 +02:00
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2020-09-18 12:57:32 +02:00
2020-09-18 12:57:32 +02:00

📒 Looking for the docs?

You find them here here:

https://haystack.deepset.ai/overview/intro

💻 How to update docs?

Overview and Usage

We move the Overview and Usage docs to the haystack-website repository. You will find the docs in the folder docs. Please make sure to only edit the newest version of the docs. We will release the docs together with the Haystack version. We are open for contibutions to our documentation. Please make sure to check our Contribution Guidelines. You will find a step by step introduction to our docs here.

Tutorials

The Tutorials live in the folder tutorials. They are created as colab notebooks which can be used by users to explore new haystack features. To include tutorials into the docs website, markdowns files need to be generated from the notebook. This can be done by running the script /docs/_src/tutorials/tutorials/convert_ipynb.py. Just run python convert_ipynb.py and the script will update all existing notebooks. Furthermore, plaese make sure to update the headers.py file with headers for the new tutorials. These headers are important for the docs website workflow. After the markdown files are generated successfully, you can raise a PR. We will review it and as soons as the markdown file is merged to master, it can be added to our website. Please follow the steps described here under Tutorial & Reference Docs.

API Reference

We use Pydoc-Markdown to create markdown files from the docstrings in our code.

Update docstrings

Execute the following commands in /haystack/docs/_src/api/api:

pip install 'pydoc-markdown==3.11.0'
./generate_docstrings.sh

If you want to generate a new markdown file for a new haystack module, please create a .yml which is inline with the following configuration and a a new line to generate_docstrings.sh for the module. After you ran the generate_docstrings.sh again, there should be a new markdown file for the module. To include it into the docs website, push it to master and follow the steps described here under Tutorial & Reference Docs.

Configuration

Pydoc will read the configuration from a .yml file which is located in the current working directory. Our files contains three main sections:

  • loader: A list of plugins that load API objects from python source files.
    • type: Loader for python source files
    • search_path: Location of source files
    • modules: Module which are used for generating the markdown file
    • ignore_when_discovered: Define which files should be ignored
  • processor: A list of plugins that process API objects to modify their docstrings (e.g. to adapt them from a documentation format to Markdown or to remove items that should not be rendered into the documentation).
    • type: filter: Filter for specific modules
    • documented_only: Only documented API objects
    • do_not_filter_modules: Do not filter module objects
    • skip_empty_modules: Skip modules without content
  • renderer: A plugin that produces the output files.
    • type: Define the renderer which you want to use. We are using the Markdown renderer as it can be configured in very detail.
    • descriptive_class_title: Remove the word "Object" from class titles.
    • descriptive_module_title: Adding the word “Module” before the module name
    • add_method_class_prefix: Add the class name as a prefix to method names
    • add_member_class_prefix: Add the class name as a prefix to member names
    • filename: file name of the generated file