16 Commits

Author SHA1 Message Date
tstadel
fc8df2163d
Fix Windows CI OOM (#1878)
* set fixture scope to "function"

* run FARMReader without multiprocessing

* dispose off ray after tests

* run most expensive tasks first in test files

* run expensive tests first

* run garbage collector between tests

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-12-22 17:20:23 +01:00
Sara Zan
ea3abd305b
Fix a few details of some tutorials (#1733)
* Make Tutorial10 use print instead of logs and fix a typo in Tutoria15

* Add a type check in 'print_answers'

* Add same checks to print_documents and print_questions

* Make RAGenerator return Answers instead of dictionaries

* Fix RAGenerator tests

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-12 16:44:28 +01:00
Lalit Pagaria
e5b4b62d75
Add CI for windows runner (#1458)
* Feat: Removing use of temp file while downloading archive from url along with adding CI for windows and mac platform

* Windows CI by default installing pytorch gpu hence updating CI to pick cpu version

* fixing mac cache build issue

* updating windows pip install command for torch

* another attempt

* updating ci

* Adding sudo

* fixing ls failure on windows

* another attempt to fix build issue

* Saving env variable of test files

* Adding debug log

* Github action differ on windows

* adding debug

* anohter attempt

* Windows have different ways to receive env

* fixing template

* minor fx

* Adding debug

* Removing use of json

* Adding back fromJson

* addin toJson

* removing print

* anohter attempt

* disabling parallel run at least for testing

* installing docker for mac runner

* correcting docker install command

* Linux dockers are not suported in windows

* Removing mac changes

* Upgrading pytorch

* using lts pytorch

* Separating win and ubuntu

* Install java 11

* enabling linux container env

* docker cli command

* docker cli command

* start elastic service

* List all service

* correcting service name

* Attempt to fix multiple test run

* convert to json

* another attempt to check

* Updating build cache step

* attempt

* Add tika

* Separating windows CI

* Changing CI name

* Skipping test which does not work in windows

* Skipping tests for windows

* create cleanup function in conftest

* adding skipif marker on tests

* Run windows PR on only push to master

* Addressing review comments

* Enabling windows ci for this PR

* Tika init is being called when importing tika function

* handling tika import issue

* handling tika import issue in test

* Fixing import issue

* removing tika fixure

* Removing fixture from tests

* Disable windows ci on pull request

* Add back extra pytorch install step

Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-10-29 10:22:28 +02:00
Sara Zan
13510aa753
Refactoring of the haystack package (#1624)
* Files moved, imports all broken

* Fix most imports and docstrings into

* Fix the paths to the modules in the API docs

* Add latest docstring and tutorial changes

* Add a few pipelines that were lost in the inports

* Fix a bunch of mypy warnings

* Add latest docstring and tutorial changes

* Create a file_classifier module

* Add docs for file_classifier

* Fixed most circular imports, now the REST API can start

* Add latest docstring and tutorial changes

* Tackling more mypy issues

* Reintroduce  from FARM and fix last mypy issues hopefully

* Re-enable old-style imports

* Fix some more import from the top-level  package in an attempt to sort out circular imports

* Fix some imports in tests to new-style to prevent failed class equalities from breaking tests

* Change document_store into document_stores

* Update imports in tutorials

* Add latest docstring and tutorial changes

* Probably fixes summarizer tests

* Improve the old-style import allowing module imports (should work)

* Try to fix the docs

* Remove dedicated KnowledgeGraph page from autodocs

* Remove dedicated GraphRetriever page from autodocs

* Fix generate_docstrings.sh with an updated list of yaml files to look for

* Fix some more modules in the docs

* Fix the document stores docs too

* Fix a small issue on Tutorial14

* Add latest docstring and tutorial changes

* Add deprecation warning to old-style imports

* Remove stray folder and import Dict into dense.py

* Change import path for MLFlowLogger

* Add old loggers path to the import path aliases

* Fix debug output of convert_ipynb.py

* Fix circular import on BaseRetriever

* Missed one merge block

* re-run tutorial 5

* Fix imports in tutorial 5

* Re-enable squad_to_dpr CLI from the root package and move get_batches_from_generator into document_stores.base

* Add latest docstring and tutorial changes

* Fix typo in utils __init__

* Fix a few more imports

* Fix benchmarks too

* New-style imports in test_knowledge_graph

* Rollback setup.py

* Rollback squad_to_dpr too

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-25 15:50:23 +02:00
Julian Risch
9de140110f
Use smaller model for one generator test case (#1622)
* Use smaller model for one generator test case

* Reduce max_length of generated sequences in tests
2021-10-20 17:57:15 +02:00
Sara Zan
96c05c34e4
Pipeline node names validation (#1601)
* Add node names validation

* Add tests

* Improve test and test that params exists before validating

* Fix the REST API

* Use minilm-uncased-squad2 instead of roberta-base-squad2

* Use roberta model for test_pipeline.yaml

* Turn off TOKENIZERS_PARALLELISM in generator tests (#1605)

* Account for non-targeted parameters

* Restore previous parameters handling in the rest api

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Julian Risch <julian.risch@deepset.ai>
2021-10-19 15:22:44 +02:00
Julian Risch
5ec29a5283
Limit generator tests to memory doc store; split pipeline tests (#1602)
* Limit generator tests to memory doc store; split pipeline tests

* Add latest docstring and tutorial changes

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-15 15:37:46 +02:00
Malte Pietsch
4a6c9302b3
Redesign primitives - Document, Answer, Label (#1398)
* 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

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

* WIP primitives

* 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

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

* fix meta handling

* adress review feedback

* Add latest docstring and tutorial changes

* make document=None for open domain labels

* add import

* fix print utils

* fix rest api

* adress review feedback

* Add latest docstring and tutorial changes

* fix mypy

Co-authored-by: Markus Paff <markuspaff.mp@gmail.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-13 14:23:23 +02:00
Malte Pietsch
183fd5ae5a
Simplify tests & allow running on individual doc stores (#1487)
* simplify tests for individual doc stores

* WIP refactoring markers of tests

* test alternative approach for tests with existing parametrization

* 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

* update readme and contributing.md

* update contributing

* adjust example

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-09-27 10:52:07 +02:00
oryx1729
9dd7c74f4f
Refactor communication between Pipeline Components (#1321) 2021-09-10 11:41:16 +02:00
vblagoje
02fc4c7783
Improve document stores unit test parametrization (#1202) 2021-06-22 16:08:23 +02:00
vblagoje
2a5882578a
Add Longform-QA (LFQA), Seq2SeqGenerator for generative QA and Retribert Retriever (#1086)
* Integrate LFQA with Haystack

* Integrate LFQA with Haystack - unit tests

* Properly initialize conftest default value for vector_dim

* Update PR after inital feedback

* Fix conftest.py import

* Seq2SeqGenerator uses Callables instead of subclasses for custom model input

* Update docstring

* Fix Callable use

* Add LFQA tutorials

* Improve type error reporting for invalid input converter Callable

* Generate docstrings

* Format comments in tutorial script

* Generate tutorial md

* Add usage page

Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
Co-authored-by: brandenchan <brandenchan@icloud.com>
2021-06-14 17:53:43 +02:00
Lalit Pagaria
5bd94ac5f7
Adding Translator (standalone component & wrapper for pipelines) (#782)
* Adding translator with many generic input parameter support

* Making dict_key as generic

* Fixing mypy issue

* Adding pipeline and using opus models

* Add latest docstring and tutorial changes

* Adding test cases for end-to-end translation for generator, summerizer etc

* raise error join and merge nodes

* Fix test failure

* add docstrings. add usage documentation. rm skip_special_tokens param

* Add latest docstring and tutorial changes

* fix code snippets in md

* Adding few extra configuration parameters and fixing tests

* Fixingmypy issue and updating usage document

* fix for mypy issue in pipeline.py

* reverting renaming of pytest_collection_modifyitems method

* Addressing review comments

* setting skip_special_tokens to True

* removing model_max_length argument as None type is not supported to many models

* Removing padding parameter. Better to leave it as default otherwise it cause tensor size miss match error. If this option required by used then it can be added later.

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-02-12 15:58:26 +01:00
Lalit Pagaria
9f7f95221f
Milvus integration (#771)
* Initial commit for Milvus integration

* Add latest docstring and tutorial changes

* Updating implementation of Milvus document store

* Add latest docstring and tutorial changes

* Adding tests and updating doc string

* Add latest docstring and tutorial changes

* Fixing issue caught by tests

* Addressing review comments

* Fixing mypy detected issue

* Fixing issue caught in test about sorting of vector ids

* fixing test

* Fixing generator test failure

* update docstrings

* Addressing review comments about multiple network call while fetching embedding from milvus server

* Add latest docstring and tutorial changes

* Ignoring mypy issue while converting vector_id to int

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-01-29 13:29:12 +01:00
Tanay Soni
8e52b48e1d
Add pipelines for GenerativeQA & FAQs (#645) 2020-12-03 10:27:06 +01:00
Lalit Pagaria
f13443054a
[RAG] Integrate "Retrieval-Augmented Generation" with Haystack (#484)
* Adding dummy generator implementation

* Adding tutorial to try the model

* Committing current non working code

* Committing current update where we need to call generate function directly and need to convert embedding to tensor way

* Addressing review comments.

* Refactoring finder, and implementing rag_generator class.

* Refined the implementation of RAGGenerator and now it is in clean shape

* Renaming RAGGenerator to RAGenerator

* Reverting change from finder.py and addressing review comments

* Remove support for RagSequenceForGeneration

* Utilizing embed_passage function from DensePassageRetriever

* Adding sample test data to verify generator output

* Updating testing script

* Updating testing script

* Fixing bug related to top_k

* Updating latest farm dependency

* Comment out farm dependency

* Reverting changes from TransformersReader

* Adding transformers dataset to compare transformers and haystack generator implementation

* Using generator_encoder instead of question_encoder to generate context_input_ids

* Adding workaround to install FARM dependency from master branch

* Removing unnecessary changes

* Fixing generator test

* Removing transformers datasets

* Fixing generator test

* Some cleanup and updating TODO comments

* Adding tutorial notebook

* Updating tutorials with comments

* Explicitly passing token model in RAG test

* Addressing review comments

* Fixing notebook

* Refactoring tests to reduce memory footprint

* Split generator tests in separate ci step and before running it reclaim memory by terminating containers

* Moving tika dependent test to separate dir

* Remove unwanted code

* Brining reader under session scope

* Farm is now session object hence restoring changes from default value

* Updating assert for pdf converter

* Dummy commit to trigger CI flow

* REducing memory footprint required for generator tests

* Fixing mypy issues

* Marking test with tika and elasticsearch markers. Reverting changes in CI and pytest splits

* reducing changes

* Fixing CI

* changing elastic search ci

* Fixing test error

* Disabling return of embedding

* Marking generator test as well

* Refactoring tutorials

* Increasing ES memory to 750M

* Trying another fix for ES CI

* Reverting CI changes

* Splitting tests in CI

* Generator and non-generator markers split

* Adding pytest.ini to add markers and enable strict-markers option

* Reducing elastic search container memory

* Simplifying generator test by using documents with embedding directly

* Bump up farm to 0.5.0
2020-10-30 18:06:02 +01:00