* Fist attempt at using setup.cfg for dependency management
* Trying the new package on the CI and in Docker too
* Add composite extras_require
* Add the safe_import function for document store imports and add some try-catch statements on rest_api and ui imports
* Fix bug on class import and rephrase error message
* Introduce typing for optional modules and add type: ignore in sparse.py
* Include importlib_metadata backport for py3.7
* Add colab group to extra_requires
* Fix pillow version
* Fix grpcio
* Separate out the crawler as another extra
* Make paths relative in rest_api and ui
* Update the test matrix in the CI
* Add try catch statements around the optional imports too to account for direct imports
* Never mix direct deps with self-references and add ES deps to the base install
* Refactor several paths in tests to make them insensitive to the execution path
* Include tstadel review and re-introduce Milvus1 in the tests suite, to fix
* Wrap pdf conversion utils into safe_import
* Update some tutorials and rever Milvus1 as default for now, see #2067
* Fix mypy config
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* doc store should return all documents matching ids passed to get_documents_by_id
* test for get_document_by_id should be named correctly
* add test for get_documents_by_id
* Add latest docstring and tutorial changes
* document es query limit
* Add latest docstring and tutorial changes
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* minimal DCDocumentStore
* support filters
* implement get_documents_by_id
* handle not existing documents
* add docstrings
* auth added
* add tests
* generate docs
* Add latest docstring and tutorial changes
* add responses to dev dependencies
* fix tests
* support query() and quey_by_embedding()
* Add latest docstring and tutorial changes
* query tests added
* read api_key and api_endpoint from env
* Add latest docstring and tutorial changes
* support query() and quey_by_embedding()
* query tests added
* Add latest docstring and tutorial changes
* Add latest docstring and tutorial changes
* support dynamic similarity and return_embedding values
* Add latest docstring and tutorial changes
* adjust KeywordDocumentStore description
* refactoring
* Add latest docstring and tutorial changes
* implement get_document_count and raise on all not implemented methods
* Add latest docstring and tutorial changes
* don't use abbreviation DC in comments and errors
* Add latest docstring and tutorial changes
* docstring added to KeywordDocumentStore
* Add latest docstring and tutorial changes
* enhanced api key set
* split tests into two parts
* change setup.py in order to work around build cache
* added link
* Add latest docstring and tutorial changes
* rename DCDocumentStore to DeepsetCloudDocumentStore
* Add latest docstring and tutorial changes
* remove dc.py
* reinsert link to docs
* fix imports
* Add latest docstring and tutorial changes
* better test structure
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* add ndcg and eval_mode to docstrings and reorder dataframe columns in docs
* Add latest docstring and tutorial changes
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* add parameters to allow for different hyperparameters in stage 1 and 2 of tinybert distillation
* Add latest docstring and tutorial changes
* improve default parameters
* Add latest docstring and tutorial changes
* split up distillation method
* Add latest docstring and tutorial changes
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* run predictions on ground-truth docs in reader
* build dataframe for closed/open domain eval
* fix looping through multilabel
* fix looping through multilabel's list of labels
* simplify collecting relevant docs
* switch closed-domain eval off by default
* Add latest docstring and tutorial changes
* handle edge case params not given
* renaming & generate pipeline eval report
* add test case for closed-domain eval metrics
* Add latest docstring and tutorial changes
* test report of closed-domain eval
* report closed-domain metrics only for answer metrics not doc metrics
* refactoring
* fix mypy & remove comment
* add second for-loop & use answer as method input
* renaming & add separate loop building docs eval df
* Add latest docstring and tutorial changes
* source /home/tstad/miniconda3/bin/activatechange column order for evaluatation dataframe (#1957)
conda activate haystack-dev2
* change column order for evaluatation dataframe
* added missing eval column node_input
* generic order for both document and answer returning nodes; ensure no columns get lost
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* fix column reordering after renaming of node_input
* simplify tests & add docu
* Add latest docstring and tutorial changes
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* Properly fix MetaDocumentORM and MetaLabelORM with composite foreign key constraints
* update_document_meta() was not using index properly
* Exclude ES and Memory from the cosine_sanity_check test
* move ensure_ids_are_correct_uuids in conftest and move one test back to faiss & milvus suite
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* align document store similarity functions
* remove unnecessary imports
* undone accidental change
* stopped weaviate from pretending to support dot product similarity
* stopped weaviate from pretending to support dot product similarity
* Add latest docstring and tutorial changes
* fix fixture params for document stores
* use cosine similarity for most tests
* fix cosine similarity test
* fix faiss test
* fix weaviate test
* fix accidental deletion
* fix document_store fixture
* test fix; shouldn't be merged
* fix test_normalize_embeddings_diff_shapes
* probably a better fix
* fix for parameter combinations
* revert new pytest_generate_tests functionality
* simplify pytest_generate_tests
* normalize embeddings for test_dpr_embedding
* add to faiss doc that embeddings are normalized
* Add latest docstring and tutorial changes
* remove unnecessary parameters and add comments
* simplify two lines of memory.py into one
* test similarity scores with smaller language model
* fix test_similarity_score
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* Refactored code to unify vector_dim and embedding_dim parameter in DocumentStores
* Unit test cases updated to use `embedding_dim` instead of `vector_dim`
* Unit test case update to use embedding_dim instead of vector_dim
* Add latest docstring and tutorial changes
* Put usage of `vector_dim` param in same if-block as corresponding warning
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* check multiprocessing sharing strategy is available
* Change default of multiprocessing strategy to None
* Change default sharing strategy to None in retriever
* Add latest docstring and tutorial changes
* Make logging message easier to understand
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* fix#1687
* fix RuntimeError: received 0 items of ancdata
* Add an arg multiprocessing_strategy to DataSilo and DPR.train()
* Add latest docstring and tutorial changes
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* Add ParsrConverter
* Fix typing error + add Parsr to Linux CI
* Fix valid_language for all converters + fix context generation for ParsrConverter
* Remove ParsrConverter test from WindowsCI
* Add latest docstring and tutorial changes
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* retriever metrics added
* Add latest docstring and tutorial changes
* answer and document level matching metrics implemented
* Add latest docstring and tutorial changes
* answer related metrics for retriever
* basic reader metrics implemented
* handle no_answers
* fix typing
* fix tests
* fix tests without sas
* first draft for simulated top k
* rename sas and f1 columns in dataframe
* refactoring of EvaluationResult
* Add latest docstring and tutorial changes
* more eval tests added
* fix sas expected value precision
* distinction between ir and qa recall
* EvaluationResult.worst_queries() implemented
* print_evaluation_report() added
* eval report for QA Pipeline improved
* dynamic metrics for worst queries calc
* Add latest docstring and tutorial changes
* method names adjusted
* simple test for print_eval_report() added
* improved documentation
* Add latest docstring and tutorial changes
* minor formatting
* Add latest docstring and tutorial changes
* fix no_answer cases
* adjust one docstring
* Add latest docstring and tutorial changes
* fix no_answer cases for sas
* batchmode for sas implemented
* fix for retriever metrics if there are only no_answers
* fix multilabel tests
* improve documentation for pipeline.eval()
* streamline multilabel aggregates and docs
* Add latest docstring and tutorial changes
* fix multilabel tests
* unify document_id
* add dataframe schema description to EvaluationResult
* Add latest docstring and tutorial changes
* rename worst_queries to wrong_examples
* Add latest docstring and tutorial changes
* make query digesting standard pipelines work with pipeline.eval()
* Add latest docstring and tutorial changes
* tests for multi retriever pipelines added
* remove unnecessary import
* print_eval_report(): support all pipelines without junctions
* Add latest docstring and tutorial changes
* fix typos
* Add latest docstring and tutorial changes
* fix minor simulated_top_k bug and use memory documentstore throughout tests
* sas model param description improved
* Add latest docstring and tutorial changes
* rename recall metrics
* Add latest docstring and tutorial changes
* fix mean average precision link
* Add latest docstring and tutorial changes
* adjust sas description docstring
* Add latest docstring and tutorial changes
* Add latest docstring and tutorial changes
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* Introduced an arg add synonyms to Elasticsearch
* Added the test code, removed the whitespace formatting changes, and overwrote the relevant parts from the already existing mapping instead of creating new mapping.
* Added the test code
* Remove whitespace change
* Added the doc_string with examples and link
* Removed unneccessary spaces
* Add latest docstring and tutorial changes
* fix text_field -> content_field
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* adding yaml functionality to BaseStandardPipeline
fixes#1681
* Add latest docstring and tutorial changes
* Update API Reference Pages for v1.0 (#1729)
* Create new API pages and update existing ones
* Create query classifier page
* Remove Objects suffix
* Change answer aggregation key to doc_id, query instead of label_id, query (#1726)
* Add debugging example to tutorial (#1731)
* Add debugging example to tutorial
* Add latest docstring and tutorial changes
* Remove Objects suffix
* Add latest docstring and tutorial changes
* Revert "Remove Objects suffix"
This reverts commit 6681cb06510b080775994effe6a50bae42254be4.
* Revert unintentional commit
* Add third debugging option
* Add latest docstring and tutorial changes
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* Fix another self.device/s typo (#1734)
* Fix yet another self.device(s) typo
* Add typing to 'initialize_device_settings' to try prevent future issues
* Fix bug in Tutorial5
* Fix the same bug in the notebook
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* added test for saving and loading prebuilt pipelines
* fixed typo, changed variable name and added comments
* Add latest docstring and tutorial changes
* 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
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* Fix `print_answers` (#1743)
* Fix a specific path of print_answers that was assuming answers are dictionaries
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* Split pipeline tests into three suites (#1755)
* Split pipeline tests into three suites
* Will this trigger the CI?
* Rename duplicate test into test_most_similar_documents_pipeline
* Fixing a bug that was probably never noticed
* Capitalize starting letter in params (#1750)
* Capitalize starting letter in params
Capitalized the starting letter in code examples for params in keeping with the latest names for nodes where first letter is capitalized.
Refer: https://github.com/deepset-ai/haystack/issues/1748
* Update standard_pipelines.py
Capitalized some starting letters in the docstrings in keeping with the updated node names for standard pipelines
* Multi query eval (#1746)
* add eval() to pipeline
* Add latest docstring and tutorial changes
* support multiple queries in eval()
* Add latest docstring and tutorial changes
* keep single query test
* fix EvaluationResult node_results default
* adjust docstrings
* Add latest docstring and tutorial changes
* minor improvements from comments
* Add latest docstring and tutorial changes
* move EvaluationResult and calculate_metrics to schema
* Add latest docstring and tutorial changes
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* Split summarizer tests in order to make windows CI work again (#1757)
* separate testfile for summarizer with translation
* Add latest docstring and tutorial changes
* import SPLIT_DOCS from test_summarizer
* add workflow_dispatch to windows_ci
* add worflow_dispatch to linux_ci
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* fix import of EvaluationResult in test case
* exclude test_summarizer_translation.py for windows_ci (#1759)
* Pipelines now tolerate custom _debug content (#1756)
* Pipelines now tolerate custom _debug content
* Support Tables in all DocumentStores (#1744)
* Add support for tables in SQLDocumentStore, FAISSDocumentStore and MilvuDocumentStore
* Add support for WeaviateDocumentStore
* Make sure that embedded meta fields are strings + add embedding_dim to WeaviateDocStore in test config
* Add latest docstring and tutorial changes
* Represent tables in WeaviateDocumentStore as nested lists
* Fix mypy
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* Allow TableReader models without aggregation classifier (#1772)
* Fix usage of filters in `/query` endpoint in REST API (#1774)
* WIP filter refactoring
* fix filter formatting
* remove inplace modification of filters
* Public demo (#1747)
* Queries now run only when pressing RUN. File upload hidden. Question is not sent if the textbox is empty.
* Add latest docstring and tutorial changes
* Tidy up: remove needless state, add comments, fix minor bugs
* Had to add results to the status to avoid some bugs in eval mode
* Added 'credits'
* Add footers, update requirements, some random questions for the evaluation
* Add requested changes
* Temporary rollback the UI to the old GoT dataset
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* Facilitate concurrent query / indexing in Elasticsearch with dense retrievers (new `skip_missing_embeddings` param) (#1762)
* Filtering records not having embeddings
* Added support for skip_missing_embeddings Flag. Default behavior is throw error when embeddings are missing. If skip_missing_embeddings=True then documents without embeddings are ignored for vector similarity
* Fix for below error:
haystack/document_stores/elasticsearch.py:852: error: Need type annotation for "script_score_query"
* docstring for skip_missing_embeddings parameter
* Raise exception where no documents with embeddings is found for Embedding retriever.
* Default skip_missing_embeddings to True
* Explicitly check if embeddings are present if no results are returned by EmbeddingRetriever for Elasticsearch
* Added test case for based on Julian's input
* Added test case for based on Julian's input. Fix pytest error on the testcase
* Added test case for based on Julian's input. Fix pytest error on the testcase
* Added test case for based on Julian's input. Fix pytest error on the testcase
* Simplify code by using get_embed_count
* Adjust docstring & error msg slightly
* Revert error msg
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
* Huggingface private model support via API tokens (FARMReader) (#1775)
* passed kwargs to model loading
* Pass Auth token explicitly
* add use_auth_token to get_language_model_class
* added use_auth_token parameter at FARMReader
* Add latest docstring and tutorial changes
* added docs for parameter `use_auth_token`
* Add latest docstring and tutorial changes
* adding docs link
* Add latest docstring and tutorial changes
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* private hugging face models for retrievers (#1785)
* private dpr
* Add latest docstring and tutorial changes
* added parameters to child functions
* Add latest docstring and tutorial changes
* added tableextractor
* Add latest docstring and tutorial changes
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* ignore empty filters parameter (#1783)
* ignore empty filters parameter
* Add latest docstring and tutorial changes
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* initialize doc store with doc and label index in tutorial 5 (#1730)
* initialize doc store with doc and label index
* change ipynb according to py for tutorial 5
* Add latest docstring and tutorial changes
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* Small fixes to the public demo (#1781)
* Make strealit tolerant to haystack not knowing its version, and adding special error for docstore issues
* Add workaround for a Streamlit bug
* Make default filters value an empty dict
* Return more context for each answer in the rest api
* Make the hs_version call not-blocking by adding a very quick timeout
* Add disclaimer on low confidence answer
* Use the no-answer feature of the reader to highlight questions with no good answer
* Upgrade torch to v1.10.0 (#1789)
* Upgrade torch to v1.10.0
* Adapt torch version for torch-scatter in TableQA tutorial
* Add latest docstring and tutorial changes
* Make torch version more flexible
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* adding yaml functionality to BaseStandardPipeline
fixes#1681
* Add latest docstring and tutorial changes
* added test for saving and loading prebuilt pipelines
* fixed typo, changed variable name and added comments
* Add latest docstring and tutorial changes
* fix code rendering for example
* Add latest docstring and tutorial changes
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* separate testfile for summarizer with translation
* Add latest docstring and tutorial changes
* import SPLIT_DOCS from test_summarizer
* add workflow_dispatch to windows_ci
* add worflow_dispatch to linux_ci
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* Fix a specific path of print_answers that was assuming answers are dictionaries
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* Move each haystack module's logger configuration into the respective file and configure the handlers properly
* Implement most changes from #1714
* Remove accidentally committed git merge tags ':D
* Remove the debug logs capture feature
* Remove more references to debug_logs
* Fix issue with FARMReader that somehow made it to master
* Add devices parameter to Inferencer
* Change log of APEX message to DEBUG and lower the 'Starting <docstore>...' messages to DEBUG as well
* Change log level of a few logs from modeling
* Silence the transformers warning
* Remove empty line below the workers :)
* Fix two more levels in the tutorials logs
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* Use initialize_device_settings in all nodes
* Set StreamHandler level to INFO
* Add latest docstring and tutorial changes
* work in progress
* Standardize device initialization
* Add latest docstring and tutorial changes
* Adapt device initialization in Reader's train method
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* create uuid and dummy embeddding in weaviate doc store
* handle and test for duplicate non-uuid-formatted ids in weaviate
* add uuid and dummy embedding to doc strings
* Add latest docstring and tutorial changes
* Upgrade weaviate
* Include weaviate in common doc store test cases
* Add latest docstring and tutorial changes
* Exclude weaviate doc store from eval tests
* Incorporate index name in uuid generation
* Ignore mypy error
* Fix typo
* Restore DOCS without uuid and embeddings generated by weaviate
* Supply docs for retriever tests as fixture
* Limit scope of fixture to function instead of session
* Add comments
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* Added uniform normalization method to each of the DocStores (implemented), so that now Milvus and Weaviate doc stores can use cosine similarity, plus future method for making existing embeddings normaziled (empty for now).
* Fixed a typo.
* Fixed lots of stuff. Performed local tests.
* Fixed scores representation for cosine. Assuming Weavieate's rep needs no change.
* fixes as per discussion
* Trigger CI
* resolving conflicts
* small typo
* fixed a param type
* cleaned some conflicts resolving left overs
* commented out fastmath for a moment
* fixing tests
* added docstore for small vectors
* test
* fixed document_store_cosine_small
* cosine tests fixes
* fixed document_store_cosine_small
* fixed weaviate index name and lowered rtol for ES
* increased rtol
* added explicit doc_ids for weaviate, excluded ES, included Inmemory
* resolving mismatch
* fixing a typo
* flatten normalize_embedding()
* fix import for test
* standardize normalize_embeddings across doc stores
* Add latest docstring and tutorial changes
* going for the faster plain dot prod
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Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
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* ensure tf-idf matrix calculation before retrieval
* Run fit() automatically if new documents have been added
* Add latest docstring and tutorial changes
* Fix type error
* Add test case for tfidf retriever yaml pipeline
* Use InMemoryDocStore and add 2nd test case
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* Truncate too large tables for TableReader
* Add documentation
* Add latest docstring and tutorial changes
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* 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
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