* Upgrade pydoc-markdown and fix the YAMLs to work with it
* Pin pydoc-markdown to major version
* Generalize pydoc-markdown workflow
* Make a single Action to perform all tasks that require committing into the local branch
* Merge the code updates and the docs in the Linux CI to prevent the bot from always show the pipeline as green
* Installing Jupyter deps for Black
* Build cache before running generation tasks
* Add check not to run the code generation on master
* Simplify push action
* Add more test deps in setup.cfg and remove from GH Action workflow
* Remove forced upgrades on pip install
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* Conversion to df does not need initialization
* Apply Black
* fix test case
* Apply Black
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* add filters attribute to labels and use in eval
* Add latest docstring and tutorial changes
* overwrite params if None
* populate filters from Label to MultiLabel
* add query_id in eval df and deepcopy params for each label
* fix mypy
* add test for aggregating filters in multilabel
* use query ids also in answers df
* loop through unique query_ids
* hash filters and query text as id
* Add latest docstring and tutorial changes
* fix top_k reader eval
* Apply Black
* rename query_id to id/multilabel_id
* Apply Black
* json dump filters in dataframe
* add filters and id to wrong_examples()
* Apply Black
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Co-authored-by: Sara Zan <sara.zanzottera@deepset.ai>
* Testing black on ui/
* Applying black on docstores
* Add latest docstring and tutorial changes
* Create a single GH action for Black and docs to reduce commit noise to the minimum, slightly refactor the OpenAPI action too
* Remove comments
* Relax constraints on pydoc-markdown
* Split temporary black from the docs. Pydoc-markdown was obsolete and needs a separate PR to upgrade
* Fix a couple of bugs
* Add a type: ignore that was missing somehow
* Give path to black
* Apply Black
* Apply Black
* Relocate a couple of type: ignore
* Update documentation
* Make Linux CI run after applying Black
* Triggering Black
* Apply Black
* Remove dependency, does not work well
* Remove manually double trailing commas
* Update documentation
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* Make FileTypeClassifier more flexible
* Make supported_types a init parameter
* Add tests and fix a couple of bugs
* Formatting
* Fix mypy
* Implement feedback
* provide option to recreate es doc store on initialization
* Add latest docstring and tutorial changes
* Label expects more arguments
* Label expects also an answer
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* Review changes
* Added the synonym analyser for search fields
* Added the review requests.
* Added the synonyms the OpenSearchDocumentStore and review requests.
* 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 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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Co-authored-by: Thomas Stadelmann <thomas.stadelmann@deepset.ai>
* 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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* add tinybert data augmentation
* don't reload glove in tinybert data augmentation
* fix unnecessary load_glove call
* fix type hints
* add comments and type hints
* add batch_size argument
* don't predict subwords as alternative for words
* fix subword predictions
* limit sequence length
* actually limit sequence length
* improve performance by calculating nearest glove vector on gpu
* add model and tokenizer parameter
* fix type hints
* improve data augmentation performance
* explained limits of script
* corrected comment
* added data augmentation test
* don't label every question in augmented dataset as impossible
* add sample glove
* better handling of downloading of glove
* fix typo of last commit
* 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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* 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
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* Rely api healthcheck on status code rather than json decoding
* Install UI dependencies on the Linux and Windows CI
Co-authored-by: Fabrice Depaulis <fabrice.depaulis@orange.com>
Co-authored-by: ZanSara <sarazanzo94@gmail.com>
* Fix bug ranker: wrong lambda function
The zip function used in line 110 intends to choose the logits array to be the key for the lambda function while it should be the first/second logit of the logit array which corresponds to the classification label (has_answer)
* Use label 1 as has_answer label
* generic ranker (add if-cond for logits vector shape)
* remove test code
* remove test code...
* add two_logits test case for ranker module.
* complete the documentation of ranker, support rankers with 1 or 2 logits as output
* diable problematic eval tests for windows ci
* move standard pipeline eval tests to separate test file
* switch to elasticsearch documentstore to reduce inproc mem
* Revert "switch to elasticsearch documentstore to reduce inproc mem"
This reverts commit 7a75871909c3317a252dff3a4df17e99eff69d05.
* get retiever from conftest
* use smaller embedding model for summarizer
* use smaller summarizer model
* remove queries param from pipeline.eval()
* isolate problematic tests
* rename separate test file
* Add latest docstring and tutorial changes
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* Aliasing the join is not sufficient yet
* Update the filter query in some other functions of SQLDocumentStore - this functionality should be centralized
* Adding tests for get_all_documents, now failing
* Fix tests
* Fix typo spotted by mypy
* 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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* Add FormRecognizerConverter
* Change signature of convert method + change return type of all converters
* Adapt preprocessing util to new return type of converters
* Parametrize number of lines used for surrounding context of table
* Change name from FormRecognizerConverter to AzureConverter
* Set version of azure-ai-formrecognizer package
* Change tutorial 8 based on new return type of converters
* Add tests
* Add latest docstring and tutorial changes
* Fix typo
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* Fix the feedback function of the demo with a workaround
* Some docstring
* Update tests and rename methods in feedback.py
* Fix tests
* Remove operation_ids
* Add a couple of status code checks
* 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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Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
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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
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* 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
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* 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
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* 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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Co-authored-by: Branden Chan <33759007+brandenchan@users.noreply.github.com>
Co-authored-by: Julian Risch <julian.risch@deepset.ai>
Co-authored-by: Sara Zan <sara.zanzottera@deepset.ai>
Co-authored-by: nishanthcgit <5066268+nishanthcgit@users.noreply.github.com>
Co-authored-by: tstadel <60758086+tstadel@users.noreply.github.com>
Co-authored-by: bogdankostic <bogdankostic@web.de>
Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
Co-authored-by: C V Goudar <cvgoudar@users.noreply.github.com>
Co-authored-by: Kristof Herrmann <37148029+ArzelaAscoIi@users.noreply.github.com>
* 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>
* 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
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* 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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