Annif 1.1

This release introduces CLI commands to share projects via Hugging Face Hub, takes care of various maintenance tasks and fixes minor bugs.

The 🤗 Hugging Face Hub intends to facilitate the sharing of AI models and datasets, and now Annif CLI includes upload and download commands, which can be used to push and pull a set of selected projects and vocabularies to and from a Hugging Face Hub repository. In this release these commands are regarded experimental; there can be changes in them in the future. See this Wiki page for more information about the commands. See also this Hugging Face Hub collection which contains the projects served at Finto AI.

Connexion dependency is upgraded to Connexion 3. From now on, when running Annif with Gunicorn, it is required to use Uvicorn workers; the workers can be set using the option --worker-class uvicorn.workers.UvicornWorker, see Connexion 3 documentation for more details. However, Docker image users do not have to add this option because an enviroment variable in the Docker image sets the worker-class. Two changes due to the upgrade to Connexion 3 relate to the REST API:

• the header Access-Control-Allow-Origin: * is now included in the response only if there's an Origin header in the request, whereas before that header was sent if the Origin header was not present in the request,
• the URL /v1/projects/ used to give a 404 response, but now it redirects to the correct URL /v1/projects.

Support for Python 3.8 is removed. Python 3.12 is supported except for NN-ensemble and STWFSA backends.

It is now possible to select the projects that Annif loads on startup using the environment variable ANNIF_PROJECTS_INIT, which can be useful in container environments as this allows distributing resource demand across multiple Annif processes.

Supported Python versions

• 3.9, 3.10 and 3.11 are fully supported
• 3.12 is supported except NN-ensemble and STWFSA backends

Backward compatibility

• NN ensemble projects trained with Annif v1.0 or older need to be retrained; for other projects the warnings by SciKit-learn are harmless
• When using Annif with Gunicorn HTTP server the worker class needs to be set to Uvicorn with the option --worker-class uvicorn.workers.UvicornWorker

Enhancements
#762/#760 Implement annif upload and annif download commands for Hugging Face Hub integration
#774/#733 Allow loading selected projects using environment variable
#736 Optimization: load a vocabulary only once even if used in different languages
#745 Show Annif version in WebUI
#751 Create SECURITY.md

Maintenance
#702/#689/#698 Upgrade to Connexion3
#780 Add partial Python 3.12 support
#770 Drop Python 3.8 support
#771/#786 Update dependencies for v1.1 release
#739 Harden GitHub Actions
#781 Make Dependabot group GitHub Actions updates into one PR
#740-#744/#750/#757/#758/#763-#766/#783 Upgrade GitHub Actions

Bug fixes
#784/#785 Add informational error message for failed loading of nn-ensemble model
#732 Fix: Add missing completion command to commands list in RTD
#773 Fix blocked http-request for version number on https site
#778 Fix project data files detection
#752 Fix tests error due to pinned Schemathesis version 3.19.* / Docker rebuild
#759 Fix installation on Python 3.8 due to missing Tensorflow-io wheel
#767 Fix tests and Docker rebuild due to defunct Schemathesis and pytest dependencies resolution
#768 Fix ReadTheDocs builds by upgrading docs build dependencies

Annif 1.0.2

This is a patch release that fixes bugs arisen after the Annif 1.0.1 release.

Bugs fixed:
#759 Fix installation on Python 3.8 due to missing Tensorflow-io wheel
#767 Fix tests and Docker rebuild due to defunct Schemathesis and pytest dependencies resolution

Annif 1.0.1

This is a patch release that fixes a bug arisen after Annif 1.0 release.

The bug affected only running unit tests, but the side-effect was that it also prevented rebuilding the Docker image of version 1.0.

Bugs fixed:
#747/#752 Tests error due to pinned schemathesis version 3.19.* / Docker rebuild fails

Annif 1.0

We are excited to introduce Annif version 1.0!

Advancing the version number to the 1.x series means that Annif is considered ready for more general, production use. The upcoming releases in the series (patches 1.0.x and minor feature releases 1.x.x) will be backward compatible, following the semantic versioning principle. See a Wiki page describing the aspects of the compatibility.

The changes in this release include enhancements to the command-line interface as well as many bug fixes and maintenance updates. The CLI commands, options and most parameters can now be tab-completed when the support is enabled: see instructions in README.md. Also the CLI startup time has been optimized, and the output of many commands has been refined.

Python 3.11 is now mostly supported; the Omikuji backend cannot yet be used on Python 3.11 because the Omikuji library does not support it at the moment.

From now on the Docker image of the latest release in the quay.io repository is going to be rebuilt from time to time in order to apply security updates to the image. The rebuilds will not change Annif itself. Version tags (<major>.<minor>[.<patch>]) can be used to reference the latest build of the version. To allow more strict pinning to a particular build, the images will also be tagged with the build date as a suffix: <major>.<minor>.<patch>-<YYYYMMDD>.

Supported Python versions:

• 3.8, 3.9 and 3.10 are fully supported
• 3.11 is supported except Omikuji backend

Backward compatibility:

• MLLM, STWFSA and NN ensemble projects trained with Annif v0.61 or older need to be retrained; for other projects the warnings by SciKit-learn are harmless
• Using STWFSA backend now requires installing an optional dependency

New features:
#684/#693 Support for CLI command completions
#703/#727 Python 3.11 support

Improvements:
#696 Optimize CLI startup time
#686/#694 Improve outputs of project inspection CLI commands
#704 Show scores in outputs of suggest, eval and index with only 4 decimals

Maintenance:
#690/#708 Use Python type hints
#699/#700 Make stwfsapy an optional dependency (credit: @cbartz)
#315/#712/#714 Add CI/CD job for testing Docker image
#707/#711 Ensure system packages are up-to-date in Docker image
#715 Add CI/CD workflow for rebuilding Docker image
#706/#725 Test CLI startup time with CI/CD job
#723 Update ReadTheDocs documentation
#726/#697/#532 Update and pin dependencies v1.0
#730 Switch to Keras v3 save format for nn_ensemble
#731 Upgrade Docker baseimage to Debian Bookworm

Bug fixes:
#705 Fix crashing index command when targeted directory contains subject files
#717 Fix Python version in GitHub Actions CI/CD pipeline
#718 Fix missing limit parameter in STWFSA backend
#722 Fix train state and modification time for unfinished project training
#720/#721 Suppress TensorFlow info messages to debug level
#695 Fix displaying of modification time for null value in Web UI project information
#701 Remove duplicated fasttext entry in optional dependencies list in Dockerfile
#728 Avoid PytestUnknownMarkWarning due to "slow" marker
#729 Avoid scikit-learn UserWarning for vectorizer parameter token_pattern

Other:
#616 Discussion on semantic versioning for Annif releases beyond 1.0

Annif 0.61

The main improvements in this release are internal changes to allow batch processing of documents for better suggestion performance and the streamlining of suggestion result representation by using sparse arrays. Currently batched processing of documents is implemented in the Omikuji, SVC, and all ensemble backends. Also a new REST API method for suggesting subjects for multiple documents has been added.

The new REST API method /v1/projects/{project_id}/suggest-batch accepts at most 32 documents in one POST request; the documents in the batch are processed in parallel when the used backend provides support for this. The request body is given in JSON format and, like in the case of the regular single-document suggest method, the limit, threshold and language parameters are optional and can be given as URL query parameters. For details see the interactive OpenAPI documention of the REST API of annif.org.

The annif suggest CLI command is augmented to accept path(s) to file(s) to be processed, in addition to stdin, to enable it to operate on multiple documents. The annif optimize command is now much faster than before and supports using a --jobs parameter for parallel processing.

The Annif Docker image has been updated to use Python 3.10.

Also various maintenance tasks have been performed, for example, the default branch of the git repository has been renamed from master to main, the Schemathesis tool has been introduced for testing the REST API and many dependendencies have been updated. A bug causing a memory leak in the neural network ensemble backend bas been fixed.

The next release of Annif will be version 1.0. For this purpose we have opened the issue #616 for discussing the expectations of backward compatibility and Semantic Versioning in releases beyond 1.0.

Backward compatibility:

• Models trained with Annif v0.60 should remain working; the warnings by SciKit-learn are harmless
• LRAP metric has been removed from evaluation results

New features:
#664 Add REST API method /v1/projects/{project_id}/suggest-batch
#663 Support for batch suggest operations for CLI commands
#423/#681 Parallelize optimize command

Improvements:
#678/#681 Represent suggestion results as sparse arrays
#665/#669 Batch suggest in Omikuji backend
#667/#670 Batch suggest in SVC backend
#677 Batch suggest in ensemble backends
#671 Add log message indicating finishing projects initialization
#673 Suppress duplicate log messages from subject module

Maintenance:
#668 Migrate codestyle to Black v23
#679/#680 Switch default git branch to main
#672 Fix slow CI/CD runs for Python 3.10
#675 Refactor and cleanup CLI module
#682/#685 Schemathesis tests for REST API and OpenAPI schema fixes
#683 Update dependencies v0.61
#691 Upgrade Docker image to Python 3.10

Bug fixes:
#674/#677 Memory leak in NN ensemble backend

Annif 0.60

This release includes improvements and maintenance updates in particular to the Web UI and REST API as well as some new functionality, especially related to multilingual support. The Web UI no longer relies on jQuery, as the last parts that were used were replaced with Axios. The REST API and Web UI updates are by @UnniKohonen, who has joined @NatLibFi as a trainee in the Annif & Finto development teams.

It is now possible to override the language for subject suggestion labels instead of always using the project language: when using the annif suggest command by giving the new --language/-L option, and when using the REST API suggest method by the new optional language parameter.

A new resource is added to the root of the REST API (i.e. http://<annif_host>/v1/) that gives basic information on the API (a title for the API and the version of Annif being used). Also, the REST API spec has been updated to OpenAPI 3.0. In the Web UI it is now possible to see detailed information about a project (language, backend type, modification timestamp etc.). 

Multiprocessing support for Mac OS and Windows environments has been improved by supporting the 'spawn' multiprocessing mode.

The language detection is now performed with Simplemma instead of pycld3. This functionality is now installed by default instead of being an optional extra.

New code style tools Black and isort are now used to help maintaining good code quality; see CONTRIBUTING.md how they can be used and instructions to how best participate in Annif development.

Many dependendencies have been updated to their most recent versions.

Note also that we are preparing for Annif 1.0 release. For this purpose we have opened the issue #616 for discussing the expectations of backward compatibility and Semantic Versioning in releases beyond 1.0.

Backward compatibility:

• Models trained with Annif v0.59 should remain working; the warnings by SciKit-learn are harmless
• The annif loadvoc command has been removed, as in the previous release it was deprecated and replaced by the annif load-vocab command.

New features:
#628/#630 Allow overriding subject label language in CLI and REST suggest operations
#637/#638 Add support for spawn multiprocessing mode
#654 Add project info to web UI
#655/#658 Add REST API root resource

Improvements:
#593/#626 Use Simplemma instead of pycld3 for language detection
#643 Add CONTRIBUTING.md file
#645 Use tailored user-agent in requests by HTTP-backend
#644/#649 Upgrade REST API spec to OpenAPI 3
#627 Upgrade joblib to 1.2.x
#642 Upgrade jQuery to version 3.6.1
#646 Use axios in web UI; remove jQuery
#648 Upgrade Bootstrap to version 5.2.2
#651 Upgrade TensorFlow to version 2.11.*
#660 Update dependencies v0.60
#647/661 Order of projects when using project configuration directory

Maintenance:
#609/#640 Use black code style
#641 Use isort to order import statements
#656 Install linting tools with Poetry in CI/CD pipeline
#624 Increase timeout of test and publish GH Actions jobs
#653 Add CodeQL workflow for GitHub code scanning
#599/#650 Avoid using pytest-flake8 plugin
 #657/#662 Upgrade GitHub Actions
#636 Better set up for docker-compose

Annif 0.59

This release makes many changes to how Annif handles vocabularies.

First, the vocabularies are now multilingual: projects with different languages can share the same vocabulary by using a common vocabulary id in the project configurations. The vocabulary id should no longer include a language specifier, which has been the practice until now. The language of the labels of subject suggestions is now defined by the project's language setting, or it can be overridden in a project by giving the language code in parentheses after the vocabulary id (e.g. vocab=lcsh(en) in a Finnish language project). These changes break the backward compatibility of existing projects and vocabularies.

The CLI command for loading a vocabulary has changed: the command is now annif load-vocab to align with the other annif commands and its first argument is a vocabulary id instead of a project id. When loading a vocabulary from a TSV file the --language option needs to be given to set the language. A command annif list-vocabs is introduced for listing vocabularies. The old annif loadvoc command still works in this release, but it has been deprecated and will be removed in the next Annif release.

The CLI commands are now documented in a page on the ReadTheDocs instead of the Annif wiki. The development installations of Annif now use Poetry for managing Python virtual environments and dependencies. There are also a few other minor changes, including an upgrade to Simplemma v0.8 series that introduced support for new languages.

Note also that we are starting to prepare for Annif 1.0 release. For this purpose we have opened the issue #616 for discussing the expectations of backward compatibility and Semantic Versioning in releases beyond 1.0.

Backward compatibility

The changes in the vocabulary functionality require reloading of previously loaded vocabularies and retraining of existing models.

New features

#559/#600 Make vocabularies multilingual
#602/#614 Implement load-vocab and list-vocabs commands
#603/#610 Store vocabs in AnnifRegistry so they are shared between projects
#597 Include labels without language tag and concepts without labels in vocabulary

Improvements

#617/#618 Upgrade to simplemma 0.8 and disable unnecessary cache
#595/#611 Autogenerated CLI commands documentation on ReadTheDocs
#612 Add Annif logo to ReadTheDocs sidebar
#608 Multilingual SubjectIndex backed by CSV file
#604 Refactor SubjectSuggestion to store subject_id - not uri, label, notation

Maintenance

#607 Remove language suffixes from vocabulary ids in example config
#606 Refactor SubjectSet and Document to store subject IDs instead of URIs and labels
#601/#605 Switch to Poetry for dependency management
#621 Remove curl from Docker image
#622 Remove Poetry cache from Docker image

Fixes

#613 Restore ability to use vocab language different from project language
#619 Allow use of hyphens in vocabulary IDs
#620 Make NN ensemble suggest operations silent

Annif 0.58

This release introduces a new Simplemma analyzer, support for multiple configuration files in a directory, and support for Python 3.10; support for Python 3.7 is removed.

Simplemma is a lightweight multilingual lemmatizer, which currently supports 38 languages; an analyzer based on Simplemma is now implemented as a core feature of Annif. Using multiple project configuration files is made possible by implementing support for a project configuration directory: Annif reads all files matching pattern *.cfg and *.toml in the directory and merges their contents. The default name of the configuration directory is projects.d, but any directory can be selected with -p/--projects command option or ANNIF_PROJECTS environment variable.

Python 3.10 support is reached by updating multiple dependencies; retraining of existing projects should not be necessary. The language filtering optional feature is not yet available on Python 3.10, because of the lack of support of pycld3 for Python 3.10.

New features:

• #584/#585 Support for multiple configuration files in a directory
• #590/#591 Add simplemma analyzer

Improvements:

• #589/#592 Add Python 3.10 support & update dependencies

Maintenance:

• #594 Upgrade Simplemma to version 0.7
• #587 Update GitHub Actions
• #588 Delete .coveragerc configuration file
• #598 Pin flake8 to version 4.x to avoid pytest-flake8 breakage

Bug fixes:

• #586 Fix readthedocs documentation builds

Annif 0.57

Training of NN ensemble models can now be performed in parallel (running suggest operations simultaneously for all source projects) on multiple CPUs; this is controlled by using the --jobs parameter of the train command. The compatibility of Annif with DVC is improved by supporting TOML file format for configuring Annif projects. The --force option is added to the loadvoc command that can be used to replace an existing vocabulary instead of updating it. This release includes many small maintenance tasks for the CI/CD pipeline, e.g. migrating Docker image builds to GitHub Actions from the Drone platform.

Omikuji, TensorFlow and Connexion dependencies are upgraded to the latest available versions; retraining of projects should not be necessary.

New features:
#526/#567 Add --force option to loadvoc CLI command

Improvements:
#429/#568 Perform suggest operations in parallel using multiprocessing in nn_ensemble
#547/#560 Support TOML as a configuration file format alongside CFG/INI for DVC compatibility

Maintenance:
#570 Use fulltext corpus in MLLM tests which is much faster
#571 Docker builds on GitHub Actions CI/CD
#572 Update Dockerfile v0.57
#573 Ensure setuptools and wheel are installed & up-to-date for tests in GitHub Actions CI
#574 Avoid running duplicated tests on PRs in GitHub Actions CI
#575 Resolve some Warnings by tests
#576 Enable pip cache in GitHub Actions CI
#577 Improved Project links in PyPI page
#578 Update dependencies v0.57
#581/#582 Add tags trigger to GH Actions CI/CD workflow

Annif 0.56

This release introduces a new spaCy analyzer and takes care of many maintenance tasks. The CLI usage is improved by shortening the startup time of some commands, the Docker images are now easier to customize, there are improvements to the eval command, and minor bugs are fixed.

The spaCy analyzer enables support for some new languages and can improve subject suggestion results. The spaCy analyzer and the language-specific models need to be installed separately. The Docker image distributed via quay.io includes the spaCy analyzer and the English language model, but no other languages.

The maintenance tasks include upgrading many dependencies, notably Omikuji to v0.4. The Omikuji upgrade brings faster training and predictions as well as reduced memory usage, but the Annif projects using the omikuji backend need to be retrained. The projects using other backends should not require retraining, although warnings may be shown in some cases.

The support for Python 3.6 is removed, which is necessitated by the dependency upgrades.

This release also removes the Maui and vw_multi (Vowpal Wabbit) backends.

New features:
#374/#527/#563 spaCy analyzer

Improvements:
#514/#544 Optimize startup time using local & lazy imports
#548 Allow selecting installed optional dependencies in Docker build
#545/#558 Select metrics for eval command using an option
#546/#557 Output eval metrics as a JSON file compatible with DVC

Bug fixes:
#552/#554 LMDB can overflow (credit: @mo-fu)
#562 Add missing import of annif.eval in MLLM backend

Maintenance:
#549 Update dependencies for v0.56
#550 Drop Python 3.6 support
#541 Remove Maui and Vowpal Wabbit multi backends
#551 Remove swagger-tester dependency
#542/#555 Add CITATION.cff file
#553 Update Scrutinizer config
#561 Set a 10 minute timeout for GitHub Actions CI jobs
#565 Avoid coverage 6.3 as it causes some tests to hang