Merge branch 'main' into upgrade-simplemma

NatLibFi · Jun 6, 2024 · 9b45e09 · 9b45e09
2 parents ec7d640 + aebb995
commit 9b45e09
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -2,3 +2,5 @@
 3bc18907354a40f1d89dca1833a2719ba7fb0933
 # Reorder import statements with isort
 68a72c5a603283f70abce2651dcde9c6f0177c41
+# Migrate code style to Black 24
+d4dbd73fe6a91964af82fbf6e6cb8d70b77569a3
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"
diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml
@@ -10,18 +10,20 @@ on:
 env:
   PIPX_HOME: "/home/runner/.cache/pipx"
   PIPX_BIN_DIR: "/home/runner/.local/bin"
-  POETRY_VERSION: "1.5.1"
+  POETRY_VERSION: "1.8.2"
+permissions:
+  contents: read
 jobs:
 
   lint:
     runs-on: ubuntu-22.04
     name: lint with isort, Black & flake8
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
     - name: "Prepare: restore caches, install Poetry, set up Python"
       uses: ./.github/actions/prepare
       with:
-        python-version: "3.10"
+        python-version: "3.11"
         poetry-version: ${{ env.POETRY_VERSION }}
     - name: Install Python dev dependencies
       run: |
@@ -40,12 +42,12 @@ jobs:
     runs-on: ubuntu-22.04
     name: check CLI startup time
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
     - name: "Prepare: restore caches, install Poetry, set up Python"
       id: prepare
       uses: ./.github/actions/prepare
       with:
-        python-version: "3.9"
+        python-version: "3.10"
         poetry-version: ${{ env.POETRY_VERSION }}
     - name: Install Python dependencies
       run: |
@@ -59,10 +61,10 @@ jobs:
     timeout-minutes: 15
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     name: test on Python ${{ matrix.python-version }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
     - name: Install system packages
       run: |
         sudo apt-get install \
@@ -77,32 +79,42 @@ jobs:
     - name: Install Python dependencies
       run: |
         # Selectively install the optional dependencies for some Python versions
-        # For Python 3.8:
-        if [[ ${{ matrix.python-version }} == '3.8' ]]; then
-          poetry install -E "nn omikuji yake voikko stwfsa";
-        fi
         # For Python 3.9:
         if [[ ${{ matrix.python-version }} == '3.9' ]]; then
+          poetry install -E "nn omikuji yake voikko stwfsa";
+        fi
+        # For Python 3.10:
+        if [[ ${{ matrix.python-version }} == '3.10' ]]; then
           poetry install -E "fasttext spacy";
           # download the small English pretrained spaCy model needed by spacy analyzer
           poetry run python -m spacy download en_core_web_sm --upgrade-strategy only-if-needed
         fi
-        # For Python 3.10:
-        if [[ ${{ matrix.python-version }} == '3.10' ]]; then
-          poetry install -E "nn omikuji yake stwfsa";
+        # For Python 3.11:
+        if [[ ${{ matrix.python-version }} == '3.11' ]]; then
+          poetry install -E "nn fasttext yake stwfsa voikko spacy";
+          # download the small English pretrained spaCy model needed by spacy analyzer
+          poetry run python -m spacy download en_core_web_sm --upgrade-strategy only-if-needed
+        fi
+        # For Python 3.12:
+        if [[ ${{ matrix.python-version }} == '3.12' ]]; then
+          poetry install -E "fasttext yake voikko spacy";
+          # download the small English pretrained spaCy model needed by spacy analyzer
+          poetry run python -m spacy download en_core_web_sm --upgrade-strategy only-if-needed
         fi
         poetry run python -m nltk.downloader punkt
     - name: Test with pytest
       run: |
         poetry run pytest --cov=./ --cov-report xml
-        if [[ ${{ matrix.python-version }} == '3.9' ]]; then
+        if [[ ${{ matrix.python-version }} == '3.10' ]]; then
           poetry run pytest --cov=./ --cov-report xml --cov-append -m slow
         fi
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@81cd2dc8148241f03f5839d295e000b8f761e378  # v3.1.0
+      uses: codecov/codecov-action@c16abc29c95fcf9174b58eb7e1abf4c866893bc8  # v4.1.1
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     - name: Save cache
       if: steps.prepare.outputs.cache-matched-key != format('poetry-installation-and-cache-{0}-{1}-{2}', matrix.python-version, env.POETRY_VERSION, hashFiles('**/poetry.lock'))
-      uses: actions/cache/save@v3
+      uses: actions/cache/save@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
       with:
         path: |
           ~/.cache/pipx/venvs
@@ -117,7 +129,7 @@ jobs:
     timeout-minutes: 15
     steps:
     - name: "Build image for testing"
-      uses: docker/build-push-action@c56af957549030174b10d6867f20e78cfd7debc5  # v3.2.0
+      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0  # v5.3.0
       with:
         push: false
         tags: test-image
@@ -133,20 +145,20 @@ jobs:
     if: github.event_name == 'push' && github.ref == 'refs/heads/main'
     steps:
     - name: Login to Quay.io
-      uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a  # v2.1.0
+      uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20  # v3.1.0
       with:
         registry: quay.io
         username: ${{ secrets.YHTEENTOIMIVUUSPALVELUT_QUAY_IO_USERNAME }}
         password: ${{ secrets.YHTEENTOIMIVUUSPALVELUT_QUAY_IO_PASSWORD }}
     - name: Docker meta
       id: meta
-      uses: docker/metadata-action@57396166ad8aefe6098280995947635806a0e6ea  # v4.1.1
+      uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81  # v5.5.1
       with:
         images: quay.io/natlibfi/annif
         tags: |
           latest
     - name: Build and push to Quay.io
-      uses: docker/build-push-action@c56af957549030174b10d6867f20e78cfd7debc5  # v3.2.0
+      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0  # v5.3.0
       with:
         push: true
         tags: ${{ steps.meta.outputs.tags }}
@@ -158,7 +170,7 @@ jobs:
     runs-on: ubuntu-22.04
     if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
     - name: "Prepare: restore caches, install Poetry, set up Python"
       uses: ./.github/actions/prepare
       with:
@@ -172,22 +184,22 @@ jobs:
         poetry publish --build
 
     - name: Login to Quay.io
-      uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a  # v2.1.0
+      uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20  # v3.1.0
       with:
         registry: quay.io
         username: ${{ secrets.YHTEENTOIMIVUUSPALVELUT_QUAY_IO_USERNAME }}
         password: ${{ secrets.YHTEENTOIMIVUUSPALVELUT_QUAY_IO_PASSWORD }}
     - name: Docker meta
       id: meta
-      uses: docker/metadata-action@57396166ad8aefe6098280995947635806a0e6ea  # v4.1.1
+      uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81  # v5.5.1
       with:
         images: quay.io/natlibfi/annif
         tags: |
           type=semver,pattern={{version}},suffix=-{{date 'YYYYMMDD'}}
           type=semver,pattern={{version}}
           type=semver,pattern={{major}}.{{minor}}
     - name: Build and push to Quay.io
-      uses: docker/build-push-action@c56af957549030174b10d6867f20e78cfd7debc5  # v3.2.0
+      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0  # v5.3.0
       with:
         push: true
         tags: ${{ steps.meta.outputs.tags }}

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -8,6 +8,9 @@ on:
   schedule:
     - cron: "22 11 * * 6"
 
+permissions:
+  contents: read
+
 jobs:
   analyze:
     name: Analyze
@@ -24,18 +27,18 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@1b1aada464948af03b950897e5eb522f92603cc2 # v3.24.9
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@1b1aada464948af03b950897e5eb522f92603cc2 # v3.24.9
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@1b1aada464948af03b950897e5eb522f92603cc2 # v3.24.9
         with:
           category: "/language:${{ matrix.language }}"
diff --git a/.github/workflows/docker-rebuild.yml b/.github/workflows/docker-rebuild.yml
@@ -1,28 +1,31 @@
 name: "Docker rebuild"
 on: workflow_dispatch
+permissions:
+  contents: read
+
 jobs:
   rebuild-docker-images:
     name: "Docker rebuild"
     runs-on: ubuntu-22.04
     timeout-minutes: 15
     steps:
     - name: "Build for testing"
-      uses: docker/build-push-action@c56af957549030174b10d6867f20e78cfd7debc5  # v3.2.0
+      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0  # v5.3.0
       with:
         push: false
         tags: test-image
     - name: "Test with pytest"
       run: |
         docker run --rm --workdir /Annif test-image pytest -p no:cacheprovider
     - name: Login to Quay.io
-      uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc  # v2.2.0
+      uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20  # v3.1.0
       with:
         registry: quay.io
         username: ${{ secrets.YHTEENTOIMIVUUSPALVELUT_QUAY_IO_USERNAME }}
         password: ${{ secrets.YHTEENTOIMIVUUSPALVELUT_QUAY_IO_PASSWORD }}
     - name: Docker meta
       id: meta
-      uses: docker/metadata-action@2c0bd771b40637d97bf205cbccdd294a32112176  # v4.5.0
+      uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81  # v5.5.1
       with:
         images: quay.io/natlibfi/annif
         flavor: |
@@ -32,7 +35,7 @@ jobs:
           type=semver,pattern={{version}}
           type=semver,pattern={{major}}.{{minor}}
     - name: Build and push to Quay.io
-      uses: docker/build-push-action@44ea916f6c540f9302d50c2b1e5a8dc071f15cdf  # v4.1.0
+      uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0  # v5.3.0
       with:
         push: true
         tags: ${{ steps.meta.outputs.tags }}

diff --git a/.scrutinizer.yml b/.scrutinizer.yml
@@ -4,7 +4,7 @@ checks:
     duplicate_code: true
 build:
   environment:
-    python: 3.8.12
+    python: 3.9.17
   dependencies:
     override:
      - pip install .[dev]

diff --git a/CITATION.cff b/CITATION.cff
@@ -33,11 +33,11 @@ authors:
     affiliation: "National Library of Finland"
 title: "Annif"
 abstract: "Annif is an automatic indexing software."
-version: 1.0.0-dev
+version: 1.2.0-dev
 license: 
   - Apache-2.0
   - GPL-3.0
-date-released: 2023-04-18
+date-released: 2024-04-25
 doi: 10.5281/zenodo.2578948
 repository-code: "https://github.com/NatLibFi/Annif"
 contact:

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.10-slim-bullseye
+FROM python:3.10-slim-bookworm
 LABEL org.opencontainers.image.authors="[email protected]"
 SHELL ["/bin/bash", "-c"]
 
@@ -50,8 +50,11 @@ RUN annif completion --bash >> /etc/bash.bashrc  # Enable tab completion
 RUN groupadd -g 998 annif_user && \
     useradd -r -u 998 -g annif_user annif_user && \
     chmod -R a+rX /Annif && \
-    mkdir -p /Annif/tests/data && \
+    mkdir -p /Annif/tests/data /Annif/projects.d && \
     chown -R annif_user:annif_user /annif-projects /Annif/tests/data
 USER annif_user
+ENV HF_HOME="/tmp"
+
+ENV GUNICORN_CMD_ARGS="--worker-class uvicorn.workers.UvicornWorker"
 
 CMD annif
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2017-2022 University Of Helsinki (The National Library Of Finland)
+Copyright (c) 2017-2024 University Of Helsinki (The National Library Of Finland)
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

diff --git a/README.md b/README.md
@@ -2,10 +2,12 @@
 
 [![DOI](https://zenodo.org/badge/100936800.svg)](https://zenodo.org/badge/latestdoi/100936800)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Container image](https://img.shields.io/badge/container_image-quay.io-blue.svg)](https://quay.io/repository/natlibfi/annif)
 [![CI/CD](https://github.com/NatLibFi/Annif/actions/workflows/cicd.yml/badge.svg)](https://github.com/NatLibFi/Annif/actions/workflows/cicd.yml)
 [![codecov](https://codecov.io/gh/NatLibFi/Annif/branch/main/graph/badge.svg)](https://codecov.io/gh/NatLibFi/Annif)
-[![Code Climate](https://codeclimate.com/github/NatLibFi/Annif/badges/gpa.svg)](https://codeclimate.com/github/NatLibFi/Annif)
 [![Scrutinizer Code Quality](https://scrutinizer-ci.com/g/NatLibFi/Annif/badges/quality-score.png?b=main)](https://scrutinizer-ci.com/g/NatLibFi/Annif/?branch=main)
+[![Code Climate](https://codeclimate.com/github/NatLibFi/Annif/badges/gpa.svg)](https://codeclimate.com/github/NatLibFi/Annif)
+[![OpenSSF Scorecard](https://api.securityscorecards.dev/projects/github.com/NatLibFi/Annif/badge)](https://securityscorecards.dev/viewer/?uri=github.com/NatLibFi/Annif)
 [![codebeat badge](https://codebeat.co/badges/7a8ef539-0094-48b8-84c2-c413b4a50d57)](https://codebeat.co/projects/github-com-natlibfi-annif-main)
 [![CodeQL](https://github.com/NatLibFi/Annif/actions/workflows/codeql.yml/badge.svg)](https://github.com/NatLibFi/Annif/actions/workflows/codeql.yml)
 [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=NatLibFi_Annif&metric=alert_status)](https://sonarcloud.io/dashboard?id=NatLibFi_Annif)
@@ -17,16 +19,16 @@ a statistical automated indexing tool that used metadata from the
 [Finna.fi](https://finna.fi) discovery interface as a training corpus.
 
 This repo contains a rewritten production version of Annif based on the
-[prototype](https://github.com/osma/annif). It is a work in progress, but
-already functional for many common tasks.
+[prototype](https://github.com/osma/annif).
 
-[Finto AI](https://ai.finto.fi/) is a service based on Annif; see the [source code for Finto AI](https://github.com/NatLibFi/FintoAI).
+[Finto AI](https://ai.finto.fi/) is a service based on Annif; see the [source code of Finto AI](https://github.com/NatLibFi/FintoAI)
+and the [🤗 Hugging Face Hub collection](https://huggingface.co/collections/NatLibFi/annif-models-65b35fb98b7c508c8e8a1570) containing the models Finto AI uses.
 
 # Basic install
 
 Annif is developed and tested on Linux. If you want to run Annif on Windows or Mac OS, the recommended way is to use Docker (see below) or a Linux virtual machine.
 
-You will need Python 3.8+ to install Annif.
+You will need Python 3.9-3.12 to install Annif.
 
 The recommended way is to install Annif from
 [PyPI](https://pypi.org/project/annif/) into a virtual environment.
@@ -71,7 +73,7 @@ For details and usage for other shells see
 [Click documentation](https://click.palletsprojects.com/en/8.1.x/shell-completion/).
 # Docker install
 
-You can use Annif as a pre-built Docker container. Please see the
+You can use Annif as a pre-built Docker container image from [quay.io/natlibfi/annif](https://quay.io/repository/natlibfi/annif) repository. Please see the
 [wiki documentation](https://github.com/NatLibFi/Annif/wiki/Usage-with-Docker)
 for details.
 
@@ -130,7 +132,7 @@ Many resources are available:
 
 # Publications / How to cite
 
-Two articles about Annif have been published in peer-reviewed Open Access
+See below for some articles about Annif in peer-reviewed Open Access
 journals. The software itself is also archived on Zenodo and
 has a [citable DOI](https://doi.org/10.5281/zenodo.5654173).
 
@@ -141,6 +143,24 @@ See "Cite this repository" in the details of the repository.
 ## Annif articles
 <ul>
 <li>
+Golub, K.; Suominen, O.; Mohammed, A.; Aagaard, H.; Osterman, O, 2024.
+Automated Dewey Decimal Classification of Swedish library metadata using Annif software.
+Journal of Documentation, in press.
+https://doi.org/10.1108/JD-01-2022-0026
+<details>
+<summary>See BibTex</summary>
+
+    @article{golub2024annif,
+      title={Automated Dewey Decimal Classification of Swedish library metadata using Annif software},
+      author={Golub, Koraljka and Suominen, Osma and Mohammed, Ahmed Taiye and Aagaard, Harriet and Osterman, Olof},
+      journal={J. Doc.},
+      year={in press},
+      doi = {10.1108/JD-01-2022-0026},
+      url={https://www.emerald.com/insight/content/doi/10.1108/JD-01-2022-0026},
+    }
+</details>
+</li>
+<li>
 Suominen, O.; Inkinen, J.; Lehtinen, M., 2022.
 Annif and Finto AI: Developing and Implementing Automated Subject Indexing.
 JLIS.It, 13(1), pp. 265–282. URL: