From 092aeceaa1ec0fba2e5243955d8b691a146606fe Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 12:11:20 +0200
Subject: [PATCH 01/17] Upgrade to jsonschema 4.21.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6a06219b4..270202c14 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,7 +47,7 @@ optuna = "3.3.*"
 python-dateutil = "2.8.*"
 tomli = { version = "2.0.*", python = "<3.11" }
 simplemma = "0.9.*"
-jsonschema = "4.17.*"
+jsonschema = "4.21.*"
 
 fasttext-wheel = {version = "0.9.2", optional = true}
 voikko = {version = "0.5.*", optional = true}

From f37d601ec1d07561e6015768acb7546c4761f075 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 12:15:27 +0200
Subject: [PATCH 02/17] Upgrade to optuna 3.5.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 270202c14..f836f1c83 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ scipy = "1.10.*"
 rdflib = "6.3.*"
 gunicorn = "21.2.*"
 numpy = "1.24.*"
-optuna = "3.3.*"
+optuna = "3.5.*"
 python-dateutil = "2.8.*"
 tomli = { version = "2.0.*", python = "<3.11" }
 simplemma = "0.9.*"

From 14b320d2c4bc64fdb5462b395e79334c6db80a17 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 14:38:36 +0200
Subject: [PATCH 03/17] Upgrade to numpy 1.26.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index f836f1c83..e7a14619e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,7 +42,7 @@ scikit-learn = "1.3.*"
 scipy = "1.10.*"
 rdflib = "6.3.*"
 gunicorn = "21.2.*"
-numpy = "1.24.*"
+numpy = "1.26.*"
 optuna = "3.5.*"
 python-dateutil = "2.8.*"
 tomli = { version = "2.0.*", python = "<3.11" }

From 4268d7668ea55b4383d55b316fee57c6d7a80ba0 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 14:39:24 +0200
Subject: [PATCH 04/17] Upgrade to tensorflow 2.15.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e7a14619e..f55e03256 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,7 @@ jsonschema = "4.21.*"
 
 fasttext-wheel = {version = "0.9.2", optional = true}
 voikko = {version = "0.5.*", optional = true}
-tensorflow-cpu = {version = "2.13.*", optional = true}
+tensorflow-cpu = {version = "2.15.*", optional = true}
 lmdb = {version = "1.4.1", optional = true}
 omikuji = {version = "0.5.*", optional = true}
 yake = {version = "0.4.5", optional = true}

From f5fa9492723c5bfe3d65eed5e053e03f782b4a65 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 14:42:39 +0200
Subject: [PATCH 05/17] Upgrade to scipy 1.12.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index f55e03256..bd5750ead 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ joblib = "1.3.*"
 nltk = "3.8.*"
 gensim = "4.3.*"
 scikit-learn = "1.3.*"
-scipy = "1.10.*"
+scipy = "1.12.*"
 rdflib = "6.3.*"
 gunicorn = "21.2.*"
 numpy = "1.26.*"

From d50ee8231533da25acc4fbea0de354b0fcdfb10b Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 14:46:53 +0200
Subject: [PATCH 06/17] Upgrade to spacy 3.7.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index bd5750ead..3ad90f1d3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,7 +55,7 @@ tensorflow-cpu = {version = "2.15.*", optional = true}
 lmdb = {version = "1.4.1", optional = true}
 omikuji = {version = "0.5.*", optional = true}
 yake = {version = "0.4.5", optional = true}
-spacy = {version = "3.6.*", optional = true}
+spacy = {version = "3.7.*", optional = true}
 stwfsapy = {version="0.3.*", optional = true}
 
 [tool.poetry.dev-dependencies]

From 3b4a22ec9cee1d4150a87d5a55476917886e1cea Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 14:51:30 +0200
Subject: [PATCH 07/17] Upgrade to pytest 8.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3ad90f1d3..b72380ac8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ stwfsapy = {version="0.3.*", optional = true}
 
 [tool.poetry.dev-dependencies]
 py = "*"
-pytest = "7.*"
+pytest = "8.*"
 requests = "*"
 pytest-cov = "*"
 pytest-watch = "*"

From 71b79b0d21e6dcb271344fadd99e86a266b3eb7a Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 16:04:05 +0200
Subject: [PATCH 08/17] Upgrade to yake 0.4.8

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b72380ac8..dcfb6edb3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,7 +54,7 @@ voikko = {version = "0.5.*", optional = true}
 tensorflow-cpu = {version = "2.15.*", optional = true}
 lmdb = {version = "1.4.1", optional = true}
 omikuji = {version = "0.5.*", optional = true}
-yake = {version = "0.4.5", optional = true}
+yake = {version = "0.4.8", optional = true}
 spacy = {version = "3.7.*", optional = true}
 stwfsapy = {version="0.3.*", optional = true}
 

From 888a17e0aeea0bf92b9fd04cb585383b51c8d35c Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Fri, 23 Feb 2024 17:32:06 +0200
Subject: [PATCH 09/17] Resolve DeprecationWarning by Scipy

DeprecationWarning: "getrow" is deprecated and will be removed in v1.14.0; use "X[[0]]"" instead.
---
 annif/eval.py       | 4 ++--
 annif/suggestion.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/annif/eval.py b/annif/eval.py
index 5ec5bd17a..eb6d80f4a 100644
--- a/annif/eval.py
+++ b/annif/eval.py
@@ -63,10 +63,10 @@ def ndcg_score(y_true: csr_array, y_pred: csr_array, limit: int | None = None) -
 
     scores = np.ones(y_true.shape[0], dtype=np.float32)
     for i in range(y_true.shape[0]):
-        true = y_true.getrow(i)
+        true = y_true[[i]]
         idcg = dcg_score(true, true, limit)
         if idcg > 0:
-            pred = y_pred.getrow(i)
+            pred = y_pred[[i]]
             dcg = dcg_score(true, pred, limit)
             scores[i] = dcg / idcg
 
diff --git a/annif/suggestion.py b/annif/suggestion.py
index ddf3ec2e5..fd7c0c12e 100644
--- a/annif/suggestion.py
+++ b/annif/suggestion.py
@@ -38,7 +38,7 @@ def filter_suggestion(
 
     data, rows, cols = [], [], []
     for row in range(preds.shape[0]):
-        arow = preds.getrow(row)
+        arow = preds[[row]]
         if limit is not None and limit < len(arow.data):
             topk_idx = arow.data.argpartition(-limit)[-limit:]
         else:

From 14b8ed70e6ba955606df8961eead41ddb607ca9d Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Mon, 26 Feb 2024 14:17:08 +0200
Subject: [PATCH 10/17] Upgrade to poetry 1.8.0 in CI/CD

---
 .github/workflows/cicd.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml
index 716bccddc..3b2e1aa92 100644
--- a/.github/workflows/cicd.yml
+++ b/.github/workflows/cicd.yml
@@ -10,7 +10,7 @@ on:
 env:
   PIPX_HOME: "/home/runner/.cache/pipx"
   PIPX_BIN_DIR: "/home/runner/.local/bin"
-  POETRY_VERSION: "1.5.1"
+  POETRY_VERSION: "1.8.0"
 permissions:
   contents: read
 jobs:

From 0d620dc4b81a3cb252746ea4bbaa8d131b6c9c65 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Mon, 26 Feb 2024 14:24:08 +0200
Subject: [PATCH 11/17] Upgrade to black 24.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index dcfb6edb3..2d0d29db0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -67,7 +67,7 @@ pytest-watch = "*"
 pytest-flask = "*"
 flake8 = "*"
 bumpversion = "*"
-black = "23.*"
+black = "24.*"
 isort = "*"
 schemathesis = "3.*.*"
 

From d4dbd73fe6a91964af82fbf6e6cb8d70b77569a3 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Mon, 26 Feb 2024 14:39:39 +0200
Subject: [PATCH 12/17] Migrate codestyle to Black v24

---
 annif/analyzer/__init__.py      |  1 +
 annif/analyzer/analyzer.py      |  1 +
 annif/analyzer/simple.py        |  1 +
 annif/analyzer/simplemma.py     |  1 +
 annif/analyzer/snowball.py      |  1 +
 annif/analyzer/spacy.py         |  1 +
 annif/analyzer/voikko.py        |  1 +
 annif/backend/__init__.py       |  1 +
 annif/backend/backend.py        |  1 +
 annif/backend/dummy.py          |  1 +
 annif/backend/ensemble.py       |  1 +
 annif/backend/fasttext.py       |  1 +
 annif/backend/http.py           |  1 +
 annif/backend/hyperopt.py       |  1 +
 annif/backend/mixins.py         |  1 +
 annif/backend/mllm.py           |  1 +
 annif/backend/nn_ensemble.py    |  1 +
 annif/backend/omikuji.py        |  1 +
 annif/backend/pav.py            | 17 ++++++++++-------
 annif/backend/svc.py            |  1 +
 annif/backend/tfidf.py          |  1 +
 annif/backend/yake.py           |  1 +
 annif/cli.py                    |  1 -
 annif/cli_util.py               |  1 +
 annif/config.py                 |  1 +
 annif/corpus/__init__.py        |  1 -
 annif/corpus/combine.py         |  1 +
 annif/corpus/document.py        |  1 +
 annif/corpus/skos.py            | 15 ++++++++++-----
 annif/corpus/subject.py         |  1 +
 annif/corpus/types.py           |  1 +
 annif/datadir.py                |  1 +
 annif/eval.py                   |  7 ++++---
 annif/exception.py              |  1 +
 annif/lexical/mllm.py           |  1 +
 annif/lexical/tokenset.py       |  1 +
 annif/lexical/util.py           |  1 +
 annif/openapi/validation.py     |  1 +
 annif/parallel.py               |  1 +
 annif/project.py                |  1 +
 annif/registry.py               |  1 +
 annif/rest.py                   |  1 +
 annif/suggestion.py             |  1 +
 annif/transform/__init__.py     |  1 +
 annif/transform/inputlimiter.py |  1 +
 annif/transform/langfilter.py   |  1 +
 annif/transform/transform.py    |  1 +
 annif/util.py                   |  1 +
 annif/vocab.py                  |  1 +
 pyproject.toml                  | 28 +++++++++++++---------------
 tests/test_vocab_csv.py         |  1 -
 tests/test_vocab_skos.py        |  1 -
 tests/test_vocab_tsv.py         |  1 -
 53 files changed, 81 insertions(+), 35 deletions(-)

diff --git a/annif/analyzer/__init__.py b/annif/analyzer/__init__.py
index a0f93ced3..27a2cd792 100644
--- a/annif/analyzer/__init__.py
+++ b/annif/analyzer/__init__.py
@@ -1,4 +1,5 @@
 """Collection of language-specific analyzers and analyzer registry for Annif"""
+
 from __future__ import annotations
 
 import re
diff --git a/annif/analyzer/analyzer.py b/annif/analyzer/analyzer.py
index 5ba876f9d..25bdb6b57 100644
--- a/annif/analyzer/analyzer.py
+++ b/annif/analyzer/analyzer.py
@@ -1,4 +1,5 @@
 """Common functionality for analyzers."""
+
 from __future__ import annotations
 
 import abc
diff --git a/annif/analyzer/simple.py b/annif/analyzer/simple.py
index 4cc35e6f1..c3ff7240a 100644
--- a/annif/analyzer/simple.py
+++ b/annif/analyzer/simple.py
@@ -1,4 +1,5 @@
 """Simple analyzer for Annif. Only folds words to lower case."""
+
 from __future__ import annotations
 
 from . import analyzer
diff --git a/annif/analyzer/simplemma.py b/annif/analyzer/simplemma.py
index e535b25de..e549a2585 100644
--- a/annif/analyzer/simplemma.py
+++ b/annif/analyzer/simplemma.py
@@ -1,4 +1,5 @@
 """Simplemma analyzer for Annif, based on simplemma lemmatizer."""
+
 from __future__ import annotations
 
 import simplemma
diff --git a/annif/analyzer/snowball.py b/annif/analyzer/snowball.py
index 57990c2a1..1a17702eb 100644
--- a/annif/analyzer/snowball.py
+++ b/annif/analyzer/snowball.py
@@ -1,4 +1,5 @@
 """Snowball analyzer for Annif, based on nltk Snowball stemmer."""
+
 from __future__ import annotations
 
 import functools
diff --git a/annif/analyzer/spacy.py b/annif/analyzer/spacy.py
index b5e9cbc55..184f03ffc 100644
--- a/annif/analyzer/spacy.py
+++ b/annif/analyzer/spacy.py
@@ -1,4 +1,5 @@
 """spaCy analyzer for Annif which uses spaCy for lemmatization"""
+
 from __future__ import annotations
 
 import annif.util
diff --git a/annif/analyzer/voikko.py b/annif/analyzer/voikko.py
index e6e693d65..b3e7d5007 100644
--- a/annif/analyzer/voikko.py
+++ b/annif/analyzer/voikko.py
@@ -1,4 +1,5 @@
 """Voikko analyzer for Annif, based on libvoikko library."""
+
 from __future__ import annotations
 
 import functools
diff --git a/annif/backend/__init__.py b/annif/backend/__init__.py
index cbeeb648e..7be1264b4 100644
--- a/annif/backend/__init__.py
+++ b/annif/backend/__init__.py
@@ -1,4 +1,5 @@
 """Registry of backend types for Annif"""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Type
diff --git a/annif/backend/backend.py b/annif/backend/backend.py
index 6a63c86b2..84465e460 100644
--- a/annif/backend/backend.py
+++ b/annif/backend/backend.py
@@ -1,4 +1,5 @@
 """Common functionality for backends."""
+
 from __future__ import annotations
 
 import abc
diff --git a/annif/backend/dummy.py b/annif/backend/dummy.py
index bb52e22e6..d10ce8d16 100644
--- a/annif/backend/dummy.py
+++ b/annif/backend/dummy.py
@@ -1,4 +1,5 @@
 """Dummy backend for testing basic interaction of projects and backends"""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any
diff --git a/annif/backend/ensemble.py b/annif/backend/ensemble.py
index 9953c9e6c..a25e8a03f 100644
--- a/annif/backend/ensemble.py
+++ b/annif/backend/ensemble.py
@@ -1,4 +1,5 @@
 """Ensemble backend that combines results from multiple projects"""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Any
diff --git a/annif/backend/fasttext.py b/annif/backend/fasttext.py
index 23c33539a..e102b02ba 100644
--- a/annif/backend/fasttext.py
+++ b/annif/backend/fasttext.py
@@ -1,4 +1,5 @@
 """Annif backend using the fastText classifier"""
+
 from __future__ import annotations
 
 import collections
diff --git a/annif/backend/http.py b/annif/backend/http.py
index 0fce7f8e4..9036ec152 100644
--- a/annif/backend/http.py
+++ b/annif/backend/http.py
@@ -1,5 +1,6 @@
 """HTTP/REST client backend that makes calls to a web service
 and returns the results"""
+
 from __future__ import annotations
 
 import importlib
diff --git a/annif/backend/hyperopt.py b/annif/backend/hyperopt.py
index 2c2e7422c..efbc10513 100644
--- a/annif/backend/hyperopt.py
+++ b/annif/backend/hyperopt.py
@@ -1,4 +1,5 @@
 """Hyperparameter optimization functionality for backends"""
+
 from __future__ import annotations
 
 import abc
diff --git a/annif/backend/mixins.py b/annif/backend/mixins.py
index 2bb094641..e4af03d26 100644
--- a/annif/backend/mixins.py
+++ b/annif/backend/mixins.py
@@ -1,4 +1,5 @@
 """Annif backend mixins that can be used to implement features"""
+
 from __future__ import annotations
 
 import abc
diff --git a/annif/backend/mllm.py b/annif/backend/mllm.py
index cbcef11b1..cd274cf65 100644
--- a/annif/backend/mllm.py
+++ b/annif/backend/mllm.py
@@ -1,4 +1,5 @@
 """Maui-like Lexical Matching backend"""
+
 from __future__ import annotations
 
 import os.path
diff --git a/annif/backend/nn_ensemble.py b/annif/backend/nn_ensemble.py
index d4bc09058..e1daab00a 100644
--- a/annif/backend/nn_ensemble.py
+++ b/annif/backend/nn_ensemble.py
@@ -1,5 +1,6 @@
 """Neural network based ensemble backend that combines results from multiple
 projects."""
+
 from __future__ import annotations
 
 import os.path
diff --git a/annif/backend/omikuji.py b/annif/backend/omikuji.py
index 7a2e6a1bb..89d8f0ea9 100644
--- a/annif/backend/omikuji.py
+++ b/annif/backend/omikuji.py
@@ -1,4 +1,5 @@
 """Annif backend using the Omikuji classifier"""
+
 from __future__ import annotations
 
 import os.path
diff --git a/annif/backend/pav.py b/annif/backend/pav.py
index 61f4362d1..2ee30337a 100644
--- a/annif/backend/pav.py
+++ b/annif/backend/pav.py
@@ -2,6 +2,7 @@
 learns which concept suggestions from each backend are trustworthy using the
 PAV algorithm, a.k.a. isotonic regression, to turn raw scores returned by
 individual backends into probabilities."""
+
 from __future__ import annotations
 
 import os.path
@@ -69,13 +70,15 @@ def _merge_source_batches(
             reg_models = self._get_model(project_id)
             pav_batch = [
                 [
-                    SubjectSuggestion(
-                        subject_id=sugg.subject_id,
-                        score=reg_models[sugg.subject_id].predict([sugg.score])[0],
-                    )
-                    if sugg.subject_id in reg_models
-                    else SubjectSuggestion(
-                        subject_id=sugg.subject_id, score=sugg.score
+                    (
+                        SubjectSuggestion(
+                            subject_id=sugg.subject_id,
+                            score=reg_models[sugg.subject_id].predict([sugg.score])[0],
+                        )
+                        if sugg.subject_id in reg_models
+                        else SubjectSuggestion(
+                            subject_id=sugg.subject_id, score=sugg.score
+                        )
                     )  # default to raw score
                     for sugg in result
                 ]
diff --git a/annif/backend/svc.py b/annif/backend/svc.py
index 30fb23eb4..c18f1410b 100644
--- a/annif/backend/svc.py
+++ b/annif/backend/svc.py
@@ -1,4 +1,5 @@
 """Annif backend using a SVM classifier"""
+
 from __future__ import annotations
 
 import os.path
diff --git a/annif/backend/tfidf.py b/annif/backend/tfidf.py
index 1cca639ca..a77704446 100644
--- a/annif/backend/tfidf.py
+++ b/annif/backend/tfidf.py
@@ -1,5 +1,6 @@
 """Backend that returns most similar subjects based on similarity in sparse
 TF-IDF normalized bag-of-words vector space"""
+
 from __future__ import annotations
 
 import os.path
diff --git a/annif/backend/yake.py b/annif/backend/yake.py
index 2eeef9a9c..c8b933c9b 100644
--- a/annif/backend/yake.py
+++ b/annif/backend/yake.py
@@ -1,4 +1,5 @@
 """Annif backend using Yake keyword extraction"""
+
 # For license remarks of this backend see README.md:
 # https://github.com/NatLibFi/Annif#license.
 from __future__ import annotations
diff --git a/annif/cli.py b/annif/cli.py
index 73f18f02e..d8ca1ea56 100644
--- a/annif/cli.py
+++ b/annif/cli.py
@@ -1,7 +1,6 @@
 """Definitions for command-line (Click) commands for invoking Annif
 operations and printing the results to console."""
 
-
 import collections
 import importlib
 import json
diff --git a/annif/cli_util.py b/annif/cli_util.py
index bbfa96df4..9f33f8153 100644
--- a/annif/cli_util.py
+++ b/annif/cli_util.py
@@ -1,4 +1,5 @@
 """Utility functions for Annif CLI commands"""
+
 from __future__ import annotations
 
 import collections
diff --git a/annif/config.py b/annif/config.py
index 810249bd6..8cdc7d04f 100644
--- a/annif/config.py
+++ b/annif/config.py
@@ -1,4 +1,5 @@
 """Configuration file handling"""
+
 from __future__ import annotations
 
 import configparser
diff --git a/annif/corpus/__init__.py b/annif/corpus/__init__.py
index 4200d2f87..fb0ceef86 100644
--- a/annif/corpus/__init__.py
+++ b/annif/corpus/__init__.py
@@ -1,6 +1,5 @@
 """Annif corpus operations"""
 
-
 from .combine import CombinedCorpus
 from .document import (
     DocumentDirectory,
diff --git a/annif/corpus/combine.py b/annif/corpus/combine.py
index 75fcc7f55..a0ad02147 100644
--- a/annif/corpus/combine.py
+++ b/annif/corpus/combine.py
@@ -1,4 +1,5 @@
 """Class for combining multiple corpora so they behave like a single corpus"""
+
 from __future__ import annotations
 
 import itertools
diff --git a/annif/corpus/document.py b/annif/corpus/document.py
index 09a80a309..8d4ef5319 100644
--- a/annif/corpus/document.py
+++ b/annif/corpus/document.py
@@ -1,4 +1,5 @@
 """Clases for supporting document corpora"""
+
 from __future__ import annotations
 
 import glob
diff --git a/annif/corpus/skos.py b/annif/corpus/skos.py
index 462a35241..82a8c5c13 100644
--- a/annif/corpus/skos.py
+++ b/annif/corpus/skos.py
@@ -1,4 +1,5 @@
 """Support for subjects loaded from a SKOS/RDF file"""
+
 from __future__ import annotations
 
 import collections
@@ -83,11 +84,15 @@ def languages(self) -> set[str]:
     def _concept_labels(self, concept: URIRef) -> dict[str, str]:
         by_lang = self.get_concept_labels(concept, self.PREF_LABEL_PROPERTIES)
         return {
-            lang: by_lang[lang][0]
-            if by_lang[lang]  # correct lang
-            else by_lang[None][0]
-            if by_lang[None]  # no language
-            else self.graph.namespace_manager.qname(concept)
+            lang: (
+                by_lang[lang][0]
+                if by_lang[lang]  # correct lang
+                else (
+                    by_lang[None][0]
+                    if by_lang[None]  # no language
+                    else self.graph.namespace_manager.qname(concept)
+                )
+            )
             for lang in self.languages
         }
 
diff --git a/annif/corpus/subject.py b/annif/corpus/subject.py
index a9ee06397..2e3ffe5de 100644
--- a/annif/corpus/subject.py
+++ b/annif/corpus/subject.py
@@ -1,4 +1,5 @@
 """Classes for supporting subject corpora expressed as directories or files"""
+
 from __future__ import annotations
 
 import csv
diff --git a/annif/corpus/types.py b/annif/corpus/types.py
index e6cd4b252..e94a8c1d9 100644
--- a/annif/corpus/types.py
+++ b/annif/corpus/types.py
@@ -1,4 +1,5 @@
 """Basic types for document and subject corpora"""
+
 from __future__ import annotations
 
 import abc
diff --git a/annif/datadir.py b/annif/datadir.py
index 752da32dd..02987490d 100644
--- a/annif/datadir.py
+++ b/annif/datadir.py
@@ -1,4 +1,5 @@
 """Mixin class for types that need a data directory"""
+
 from __future__ import annotations
 
 import os
diff --git a/annif/eval.py b/annif/eval.py
index eb6d80f4a..95cdf449d 100644
--- a/annif/eval.py
+++ b/annif/eval.py
@@ -1,4 +1,5 @@
 """Evaluation metrics for Annif"""
+
 from __future__ import annotations
 
 import warnings
@@ -86,9 +87,9 @@ def __init__(self, subject_index: SubjectIndex) -> None:
 
     def evaluate_many(
         self,
-        suggestion_batch: list[list[SubjectSuggestion]]
-        | SuggestionBatch
-        | list[Iterator],
+        suggestion_batch: (
+            list[list[SubjectSuggestion]] | SuggestionBatch | list[Iterator]
+        ),
         gold_subject_batch: Sequence[SubjectSet],
     ) -> None:
         if not isinstance(suggestion_batch, SuggestionBatch):
diff --git a/annif/exception.py b/annif/exception.py
index b4b9c6552..9132d0134 100644
--- a/annif/exception.py
+++ b/annif/exception.py
@@ -1,4 +1,5 @@
 """Custom exceptions used by Annif"""
+
 from __future__ import annotations
 
 from click import ClickException
diff --git a/annif/lexical/mllm.py b/annif/lexical/mllm.py
index ff8bc5894..b475d2975 100644
--- a/annif/lexical/mllm.py
+++ b/annif/lexical/mllm.py
@@ -1,4 +1,5 @@
 """MLLM (Maui-like Lexical Matchin) model for Annif"""
+
 from __future__ import annotations
 
 import collections
diff --git a/annif/lexical/tokenset.py b/annif/lexical/tokenset.py
index 07c15705d..d577527ad 100644
--- a/annif/lexical/tokenset.py
+++ b/annif/lexical/tokenset.py
@@ -1,4 +1,5 @@
 """Index for fast matching of token sets."""
+
 from __future__ import annotations
 
 import collections
diff --git a/annif/lexical/util.py b/annif/lexical/util.py
index 28d21a141..ca3cb8fb3 100644
--- a/annif/lexical/util.py
+++ b/annif/lexical/util.py
@@ -1,4 +1,5 @@
 """Utility methods for lexical algorithms"""
+
 from __future__ import annotations
 
 import collections
diff --git a/annif/openapi/validation.py b/annif/openapi/validation.py
index 7f920b35d..e57d6830d 100644
--- a/annif/openapi/validation.py
+++ b/annif/openapi/validation.py
@@ -1,4 +1,5 @@
 """Custom validator for the Annif API."""
+
 from __future__ import annotations
 
 import logging
diff --git a/annif/parallel.py b/annif/parallel.py
index c6b293f8e..2fead01b9 100644
--- a/annif/parallel.py
+++ b/annif/parallel.py
@@ -1,4 +1,5 @@
 """Parallel processing functionality for Annif"""
+
 from __future__ import annotations
 
 import multiprocessing
diff --git a/annif/project.py b/annif/project.py
index 83f7eda7c..3a4aa5566 100644
--- a/annif/project.py
+++ b/annif/project.py
@@ -1,4 +1,5 @@
 """Project management functionality for Annif"""
+
 from __future__ import annotations
 
 import enum
diff --git a/annif/registry.py b/annif/registry.py
index a97dc366e..e12b30e72 100644
--- a/annif/registry.py
+++ b/annif/registry.py
@@ -1,4 +1,5 @@
 """Registry that keeps track of Annif projects"""
+
 from __future__ import annotations
 
 import re
diff --git a/annif/rest.py b/annif/rest.py
index f848117c8..f8d9f6d7e 100644
--- a/annif/rest.py
+++ b/annif/rest.py
@@ -1,5 +1,6 @@
 """Definitions for REST API operations. These are wired via Connexion to
 methods defined in the OpenAPI specification."""
+
 from __future__ import annotations
 
 import importlib
diff --git a/annif/suggestion.py b/annif/suggestion.py
index fd7c0c12e..fd9eb48cc 100644
--- a/annif/suggestion.py
+++ b/annif/suggestion.py
@@ -1,4 +1,5 @@
 """Representing suggested subjects."""
+
 from __future__ import annotations
 
 import collections
diff --git a/annif/transform/__init__.py b/annif/transform/__init__.py
index 716d874a2..680b02cc0 100644
--- a/annif/transform/__init__.py
+++ b/annif/transform/__init__.py
@@ -1,4 +1,5 @@
 """Functionality for obtaining text transformation from string specification"""
+
 from __future__ import annotations
 
 import re
diff --git a/annif/transform/inputlimiter.py b/annif/transform/inputlimiter.py
index 229766864..d57c6a56c 100644
--- a/annif/transform/inputlimiter.py
+++ b/annif/transform/inputlimiter.py
@@ -1,5 +1,6 @@
 """A simple transformation that truncates the text of input documents to a
 given character length."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
diff --git a/annif/transform/langfilter.py b/annif/transform/langfilter.py
index 6794eb370..f7c985485 100644
--- a/annif/transform/langfilter.py
+++ b/annif/transform/langfilter.py
@@ -1,5 +1,6 @@
 """Transformation filtering out parts of a text that are in a language
 different from the language of the project."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
diff --git a/annif/transform/transform.py b/annif/transform/transform.py
index db71fef37..9a96f2877 100644
--- a/annif/transform/transform.py
+++ b/annif/transform/transform.py
@@ -1,4 +1,5 @@
 """Common functionality for transforming text of input documents."""
+
 from __future__ import annotations
 
 import abc
diff --git a/annif/util.py b/annif/util.py
index 1702c2e4b..b03c63ec2 100644
--- a/annif/util.py
+++ b/annif/util.py
@@ -1,4 +1,5 @@
 """Utility functions for Annif"""
+
 from __future__ import annotations
 
 import glob
diff --git a/annif/vocab.py b/annif/vocab.py
index 333fa0d69..7f7e125c4 100644
--- a/annif/vocab.py
+++ b/annif/vocab.py
@@ -1,4 +1,5 @@
 """Vocabulary management functionality for Annif"""
+
 from __future__ import annotations
 
 import os.path
diff --git a/pyproject.toml b/pyproject.toml
index 2d0d29db0..e83921c3b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,19 +18,19 @@ keywords = [
     "text-classification",
     "rest-api",
     "code4lib",
-    "subject-indexing"
+    "subject-indexing",
 ]
 
-classifiers=[
+classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: Apache Software License",
-    "Operating System :: OS Independent"
+    "Operating System :: OS Independent",
 ]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 
-connexion = {version = "2.14.2", extras = ["swagger-ui"]}
+connexion = { version = "2.14.2", extras = ["swagger-ui"] }
 flask = "2.2.*"
 flask-cors = "4.0.*"
 click = "8.1.*"
@@ -49,14 +49,14 @@ tomli = { version = "2.0.*", python = "<3.11" }
 simplemma = "0.9.*"
 jsonschema = "4.21.*"
 
-fasttext-wheel = {version = "0.9.2", optional = true}
-voikko = {version = "0.5.*", optional = true}
-tensorflow-cpu = {version = "2.15.*", optional = true}
-lmdb = {version = "1.4.1", optional = true}
-omikuji = {version = "0.5.*", optional = true}
-yake = {version = "0.4.8", optional = true}
-spacy = {version = "3.7.*", optional = true}
-stwfsapy = {version="0.3.*", optional = true}
+fasttext-wheel = { version = "0.9.2", optional = true }
+voikko = { version = "0.5.*", optional = true }
+tensorflow-cpu = { version = "2.15.*", optional = true }
+lmdb = { version = "1.4.1", optional = true }
+omikuji = { version = "0.5.*", optional = true }
+yake = { version = "0.4.8", optional = true }
+spacy = { version = "3.7.*", optional = true }
+stwfsapy = { version = "0.3.*", optional = true }
 
 [tool.poetry.dev-dependencies]
 py = "*"
@@ -93,7 +93,5 @@ line_length = "88"
 skip_gitignore = true
 
 [tool.pytest.ini_options]
-markers = [
-    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
-]
+markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
 addopts = "-m 'not slow'"
diff --git a/tests/test_vocab_csv.py b/tests/test_vocab_csv.py
index 0bc3820dd..bdb66e25c 100644
--- a/tests/test_vocab_csv.py
+++ b/tests/test_vocab_csv.py
@@ -1,6 +1,5 @@
 """Unit tests for CSV vocabulary functionality in Annif"""
 
-
 from annif.corpus import SubjectFileCSV, SubjectIndex
 
 
diff --git a/tests/test_vocab_skos.py b/tests/test_vocab_skos.py
index a3c1e508c..fd93ca6d1 100644
--- a/tests/test_vocab_skos.py
+++ b/tests/test_vocab_skos.py
@@ -1,6 +1,5 @@
 """Unit tests for SKOS vocabulary functionality in Annif"""
 
-
 import os.path
 
 from annif.corpus.skos import SubjectFileSKOS
diff --git a/tests/test_vocab_tsv.py b/tests/test_vocab_tsv.py
index 1fc318e0f..4d0956d5a 100644
--- a/tests/test_vocab_tsv.py
+++ b/tests/test_vocab_tsv.py
@@ -1,6 +1,5 @@
 """Unit tests for TSV vocabulary functionality in Annif"""
 
-
 from annif.corpus import SubjectFileTSV, SubjectIndex
 
 

From df20982b7b6ea48609a3ef9cb132a9d01a99527f Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Mon, 26 Feb 2024 14:46:45 +0200
Subject: [PATCH 13/17] Ignore modifications due to migration to Black v24
 codestyle in git blame

---
 .git-blame-ignore-revs | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index bbed4a471..292e8d698 100644
--- 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

From 95639ba70effce7dcb0ea74644862a3bb26aad0e Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Wed, 20 Mar 2024 11:30:49 +0200
Subject: [PATCH 14/17] Upgrade to optuna 3.6.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e83921c3b..636f99329 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ scipy = "1.12.*"
 rdflib = "6.3.*"
 gunicorn = "21.2.*"
 numpy = "1.26.*"
-optuna = "3.5.*"
+optuna = "3.6.*"
 python-dateutil = "2.8.*"
 tomli = { version = "2.0.*", python = "<3.11" }
 simplemma = "0.9.*"

From d3b39e1b3151d1899e9ec770aaef13062f718a73 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Wed, 20 Mar 2024 16:35:18 +0200
Subject: [PATCH 15/17] Upgrade to stwfsapy 0.4.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 636f99329..50c2f2b0d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,7 +56,7 @@ lmdb = { version = "1.4.1", optional = true }
 omikuji = { version = "0.5.*", optional = true }
 yake = { version = "0.4.8", optional = true }
 spacy = { version = "3.7.*", optional = true }
-stwfsapy = { version = "0.3.*", optional = true }
+stwfsapy = { version = "0.4.*", optional = true }
 
 [tool.poetry.dev-dependencies]
 py = "*"

From a8a4fc3b1d2bbc4e33519235101c5dd13f4b2495 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Wed, 20 Mar 2024 16:35:50 +0200
Subject: [PATCH 16/17] Upgrade to scikit-learn 1.4.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 50c2f2b0d..008b1f35e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,7 +38,7 @@ click-log = "0.4.*"
 joblib = "1.3.*"
 nltk = "3.8.*"
 gensim = "4.3.*"
-scikit-learn = "1.3.*"
+scikit-learn = "1.4.*"
 scipy = "1.12.*"
 rdflib = "6.3.*"
 gunicorn = "21.2.*"

From 44b47347f8f0721de0f7bdc9973519ee118a50a7 Mon Sep 17 00:00:00 2001
From: Juho Inkinen <34240031+juhoinkinen@users.noreply.github.com>
Date: Wed, 20 Mar 2024 16:36:13 +0200
Subject: [PATCH 17/17] Upgrade to rdflib 7.0.*

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 008b1f35e..ca2a30d1a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ nltk = "3.8.*"
 gensim = "4.3.*"
 scikit-learn = "1.4.*"
 scipy = "1.12.*"
-rdflib = "6.3.*"
+rdflib = "7.0.*"
 gunicorn = "21.2.*"
 numpy = "1.26.*"
 optuna = "3.6.*"