Merge pull request #641 from NatLibFi/add-isort-tool

Use isort to order import statements

.git-blame-ignore-revs

@@ -1,2 +1,4 @@
 # Migrate code style to Black
 3bc18907354a40f1d89dca1833a2719ba7fb0933
+# Reorder import statements with isort
+68a72c5a603283f70abce2651dcde9c6f0177c41

.github/workflows/cicd.yml

@@ -15,9 +15,10 @@ jobs:
 
   lint:
     runs-on: ubuntu-latest
-    name: lint with Black
+    name: lint with isort & Black
     steps:
       - uses: actions/checkout@v3
+      - uses: isort/isort-action@f14e57e1d457956c45a19c05a89cccdf087846e5  # v1.1.0
       - uses: psf/black@6b42c2b8c9f9bd666120a2c19b8da509fe477f27
 
   test:

README.md

@@ -101,12 +101,13 @@ pytest-watch by running `ptw`.
 
 ## Code style
 
-Annif code should follow the [Black style](https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html).
-The Black tool is included as a developoment dependency; you can run `black .` in the project root to autoformat code. 
-You can set up a [pre-commit hook](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) to automate linting with Black and flake8 with every git commit by using the following in the file `.git/hooks/pre-commit`, which should have execute permission set:
+Annif code should follow the [Black style](https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html) and import statements should be [grouped and ordered](https://peps.python.org/pep-0008/#imports).
+To achive this, the Black and isort tools are included as developoment dependencies; you can run `black .` and `isort .` in the project root to autoformat code. 
+You can set up a [pre-commit hook](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) to automate linting with isort, Black and flake8 with every git commit by using the following in the file `.git/hooks/pre-commit`, which should have execute permission set:
 ```bash
 #!/bin/sh
 
+isort . --check-only --diff
 black . --check --diff
 flake8
 ```

annif/__init__.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python3
 
+import logging
 import os
 import os.path
-import logging
+
 import connexion
 from flask_cors import CORS
 

annif/analyzer/__init__.py

@@ -1,12 +1,12 @@
 """Collection of language-specific analyzers and analyzer registry for Annif"""
 
 import re
-from . import simple
-from . import snowball
-from . import simplemma
+
 import annif
 from annif.util import parse_args
 
+from . import simple, simplemma, snowball
+
 _analyzers = {}
 
 

annif/analyzer/simplemma.py

@@ -1,6 +1,7 @@
 """Simplemma analyzer for Annif, based on simplemma lemmatizer."""
 
 import simplemma
+
 from . import analyzer
 
 

annif/analyzer/snowball.py

@@ -1,6 +1,7 @@
 """Snowball analyzer for Annif, based on nltk Snowball stemmer."""
 
 import functools
+
 from . import analyzer
 
 

annif/analyzer/spacy.py

@@ -1,8 +1,9 @@
 """spaCy analyzer for Annif which uses spaCy for lemmatization"""
 
-from . import analyzer
-from annif.exception import OperationFailedException
 import annif.util
+from annif.exception import OperationFailedException
+
+from . import analyzer
 
 _KEY_LOWERCASE = "lowercase"
 

annif/analyzer/voikko.py

@@ -1,7 +1,9 @@
 """Voikko analyzer for Annif, based on libvoikko library."""
 
 import functools
+
 import voikko.libvoikko
+
 from . import analyzer
 
 

annif/backend/backend.py

@@ -4,6 +4,7 @@
 import os.path
 from datetime import datetime, timezone
 from glob import glob
+
 from annif import logger
 
 

annif/backend/dummy.py

@@ -1,7 +1,8 @@
 """Dummy backend for testing basic interaction of projects and backends"""
 
 
-from annif.suggestion import SubjectSuggestion, ListSuggestionResult
+from annif.suggestion import ListSuggestionResult, SubjectSuggestion
+
 from . import backend
 
 

annif/backend/ensemble.py

@@ -1,14 +1,14 @@
 """Ensemble backend that combines results from multiple projects"""
 
 
+import annif.eval
 import annif.parallel
 import annif.suggestion
 import annif.util
-import annif.eval
-from . import backend
-from . import hyperopt
 from annif.exception import NotSupportedException
 
+from . import backend, hyperopt
+
 
 class BaseEnsembleBackend(backend.AnnifBackend):
     """Base class for ensemble backends"""

annif/backend/fasttext.py

@@ -2,12 +2,14 @@
 
 import collections
 import os.path
+
+import fasttext
+
 import annif.util
-from annif.suggestion import SubjectSuggestion, ListSuggestionResult
 from annif.exception import NotInitializedException, NotSupportedException
-import fasttext
-from . import backend
-from . import mixins
+from annif.suggestion import ListSuggestionResult, SubjectSuggestion
+
+from . import backend, mixins
 
 
 class FastTextBackend(mixins.ChunkingBackend, backend.AnnifBackend):

annif/backend/http.py

@@ -5,8 +5,10 @@
 import dateutil.parser
 import requests
 import requests.exceptions
-from annif.suggestion import SubjectSuggestion, ListSuggestionResult
+
 from annif.exception import OperationFailedException
+from annif.suggestion import ListSuggestionResult, SubjectSuggestion
+
 from . import backend
 
 

annif/backend/hyperopt.py

@@ -3,10 +3,11 @@
 import abc
 import collections
 import warnings
+
 import optuna
 import optuna.exceptions
-from .backend import AnnifBackend
 
+from .backend import AnnifBackend
 
 HPRecommendation = collections.namedtuple("HPRecommendation", "lines score")
 

annif/backend/mixins.py

@@ -3,8 +3,10 @@
 
 import abc
 import os.path
+
 import joblib
 from sklearn.feature_extraction.text import TfidfVectorizer
+
 import annif.util
 from annif.exception import NotInitializedException
 from annif.suggestion import ListSuggestionResult

annif/backend/mllm.py

@@ -1,16 +1,17 @@
 """Maui-like Lexical Matching backend"""
 
 import os.path
+
 import joblib
 import numpy as np
+
 import annif.eval
 import annif.util
-from annif.exception import NotInitializedException
-from annif.exception import NotSupportedException
+from annif.exception import NotInitializedException, NotSupportedException
 from annif.lexical.mllm import MLLMModel
 from annif.suggestion import VectorSuggestionResult
-from . import backend
-from . import hyperopt
+
+from . import backend, hyperopt
 
 
 class MLLMOptimizer(hyperopt.HyperparameterOptimizer):

annif/backend/nn_ensemble.py

@@ -2,24 +2,26 @@
 projects."""
 
 
-from io import BytesIO
-import shutil
 import os.path
-import numpy as np
-from scipy.sparse import csr_matrix, csc_matrix
+import shutil
+from io import BytesIO
+
 import joblib
 import lmdb
-from tensorflow.keras.layers import Input, Dense, Add, Flatten, Dropout, Layer
+import numpy as np
+import tensorflow.keras.backend as K
+from scipy.sparse import csc_matrix, csr_matrix
+from tensorflow.keras.layers import Add, Dense, Dropout, Flatten, Input, Layer
 from tensorflow.keras.models import Model, load_model
 from tensorflow.keras.utils import Sequence
-import tensorflow.keras.backend as K
+
 import annif.corpus
 import annif.parallel
 import annif.util
 from annif.exception import NotInitializedException, NotSupportedException
 from annif.suggestion import VectorSuggestionResult
-from . import backend
-from . import ensemble
+
+from . import backend, ensemble
 
 
 def idx_to_key(idx):

annif/backend/omikuji.py

@@ -1,17 +1,19 @@
 """Annif backend using the Omikuji classifier"""
 
-import omikuji
 import os.path
 import shutil
+
+import omikuji
+
 import annif.util
-from annif.suggestion import SubjectSuggestion, ListSuggestionResult
 from annif.exception import (
     NotInitializedException,
     NotSupportedException,
     OperationFailedException,
 )
-from . import backend
-from . import mixins
+from annif.suggestion import ListSuggestionResult, SubjectSuggestion
+
+from . import backend, mixins
 
 
 class OmikujiBackend(mixins.TfidfVectorizerMixin, backend.AnnifBackend):

annif/backend/pav.py

@@ -4,16 +4,18 @@
 individual backends into probabilities."""
 
 import os.path
+
 import joblib
+import numpy as np
 from scipy.sparse import coo_matrix, csc_matrix
 from sklearn.isotonic import IsotonicRegression
-import numpy as np
+
 import annif.corpus
 import annif.suggestion
 import annif.util
 from annif.exception import NotInitializedException, NotSupportedException
-from . import backend
-from . import ensemble
+
+from . import backend, ensemble
 
 
 class PAVBackend(ensemble.BaseEnsembleBackend):

annif/backend/stwfsa.py

@@ -1,10 +1,12 @@
 import os
+
 from stwfsapy.predictor import StwfsapyPredictor
+
 from annif.exception import NotInitializedException, NotSupportedException
 from annif.suggestion import ListSuggestionResult, SubjectSuggestion
-from . import backend
 from annif.util import atomic_save, boolean
 
+from . import backend
 
 _KEY_CONCEPT_TYPE_URI = "concept_type_uri"
 _KEY_SUBTHESAURUS_TYPE_URI = "sub_thesaurus_type_uri"

annif/backend/svc.py

@@ -1,15 +1,17 @@
 """Annif backend using a SVM classifier"""
 
 import os.path
+
 import joblib
 import numpy as np
 import scipy.special
 from sklearn.svm import LinearSVC
+
 import annif.util
-from annif.suggestion import SubjectSuggestion, ListSuggestionResult
 from annif.exception import NotInitializedException, NotSupportedException
-from . import backend
-from . import mixins
+from annif.suggestion import ListSuggestionResult, SubjectSuggestion
+
+from . import backend, mixins
 
 
 class SVCBackend(mixins.TfidfVectorizerMixin, backend.AnnifBackend):

annif/backend/tfidf.py

@@ -3,13 +3,15 @@
 
 import os.path
 import tempfile
-import annif.util
+
 import gensim.similarities
 from gensim.matutils import Sparse2Corpus
-from annif.suggestion import VectorSuggestionResult
+
+import annif.util
 from annif.exception import NotInitializedException, NotSupportedException
-from . import backend
-from . import mixins
+from annif.suggestion import VectorSuggestionResult
+
+from . import backend, mixins
 
 
 class SubjectBuffer:

annif/backend/yake.py

@@ -2,16 +2,19 @@
 # For license remarks of this backend see README.md:
 # https://github.com/NatLibFi/Annif#license.
 
-import yake
-import joblib
 import os.path
 import re
 from collections import defaultdict
+
+import joblib
+import yake
 from rdflib.namespace import SKOS
+
 import annif.util
-from . import backend
-from annif.suggestion import SubjectSuggestion, ListSuggestionResult
 from annif.exception import ConfigurationException, NotSupportedException
+from annif.suggestion import ListSuggestionResult, SubjectSuggestion
+
+from . import backend
 
 
 class YakeBackend(backend.AnnifBackend):