Merge pull request #244 from IFCA-Advanced-Computing/feature/isort

Set up isort to format imports

.pre-commit-config.yaml

@@ -9,11 +9,21 @@ repos:
   - id: check-yaml
   - id: check-added-large-files
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 23.12.0
+  rev: 24.3.0
   hooks:
   - id: black
 - repo: https://github.com/PyCQA/docformatter
   rev: v1.7.5
   hooks:
   - id: docformatter
     additional_dependencies: [tomli]
+- repo: https://github.com/pre-commit/mirrors-isort
+  rev: v5.10.1
+  hooks:
+    - id: isort
+      additional_dependencies: [toml]
+        # - repo: https://github.com/pycqa/isort
+        #   rev: 5.11.2
+        #   hooks:
+        #     - id: isort
+        #       name: isort (python)

api/evaluator.py

@@ -1,18 +1,19 @@
 import ast
+import csv
 import gettext
-import idutils
 import logging
-import csv
 import os
-import pandas as pd
+import sys
+import urllib
 import xml.etree.ElementTree as ET
+from functools import wraps
+
+import idutils
+import pandas as pd
 import requests
-import urllib
-import sys
+
 import api.utils as ut
 from fair import load_config
-from functools import wraps
-
 
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"

api/rda.py

@@ -1,14 +1,16 @@
-import os
-import yaml
-from api.evaluator import Evaluator
-import api.utils as ut
-from connexion import NoContent
-from fair import app_dirname, load_config
 import importlib
 import logging
+import os
 import sys
 from functools import wraps
 
+import yaml
+from connexion import NoContent
+
+import api.utils as ut
+from api.evaluator import Evaluator
+from fair import app_dirname, load_config
+
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"
 )

api/utils.py

@@ -1,16 +1,16 @@
-from bs4 import BeautifulSoup
-import idutils
-import logging
 import json
-import uuid
-import pandas as pd
-import xml.etree.ElementTree as ET
+import logging
 import re
-import requests
 import sys
 import urllib
+import uuid
+import xml.etree.ElementTree as ET
 from urllib.parse import urljoin
 
+import idutils
+import pandas as pd
+import requests
+from bs4 import BeautifulSoup
 
 logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
 

docs/conf.py

@@ -12,9 +12,9 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
 import shlex
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the

fair.py

@@ -3,10 +3,10 @@
 import configparser
 import logging
 import os
+import sys
 
 import connexion
 from connexion.resolver import RestyResolver
-import sys
 
 logging.basicConfig(
     stream=sys.stdout,

plugins/digital_csic/plugin.py

@@ -1,20 +1,22 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 import ast
-import idutils
 import json
 import logging
 import os
-import psycopg2
-import requests
-from api.evaluator import Evaluator
-import pandas as pd
-import api.utils as ut
 import sys
-from functools import wraps
 import urllib
+from functools import wraps
+
+import idutils
+import pandas as pd
+import psycopg2
+import requests
 from bs4 import BeautifulSoup
 
+import api.utils as ut
+from api.evaluator import Evaluator
+
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"
 )

plugins/dspace7/plugin.py

@@ -1,14 +1,15 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
-import api.utils as ut
 import ast
 import gettext
 import json
 import logging
-import pandas as pd
+import sys
 import xml.etree.ElementTree as ET
+
+import pandas as pd
 import requests
-import sys
+
 import api.utils as ut
 from api.evaluator import Evaluator
 

plugins/epos/plugin.py

@@ -2,24 +2,23 @@
 # -*- coding: utf-8 -*-
 import ast
 import configparser
-import idutils
+import csv
+import json
 import logging
 import os
+import sys
 import urllib
+import xml.etree.ElementTree as ET
 
-from api.evaluator import Evaluator
-from api.evaluator import ConfigTerms
-from fair import load_config
-import pandas as pd
+import idutils
 import numpy as np
+import pandas as pd
 import requests
-import sys
-import csv
-import xml.etree.ElementTree as ET
-import json
-import api.utils as ut
 from dicttoxml import dicttoxml
 
+import api.utils as ut
+from api.evaluator import ConfigTerms, Evaluator
+from fair import load_config
 
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"

plugins/example_plugin/plugin.py

@@ -4,10 +4,12 @@
 import configparser
 import logging
 import os
-from api.evaluator import Evaluator
-import pandas as pd
 import sys
 
+import pandas as pd
+
+from api.evaluator import Evaluator
+
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"
 )

plugins/gbif/plugin.py

@@ -1,15 +1,17 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 import ast
-import idutils
 import logging
 import os
-from api.evaluator import Evaluator
-import pandas as pd
-import requests
 import sys
 import xml.etree.ElementTree as ET
 
+import idutils
+import pandas as pd
+import requests
+
+from api.evaluator import Evaluator
+
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"
 )

plugins/signposting/plugin.py

@@ -1,17 +1,18 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 import ast
-from bs4 import BeautifulSoup
 import configparser
-import idutils
 import logging
 import os
-from api.evaluator import Evaluator
-import pandas as pd
-import requests
 import sys
 import xml.etree.ElementTree as ET
 
+import idutils
+import pandas as pd
+import requests
+from bs4 import BeautifulSoup
+
+from api.evaluator import Evaluator
 
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"

pyproject.toml

@@ -45,3 +45,6 @@ black = true
 recursive = true
 non-strict = false
 in-place = true
+
+[tool.isort]
+profile = "black"

scripts/fair-eva.py

@@ -23,11 +23,13 @@
 import argparse
 import json
 import logging
-import requests
 import socket
 import sys
 import time
-from flask_babel import Babel, gettext, lazy_gettext as _l
+
+import requests
+from flask_babel import Babel, gettext
+from flask_babel import lazy_gettext as _l
 
 
 def get_input_args():

setup.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 NAME = "fair_eva"
 VERSION = "1.0.0"

test-requirements.txt

@@ -1,3 +1,4 @@
 black
 pre-commit
 docformatter
+isort

utils/pdf_gen.py

@@ -1,19 +1,20 @@
 import logging
 import os
 import sys
+from datetime import datetime
+from io import BytesIO
+
 from bs4 import BeautifulSoup
 from flask_babel import gettext as _l
+from PyPDF2 import PdfFileMerger
+from reportlab.graphics.charts.barcharts import VerticalBarChart
+from reportlab.graphics.shapes import Drawing
+from reportlab.lib import colors
 from reportlab.lib.pagesizes import letter
-from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Image
-from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
+from reportlab.lib.styles import ParagraphStyle, getSampleStyleSheet
 from reportlab.lib.units import inch
+from reportlab.platypus import Image, Paragraph, SimpleDocTemplate, Spacer
 from reportlab.platypus.tables import Table
-from reportlab.lib import colors
-from reportlab.graphics.shapes import Drawing
-from reportlab.graphics.charts.barcharts import VerticalBarChart
-from datetime import datetime
-from PyPDF2 import PdfFileMerger
-from io import BytesIO
 
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"

utils/smart_plugin.py

@@ -1,14 +1,15 @@
-import idutils
 import json
 import logging
 import os
-import requests
-from rdflib import Graph
-from rdflib.plugins.sparql import prepareQuery
 import sys
 import xml.etree.ElementTree as ET
 from urllib.parse import urlparse
 
+import idutils
+import requests
+from rdflib import Graph
+from rdflib.plugins.sparql import prepareQuery
+
 logging.basicConfig(
     stream=sys.stdout, level=logging.DEBUG, format="'%(name)s:%(lineno)s' | %(message)s"
 )