applied precommit (black, isort, etc)

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+
+files: '\.(py|rst|sh)$'
+fail_fast: false
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    #-   id: check-executables-have-shebangs
+    -   id: check-ast
+
+-   repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+    -   id: flake8
+        args: ["-j8", "--ignore=E203,E501,W503,E722", "--max-line-length=120", "--exit-zero"]
+
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
+        args: ["--line-length=120"]
+        exclude: E501
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"] # solves conflicts between black and isort
+

README.rst

@@ -46,7 +46,7 @@ This tool uses a registry so it will work only with resgistered tools, which lis
 
 Type::
 
-    versionix --help 
+    versionix --help
 
 to get more help like this example:
 
@@ -67,6 +67,7 @@ Changelog
 ========= ========================================================================
 Version   Description
 ========= ========================================================================
+0.2.4     More tools in the registry and added precommit
 0.2.3     More tools in the registry
 0.2.2     add all tools required by sequana pipelines (oct 2023)
 0.2.1     More tools added.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "versionix"
-version = "0.2.3"
+version = "0.2.4"
 description = "Get version of any tools"
 authors = ["Sequana Team"]
 license = "BSD-3"

test/test_parser.py

@@ -1,51 +1,52 @@
+import sys
+
 from versionix.parser import get_version as get_version
 from versionix.scripts import main
 
-import sys
-
 # for testing we do not want to install all those tools/software so
 # we have set testing=True, in which case some sanity checks and
 # error won't be raised.
 # def get_version(standalone):
 #    return get_version_orig(standalone, testing=True)
 
-#The mocker which is set so that when we test the presence of e.G. macs3, which is not installed,
-#no error is raise
+# The mocker which is set so that when we test the presence of e.G. macs3, which is not installed,
+# no error is raise
+
 
 def test_sequana(fp, mocker):
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(["sequana_coverage", "--version"], stdout=["sequana_coverage, version 0.15.4"])
     assert get_version("sequana_coverage") == "0.15.4"
 
 
 def test_macs3(fp, mocker):
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(["macs3", "--version"], stdout=["macs3 3.0.0b1"])
     assert get_version("macs3") == "3.0.0b1"
 
 
 def test_kallisto(fp, mocker):
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(["kallisto", "version"], stdout=["kallisto, version 0.48.0"])
     assert get_version("kallisto") == "0.48.0"
 
 
 def test_pigz(fp, mocker):
     # stderr parser
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(["pigz", "--version"], stderr=["pigz 2.4"])
     assert get_version("pigz") == "2.4"
 
 
 def test_fastqc(fp, mocker):
     # stderr parser
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(["fastqc", "--version"], stderr=["fastqc v1.0.0"])
     assert get_version("fastqc") == "1.0.0"
 
 
 def _test_bwa(fp, mocker):
-    mocker.patch('shutil.which', return_value="something")
+    mocker.patch("shutil.which", return_value="something")
     fp.register(
         ["bwa"],
         stderr=[
@@ -92,7 +93,10 @@ def test_script(fp, mocker):
 
     runner.invoke(main, ["--registered"])
     runner.invoke(main, ["--stats"])
-    runner.invoke(main, )
+    runner.invoke(
+        main,
+    )
+
 
 def test_bedtools_error(fp, mocker):
     # registered tool but if not installed, should raise a SystemExit error

versionix/__init__.py

@@ -2,5 +2,5 @@
 
 try:
     version = pkg_resources.require("versionix")[0].version
-except: #pragma: no cover
+except:  # pragma: no cover
     version = ">=0.1.0"

versionix/parser.py

@@ -52,6 +52,6 @@ def get_version(standalone, verbose=True):
         version = parser(p)
         return version
 
-    except Exception as err: #pragma: no cover
+    except Exception as err:  # pragma: no cover
         print(err)
         sys.exit(1)