setting up dev environment

Makefile

@@ -51,11 +51,15 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint: ## check style with flake8
+	black s2rename tests setup.py
 	flake8 s2rename tests
 
-test: ## run tests quickly with the default Python
+alltests: ## run all tests with the default Python
 	py.test
 
+test: ## run tests quickly with the default Python, exit on first error
+	py.test --exitfirst -s
+
 coverage: ## check code coverage quickly with the default Python
 	coverage run --source s2rename -m pytest
 	coverage report -m

requirements_dev.txt

@@ -4,7 +4,7 @@ wheel==0.32.1
 watchdog==0.9.0
 flake8==3.5.0
 coverage==4.5.1
-black>=18.9
+black>=18.9b0
 
 pytest==3.8.2
 pytest-runner==4.2

s2rename/__init__.py

@@ -3,5 +3,5 @@
 """Top-level package for S2Rename."""
 
 __author__ = """Holger Frey"""
-__email__ = 'frey@imtek.de'
+__email__ = "frey@imtek.de"
-__version__ = '0.0.1'
+__version__ = "0.0.1"

s2rename/cli.py

@@ -8,8 +8,7 @@ import click
 @click.command()
 def main(args=None):
     """Console script for s2rename."""
-    click.echo("Replace this message by putting your code into "
+    click.echo("Replace this message by putting your code into " "s2rename.cli.main")
-               "s2rename.cli.main")
     click.echo("See click documentation at http://click.pocoo.org/")
     return 0
 

s2rename/s2rename.py

@@ -1,3 +1,64 @@
 # -*- coding: utf-8 -*-
 
 """Main module."""
+
+import re
+
+from collections import namedtuple
+from pathlib import Path
+
+REGEX_ID = r"(?P<row>[A-H])(?P<col>(0?[1-9]|1[0-2]))_(?P<channel>\d)"
+REGEX_SENSOVATION = r"(?P<stem>(.+_|))" + REGEX_ID
+REGEX_SCIENION = REGEX_ID + r"(?P<stem>(.+_|))"
+
+RE_SENSOVATION = re.compile(REGEX_SENSOVATION)
+RE_SCIENION = re.compile(REGEX_SENSOVATION)
+
+
+TPL_SENSOVATION = '{r.stem}_{r.row}{r.col:0>{dec}d}_{r.channel}'
+
+class S2IOError(IOError):
+    """ custom IO Exception """
+
+
+Renamable = namedtuple("Renamable", "path,stem,row,col,channel")
+
+
+def get_source_list(folder, suffix=None):
+    """ returns the files in a directory that are not hidden
+
+    if 'suffix' is given, the list will only return files with the given
+    extension
+    """
+    src_dir = Path(folder)
+    if not src_dir.is_dir():
+        raise S2IOError(f"{src_dir} is not a directory")
+    all_files = (f for f in src_dir.iterdir() if f.is_file())
+    non_hidden_files = (f for f in all_files if not f.stem.startswith("."))
+    if suffix is None:
+        return non_hidden_files
+    else:
+        return filter_source_list(non_hidden_files, suffix)
+
+
+def filter_source_list(source_list, suffix):
+    """ filters pathlib.Path objects by only containing a given suffix """
+    return (f for f in source_list if f.suffix.lower() == suffix)
+
+
+def parse_source_list(source_list, regex):
+    """ returns a list of items that can be renamed """
+    for path in source_list:
+        groups = regex.match(path.stem)
+        if groups:
+            stem = groups["stem"]
+            if stem.endswith('_'):
+                stem = stem[:-1]
+            entry = Renamable(
+                path=path,
+                stem=stem,
+                row=groups["row"],
+                col=int(groups["col"]),
+                channel=groups["channel"],
+            )
+            yield entry

setup.cfg

@@ -15,7 +15,10 @@ replace = __version__ = '{new_version}'
 universal = 1
 
 [flake8]
-exclude = docs
+max-line-length = 88
+exclude =
+    .venv,
+    docs
 
 [aliases]
 # Define setup.py command aliases here

setup.py

@@ -5,42 +5,38 @@
 
 from setuptools import setup, find_packages
 
-with open('README.md') as readme_file:
+with open("README.md") as readme_file:
     readme = readme_file.read()
 
-requirements = ['Click>=6.0', ]
+requirements = ["Click>=6.0"]
 
-setup_requirements = ['pytest-runner', ]
+setup_requirements = ["pytest-runner"]
 
-test_requirements = ['pytest', ]
+test_requirements = ["pytest"]
 
 setup(
     author="Holger Frey",
-    author_email='frey@imtek.de',
+    author_email="frey@imtek.de",
     classifiers=[
-        'Development Status :: 2 - Pre-Alpha',
+        "Development Status :: 2 - Pre-Alpha",
-        'Intended Audience :: Developers',
+        "Intended Audience :: Developers",
-        'Natural Language :: English',
+        "Natural Language :: English",
-        'Programming Language :: Python :: 3',
+        "Programming Language :: Python :: 3",
-        'Programming Language :: Python :: 3.6',
+        "Programming Language :: Python :: 3.6",
-        'Programming Language :: Python :: 3.7',
+        "Programming Language :: Python :: 3.7",
     ],
     description="Renaming files for SensoSpot and Scienion software",
-    entry_points={
+    entry_points={"console_scripts": ["s2rename=s2rename.cli:main"]},
-        'console_scripts': [
-            's2rename=s2rename.cli:main',
-        ],
-    },
     install_requires=requirements,
     long_description=readme,
     include_package_data=True,
-    keywords='s2rename',
+    keywords="s2rename",
-    name='s2rename',
+    name="s2rename",
-    packages=find_packages(include=['s2rename']),
+    packages=find_packages(include=["s2rename"]),
     setup_requires=setup_requirements,
-    test_suite='tests',
+    test_suite="tests",
     tests_require=test_requirements,
-    url='https://github.com/audreyr/s2rename',
+    url="https://github.com/audreyr/s2rename",
-    version='0.0.1',
+    version="0.0.1",
     zip_safe=False,
 )

tests/test_cli.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""Tests for `s2rename` package."""
+
+import pytest
+
+from click.testing import CliRunner
+
+from s2rename import cli
+
+
+def test_command_line_interface():
+    """Test the CLI."""
+    runner = CliRunner()
+    result = runner.invoke(cli.main)
+    assert result.exit_code == 0
+    assert "s2rename.cli.main" in result.output
+    help_result = runner.invoke(cli.main, ["--help"])
+    assert help_result.exit_code == 0
+    assert "--help  Show this message and exit." in help_result.output

tests/test_s2rename.py

@@ -5,34 +5,107 @@
 
 import pytest
 
-from click.testing import CliRunner
+from pathlib import Path
 
+
+sensovation_source_list = [
+    Path("some prefix thing_A1_1.tif"),
+    Path("some prefix thing_A02_2.tif"),
+    Path("A03_3.tif"),
+    Path("some prefix thing_A10_4"),
+    Path("some prefix thing_A11_5.csv"),
+    Path("some prefix thing_A12_6.xml"),
+    Path("some prefix thing_B01_1.tif"),
+    Path("some prefix thing_C01_1.tif"),
+    Path("some prefix thing_D01_1.tif"),
+    Path("some prefix thing_E01_1.tif"),
+    Path("some prefix thing_F01_1.tif"),
+    Path("some prefix thing_G01_1.tif"),
+    Path("some prefix thing_H01_1.tif"),
+    Path("some prefix thing_I01_1.tif"),
+    Path("some prefix thing_FF01_1.tif"),
+    Path("some prefix thing_F21_1.tif"),
+    Path("some prefix thing_F00_1.tif"),
+    Path("some prefix thing_F0_1.tif"),
+    Path("some prefix thing_F13_1.tif"),
+    Path("some prefix thing_F08.tif"),
+    Path(".some prefix thing_F09_1.tif"),
+]
+
+scienion_source_list = [
+    Path("A1_1_some suffix thing.tif"),
+    Path("A02_2_some suffix thing.tif"),
+    Path("A03_3.tif"),
+    Path("A10_3_some suffix thing"),
+    Path("A11_4_some suffix thing.csv"),
+    Path("A12_5_some suffix thing.xml"),
+    Path("B01_1_some suffix thing.tif"),
+    Path("C01_1_some suffix thing.tif"),
+    Path("D01_1_some suffix thing.tif"),
+    Path("E01_1_some suffix thing.tif"),
+    Path("F01_1_some suffix thing.tif"),
+    Path("G01_1_some suffix thing.tif"),
+    Path("H01_1_some suffix thing.tif"),
+    Path("I01_1_some suffix thing.tif"),
+    Path("FF01_1_some suffix thing.tif"),
+    Path("F21_1_some suffix thing.tif"),
+    Path("F00_1_some suffix thing.tif"),
+    Path("F0_1_some suffix thing.tif"),
+    Path("F13_1_some suffix thing.tif"),
+    Path("F08_some suffix thing.tif"),
+    Path(".F09_1_some suffix thing.tif"),
+]
+
+
+@pytest.mark.parametrize("sources", [sensovation_source_list, scienion_source_list])
+def test_parse_source_list_sensovation(sources):
+    from s2rename import s2rename
+
+    if sources == sensovation_source_list:
+        regex = s2rename.RE_SENSOVATION
+    else:
+        regex = s2rename.RE_SCIENION
+
+    result = list(s2rename.parse_source_list(sensovation_source_list, regex))
+    assert len(result) == 14
+    assert {r.row for r in result} == set("ABCDEFGH")
+    assert {r.col for r in result} == set([1, 2, 3, 9, 10, 11, 12])
+
+
+def test_get_source_list():
+    from s2rename import s2rename
+
+    result = list(s2rename.get_source_list("."))
+    assert {p.name for p in result} == {
+        "LICENSE",
+        "Pipfile",
+        "requirements_dev.txt",
+        "setup.cfg",
+        "Makefile",
+        "README.md",
+        "setup.py",
+    }
+
+
+@pytest.mark.parametrize("path", ["/i/hope/this/doesnt/exist", "setup.py"])
+def test_get_source_list_raises_error(path):
     from s2rename import s2rename
-from s2rename import cli
+
+    with pytest.raises(s2rename.S2IOError):
+        result = s2rename.get_source_list(path)
 
 
-@pytest.fixture
+def test_get_source_list_with_type():
-def response():
+    from s2rename import s2rename
-    """Sample pytest fixture.
 
-    See more at: http://doc.pytest.org/en/latest/fixture.html
+    result = s2rename.get_source_list(".", ".txt")
-    """
+    assert {p.name for p in result} == {"requirements_dev.txt"}
-    # import requests
-    # return requests.get('https://github.com/audreyr/cookiecutter-pypackage')
 
 
-def test_content(response):
+def test_filter_source_list_type():
-    """Sample pytest test function with the pytest fixture as an argument."""
+    from s2rename import s2rename
-    # from bs4 import BeautifulSoup
-    # assert 'GitHub' in BeautifulSoup(response.content).title.string
 
+    result = list(s2rename.filter_source_list(sensovation_source_list, ".csv"))
+    assert len(result) == 1
+    assert result[0].name == "some prefix thing_A11_5.csv"
 
-def test_command_line_interface():
-    """Test the CLI."""
-    runner = CliRunner()
-    result = runner.invoke(cli.main)
-    assert result.exit_code == 0
-    assert 's2rename.cli.main' in result.output
-    help_result = runner.invoke(cli.main, ['--help'])
-    assert help_result.exit_code == 0
-    assert '--help  Show this message and exit.' in help_result.output