Merge pull request #28 from databio/dev

Dev

.github/workflows/black.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: psf/black@20.8b1

.github/workflows/python-publish.yml

@@ -1,6 +1,3 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: Upload Python Package
 
 on:
@@ -9,22 +6,24 @@ on:
 
 jobs:
   deploy:
+
     runs-on: ubuntu-latest
+    name: upload release to PyPI
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          python setup.py sdist bdist_wheel
-          twine upload dist/*
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      run: |
+        python setup.py sdist bdist_wheel
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/run-pytest.yml

@@ -11,7 +11,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.9]
+
+        python-version: ["3.8", "3.12"]
         os: [ubuntu-latest]
 
     steps:

docs/changelog.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.2.8] -- 2024-04-04
+### Changed
+- Updated Python versions to >3.8
+
 ## [0.2.7] -- 2021-09-08
 ### Changed
 - Drop support 2to3 for RTD compatibility

logmuse/_version.py

@@ -1 +1 @@
-__version__ = "0.2.7"
+__version__ = "0.2.8"

logmuse/est.py

@@ -285,10 +285,12 @@ def init_logger(
         (lambda _: fmt)
         if fmt
         else (
-            lambda hdlr: BASIC_LOGGING_FORMAT
-            if plain_format
-            or not (devmode or fine or isinstance(hdlr, logging.FileHandler))
-            else (FULL_DEV_LOGGING_FMT if use_full_names else DEV_LOGGING_FMT)
+            lambda hdlr: (
+                BASIC_LOGGING_FORMAT
+                if plain_format
+                or not (devmode or fine or isinstance(hdlr, logging.FileHandler))
+                else (FULL_DEV_LOGGING_FMT if use_full_names else DEV_LOGGING_FMT)
+            )
         )
     )
 
@@ -329,7 +331,7 @@ def setup_logger(
     plain_format=False,
     style=None,
 ):
-    """ Old alias for init_logger for backwards compatibility """
+    """Old alias for init_logger for backwards compatibility"""
     warnings.warn("Please use init_logger in place of setup_logger", DeprecationWarning)
     return init_logger(
         name,
@@ -386,7 +388,7 @@ def _level_from_verbosity(verbosity):
 
 
 class AbsentOptionException(Exception):
-    """ Exception subtype suggesting that client should add log options. """
+    """Exception subtype suggesting that client should add log options."""
 
     def __init__(self, missing_optname):
         likely_reason = (

requirements/requirements-all.txt

@@ -0,0 +1 @@
+setuptools

setup.py

@@ -9,7 +9,7 @@
 def read_reqs(reqs_name):
     deps = []
     depsfile = os.path.join(REQDIR, "requirements-{}.txt".format(reqs_name))
-    with open(depsfile, 'r') as f:
+    with open(depsfile, "r") as f:
         for l in f:
             if not l.strip():
                 continue
@@ -20,13 +20,21 @@ def read_reqs(reqs_name):
 # Additional keyword arguments for setup().
 extra = {}
 
-extra["install_requires"] = []
+DEPENDENCIES = []
+with open("requirements/requirements-all.txt", "r") as reqs_file:
+    for line in reqs_file:
+        if not line.strip():
+            continue
+        DEPENDENCIES.append(line)
 
-with open(os.path.join(PKG, "_version.py"), 'r') as versionfile:
+extra["install_requires"] = DEPENDENCIES
+
+
+with open(os.path.join(PKG, "_version.py"), "r") as versionfile:
     version = versionfile.readline().split()[-1].strip("\"'\n")
 
 # Handle the pypi README formatting.
-with open('README.md') as f:
+with open("README.md") as f:
     long_description = f.read()
 
 setup(
@@ -35,22 +43,26 @@ def read_reqs(reqs_name):
     version=version,
     description="Logging setup",
     long_description=long_description,
-    long_description_content_type='text/markdown', 
+    long_description_content_type="text/markdown",
     classifiers=[
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python :: 2.7",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 2.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     keywords="logging, workflow, logger, logs",
     url="https://github.com/databio/{}/".format(PKG),
-    author=u"Vince Reuter, Nathan Sheffield",
+    author="Vince Reuter, Nathan Sheffield",
     license="BSD-2-Clause",
     scripts=None,
     include_package_data=True,
     test_suite="tests",
     tests_require=read_reqs("dev"),
-    setup_requires=(["pytest-runner"] if {"test", "pytest", "ptr"} & set(sys.argv) else []),
+    setup_requires=(
+        ["pytest-runner"] if {"test", "pytest", "ptr"} & set(sys.argv) else []
+    ),
     **extra
 )

tests/conftest.py

@@ -9,5 +9,5 @@
 
 @pytest.fixture
 def parser():
-    """ Clean/fresh, blank-slate argument parser instance for a test case """
+    """Clean/fresh, blank-slate argument parser instance for a test case"""
     return argparse.ArgumentParser()

tests/test_add_logging_options.py

@@ -12,28 +12,33 @@
 
 
 def pytest_generate_tests(metafunc):
-    """ Generation and parameterization of tests in this module. """
+    """Generation and parameterization of tests in this module."""
     if "opt" in metafunc.fixturenames:
-        metafunc.parametrize("opt", list(["--" + x for x in LOGGING_CLI_OPTDATA.keys()]))
+        metafunc.parametrize(
+            "opt", list(["--" + x for x in LOGGING_CLI_OPTDATA.keys()])
+        )
 
 
 def test_all_options_are_added(parser, opt):
-    """ If requested, all of the standard logging options are added. """
+    """If requested, all of the standard logging options are added."""
     assert opt not in _get_optnames(parser)
     add_logging_options(parser)
     assert opt in _get_optnames(parser)
 
 
 def test_each_option_gis_functional(parser, opt):
-    """ Each added CLI opt can be used as expected. """
+    """Each added CLI opt can be used as expected."""
     add_logging_options(parser)
     for a in parser._actions:
         if opt in a.option_strings:
             use = get_act_use(parser, a)
             break
     else:
-        pytest.fail("Parser lacks action with name: {}; available: {}".
-                    format(opt, _get_optnames(parser)))
+        pytest.fail(
+            "Parser lacks action with name: {}; available: {}".format(
+                opt, _get_optnames(parser)
+            )
+        )
     try:
         parser.parse_args(use)
     except Exception as e:
@@ -64,21 +69,29 @@ def _build_action_usage(act_kind):
         given a CLI action will create the representative command line chunks
     """
     from logmuse.est import _VERBOSITY_CHOICES, VERBOSITY_OPTNAME
+
     def get_general_use(act):
         name = _get_opt_first_name(act)
-        arg = random.choice(_VERBOSITY_CHOICES) \
-            if name == "--" + VERBOSITY_OPTNAME else _random_chars_option()
+        arg = (
+            random.choice(_VERBOSITY_CHOICES)
+            if name == "--" + VERBOSITY_OPTNAME
+            else _random_chars_option()
+        )
         return [name, arg]
+
     strategies = [
-        ((argparse._StoreTrueAction, argparse._StoreFalseAction),
-         lambda a: [a.option_strings[0]]),
-        ((argparse._StoreAction), get_general_use)
+        (
+            (argparse._StoreTrueAction, argparse._StoreFalseAction),
+            lambda a: [a.option_strings[0]],
+        ),
+        ((argparse._StoreAction), get_general_use),
     ]
     for kinds, strat in strategies:
         if issubclass(act_kind, kinds):
             return strat
-    raise ValueError("No usage strategies for given kind of option: {}".
-                     format(act_kind))
+    raise ValueError(
+        "No usage strategies for given kind of option: {}".format(act_kind)
+    )
 
 
 def _get_optnames(p):
@@ -93,11 +106,11 @@ def _get_optnames(p):
 
 
 def _random_chars_option():
-    """ Randomly generate arbitrary text value for use as CLI opt argument. """
+    """Randomly generate arbitrary text value for use as CLI opt argument."""
     pool = string.ascii_letters + string.digits
     return "".join(random.choice(pool) for _ in range(10))
 
 
 def _get_opt_first_name(a):
-    """ Get the first of an action's option names. """
+    """Get the first of an action's option names."""
     return a.option_strings[0]