Merge branch 'main' of github.com:Countess-project/countess

.github/workflows/run-tests-push.yml

@@ -11,148 +11,60 @@ jobs:
  - uses: actions/setup-python@v5
  with:
  python-version: "3.9"
+ cache: 'pip'
  - run: sudo apt install xvfb
  - run: pip install --upgrade pip
  - run: pip install .[dev]
- - run: xvfb-run pytest tests/
+ - run: xvfb-run pytest -v -rP --doctest-modules countess/ tests/
 
- run-tests-ubuntu-22_04-python-3_10-with-coverage:
+ run-tests-ubuntu-22_04-python-3_10:
  runs-on: ubuntu-22.04
- name: Ubuntu 22.04, Python 3.10 (with coverage)
+ name: Ubuntu 22.04, Python 3.10
  steps:
  - uses: actions/checkout@v4
  - uses: actions/setup-python@v5
  with:
  python-version: "3.10"
+ cache: 'pip'
  - run: sudo apt install xvfb
  - run: pip install --upgrade pip
  - run: pip install .[dev]
- - run: xvfb-run coverage run --source countess -m pytest tests/
-# - run: coverage html
-# - uses: actions/upload-artifact@v3
-# with:
-# name: test coverage report
-# path: htmlcov/*
- - run: echo '### Coverage Report' >> $GITHUB_STEP_SUMMARY
- - run: coverage report --format=markdown --skip-empty --sort=-cover >> $GITHUB_STEP_SUMMARY
-
-# run-tests-ubuntu-22_04-python-3_11_0rc2:
-# runs-on: ubuntu-22.04
-# name: Ubuntu 22.04, Python 3.11.0rc2
-# steps:
-# - uses: actions/checkout@v4
-# - uses: actions/setup-python@v4
-# with:
-# python-version: "3.11.0-rc.2"
-# - run: sudo apt install xvfb
-# - run: pip install --upgrade pip
-# - run: pip install .[dev]
-# - run: xvfb-run pytest tests/
-#
-# run-tests-ubuntu-22_04-python-3_11_0:
-# runs-on: ubuntu-22.04
-# name: Ubuntu 22.04, Python 3.11.1
-# steps:
-# - uses: actions/checkout@v4
-# - uses: actions/setup-python@v4
-# with:
-# python-version: "3.11.0"
-# - run: sudo apt install xvfb
-# - run: pip install --upgrade pip
-# - run: pip install .[dev]
-# - run: xvfb-run pytest tests/
-#
-# run-tests-ubuntu-22_04-python-3_11_1:
-# runs-on: ubuntu-22.04
-# name: Ubuntu 22.04, Python 3.11.1
-# steps:
-# - uses: actions/checkout@v4
-# - uses: actions/setup-python@v4
-# with:
-# python-version: "3.11.1"
-# - run: sudo apt install xvfb
-# - run: pip install --upgrade pip
-# - run: pip install .[dev]
-# - run: xvfb-run pytest tests/
-
- run-tests-ubuntu-22_04-python-3_11_2:
- runs-on: ubuntu-22.04
- name: Ubuntu 22.04, Python 3.11.2
- steps:
- - uses: actions/checkout@v4
- - uses: actions/setup-python@v5
- with:
- python-version: "3.11.2"
- - run: sudo apt install xvfb
- - run: pip install --upgrade pip
- - run: pip install .[dev]
- - run: xvfb-run pytest tests/
-
- run-tests-ubuntu-22_04-python-3_11:
- runs-on: ubuntu-22.04
- name: Ubuntu 22.04, Python 3.11
- steps:
- - uses: actions/checkout@v4
- - uses: actions/setup-python@v5
- with:
- python-version: "3.11"
- - run: sudo apt install xvfb
- - run: pip install --upgrade pip
- - run: pip install .[dev]
- - run: xvfb-run pytest tests/
-
-# run-tests-ubuntu-22_04-python-3_12_0_alpha5:
-# runs-on: ubuntu-22.04
-# name: Ubuntu 22.04, Python 3.12.0alpha5
-# steps:
-# - uses: actions/checkout@v4
-# - uses: actions/setup-python@v4
-# with:
-# python-version: "3.12.0-alpha.5"
-# - run: sudo apt install xvfb
-# - run: pip install --upgrade pip
-# - run: pip install .[dev]
-# - run: xvfb-run pytest tests/
+ - run: xvfb-run pytest -v -rP --doctest-modules countess/ tests/
 
  run-tests-ubuntu-22_04-python-3_11_from_apt:
  runs-on: ubuntu-22.04
- name: Ubuntu 22.04, Python from Apt
+ name: Ubuntu 22.04, Python 3.11 from Apt
  steps:
  - uses: actions/checkout@v4
  - run: sudo apt install python3.11-full python3-pip xvfb
  - run: python3.11 -m pip install --upgrade pip
  - run: python3.11 -m pip install -e .[dev]
- - run: xvfb-run python3.11 -mpytest tests/
+ - run: xvfb-run python3.11 -m pytest -v -rP --doctest-modules countess/ tests/
 
- # run-tests-ubuntu-22_10-python-3_11_from_apt:
- #runs-on: ubuntu-22.10
- #name: Ubuntu 22.10, Python from Apt
- #steps:
- #- uses: actions/checkout@v4
- #- run: sudo apt install python3.11-full python3-pip xvfb
- #- run: python3.11 -m pip install --upgrade pip
- #- run: python3.11 -m pip install -e .[dev]
- #- run: xvfb-run python3.11 -mpytest tests/
-
- #run-tests-ubuntu-23_04-python-3_11_from_apt:
- #runs-on: ubuntu-23.04
- #name: Ubuntu 23.04, Python from Apt
- #steps:
- #- uses: actions/checkout@v4
- #- run: sudo apt install python3.11-full python3-pip xvfb
- #- run: python3.11 -m pip install --upgrade pip
- #- run: python3.11 -m pip install -e .[dev]
- #- run: xvfb-run python3.11 -mpytest tests/
+ run-tests-ubuntu-24_04-python-3_12_from_apt:
+ runs-on: ubuntu-24.04
+ name: Ubuntu 24.04, Python 3.12 from Apt
+ steps:
+ - uses: actions/checkout@v4
+ - run: sudo apt install python3.12-full python3-pip xvfb
+ - run: python3.12 -m venv /tmp/venv
+ - run: /tmp/venv/bin/python -m pip install --upgrade pip
+ - run: /tmp/venv/bin/python -m pip install -e .[dev]
+ - run: xvfb-run /tmp/venv/bin/python -m pytest -v -rP --doctest-modules countess/ tests/
 
-# run-tests-ubuntu-22_04-pypy3:
-# runs-on: ubuntu-22.04
-# name: Ubuntu 22.04, PyPy 3
-# steps:
-# - uses: actions/checkout@v4
-# - uses: actions/setup-python@v4
-# with:
-# python-version: "pypy3.9"
-# - run: sudo apt install pypy3 pypy3-tk pypy3-dev xvfb
-# - run: pypy3 -mpip install -U pip wheel
-# - run: pypy3 -mpip install .[dev]
-# - run: xvfb-run pytest tests/
+ run-tests-ubuntu-24_04-python-3_x:
+ runs-on: ubuntu-24.04
+ name: Ubuntu 24.04, Python 3.x
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v5
+ with:
+ python-version: "3.x"
+ cache: 'pip'
+ - run: sudo apt install xvfb
+ - run: python3 -m venv /tmp/venv
+ - run: /tmp/venv/bin/python -m pip install --upgrade pip
+ - run: /tmp/venv/bin/python -m pip install -e .[dev]
+ - run: xvfb-run /tmp/venv/bin/coverage run --source countess -m pytest -v -rP --doctest-modules countess/ tests/
+ - run: echo '### Coverage Report' >> $GITHUB_STEP_SUMMARY
+ - run: /tmp/venv/bin/coverage report --format=markdown --skip-empty --sort=-cover >> $GITHUB_STEP_SUMMARY

countess/core/cmd.py

@@ -17,17 +17,27 @@ def run(argv) -> None:
 
 
 def main() -> None:
+ # set up a default stderr StreamHandler for logs
+ logging_handler = logging.StreamHandler()
+
+ # set up a QueueHandler/QueueListener to forward the logs between
+ # processes and send them to the logging_handler
  logging_queue: multiprocessing.Queue = multiprocessing.Queue()
- logging.getLogger().addHandler(logging.handlers.QueueHandler(logging_queue))
- logging.getLogger().setLevel(logging.INFO)
- logging_handler = logging.handlers.QueueListener(logging_queue, logging.StreamHandler())
- logging_handler.start()
+ logging_queue_handler = logging.handlers.QueueHandler(logging_queue)
+ logging_queue_listener = logging.handlers.QueueListener(logging_queue, logging_handler)
+ logging_queue_listener.start()
+
+ # set up all loggers to be handled by the QueueHandler.
+ root_logger = logging.getLogger()
+ root_logger.addHandler(logging_queue_handler)
+ root_logger.setLevel(logging.INFO)
 
  run(sys.argv[1:])
 
- # tidy up just in case we're not just about to exit
- logging.getLogger().handlers.clear()
- logging_handler.stop()
+ # shut down the logging subsystem, in case this function is being
+ # called as part of something else (eg: tests)
+ root_logger.handlers.clear()
+ logging_queue_listener.stop()
  logging_queue.close()
 
 

countess/core/parameters.py

@@ -110,13 +110,13 @@ def __ne__(self, other):
  def __gt__(self, other):
  return self._value > other
 
- def __gte__(self, other):
+ def __ge__(self, other):
  return self._value >= other
 
  def __lt__(self, other):
  return self._value < other
 
- def __lte__(self, other):
+ def __le__(self, other):
  return self._value <= other
 
 
@@ -187,6 +187,15 @@ def __int__(self):
  def __float__(self):
  return float(self._value)
 
+ def __abs__(self):
+ return abs(self._value)
+
+ def __pos__(self):
+ return self._value
+
+ def __neg__(self):
+ return 0 - (self._value)
+
  # XXX should include many more numeric operator methods here, see
  # https://docs.python.org/3/reference/datamodel.html#emulating-numeric-types
  # matmul, truediv, floordiv, mod, divmod, pow, lshift, rshift, and, xor, or,
@@ -219,10 +228,12 @@ def set_value(self, value):
  if isinstance(value, str):
  if value in ("t", "T", "true", "True", "1"):
  self._value = True
- if value in ("f", "F", "false", "False", "0"):
+ elif value in ("f", "F", "false", "False", "0"):
  self._value = False
- raise ValueError(f"Can't convert {value} to boolean")
- self._value = bool(value)
+ else:
+ raise ValueError(f"Can't convert {value} to boolean")
+ else:
+ self._value = bool(value)
 
  def __bool__(self):
  return self._value or False
@@ -402,10 +413,10 @@ def __init__(self, label: str, value: Optional[str] = None, choices: Optional[It
  super().__init__(label, value, choices)
 
  def get_selected_type(self):
- if self.value is None:
- return None
- else:
+ try:
  return self.DATA_TYPES[self.value][0]
+ except KeyError:
+ return None
 
  def cast_value(self, value):
  if value is not None:
@@ -519,7 +530,7 @@ def is_not_none(self):
  def get_column_prefix(self):
  if self.is_none():
  return None
- return self.value.removesuffix("*")
+ return super().get_column_prefix()
 
 
 class ColumnOrIndexChoiceParam(ColumnChoiceParam):
@@ -548,33 +559,32 @@ class ColumnOrStringParam(ColumnChoiceParam):
  def set_column_choices(self, choices):
  self.set_choices([self.PREFIX + c for c in choices])
 
- def get_column_name(self):
- if self.value.startswith(self.PREFIX):
+ def get_column_name(self) -> Optional[str]:
+ if type(self.value) is str and self.value.startswith(self.PREFIX):
  return self.value[len(self.PREFIX) :]
  return None
 
- def get_value_from_dict(self, data: dict):
+ def get_value_from_dict(self, data: dict) -> str:
  if type(self.value) is str and self.value.startswith(self.PREFIX):
  return data[self.value[len(self.PREFIX) :]]
  else:
  return self.value
 
- def get_column_or_value(self, df: pd.DataFrame, numeric: bool):
- if self.value.startswith(self.PREFIX):
+ def get_column_or_value(self, df: pd.DataFrame, numeric: bool) -> Union[float, str, pd.Series]:
+ if type(self.value) is str and self.value.startswith(self.PREFIX):
  col = df[self.value[len(self.PREFIX) :]]
- return col.astype("f" if numeric else "string")
+ return col.astype(float if numeric else str)
  else:
  return float(self.value) if numeric else str(self.value)
 
- def get_column_or_value_numeric(self, df: pd.DataFrame):
- if self.value.startswith(self.PREFIX):
- return df[self.value[len(self.PREFIX) :]]
- else:
- return self.value
-
  def set_choices(self, choices: Iterable[str]):
  self.choices = list(choices)
- if self._value is not None and self._value.startswith(self.PREFIX) and self._value not in self.choices:
+ if (
+ self._value is not None
+ and type(self._value) is str
+ and self._value.startswith(self.PREFIX)
+ and self._value not in self.choices
+ ):
  self._value = self.DEFAULT_VALUE
  self._choice = None
 
@@ -862,17 +872,6 @@ def copy(self) -> "MultiParam":
  pp = dict(((k, p.copy()) for k, p in self.params.items()))
  return self.__class__(self.label, pp)
 
- # XXX decide if these "dict-like" accessors are worth keeping
-
- def __getitem__(self, key):
- return self.params[key]
-
- def __contains__(self, item):
- return item in self.params
-
- def __setitem__(self, key, value):
- self.params[key].value = value
-
  def __iter__(self):
  return self.params.__iter__()