sclab 0.1.7__py3-none-any.whl → 0.2.2__py3-none-any.whl

sclab/scanpy/_compat.py

@@ -0,0 +1,92 @@
+from __future__ import annotations
+
+import sys
+from dataclasses import dataclass, field
+from functools import cache, partial
+from importlib.util import find_spec
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+from packaging.version import Version
+
+if TYPE_CHECKING:
+    from importlib.metadata import PackageMetadata
+
+
+if TYPE_CHECKING:
+    # type checkers are confused and can only see …core.Array
+    from dask.array.core import Array as DaskArray
+elif find_spec("dask"):
+    from dask.array import Array as DaskArray
+else:
+
+    class DaskArray:
+        pass
+
+
+if find_spec("zappy") or TYPE_CHECKING:
+    from zappy.base import ZappyArray
+else:
+
+    class ZappyArray:
+        pass
+
+
+__all__ = [
+    "DaskArray",
+    "ZappyArray",
+    "fullname",
+    "pkg_metadata",
+    "pkg_version",
+]
+
+
+def fullname(typ: type) -> str:
+    module = typ.__module__
+    name = typ.__qualname__
+    if module == "builtins" or module is None:
+        return name
+    return f"{module}.{name}"
+
+
+if sys.version_info >= (3, 11):
+    from contextlib import chdir
+else:
+    import os
+    from contextlib import AbstractContextManager
+
+    @dataclass
+    class chdir(AbstractContextManager):
+        path: Path
+        _old_cwd: list[Path] = field(default_factory=list)
+
+        def __enter__(self) -> None:
+            self._old_cwd.append(Path.cwd())
+            os.chdir(self.path)
+
+        def __exit__(self, *_excinfo) -> None:
+            os.chdir(self._old_cwd.pop())
+
+
+def pkg_metadata(package: str) -> PackageMetadata:
+    from importlib.metadata import metadata
+
+    return metadata(package)
+
+
+@cache
+def pkg_version(package: str) -> Version:
+    from importlib.metadata import version
+
+    return Version(version(package))
+
+
+if find_spec("legacy_api_wrap") or TYPE_CHECKING:
+    from legacy_api_wrap import legacy_api  # noqa: TID251
+
+    old_positionals = partial(legacy_api, category=FutureWarning)
+else:
+    # legacy_api_wrap is currently a hard dependency,
+    # but this code makes it possible to run scanpy without it.
+    def old_positionals(*old_positionals: str):
+        return lambda func: func

sclab/scanpy/_settings.py

@@ -0,0 +1,526 @@
+from __future__ import annotations
+
+import inspect
+import sys
+from contextlib import contextmanager
+from enum import IntEnum
+from logging import getLevelName
+from pathlib import Path
+from time import time
+from typing import TYPE_CHECKING
+
+from . import logging
+from ._compat import old_positionals
+from .logging import _RootLogger, _set_log_file, _set_log_level
+
+if TYPE_CHECKING:
+    from collections.abc import Generator, Iterable
+    from typing import Any, Literal, TextIO
+
+    # Collected from the print_* functions in matplotlib.backends
+    _Format = (
+        Literal["png", "jpg", "tif", "tiff"]
+        | Literal["pdf", "ps", "eps", "svg", "svgz", "pgf"]
+        | Literal["raw", "rgba"]
+    )
+
+_VERBOSITY_TO_LOGLEVEL = {
+    "error": "ERROR",
+    "warning": "WARNING",
+    "info": "INFO",
+    "hint": "HINT",
+    "debug": "DEBUG",
+}
+# Python 3.7+ ensures iteration order
+for v, level in enumerate(list(_VERBOSITY_TO_LOGLEVEL.values())):
+    _VERBOSITY_TO_LOGLEVEL[v] = level
+
+
+class Verbosity(IntEnum):
+    """Logging verbosity levels."""
+
+    error = 0
+    warning = 1
+    info = 2
+    hint = 3
+    debug = 4
+
+    def __eq__(self, other: Verbosity | int | str) -> bool:
+        if isinstance(other, Verbosity):
+            return self is other
+        if isinstance(other, int):
+            return self.value == other
+        if isinstance(other, str):
+            return self.name == other
+        return NotImplemented
+
+    @property
+    def level(self) -> int:
+        # getLevelName(str) returns the int level…
+        return getLevelName(_VERBOSITY_TO_LOGLEVEL[self.name])
+
+    @contextmanager
+    def override(
+        self, verbosity: Verbosity | str | int
+    ) -> Generator[Verbosity, None, None]:
+        """\
+        Temporarily override verbosity
+        """
+        settings.verbosity = verbosity
+        yield self
+        settings.verbosity = self
+
+
+# backwards compat
+Verbosity.warn = Verbosity.warning
+
+
+def _type_check(var: Any, varname: str, types: type | tuple[type, ...]):
+    if isinstance(var, types):
+        return
+    if isinstance(types, type):
+        possible_types_str = types.__name__
+    else:
+        type_names = [t.__name__ for t in types]
+        possible_types_str = "{} or {}".format(
+            ", ".join(type_names[:-1]), type_names[-1]
+        )
+    raise TypeError(f"{varname} must be of type {possible_types_str}")
+
+
+class ScanpyConfig:
+    """\
+    Config manager for scanpy.
+    """
+
+    N_PCS: int
+    """Default number of principal components to use."""
+
+    def __init__(
+        self,
+        *,
+        verbosity: Verbosity | int | str = Verbosity.warning,
+        plot_suffix: str = "",
+        file_format_data: str = "h5ad",
+        file_format_figs: str = "pdf",
+        autosave: bool = False,
+        autoshow: bool = True,
+        writedir: Path | str = "./write/",
+        cachedir: Path | str = "./cache/",
+        datasetdir: Path | str = "./data/",
+        figdir: Path | str = "./figures/",
+        cache_compression: str | None = "lzf",
+        max_memory=15,
+        n_jobs=1,
+        logfile: Path | str | None = None,
+        categories_to_ignore: Iterable[str] = ("N/A", "dontknow", "no_gate", "?"),
+        _frameon: bool = True,
+        _vector_friendly: bool = False,
+        _low_resolution_warning: bool = True,
+        n_pcs=50,
+    ):
+        # logging
+        self._root_logger = _RootLogger(logging.INFO)  # level will be replaced
+        self.logfile = logfile
+        self.verbosity = verbosity
+        # rest
+        self.plot_suffix = plot_suffix
+        self.file_format_data = file_format_data
+        self.file_format_figs = file_format_figs
+        self.autosave = autosave
+        self.autoshow = autoshow
+        self.writedir = writedir
+        self.cachedir = cachedir
+        self.datasetdir = datasetdir
+        self.figdir = figdir
+        self.cache_compression = cache_compression
+        self.max_memory = max_memory
+        self.n_jobs = n_jobs
+        self.categories_to_ignore = categories_to_ignore
+        self._frameon = _frameon
+        """bool: See set_figure_params."""
+
+        self._vector_friendly = _vector_friendly
+        """Set to true if you want to include pngs in svgs and pdfs."""
+
+        self._low_resolution_warning = _low_resolution_warning
+        """Print warning when saving a figure with low resolution."""
+
+        self._start = time()
+        """Time when the settings module is first imported."""
+
+        self._previous_time = self._start
+        """Variable for timing program parts."""
+
+        self._previous_memory_usage = -1
+        """Stores the previous memory usage."""
+
+        self.N_PCS = n_pcs
+
+    @property
+    def verbosity(self) -> Verbosity:
+        """
+        Verbosity level (default `warning`)
+
+        Level 0: only show 'error' messages.
+        Level 1: also show 'warning' messages.
+        Level 2: also show 'info' messages.
+        Level 3: also show 'hint' messages.
+        Level 4: also show very detailed progress for 'debug'ging.
+        """
+        return self._verbosity
+
+    @verbosity.setter
+    def verbosity(self, verbosity: Verbosity | int | str):
+        verbosity_str_options = [
+            v for v in _VERBOSITY_TO_LOGLEVEL if isinstance(v, str)
+        ]
+        if isinstance(verbosity, Verbosity):
+            self._verbosity = verbosity
+        elif isinstance(verbosity, int):
+            self._verbosity = Verbosity(verbosity)
+        elif isinstance(verbosity, str):
+            verbosity = verbosity.lower()
+            if verbosity not in verbosity_str_options:
+                raise ValueError(
+                    f"Cannot set verbosity to {verbosity}. "
+                    f"Accepted string values are: {verbosity_str_options}"
+                )
+            else:
+                self._verbosity = Verbosity(verbosity_str_options.index(verbosity))
+        else:
+            _type_check(verbosity, "verbosity", (str, int))
+        _set_log_level(self, _VERBOSITY_TO_LOGLEVEL[self._verbosity.name])
+
+    @property
+    def plot_suffix(self) -> str:
+        """Global suffix that is appended to figure filenames."""
+        return self._plot_suffix
+
+    @plot_suffix.setter
+    def plot_suffix(self, plot_suffix: str):
+        _type_check(plot_suffix, "plot_suffix", str)
+        self._plot_suffix = plot_suffix
+
+    @property
+    def file_format_data(self) -> str:
+        """File format for saving AnnData objects.
+
+        Allowed are 'txt', 'csv' (comma separated value file) for exporting and 'h5ad'
+        (hdf5) for lossless saving.
+        """
+        return self._file_format_data
+
+    @file_format_data.setter
+    def file_format_data(self, file_format: str):
+        _type_check(file_format, "file_format_data", str)
+        file_format_options = {"txt", "csv", "h5ad"}
+        if file_format not in file_format_options:
+            raise ValueError(
+                f"Cannot set file_format_data to {file_format}. "
+                f"Must be one of {file_format_options}"
+            )
+        self._file_format_data = file_format
+
+    @property
+    def file_format_figs(self) -> str:
+        """File format for saving figures.
+
+        For example 'png', 'pdf' or 'svg'. Many other formats work as well (see
+        `matplotlib.pyplot.savefig`).
+        """
+        return self._file_format_figs
+
+    @file_format_figs.setter
+    def file_format_figs(self, figure_format: str):
+        _type_check(figure_format, "figure_format_data", str)
+        self._file_format_figs = figure_format
+
+    @property
+    def autosave(self) -> bool:
+        """\
+        Automatically save figures in :attr:`~scanpy._settings.ScanpyConfig.figdir` (default `False`).
+
+        Do not show plots/figures interactively.
+        """
+        return self._autosave
+
+    @autosave.setter
+    def autosave(self, autosave: bool):
+        _type_check(autosave, "autosave", bool)
+        self._autosave = autosave
+
+    @property
+    def autoshow(self) -> bool:
+        """\
+        Automatically show figures if `autosave == False` (default `True`).
+
+        There is no need to call the matplotlib pl.show() in this case.
+        """
+        return self._autoshow
+
+    @autoshow.setter
+    def autoshow(self, autoshow: bool):
+        _type_check(autoshow, "autoshow", bool)
+        self._autoshow = autoshow
+
+    @property
+    def writedir(self) -> Path:
+        """\
+        Directory where the function scanpy.write writes to by default.
+        """
+        return self._writedir
+
+    @writedir.setter
+    def writedir(self, writedir: Path | str):
+        _type_check(writedir, "writedir", (str, Path))
+        self._writedir = Path(writedir)
+
+    @property
+    def cachedir(self) -> Path:
+        """\
+        Directory for cache files (default `'./cache/'`).
+        """
+        return self._cachedir
+
+    @cachedir.setter
+    def cachedir(self, cachedir: Path | str):
+        _type_check(cachedir, "cachedir", (str, Path))
+        self._cachedir = Path(cachedir)
+
+    @property
+    def datasetdir(self) -> Path:
+        """\
+        Directory for example :mod:`~scanpy.datasets` (default `'./data/'`).
+        """
+        return self._datasetdir
+
+    @datasetdir.setter
+    def datasetdir(self, datasetdir: Path | str):
+        _type_check(datasetdir, "datasetdir", (str, Path))
+        self._datasetdir = Path(datasetdir).resolve()
+
+    @property
+    def figdir(self) -> Path:
+        """\
+        Directory for saving figures (default `'./figures/'`).
+        """
+        return self._figdir
+
+    @figdir.setter
+    def figdir(self, figdir: Path | str):
+        _type_check(figdir, "figdir", (str, Path))
+        self._figdir = Path(figdir)
+
+    @property
+    def cache_compression(self) -> str | None:
+        """\
+        Compression for `sc.read(..., cache=True)` (default `'lzf'`).
+
+        May be `'lzf'`, `'gzip'`, or `None`.
+        """
+        return self._cache_compression
+
+    @cache_compression.setter
+    def cache_compression(self, cache_compression: str | None):
+        if cache_compression not in {"lzf", "gzip", None}:
+            raise ValueError(
+                f"`cache_compression` ({cache_compression}) "
+                "must be in {'lzf', 'gzip', None}"
+            )
+        self._cache_compression = cache_compression
+
+    @property
+    def max_memory(self) -> int | float:
+        """\
+        Maximum memory usage in Gigabyte.
+
+        Is currently not well respected…
+        """
+        return self._max_memory
+
+    @max_memory.setter
+    def max_memory(self, max_memory: int | float):
+        _type_check(max_memory, "max_memory", (int, float))
+        self._max_memory = max_memory
+
+    @property
+    def n_jobs(self) -> int:
+        """\
+        Default number of jobs/ CPUs to use for parallel computing.
+
+        Set to `-1` in order to use all available cores.
+        Not all algorithms support special behavior for numbers < `-1`,
+        so make sure to leave this setting as >= `-1`.
+        """
+        return self._n_jobs
+
+    @n_jobs.setter
+    def n_jobs(self, n_jobs: int):
+        _type_check(n_jobs, "n_jobs", int)
+        self._n_jobs = n_jobs
+
+    @property
+    def logpath(self) -> Path | None:
+        """\
+        The file path `logfile` was set to.
+        """
+        return self._logpath
+
+    @logpath.setter
+    def logpath(self, logpath: Path | str | None):
+        _type_check(logpath, "logfile", (str, Path))
+        # set via “file object” branch of logfile.setter
+        self.logfile = Path(logpath).open("a")  # noqa: SIM115
+        self._logpath = Path(logpath)
+
+    @property
+    def logfile(self) -> TextIO:
+        """\
+        The open file to write logs to.
+
+        Set it to a :class:`~pathlib.Path` or :class:`str` to open a new one.
+        The default `None` corresponds to :obj:`sys.stdout` in jupyter notebooks
+        and to :obj:`sys.stderr` otherwise.
+
+        For backwards compatibility, setting it to `''` behaves like setting it to `None`.
+        """
+        return self._logfile
+
+    @logfile.setter
+    def logfile(self, logfile: Path | str | TextIO | None):
+        if not hasattr(logfile, "write") and logfile:
+            self.logpath = logfile
+        else:  # file object
+            if not logfile:  # None or ''
+                logfile = sys.stdout if self._is_run_from_ipython() else sys.stderr
+            self._logfile = logfile
+            self._logpath = None
+            _set_log_file(self)
+
+    @property
+    def categories_to_ignore(self) -> list[str]:
+        """\
+        Categories that are omitted in plotting etc.
+        """
+        return self._categories_to_ignore
+
+    @categories_to_ignore.setter
+    def categories_to_ignore(self, categories_to_ignore: Iterable[str]):
+        categories_to_ignore = list(categories_to_ignore)
+        for i, cat in enumerate(categories_to_ignore):
+            _type_check(cat, f"categories_to_ignore[{i}]", str)
+        self._categories_to_ignore = categories_to_ignore
+
+    # --------------------------------------------------------------------------------
+    # Functions
+    # --------------------------------------------------------------------------------
+
+    @old_positionals(
+        "scanpy",
+        "dpi",
+        "dpi_save",
+        "frameon",
+        "vector_friendly",
+        "fontsize",
+        "figsize",
+        "color_map",
+        "format",
+        "facecolor",
+        "transparent",
+        "ipython_format",
+    )
+    def set_figure_params(
+        self,
+        *,
+        scanpy: bool = True,
+        dpi: int = 80,
+        dpi_save: int = 150,
+        frameon: bool = True,
+        vector_friendly: bool = True,
+        fontsize: int = 14,
+        figsize: int | None = None,
+        color_map: str | None = None,
+        format: _Format = "pdf",
+        facecolor: str | None = None,
+        transparent: bool = False,
+        ipython_format: str = "png2x",
+    ) -> None:
+        """\
+        Set resolution/size, styling and format of figures.
+
+        Parameters
+        ----------
+        scanpy
+            Init default values for :obj:`matplotlib.rcParams` suited for Scanpy.
+        dpi
+            Resolution of rendered figures – this influences the size of figures in notebooks.
+        dpi_save
+            Resolution of saved figures. This should typically be higher to achieve
+            publication quality.
+        frameon
+            Add frames and axes labels to scatter plots.
+        vector_friendly
+            Plot scatter plots using `png` backend even when exporting as `pdf` or `svg`.
+        fontsize
+            Set the fontsize for several `rcParams` entries. Ignored if `scanpy=False`.
+        figsize
+            Set plt.rcParams['figure.figsize'].
+        color_map
+            Convenience method for setting the default color map. Ignored if `scanpy=False`.
+        format
+            This sets the default format for saving figures: `file_format_figs`.
+        facecolor
+            Sets backgrounds via `rcParams['figure.facecolor'] = facecolor` and
+            `rcParams['axes.facecolor'] = facecolor`.
+        transparent
+            Save figures with transparent back ground. Sets
+            `rcParams['savefig.transparent']`.
+        ipython_format
+            Only concerns the notebook/IPython environment; see
+            :func:`~IPython.display.set_matplotlib_formats` for details.
+        """
+        if self._is_run_from_ipython():
+            import IPython
+
+            if isinstance(ipython_format, str):
+                ipython_format = [ipython_format]
+            IPython.display.set_matplotlib_formats(*ipython_format)
+
+        from matplotlib import rcParams
+
+        self._vector_friendly = vector_friendly
+        self.file_format_figs = format
+        if dpi is not None:
+            rcParams["figure.dpi"] = dpi
+        if dpi_save is not None:
+            rcParams["savefig.dpi"] = dpi_save
+        if transparent is not None:
+            rcParams["savefig.transparent"] = transparent
+        if facecolor is not None:
+            rcParams["figure.facecolor"] = facecolor
+            rcParams["axes.facecolor"] = facecolor
+        if scanpy:
+            from .plotting._rcmod import set_rcParams_scanpy
+
+            set_rcParams_scanpy(fontsize=fontsize, color_map=color_map)
+        if figsize is not None:
+            rcParams["figure.figsize"] = figsize
+        self._frameon = frameon
+
+    @staticmethod
+    def _is_run_from_ipython():
+        """Determines whether we're currently in IPython."""
+        import builtins
+
+        return getattr(builtins, "__IPYTHON__", False)
+
+    def __str__(self) -> str:
+        return "\n".join(
+            f"{k} = {v!r}"
+            for k, v in inspect.getmembers(self)
+            if not k.startswith("_") and k != "getdoc"
+        )
+
+
+settings = ScanpyConfig()