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https://beta.ruff.rs/docs/rules +[tool.ruff] +select = ["E", "F", "W", "I", "D", "B"] +ignore = [ + "D100", + "D101", + "D104", + "D105", + "D205", + "D400", + "D401", + "D403", + "D415", + "B905", +] +src = ["src", "tests"] +line-length = 88 + +[tool.ruff.pydocstyle] +convention = "numpy" + [tool.poetry.scripts] pymsaviz = "pymsaviz.scripts.cli:main" @@ -34,15 +55,14 @@ python = "^3.8" biopython = ">=1.79" matplotlib = ">=3.5.2" -[tool.poetry.dev-dependencies] -flake8 = ">=4.0.1" +[tool.poetry.group.dev.dependencies] +pytest = ">=7.1.2" black = ">=22.10.0" -pydocstyle = ">=6.1.1" -pytest = ">=7.2.0" +ruff = ">=0.0.264" pytest-cov = ">=4.0.0" -ipykernel = ">=6.16.0" +ipykernel = ">=6.13.0" mkdocs = ">=1.2" -mkdocstrings = {version = ">=0.19.0", extras = ["python"]} +mkdocstrings = { extras = ["python"], version = ">=0.19.0" } mkdocs-jupyter = ">=0.21.0" mkdocs-material = ">=8.2" diff --git a/src/pymsaviz/__init__.py b/src/pymsaviz/__init__.py index fa3c146..8656edd 100644 --- a/src/pymsaviz/__init__.py +++ b/src/pymsaviz/__init__.py @@ -12,7 +12,7 @@ "get_msa_testdata", ] -__version__ = "0.4.0" +__version__ = "0.4.1" # Setting matplotlib rc(runtime configuration) parameters # https://matplotlib.org/stable/tutorials/introductory/customizing.html diff --git a/src/pymsaviz/msaviz.py b/src/pymsaviz/msaviz.py index 734ccc8..72446f1 100644 --- a/src/pymsaviz/msaviz.py +++ b/src/pymsaviz/msaviz.py @@ -417,7 +417,7 @@ def plotfig(self, dpi: int = 100) -> Figure: y_size_list = [ax_type2y_size[t] for t in plot_ax_types] figsize = (self._wrap_length * self._x_unit_size, sum(y_size_list)) fig: Figure = plt.figure(figsize=figsize, dpi=dpi) # type: ignore - fig.set_layout_engine("tight") + fig.tight_layout() gs = GridSpec(nrows=len(plot_ax_types), ncols=1, height_ratios=y_size_list) gs.update(left=0, right=1, bottom=0, top=1, hspace=0, wspace=0) @@ -469,6 +469,9 @@ def savefig( dpi=dpi, pad_inches=pad_inches, ) + # Clear & close figure to suppress memory leak + fig.clear() + plt.close(fig) ############################################################ # Private Method @@ -630,7 +633,7 @@ def _get_consensus_identity_list( start = 0 if start is None else start end = self.alignment_length if end is None else end consensus_identity_list = [] - for idx, seq_char in enumerate(self.consensus_seq[start:end], start): + for idx, _ in enumerate(self.consensus_seq[start:end], start): column_chars = str(self.msa[:, idx]) counter = Counter(filter(lambda c: c not in ("-", "*"), column_chars)) count = counter.most_common()[0][1] if len(counter) != 0 else 0 @@ -741,7 +744,7 @@ def _parse_positions(self, positions: list[tuple[int, int] | int]) -> list[int]: for pos in positions: if isinstance(pos, (tuple, list)): result_positions.extend(list(range(pos[0] - 1, pos[1]))) - elif type(pos) == int: + elif isinstance(pos, int): result_positions.append(pos - 1) else: raise ValueError(f"{positions=} is invalid.") diff --git a/src/pymsaviz/scripts/cli.py b/src/pymsaviz/scripts/cli.py index 7bc29ab..504a6a0 100644 --- a/src/pymsaviz/scripts/cli.py +++ b/src/pymsaviz/scripts/cli.py @@ -21,6 +21,7 @@ def run( end: int | None = None, wrap_length: int | None = None, wrap_space_size: float = 3.0, + label_type: str = "id", show_grid: bool = False, show_count: bool = False, show_consensus: bool = False, @@ -37,6 +38,7 @@ def run( end=end, wrap_length=wrap_length, wrap_space_size=wrap_space_size, + label_type=label_type, color_scheme=color_scheme, show_grid=show_grid, show_count=show_count, @@ -129,6 +131,15 @@ def get_args() -> argparse.Namespace: default=default_wrap_space_size, metavar="", ) + default_label_type = "id" + parser.add_argument( + "--label_type", + type=str, + help="Label type ('id'[default]|'description')", + default=default_label_type, + choices=("id", "description"), + metavar="", + ) parser.add_argument( "--show_grid", help="Show grid (Default: OFF)",