Merge pull request #9 from moshi4/develop

Bump to v0.4.1

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
       - name: Checkout
         uses: actions/checkout@v3
@@ -24,11 +24,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      # Install poetry v1.4.0 to avoid _WheelFileValidationError in debugpy
-      # Latest poetry v1.4.1 cannot install debugpy
       - name: Install Poetry
         run: |
-          curl -sSL https://install.python-poetry.org | python3 - --version 1.4.0
+          curl -sSL https://install.python-poetry.org | python3 -
           echo "$HOME/.local/bin" >> $GITHUB_PATH
 
       - name: Install Dependencies
@@ -37,8 +35,8 @@ jobs:
       - name: Run black format check
         run: poetry run black src tests --check --diff --verbose
 
-      - name: Run flake8 lint check
-        run: poetry run flake8 src tests --max-line-length=88 --ignore=E203,W503,W504
+      - name: Run ruff lint check
+        run: poetry run ruff .
 
       - name: Run pytest
         run: poetry run pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term

README.md

@@ -118,6 +118,7 @@ pyMSAviz provides simple MSA visualization CLI.
     --end               End position of MSA visualization (Default: 'MSA Length')
     --wrap_length       Wrap length (Default: None)
     --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
+    --label_type        Label type ('id'[default]|'description')
     --show_grid         Show grid (Default: OFF)
     --show_count        Show seq char count without gap on right side (Default: OFF)
     --show_consensus    Show consensus sequence (Default: OFF)

docs/cli-docs/pymsaviz.md

@@ -16,6 +16,7 @@
     --end               End position of MSA visualization (Default: 'MSA Length')
     --wrap_length       Wrap length (Default: None)
     --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
+    --label_type        Label type ('id'[default]|'description')
     --show_grid         Show grid (Default: OFF)
     --show_count        Show seq char count without gap on right side (Default: OFF)
     --show_consensus    Show consensus sequence (Default: OFF)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyMSAviz"
-version = "0.4.0"
+version = "0.4.1"
 description = "MSA visualization python package for sequence analysis"
 authors = ["moshi4"]
 license = "MIT"
@@ -26,6 +26,27 @@ minversion = "6.0"
 addopts = "--cov=src --tb=line --cov-report=xml --cov-report=term"
 testpaths = ["tests"]
 
+# Lint Rules: 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"
 

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

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.")

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)",