Update packages dependencies and other fixes

.github/workflows/pytest.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

.gitignore

@@ -72,6 +72,9 @@ target/
 # Jupyter Notebook
 .ipynb_checkpoints
 
+# Test file
+wgscovplot.html
+
 # pyenv
 .python-version
 

HISTORY.md

@@ -1,5 +1,12 @@
 # History
 
+## 1.0.3 (2026-04-30)
+
+- Update package dependencies
+- Fix issue: for KeyError DP when parsing VCF files with no DP INFO field (viral recon moves DP to FORMAT field)
+- Fix parsing strand in genbank file with Biopython 1.80 or newer
+- Fix issue: handles object or string dtypes across all Python versions and pandas versions in simplify_snpsift function
+
 ## 1.0.2 (2024-04-27)
 
 This patch release fixes an issue with not capturing an EmptyDataError when reading VCF files and an issue where Clair3 

README.md

@@ -86,12 +86,12 @@ Show help info with `$ wgscovplot --help`:
 │ --help                                                                                 Show this message and exit.                                                                                                                           │
 ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
 
- wgscovplot version 0.3.0; Python 3.11.6
+ wgscovplot version 1.0.3; Python 3.11.15
 ```
 
 ## Dependencies
 
-- [Python](https://www.python.org/) (>=3.9)
+- [Python](https://www.python.org/) (>=3.10)
     - [BioPython](https://github.com/biopython/biopython/) for all things bioinformatics
     - [rich](https://rich.readthedocs.io/) for pretty terminal output
     - [typer](https://github.com/tiangolo/typer) for CLI

hatch_build.py

@@ -10,7 +10,7 @@
 
 
 class CustomBuildHook(BuildHookInterface):
-    def initialize(self, version: str, build_data: dict[str, Any]) -> None:  # noqa: ARG002
+    def initialize(self, _version, build_data: dict[str, Any]) -> None:
         logger.warning("CustomBuildHook: running 'npm run build' to compile wgscovplot.js")
         workdir = Path(self.root, "web")
         has_npm = has_software("npm")
@@ -22,17 +22,15 @@ def initialize(self, version: str, build_data: dict[str, Any]) -> None:  # noqa:
                 "Please install 'npm' or 'bun' and try again."
             )
             raise RuntimeError(msg)
-        run(
-            f"{js_installer} install",
+        run(  # noqa: S603
+            [js_installer, "install"],
             cwd=str(workdir),
             check=True,
-            shell=True,  # noqa: S602
         )
-        run(
-            f"{js_installer} run build",
+        run(  # noqa: S603
+            [js_installer, "run", "build"],
             cwd=str(workdir),
             check=True,
-            shell=True,  # noqa: S602
         )
         build_data["artifacts"].append("web/build/wgscovplot.js")
         logger.warning("Done! 'wgscovplot.js' built!")

pyproject.toml

@@ -7,7 +7,7 @@ name = "wgscovplot"
 dynamic = ["version"]
 description = "Create interactive comparative sequencing coverage plots from virus sequencing data."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = "Apache-2.0"
 keywords = []
 authors = [
@@ -17,9 +17,10 @@ authors = [
 classifiers = [
     "Development Status :: 4 - Beta",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: Implementation :: CPython",
 ]
 dependencies = [
@@ -97,24 +98,24 @@ cov = [
 ]
 
 [[tool.hatch.envs.all.matrix]]
-python = ["3.9", "3.10", "3.11"]
+python = ["3.10", "3.11", "3.12", "3.13"]
 
 [tool.hatch.envs.lint]
 detached = true
 dependencies = [
     "black>=23.1.0",
     "mypy>=1.0.0",
-    "ruff>=0.0.243",
+    "ruff>=0.3.0",
 ]
 [tool.hatch.envs.lint.scripts]
 typing = "mypy --install-types --ignore-missing-imports --non-interactive {args:wgscovplot tests}"
 style = [
-    "ruff {args:.}",
+    "ruff check {args:.}",
     "black --check --diff {args:.}",
 ]
 fmt = [
     "black {args:.}",
-    "ruff --fix {args:.}",
+    "ruff check --fix {args:.}",
     "style",
 ]
 all = [
@@ -123,12 +124,12 @@ all = [
 ]
 
 [tool.black]
-target-version = ["py311"]
+target-version = ["py310"]
 line-length = 120
 skip-string-normalization = true
 
 [tool.ruff]
-target-version = "py311"
+target-version = "py310"
 line-length = 120
 [tool.ruff.lint]
 select = [
@@ -180,6 +181,8 @@ ignore = [
     "UP035",
     # Ignore "B905 [*] `zip()` without an explicit `strict=` parameter"
     "B905",
+    #   Too many positional arguments
+    "PLR0917",
 ]
 unfixable = [
     # Don't touch unused imports

recipe/meta.yaml

@@ -0,0 +1,46 @@
+{% set name = "wgscovplot" %}
+# You can set the version manually or read it dynamically
+{% set version = "1.0.3" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  path: ..  # Tells conda-build to use the local repository source files
+
+build:
+  number: 0
+  noarch: python  # Pure python package (architecture independent)
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  entry_points:
+    - wgscovplot = wgscovplot.cli:app
+
+requirements:
+  host:
+    - python >=3.10
+    - pip
+    - hatchling  # Since the project uses hatchling as the build backend
+  run:
+    - python >=3.10
+    - typer
+    - rich
+    - pandas
+    - biopython
+    - bcbio-gff
+    - pydantic >=2.0.0
+    - jinja2
+    - python-edlib
+    - pysam
+
+test:
+  imports:
+    - wgscovplot
+    - wgscovplot.tools
+  commands:
+    - wgscovplot --help
+
+about:
+  home: https://github.com/CFIA-NCFAD/wgscovplot
+  license: Apache-2.0
+  summary: wgscovplot generates interactive comparative sequencing coverage plots in self-contained, offline-friendly HTML files with optional annotation of variant calling results, PCR amplicon coverage and genetic features.

tests/test_cli.py

@@ -1,4 +1,8 @@
 #!/usr/bin/env python
+import contextlib
+import os
+import shutil
+import tempfile
 from os.path import exists
 from pathlib import Path
 
@@ -13,6 +17,21 @@
 segmented_virus_data_dir = dirpath / "data/iav"
 
 
+@contextlib.contextmanager
+def isolated_filesystem():
+    cwd = os.getcwd()
+    t = tempfile.mkdtemp()
+    os.chdir(t)
+    try:
+        yield t
+    finally:
+        os.chdir(cwd)
+        try:
+            shutil.rmtree(t)
+        except OSError:
+            pass
+
+
 def test_basic_cli():
     result = runner.invoke(app)
     assert result.exit_code != 0
@@ -24,7 +43,7 @@ def test_basic_cli():
 
 
 def test_cli_non_segment_virus():
-    with runner.isolated_filesystem():
+    with isolated_filesystem():
         out_html = "wgscovplot_test1.html"
         test_result = runner.invoke(
             app,
@@ -39,7 +58,7 @@ def test_cli_non_segment_virus():
 
 
 def test_cli_segment_virus():
-    with runner.isolated_filesystem():
+    with isolated_filesystem():
         out_html = "wgscovplot_test_segment_virus.html"
         test_result = runner.invoke(
             app, [str(segmented_virus_data_dir.resolve().absolute()), "--output-html", out_html]