Update metadata files (#248)

Author: JoshLoecker

pyproject.toml

@@ -9,7 +9,7 @@ requires-python = ">=3.11,<3.14"
 dependencies = [
     "aioftp>=0.23.1",
     "anndata>=0.12.0",
-    "bioservices>=1.12.1",
+    "bioservices>=1.13.0",
     "cobamp@git+https://github.com/JoshLoecker/cobamp@master",
     "cobra>=0.28.0",
     "joypy>=0.2.6",
@@ -28,7 +28,7 @@ dependencies = [
     "statsmodels>=0.13.0; python_version < '3.12'",
     "statsmodels>=0.14.0; python_version >= '3.12'",
     "troppo@git+https://github.com/JoshLoecker/troppo@master",
-    "zfpkm>=1.0.3",
+    "zfpkm>=1.1.0",
 ]
 
 [project.optional-dependencies]

ruff.toml

@@ -1,3 +1,4 @@
+src = ["main/como"]
 line-length = 120
 extend-include = ["docs/**/*.py", "tests/**/*.py", "**/*.ipynb"]
 
@@ -6,7 +7,11 @@ quote-style = "double"
 docstring-code-format = true
 
 [lint]
-extend-fixable = ["I001"]
+extend-fixable = [
+    "I001",
+    "RUF022",
+    "W293",
+]
 # Linting rules: https://docs.astral.sh/ruff/rules/
 unfixable = [
     "F401", # warn about, but do not remove, unused imports
@@ -45,6 +50,9 @@ ignore = [
     "TRY003", # allow exception messages outside the `Exception` class
 ]
 
+[lint.isort]
+known-first-party = ["como"]
+
 [lint.pydocstyle]
 convention = "google"