adjust dependencies

Author: dbdimitrov

pyproject.toml

@@ -23,22 +23,37 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-  "anndata",
+  "anndata>=0.7.4",
   "mudata",
   "scanpy>=1.8.0",
   "numba>=0.54.0",
   "tqdm>=4.0",
   "docrep>=0.3.1",
-  # for debug logging (referenced from the issue template)
+  "plotnine>=0.10.1",
   "session-info2",
 ]
-optional-dependencies.dev = [
-  "pre-commit",
+[project.optional-dependencies]
+dev = [
+  "pre-commit>=3.0.0",
   "twine>=4.0.2",
   "pytest<=6.0",
-  "bumpversion"
+  "bumpversion>=0.6.0",
+  "highspy>=1.9.0",
+]
+extra-requirements = [
+  "decoupler>=1.5.1",
+  "omnipath>=1.0.6",
+  "pydeseq2>=0.3.5",
+  "cell2cell",
+  "muon",
+  "mofax",
+  "mofapy2>=0.7.0",
+  "requests>=2.25.1",
+  "corneto>=0.9.1-alpha.6",
+  "cvxpy-base>=1.6.0",
+  "PySCIPOpt>=5.2.1",
 ]
-optional-dependencies.doc = [
+doc = [
   "docutils>=0.8,!=0.18.*,!=0.19.*",
   "ipykernel",
   "ipython",
@@ -53,15 +68,17 @@ optional-dependencies.doc = [
   "sphinx-tabs",
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
+  "pre-commit",
 ]
-optional-dependencies.test = [
+test = [
   "coverage",
   "pytest",
 ]
 # https://docs.pypi.org/project_metadata/#project-urls
-urls.Documentation = "https://liana.readthedocs.io/"
-urls.Homepage = "https://liana-py.readthedocs.io"
-urls.Source = "https://github.com/saezlab/liana-py"
+[project.urls]
+Documentation = "https://liana.readthedocs.io/"
+Homepage = "https://liana-py.readthedocs.io"
+Source = "https://github.com/saezlab/liana-py"
 
 [tool.hatch.envs.default]
 installer = "uv"