Python package installs and imports properly

pyproject.toml

@@ -1,6 +1,7 @@
 [build-system]
 requires = ["scikit-build-core>=0.3.3", "pybind11"] 
 build-backend = "scikit_build_core.build"
+# build-backend = "setuptools.build_meta"
 
 [project]
 name = "scdemon"
@@ -10,7 +11,18 @@ authors = [{name = "Benjamin James", email = "[email protected]"},
            {name = "Carles Boix", email = "[email protected]"}]
 license = {file = "LICENSE"}
 requires-python = ">=3.7"
-dependencies = ["numpy", "pandas", "scipy", "tqdm", "igraph", "umap-learn", "leidenalg", "scikit-learn"]
+dependencies = [
+    "numpy", "pandas",
+    "scipy", "tqdm",
+    "igraph", "umap-learn",
+    "leidenalg", "scikit-learn",
+    # Added from original modules, can prune:
+    "scanpy", "anndata",
+    "seaborn", "matplotlib",
+    "fbpca", "gprofiler-official",
+    "python-igraph", "adjustText",
+    "numba"
+]
 
 [project.urls]
 Documentation = "https://scdemon.readthedocs.io/"

scdemon/__init__.py

@@ -1,6 +1,6 @@
 from . import _core as core
 
-from .robust_se import robust_se, robust_prepare_default
+from .robust_se import robust_se_default, robust_prepare
 from .utils import ProgressManager, _interrupt_checker
 
 from .auxiliary import vcorrcoef

scdemon/modules.py

@@ -563,19 +563,3 @@ def __setstate__(self, state):
         self.__dict__.update(state)
         # Restore the adata with the h5ad_file handle:
         self.adata = sc.read(self.h5ad_file)
-
-    # DONE: Fixed graph layout (nogrid works)
-    # DONE: Enrichments on graph / other attributes on graph
-    # DONE: P-values on corr for cutoff
-    # DONE: Quantiles for corr. cutoff
-    # DONE: Expr percent dpdt. cutoffs
-    # DONE: Writing module list
-    # TODO: Saving enrichments so we don't recompute them
-    # TODO: Heatmap for the enrichments (make profiles, pass to scanpy dotplot)
-    # TODO: Compute gene properties
-    # TODO: Plot umap with any coloring (gene properties)
-    # TODO: Handle both X and adata
-    # TODO: Plot multiple graphs from the same adata
-    # TODO: Better docstrings
-    # TODO: Plot multiple graphs on the same layout (for subsetting!)
-    # TODO: CELL STATE DISCOVERY + ANNOTATION FROM GENE EXPRESSION MODULES.