version changes & minor fixes

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.9]
+        python-version: [3.9, 3.10]
 
     steps:
     - uses: actions/checkout@v2

pyproject.toml

@@ -10,8 +10,8 @@ classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Science/Research",
   "Natural Language :: English",
-  "Programming Language :: Python :: 3.7",
   "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
   "Operating System :: MacOS :: MacOS X",
   "Operating System :: Microsoft :: Windows",
   "Operating System :: POSIX :: Linux",
@@ -26,7 +26,7 @@ packages = [
   {include = "schierarchy"},
 ]
 readme = "README.md"
-version = "0.0.1"
+version = "0.0.2"
 
 [tool.poetry.dependencies]
 anndata = ">=0.7.5"
@@ -46,14 +46,14 @@ nbsphinx-link = {version = "*", optional = true}
 pre-commit = {version = ">=2.7.1", optional = true}
 pydata-sphinx-theme = {version = ">=0.4.0", optional = true}
 pytest = {version = ">=4.4", optional = true}
-python = ">=3.7.2,<4.0"
+python = ">=3.9.18"
 python-igraph = {version = "*", optional = true}
 scanpy = {version = ">=1.6", optional = true}
 scanpydoc = {version = ">=0.5", optional = true}
 scikit-misc = {version = ">=0.1.3", optional = true}
-cell2location = {git = "https://github.com/BayraktarLab/cell2location.git"}
-pyro-ppl = {git = "https://github.com/pyro-ppl/pyro.git", branch="dev"}
-scvi-tools = ">=0.16.0"
+cell2location = {git = "https://github.com/BayraktarLab/cell2location.git@hires_sliding_window"}
+pyro-ppl = {version = ">=1.8.0"}
+scvi-tools = ">=1.0.0"
 sphinx = {version = "^3.0", optional = true}
 sphinx-autodoc-typehints = {version = "*", optional = true}
 sphinx-rtd-theme = {version = "*", optional = true}

schierarchy/base/_pyro_base_regression_module.py

@@ -12,7 +12,6 @@ def __init__(
         amortised: bool = False,
         encoder_mode: Literal["single", "multiple", "single-multiple"] = "single",
         encoder_kwargs=None,
-        data_transform="log1p",
         create_autoguide_kwargs: Optional[dict] = None,
         **kwargs,
     ):
@@ -43,7 +42,6 @@ def __init__(
             model=self.model,
             amortised=self.is_amortised,
             encoder_kwargs=encoder_kwargs,
-            data_transform=data_transform,
             encoder_mode=encoder_mode,
             init_loc_fn=self.init_to_value,
             n_cat_list=[kwargs["n_batch"]],

schierarchy/logistic/_logistic_model.py

@@ -321,6 +321,7 @@ def export_posterior(
         self,
         adata,
         prediction: bool = False,
+        use_quantiles: bool = False,
         sample_kwargs: Optional[dict] = None,
         export_slot: str = "mod",
         add_to_varm: list = ["means", "stds", "q05", "q95"],
@@ -441,7 +442,6 @@ def export_posterior(
                     ].values()
                 )[i]
             )
-            print(f"level {i}", categories) 
             for k in add_to_varm:
                 sample_df = pd.DataFrame(
                     self.samples[f"post_sample_{k}"].get(f"weight_level_{i}", None),