Fix docs rendering for classes using lazy import (#651)

* Fix lazy import for docs

* Pre-commit

* Fixed error naming

* Fixed SCGEN usage display

* Run only two CI tests

* Fix cinemaot tests

.github/workflows/test.yml

@@ -27,13 +27,13 @@ jobs:
                     - os: ubuntu-latest
                       python: "3.12"
                       run_mode: "slow"
-                    - os: ubuntu-latest
-                      python: "3.12"
-                      run_mode: "fast"
-                    - os: ubuntu-latest
-                      python: "3.12"
-                      run_mode: slow
-                      pip-flags: "--pre"
+#                    - os: ubuntu-latest
+#                      python: "3.12"
+#                      run_mode: "fast"
+#                    - os: ubuntu-latest
+#                      python: "3.12"
+#                      run_mode: slow
+#                      pip-flags: "--pre"
 
         env:
             OS: ${{ matrix.os }}

docs/installation.md

@@ -78,10 +78,10 @@ Follow these steps to install pertpy on an Apple Silicon machine (tested on a Ma
     brew install --cask mambaforge
     ```
 
-3. Create a new environment using mamba (here with python 3.10) and activate it
+3. Create a new environment using mamba and activate it
 
     ```console
-    mamba create -n pertpy-env python=3.11
+    mamba create -n pertpy-env
     mamba activate pertpy-env
     ```
 

docs/usage/usage.md

@@ -450,7 +450,7 @@ See [scGen predicts single-cell perturbation responses](https://www.nature.com/a
 .. autosummary::
     :toctree: tools
 
-    tools.SCGEN
+    tools.Scgen
 ```
 
 Example implementation:

pertpy/tools/__init__.py

@@ -1,25 +1,22 @@
-from functools import wraps
 from importlib import import_module
 
 
 def lazy_import(module_path, class_name, extras):
-    def _import():
-        try:
-            for extra in extras:
-                import_module(extra)
-        except ImportError as e:
-            raise ImportError(
-                f"Extra dependencies required: {', '.join(extras)}. "
-                f"Please install with: pip install {' '.join(extras)}"
-            ) from e
+    try:
+        for extra in extras:
+            import_module(extra)
         module = import_module(module_path)
         return getattr(module, class_name)
+    except ImportError:
 
-    @wraps(_import)
-    def wrapper(*args, **kwargs):
-        return _import()(*args, **kwargs)
+        class Placeholder:
+            def __init__(self, *args, **kwargs):
+                raise ImportError(
+                    f"Extra dependencies required: {', '.join(extras)}. "
+                    f"Please install with: pip install {' '.join(extras)}"
+                )
 
-    return wrapper
+        return Placeholder
 
 
 from pertpy.tools._augur import Augur
@@ -49,7 +46,7 @@ def wrapper(*args, **kwargs):
 Tasccoda = lazy_import("pertpy.tools._coda._tasccoda", "Tasccoda", CODA_EXTRAS)
 
 DE_EXTRAS = ["formulaic", "pydeseq2"]
-EdgeR = lazy_import("pertpy.tools._differential_gene_expression", "EdgeR", DE_EXTRAS + ["edger"])
+EdgeR = lazy_import("pertpy.tools._differential_gene_expression", "EdgeR", DE_EXTRAS) # edgeR will be imported via rpy2
 PyDESeq2 = lazy_import("pertpy.tools._differential_gene_expression", "PyDESeq2", DE_EXTRAS)
 Statsmodels = lazy_import("pertpy.tools._differential_gene_expression", "Statsmodels", DE_EXTRAS + ["statsmodels"])
 TTest = lazy_import("pertpy.tools._differential_gene_expression", "TTest", DE_EXTRAS)

pertpy/tools/_cinemaot.py

@@ -190,7 +190,7 @@ def causaleffect(
         TE.obsm["X_embedding"] = embedding
 
         if return_matching:
-            TE.obsm["ot"] = ot_sink.matrix.T
+            TE.obsm["ot"] = np.asarray(ot_sink.matrix.T)
             return TE
         else:
             return TE