remove explicit alphastats dependency

Author: mffrank

grassp/io/__init__.py

@@ -1 +1,7 @@
-from .read import read, read_prolocdata
+from .read import (
+    read_alphastats,
+    read_prolocdata,
+    read_maxquant,
+    read_fragpipe,
+    read_diann,
+)

grassp/io/read.py

@@ -11,9 +11,10 @@
 import numpy as np
 import pandas as pd
 import urllib
+import protdata
 
 
-def read(
+def read_alphastats(
     loader: alphastats.BaseLoader,
     x_dtype: Union[np.dtype, type, int, float, None] = None,
     proteins_as_obs: bool = False,
@@ -41,7 +42,12 @@ def read(
     - gene_names: Gene name mapping information
     """
 
-    import alphastats
+    try:
+        import alphastats
+    except ImportError:
+        raise Exception(
+            "To read alphastats, please install the `alphastats` python package (pip install alphastats)."
+        )
 
     alphastats.DataSet._check_loader(
         1, loader
@@ -143,3 +149,27 @@ def read_prolocdata(file_name: str) -> anndata.AnnData:
     adata.uns["MIAPE_metadata"] = metadata
 
     return adata
+
+
+def read_maxquant(*args, **kwargs) -> anndata.AnnData:
+    """
+    Wrapper for protdata.read_maxquant that transposes the AnnData object.
+    """
+    adata = protdata.read_maxquant(*args, **kwargs)
+    return adata.T
+
+
+def read_fragpipe(*args, **kwargs) -> anndata.AnnData:
+    """
+    Wrapper for protdata.read_fragpipe that transposes the AnnData object.
+    """
+    adata = protdata.read_fragpipe(*args, **kwargs)
+    return adata.T
+
+
+def read_diann(*args, **kwargs) -> anndata.AnnData:
+    """
+    Wrapper for protdata.read_diann that transposes the AnnData object.
+    """
+    adata = protdata.read_diann(*args, **kwargs)
+    return adata.T

pyproject.toml

@@ -4,6 +4,13 @@ requires = [
   "wheel",
   "setuptools_scm[toml]>=3.4"
 ]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+version_scheme = "post-release"
+local_scheme = "no-local-version"
+write_to = "grassp/_version.py"
+fallback_version = "0.0.1"
 
 [project]
 name =  "grassp"
@@ -29,7 +36,8 @@ dependencies = [
     "numpy",
     "pandas",
     "scanpy[leiden]",
-    "alphastats",
+    "protdata",
+#    "alphastats",
     "anndata",
     "scipy",
     "networkx",
@@ -78,8 +86,7 @@ repository = "https://github.com/czbiohub/some-package"
 
 
 [tool.setuptools]
-# explicitly specify the package name
-# TODO: is there a better way to do this?
+# Use find_namespace_packages to discover all packages
 packages = ["grassp"]
 
 # allow use of __file__ to load data files included in the package