Refactoring (#627)

* Removed unused dependencies Signed-off-by: zethson <[email protected]> * Tutorials update Signed-off-by: zethson <[email protected]> * Readd fhiry Signed-off-by: zethson <[email protected]> * Skip jupyter_core Signed-off-by: zethson <[email protected]> * Fix import Signed-off-by: zethson <[email protected]> * Don't fail session-info Signed-off-by: zethson <[email protected]> * Revert session info change Signed-off-by: zethson <[email protected]> * Refactoring Signed-off-by: zethson <[email protected]> * Session info Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]>
theislab · Dec 18, 2023 · 8ce852d · 8ce852d
1 parent 9c2de8c
commit 8ce852d
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Showing 3 changed files with 44 additions and 47 deletions.
diff --git a/ehrapy/core/meta_information.py b/ehrapy/core/meta_information.py
@@ -17,19 +17,23 @@ def print_versions():  # pragma: no cover
         >>> import ehrapy as ep
         >>> ep.print_versions()
     """
-    session_info.show(
-        dependencies=True,
-        html=False,
-        excludes=[
-            "builtins",
-            "stdlib_list",
-            "importlib_metadata",
-            "jupyter_core"
-            # Special module present if test coverage being calculated
-            # https://gitlab.com/joelostblom/session_info/-/issues/10
-            "$coverage",
-        ],
-    )
+    try:
+        session_info.show(
+            dependencies=True,
+            html=False,
+            excludes=[
+                "builtins",
+                "stdlib_list",
+                "importlib_metadata",
+                "jupyter_core"
+                # Special module present if test coverage being calculated
+                # https://gitlab.com/joelostblom/session_info/-/issues/10
+                "$coverage",
+            ],
+        )
+    except AttributeError:
+        print("[bold yellow]Unable to fetch versions for one or more dependencies.")
+        pass
 
 
 def print_version_and_date(*, file=None):  # pragma: no cover

diff --git a/ehrapy/io/_utility_io.py b/ehrapy/io/_utility_io.py
diff --git a/ehrapy/io/_write.py b/ehrapy/io/_write.py
@@ -6,12 +6,13 @@
 import numpy as np
 
 from ehrapy import settings
-from ehrapy.io._utility_io import _get_file_extension
 from ehrapy.preprocessing._encode import encode
 
 if TYPE_CHECKING:
     from anndata import AnnData
 
+supported_extensions = {"csv", "tsv", "h5ad"}
+
 
 def write(
     filename: str | Path,
@@ -69,6 +70,31 @@ def write(
             adata.write(filename, compression=compression, compression_opts=compression_opts)
 
 
+def _get_file_extension(file_path: Path) -> str:
+    """Check whether the argument is a filename.
+
+    Args:
+        file_path: Path to the file.
+
+    Returns:
+        File extension of the specified file
+    """
+    ext = file_path.suffixes
+
+    if len(ext) > 2:
+        ext = ext[-2:]
+
+    if ext and ext[-1][1:] in supported_extensions:
+        return ext[-1][1:]
+    raise ValueError(
+        f"""\
+        {file_path!r} does not end on a valid extension.
+        Please, provide one of the available extensions.
+        {supported_extensions}
+        """
+    )
+
+
 def _get_filename_from_key(key, extension=None) -> Path:
     """Gets full file name from a key.