From 62c610c250737775475a167acf1dcbc1c356fc63 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 2 Mar 2024 01:58:41 +0000
Subject: [PATCH] Move numpy and pillow requirements to new extended-assertions
 extra

together pysam, which is also conditionally imported in
``lib/galaxy/tool_util/verify/__init__.py`` .
---
 lib/galaxy/tool_util/verify/__init__.py | 19 ++++++++++++-------
 packages/test.sh                        |  2 +-
 packages/tool_util/setup.cfg            |  6 ++++--
 3 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py
index 7adfa3321904..976c8706b684 100644
--- a/lib/galaxy/tool_util/verify/__init__.py
+++ b/lib/galaxy/tool_util/verify/__init__.py
@@ -20,13 +20,18 @@
     TYPE_CHECKING,
 )
 
-import numpy
-from PIL import Image
-
+try:
+    import numpy
+except ImportError:
+    pass
 try:
     import pysam
 except ImportError:
-    pysam = None  # type: ignore[assignment]
+    pass
+try:
+    from PIL import Image
+except ImportError:
+    pass
 
 from galaxy.tool_util.parser.util import (
     DEFAULT_DELTA,
@@ -449,7 +454,7 @@ def files_contains(file1, file2, attributes=None):
 
 def _multiobject_intersection_over_union(
     mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray", repeat_reverse: bool = True
-) -> List[numpy.floating]:
+) -> List["numpy.floating"]:
     iou_list = []
     for label1 in numpy.unique(mask1):
         cc1 = mask1 == label1
@@ -463,7 +468,7 @@ def _multiobject_intersection_over_union(
     return iou_list
 
 
-def intersection_over_union(mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray") -> numpy.floating:
+def intersection_over_union(mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray") -> "numpy.floating":
     assert mask1.dtype == mask2.dtype
     assert mask1.ndim == mask2.ndim == 2
     assert mask1.shape == mask2.shape
@@ -475,7 +480,7 @@ def intersection_over_union(mask1: "numpy.typing.NDArray", mask2: "numpy.typing.
 
 def get_image_metric(
     attributes: Dict[str, Any]
-) -> Callable[["numpy.typing.NDArray", "numpy.typing.NDArray"], numpy.floating]:
+) -> Callable[["numpy.typing.NDArray", "numpy.typing.NDArray"], "numpy.floating"]:
     metric_name = attributes.get("metric", DEFAULT_METRIC)
     metrics = {
         "mae": lambda arr1, arr2: numpy.abs(arr1 - arr2).mean(),
diff --git a/packages/test.sh b/packages/test.sh
index 5a64061bd51d..ae69d9b20516 100755
--- a/packages/test.sh
+++ b/packages/test.sh
@@ -51,7 +51,7 @@ while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.
     if [ "$package_dir" = "util" ]; then
         pip install -e '.[template,jstree]'
     elif [ "$package_dir" = "tool_util" ]; then
-        pip install -e '.[cwl,mulled,edam]'
+        pip install -e '.[cwl,mulled,edam,extended-assertions]'
     else
         pip install -e '.'
     fi
diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
index 2aecac71fbe0..5d6b9b9a378d 100644
--- a/packages/tool_util/setup.cfg
+++ b/packages/tool_util/setup.cfg
@@ -36,10 +36,8 @@ install_requires =
     galaxy-util>=22.1
     conda-package-streaming
     lxml!=4.2.2
-    numpy
     MarkupSafe
     packaging
-    pillow
     pydantic>=2,!=2.6.0,!=2.6.1
     PyYAML
     requests
@@ -68,6 +66,10 @@ mulled =
     Whoosh
 edam =
     edam-ontology
+extended-assertions =
+    numpy
+    pysam
+    pillow
 
 [options.packages.find]
 exclude =