Drop use of deprecated imghdr standard library module

which has been removed in the upcoming Python 3.13 .
galaxyproject · Oct 31, 2024 · ac480e7 · ac480e7
1 parent 695e86e
commit ac480e7
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Showing 8 changed files with 19 additions and 11 deletions.
diff --git a/lib/galaxy/util/image_util.py b/lib/galaxy/util/image_util.py
@@ -1,6 +1,5 @@
 """Provides utilities for working with image files."""
 
-import imghdr
 import logging
 from typing import (
     List,
@@ -22,11 +21,7 @@ def image_type(filename: str) -> Optional[str]:
             with Image.open(filename) as im:
                 fmt = im.format
         except Exception:
-            # We continue to try with imghdr, so this is a rare case of an
-            # exception we expect to happen frequently, so we're not logging
             pass
-    if not fmt:
-        fmt = imghdr.what(filename)
     if fmt:
         return fmt.upper()
     else:

diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
@@ -41,7 +41,7 @@ install_requires =
     galaxy-objectstore
     galaxy-tool-util[cwl,edam]
     galaxy-tours
-    galaxy-util
+    galaxy-util[image_util]
     galaxy-web-framework
     galaxy-web-stack
     Beaker

diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
@@ -36,7 +36,7 @@ install_requires =
     galaxy-objectstore
     galaxy-schema
     galaxy-tool-util
-    galaxy-util[template]
+    galaxy-util[image_util,template]
     alembic
     alembic-utils
     bdbag>=1.6.3

diff --git a/packages/test.sh b/packages/test.sh
@@ -49,7 +49,7 @@ while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.
 
     # Install extras (if needed)
     if [ "$package_dir" = "util" ]; then
-        pip install '.[template,jstree,config_template]'
+        pip install '.[image_util,template,jstree,config_template]'
     elif [ "$package_dir" = "tool_util" ]; then
         pip install '.[cwl,mulled,edam,extended-assertions]'
     else

diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg
@@ -36,7 +36,7 @@ install_requires =
     galaxy-auth
     galaxy-config
     galaxy-data
-    galaxy-util
+    galaxy-util[image_util]
     galaxy-web-framework
     galaxy-web-stack
     galaxy-web-apps

diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
@@ -33,7 +33,7 @@ version = 24.2.dev0
 [options]
 include_package_data = True
 install_requires =
-    galaxy-util>=22.1
+    galaxy-util[image_util]>=22.1
     conda-package-streaming
     lxml!=4.2.2
     MarkupSafe

diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg
@@ -48,6 +48,8 @@ packages = find:
 python_requires = >=3.7
 
 [options.extras_require]
+image_util =
+    pillow
 jstree =
     dictobj
 template =

diff --git a/test/unit/util/test_checkers.py b/test/unit/util/test_checkers.py
@@ -1,6 +1,10 @@
+import os.path
 import tempfile
 
-from galaxy.util.checkers import check_html
+from galaxy.util.checkers import (
+    check_html,
+    check_image,
+)
 
 
 def test_check_html():
@@ -17,3 +21,10 @@ def test_check_html():
         tmpb.write(b"\x1f\x8b")
         tmpb.flush()
         assert not check_html(tmpb.name)
+
+
+def test_check_image():
+    for filename, expected in (("1.tiff", True), ("454Score.png", True), ("1.bam", False)):
+        path = f"test-data/{filename}"
+        assert os.path.exists(path)
+        assert check_image(path) is expected