From 6231f4feb04157d46c4123898edf85f7f7df574c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 7 Mar 2025 10:39:27 +0100
Subject: [PATCH 1/5] Remove ``num_unique_values`` tiff metadata element

This was added in https://github.com/galaxyproject/galaxy/pull/18951 but
it's memory consumption scales with input size. On a 5.5GB TIFF file
this consumed a peak of 18GB of memory.

@kostrykin added a workaround for the memory consumption in
https://github.com/galaxyproject/galaxy/pull/19830, but this now very
slow.

Besides improving the efficient, Perhaps there is a more gentle way to approach

> Many tools assume that images are binary, or label maps, for example, and it makes no sense to run those tools on other images.

?

Could those tools just error out, and/or consume a different datatype ?
Do we need the full unique values, or is it ok to just check if it's
more than `n` unique values ?
---
 lib/galaxy/datatypes/images.py          | 12 ------------
 test/unit/data/datatypes/test_images.py |  9 ---------
 2 files changed, 21 deletions(-)

diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py
index 64067c203ac..2f851b0f00f 100644
--- a/lib/galaxy/datatypes/images.py
+++ b/lib/galaxy/datatypes/images.py
@@ -84,14 +84,6 @@ class Image(data.Data):
         optional=True,
     )
 
-    MetadataElement(
-        name="num_unique_values",
-        desc="Number of unique values in the image data (e.g., should be 2 for binary images)",
-        readonly=True,
-        visible=True,
-        optional=True,
-    )
-
     MetadataElement(
         name="width",
         desc="Width of the image (in pixels)",
@@ -271,7 +263,6 @@ class Tiff(Image):
                         "channels",
                         "depth",
                         "frames",
-                        "num_unique_values",
                     ]
                 }
 
@@ -289,9 +280,6 @@ class Tiff(Image):
                     metadata["depth"].append(Tiff._get_axis_size(series.shape, axes, "Z"))
                     metadata["frames"].append(Tiff._get_axis_size(series.shape, axes, "T"))
 
-                    # Determine the metadata values that require reading the image data
-                    metadata["num_unique_values"].append(Tiff._get_num_unique_values(series))
-
                 # Populate the metadata fields based on the values determined above
                 for key, values in metadata.items():
                     if len(values) > 0:
diff --git a/test/unit/data/datatypes/test_images.py b/test/unit/data/datatypes/test_images.py
index 167090c4cff..b05be9f40bd 100644
--- a/test/unit/data/datatypes/test_images.py
+++ b/test/unit/data/datatypes/test_images.py
@@ -52,7 +52,6 @@ def __assert_empty_metadata(metadata):
     for key in (
         "axes",
         "dtype",
-        "num_unique_values",
         "width",
         "height",
         "channels",
@@ -69,8 +68,6 @@ test_tiff_axes_zcyx = __create_test(Tiff, "im6_uint8.tif", "axes", "ZCYX")
 test_tiff_dtype_uint8 = __create_test(Tiff, "im6_uint8.tif", "dtype", "uint8")
 test_tiff_dtype_uint16 = __create_test(Tiff, "im8_uint16.tif", "dtype", "uint16")
 test_tiff_dtype_float64 = __create_test(Tiff, "im4_float.tif", "dtype", "float64")
-test_tiff_num_unique_values_2 = __create_test(Tiff, "im3_b.tif", "num_unique_values", 2)
-test_tiff_num_unique_values_618 = __create_test(Tiff, "im4_float.tif", "num_unique_values", 618)
 test_tiff_width_16 = __create_test(Tiff, "im7_uint8.tif", "width", 16)  # axes: ZYX
 test_tiff_width_32 = __create_test(Tiff, "im3_b.tif", "width", 32)  # axes: YXS
 test_tiff_height_8 = __create_test(Tiff, "im7_uint8.tif", "height", 8)  # axes: ZYX
@@ -100,15 +97,11 @@ def test_tiff_unsupported_compression(metadata):
     assert metadata.depth == 0
     assert metadata.frames == 0
 
-    # The other fields should be missing
-    assert getattr(metadata, "num_unique_values", None) is None
-
 
 @__test(Tiff, "im9_multiseries.tif")
 def test_tiff_multiseries(metadata):
     assert metadata.axes == ["YXS", "YX"]
     assert metadata.dtype == ["uint8", "uint16"]
-    assert metadata.num_unique_values == [2, 255]
     assert metadata.width == [32, 256]
     assert metadata.height == [32, 256]
     assert metadata.channels == [3, 0]
@@ -121,8 +114,6 @@ def test_tiff_multiseries(metadata):
 test_png_axes_yx = __create_test(Image, "im1_uint8.png", "axes", "YX")
 test_png_axes_yxc = __create_test(Image, "im3_a.png", "axes", "YXC")
 test_png_dtype_uint8 = __create_test(Image, "im1_uint8.png", "dtype", "uint8")
-test_png_num_unique_values_1 = __create_test(Image, "im2_a.png", "num_unique_values", None)
-test_png_num_unique_values_2 = __create_test(Image, "im2_b.png", "num_unique_values", None)
 test_png_width_32 = __create_test(Image, "im2_b.png", "width", 32)
 test_png_height_32 = __create_test(Image, "im2_b.png", "height", 32)
 test_png_channels_0 = __create_test(Image, "im1_uint8.png", "channels", 0)

From bfd1f3347a6b2a43140536d6d1f2f5efd60362c6 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 20 Jun 2025 12:18:27 -0500
Subject: [PATCH 2/5] [25.0] Prevent DCE collections from being renamed

Fixes https://help.galaxyproject.org/t/how-can-i-rename-a-paired-fastq-file/15784

Adds a `renameable` prop to `DetailsLayout` in addition to the existing `writeable` prop, because this way, we allow anonymous user histories to still be renamed (https://github.com/galaxyproject/galaxy/issues/20197) and in the case of the collection layout, DCEs are made not-renamaeable and unwriteable.
---
 .../CurrentCollection/CollectionDetails.vue   |  1 +
 .../History/Layout/DetailsLayout.test.js      | 31 +++++++++++++++++--
 .../History/Layout/DetailsLayout.vue          | 23 +++++++++-----
 3 files changed, 44 insertions(+), 11 deletions(-)

diff --git a/client/src/components/History/CurrentCollection/CollectionDetails.vue b/client/src/components/History/CurrentCollection/CollectionDetails.vue
index 81af7a85e0c..170986dfcb6 100644
--- a/client/src/components/History/CurrentCollection/CollectionDetails.vue
+++ b/client/src/components/History/CurrentCollection/CollectionDetails.vue
@@ -24,6 +24,7 @@ const jobState = computed(() => {
         :name="dsc.name ?? ''"
         :tags="dsc.tags"
         :writeable="writeable"
+        :renameable="writeable"
         :show-annotation="false"
         @save="$emit('update:dsc', $event)">
         <template v-slot:description>
diff --git a/client/src/components/History/Layout/DetailsLayout.test.js b/client/src/components/History/Layout/DetailsLayout.test.js
index cee10bd05d8..6a8e8036686 100644
--- a/client/src/components/History/Layout/DetailsLayout.test.js
+++ b/client/src/components/History/Layout/DetailsLayout.test.js
@@ -7,11 +7,15 @@ import DetailsLayout from "./DetailsLayout";
 
 const localVue = getLocalVue();
 
-async function createWrapper(component, localVue, userData) {
+async function createWrapper(component, localVue, userData, unwritable = false) {
     const pinia = createPinia();
     const wrapper = mount(component, {
         localVue,
         pinia,
+        propsData: {
+            writeable: !unwritable,
+            renameable: !unwritable,
+        },
     });
     const userStore = useUserStore();
     userStore.currentUser = { ...userStore.currentUser, ...userData };
@@ -19,18 +23,39 @@ async function createWrapper(component, localVue, userData) {
 }
 
 describe("DetailsLayout", () => {
-    it("allows logged-in users to edit details", async () => {
+    it("allows logged-in users to edit all details", async () => {
         const wrapper = await createWrapper(DetailsLayout, localVue, {
             id: "user.id",
             email: "user.email",
         });
 
         expect(wrapper.find(".edit-button").attributes("title")).toBe("Edit");
+
+        // Click to edit and rename
+        expect(wrapper.find(".click-to-edit-label").exists()).toBe(true);
     });
 
-    it("prompts anonymous users to log in", async () => {
+    it("prompts anonymous users to log in to edit all details, but allows rename", async () => {
         const wrapper = await createWrapper(DetailsLayout, localVue, {});
 
         expect(wrapper.find(".edit-button").attributes("title")).toContain("Log in");
+
+        // Click to edit and rename should still be available
+        expect(wrapper.find(".click-to-edit-label").exists()).toBe(true);
+    });
+
+    it("disallows editing and renaming if props set them to false", async () => {
+        const wrapper = await createWrapper(
+            DetailsLayout,
+            localVue,
+            {
+                id: "user.id",
+                email: "user.email",
+            },
+            true
+        );
+
+        expect(wrapper.find(".edit-button").attributes("title")).toContain("Not Editable");
+        expect(wrapper.find(".click-to-edit-label").exists()).toBe(false);
     });
 });
diff --git a/client/src/components/History/Layout/DetailsLayout.vue b/client/src/components/History/Layout/DetailsLayout.vue
index 916f0c77ba2..657d6306ac4 100644
--- a/client/src/components/History/Layout/DetailsLayout.vue
+++ b/client/src/components/History/Layout/DetailsLayout.vue
@@ -21,6 +21,7 @@ interface Props {
     name?: string;
     tags?: string[];
     writeable?: boolean;
+    renameable?: boolean;
     annotation?: string;
     showAnnotation?: boolean;
     summarized?: DetailsLayoutSummarized;
@@ -30,6 +31,7 @@ const props = withDefaults(defineProps<Props>(), {
     name: undefined,
     tags: undefined,
     writeable: true,
+    renameable: true,
     annotation: undefined,
     showAnnotation: true,
     summarized: undefined,
@@ -119,14 +121,19 @@ function selectText() {
 <template>
     <section :class="detailsClass" data-description="edit details">
         <div class="d-flex justify-content-between w-100">
-            <ClickToEdit
-                v-if="!summarized && !editing"
-                v-model="clickToEditName"
-                component="h3"
-                title="..."
-                data-description="name display"
-                no-save-on-blur
-                class="my-2 w-100" />
+            <template v-if="!summarized && !editing">
+                <ClickToEdit
+                    v-if="renameable"
+                    v-model="clickToEditName"
+                    component="h3"
+                    title="..."
+                    data-description="name display"
+                    no-save-on-blur
+                    class="my-2 w-100" />
+                <h3 v-else class="my-2 w-100">
+                    {{ props.name || "..." }}
+                </h3>
+            </template>
             <div v-else style="max-width: 80%">
                 <TextSummary
                     :description="name"

From a90c1c3d04e645722fd303a3c00fbeee2bf2bedc Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 20 Jun 2025 12:20:57 -0500
Subject: [PATCH 3/5] adds a title to the click to edit component to make enter
 to save obvious

---
 client/src/components/Collections/common/ClickToEdit.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Collections/common/ClickToEdit.vue b/client/src/components/Collections/common/ClickToEdit.vue
index c01a1ea7f1f..f04972b4a45 100644
--- a/client/src/components/Collections/common/ClickToEdit.vue
+++ b/client/src/components/Collections/common/ClickToEdit.vue
@@ -67,6 +67,7 @@ function revertToOriginal() {
             v-model="localValue"
             class="w-100 input-with-icon"
             tabindex="0"
+            title="Press enter/return to save, esc to revert changes"
             contenteditable
             max-rows="4"
             @blur.prevent.stop="onBlur"

From 414019da342aef4e4d64bb56078dc25e7f6b511f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sat, 21 Jun 2025 20:00:16 +0100
Subject: [PATCH 4/5] Fix docs versioning

for Galaxy releases (e.g. 24.2 and 25.0) that have only tags with
2 dots.
---
 doc/source/conf.versioning.py | 29 +++++++++++++++++++----------
 1 file changed, 19 insertions(+), 10 deletions(-)

diff --git a/doc/source/conf.versioning.py b/doc/source/conf.versioning.py
index 6aef635aa0c..9ed1cd9f04b 100644
--- a/doc/source/conf.versioning.py
+++ b/doc/source/conf.versioning.py
@@ -34,18 +34,27 @@ simpleversioning_versions = [
     # Additional versions added below
 ]
 
-# Used for determining the latest stable release so the banner can be added to older releases.
-_stable = None
 # Use tags to determine versions - a stable version will have a branch before it's released, but not a tag.
 tags = check_output(("git", "tag")).decode().splitlines()
-for _tag in reversed(tags):
-    if _tag.startswith("v") and _tag.count(".") == 1:
-        # this version is released
-        _ver = _tag[1:]
-        if not _stable:
-            _stable = _ver
-        if Version(_ver) >= MIN_DOC_VERSION:
-            simpleversioning_versions.append({"id": f"release_{_ver}", "name": _ver})
+found_versions = []
+for _tag in sorted(tags, reverse=True):
+    if not _tag.startswith("v"):
+        continue
+    _ver_parts = _tag[1:].split(".")
+    if len(_ver_parts) == 1:
+        # No "."
+        continue
+    # Keep only major and minor version numbers
+    _ver = ".".join(_ver_parts[:2])
+    if Version(_ver) < MIN_DOC_VERSION:
+        continue
+    if _ver in found_versions:
+        continue
+    found_versions.append(_ver)
+    simpleversioning_versions.append({"id": f"release_{_ver}", "name": _ver})
+
+# The latest stable release
+_stable = found_versions[0] if found_versions else None
 
 if re.fullmatch(r"release_\d{2}\.\d{1,2}", TARGET_GIT_BRANCH):
     if _stable:

From 97aa3a3adda161e8b382ddf70b02e96186ec1832 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 21 Jun 2025 17:31:54 -0500
Subject: [PATCH 5/5] fix AXE error

---
 client/src/components/Collections/common/ClickToEdit.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Collections/common/ClickToEdit.vue b/client/src/components/Collections/common/ClickToEdit.vue
index f04972b4a45..3d153b1c48d 100644
--- a/client/src/components/Collections/common/ClickToEdit.vue
+++ b/client/src/components/Collections/common/ClickToEdit.vue
@@ -70,6 +70,7 @@ function revertToOriginal() {
             title="Press enter/return to save, esc to revert changes"
             contenteditable
             max-rows="4"
+            aria-label="Press enter/return to save, esc to revert changes"
             @blur.prevent.stop="onBlur"
             @keyup.prevent.stop.enter="editable = false"
             @keyup.prevent.stop.escape="revertToOriginal"