From 3d7bfe08084b81cc1d96a42a00f3fca3c700021d Mon Sep 17 00:00:00 2001
From: ehennestad <ehennestad@gmail.com>
Date: Fri, 18 Sep 2026 05:00:18 +0200
Subject: [PATCH 1/2] fix(stack): initialize binary files on Linux

Binary.initializeFile only assigned status inside an ispc/ismac
branch, so on Linux the variable was never defined and `if status`
threw "Unrecognized function or variable 'status'". Every code path
that creates a new .raw file failed on Linux, which surfaced in CI as
five CropTest errors with the identifier
NANSEN:Stack:Crop:FileNotCreated.

Default status to the fallback path and only override it on Windows,
where fsutil preallocates the file. Also check the fopen handle before
writing, so a folder that does not exist or is not writable reports
the reason instead of failing on an invalid file id, and close the
file through onCleanup so it is released if fwrite errors.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---
 code/datatypes/+nansen/+stack/+virtual/Binary.m | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/code/datatypes/+nansen/+stack/+virtual/Binary.m b/code/datatypes/+nansen/+stack/+virtual/Binary.m
index 7e89cef1..5a4a6d36 100644
--- a/code/datatypes/+nansen/+stack/+virtual/Binary.m
+++ b/code/datatypes/+nansen/+stack/+virtual/Binary.m
@@ -360,16 +360,25 @@ function initializeFile(filePath, arraySize, arrayClass)
                 numBytes = nansen.stack.ImageStack.getImageDataByteSize(...
                     arraySize, arrayClass);
 
+                % On Windows, fsutil preallocates the file without writing
+                % its contents. Every other platform, and a failed fsutil
+                % call, falls back to writing a sparse file with fwrite.
+                status = 1;
                 if ispc
                     [status, ~] = system(sprintf('cmd /C fsutil file createnew %s %i', filePath, numBytes));
-                elseif ismac
-                    status = 1;
                 end
 
                 if status % Backup solution
-                    fileId = fopen(filePath, 'w');
+                    [fileId, errorMessage] = fopen(filePath, 'w');
+                    if fileId == -1
+                        error('NANSEN:Stack:Binary:FileNotCreated', ...
+                            ['Could not create the binary file "%s": %s. ', ...
+                            'Check that the folder exists and is writable.'], ...
+                            filePath, errorMessage)
+                    end
+                    fileCleanup = onCleanup(@() fclose(fileId));
                     fwrite(fileId, 0, 'uint8', numBytes-1); % 4th arg: skip
-                    fclose(fileId);
+                    clear fileCleanup % Close the file before it is mapped
                 end
 
             else

From c11f49b58a0d86642cd6d39341ef1a22be914662 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 18 Sep 2026 03:04:39 +0000
Subject: [PATCH 2/2] Update GitHub badges [skip ci]

---
 .github/badges/tests.svg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/badges/tests.svg b/.github/badges/tests.svg
index 007b7eff..fd00e9b1 100644
--- a/.github/badges/tests.svg
+++ b/.github/badges/tests.svg
@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" width="110" height="20" role="img" aria-label="tests: 333 passed"><title>tests: 333 passed</title><filter id="blur"><feGaussianBlur stdDeviation="16"/></filter><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="110" height="20" rx="3"/></clipPath><g clip-path="url(#r)"><rect width="37" height="20" fill="#555"/><rect x="37" width="73" height="20" fill="#67ac09"/><rect width="110" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><g transform="scale(.1)"><g aria-hidden="true" fill="#010101"><text x="195" y="150" fill-opacity=".8" filter="url(#blur)" textLength="270">tests</text><text x="195" y="150" fill-opacity=".3" textLength="270">tests</text></g><text x="195" y="140" textLength="270">tests</text></g><g transform="scale(.1)"><g aria-hidden="true" fill="#010101"><text x="725" y="150" fill-opacity=".8" filter="url(#blur)" textLength="630">333 passed</text><text x="725" y="150" fill-opacity=".3" textLength="630">333 passed</text></g><text x="725" y="140" textLength="630">333 passed</text></g></g></svg>
+<svg xmlns="http://www.w3.org/2000/svg" width="110" height="20" role="img" aria-label="tests: 369 passed"><title>tests: 369 passed</title><filter id="blur"><feGaussianBlur stdDeviation="16"/></filter><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="110" height="20" rx="3"/></clipPath><g clip-path="url(#r)"><rect width="37" height="20" fill="#555"/><rect x="37" width="73" height="20" fill="#67ac09"/><rect width="110" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><g transform="scale(.1)"><g aria-hidden="true" fill="#010101"><text x="195" y="150" fill-opacity=".8" filter="url(#blur)" textLength="270">tests</text><text x="195" y="150" fill-opacity=".3" textLength="270">tests</text></g><text x="195" y="140" textLength="270">tests</text></g><g transform="scale(.1)"><g aria-hidden="true" fill="#010101"><text x="725" y="150" fill-opacity=".8" filter="url(#blur)" textLength="630">369 passed</text><text x="725" y="150" fill-opacity=".3" textLength="630">369 passed</text></g><text x="725" y="140" textLength="630">369 passed</text></g></g></svg>