Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release - #36

Merged
harryswift01 merged 4 commits into
mainfrom
33-feature-clean-repository
Aug 13, 2026
Merged

Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release#36
harryswift01 merged 4 commits into
mainfrom
33-feature-clean-repository

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@harryswift01

@harryswift01harryswift01 commented Aug 13, 2026

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Summary

This PR cleans up the SIST repository ahead of the 1.0.0 release by removing tracked build artefacts and ensuring generated files are ignored correctly.

The repository has also been rebuilt and tested after the cleanup to confirm that SIST can still be built from source without changing the established scientific results.

Changes

Repository cleanup:

  • Removed the tracked cmake-build-debug/ directory.
  • Removed tracked C++ object files from trans_three/ and trans_compete/.
  • Removed the tracked qsidd executables.
  • Removed generated depend files from version control.
  • Reviewed the existing files under example/ and retained them as intentional worked-example inputs and outputs.

Git ignore rules:

  • Added ignore rules for generated SIST qsidd executables.
  • Added ignore rules for generated dependency files.
  • Retained the existing rules for object files, build directories, documentation output, Python artefacts, and regression test output.
  • Left irf308.linux.exe unchanged pending the separate platform and dependency investigation.

Build and regression verification:

  • Rebuilt both trans_three and trans_compete successfully from source.
  • Confirmed regenerated build artefacts do not appear as untracked files.
  • Ran the full regression suite successfully after cleanup.
  • Confirmed the maintained scientific baseline remains unchanged.

Impact

  • Provides a cleaner and more maintainable source repository.
  • Prevents stale compiled artefacts from being accidentally used.
  • Ensures SIST executables are built from the maintained source rather than inherited binaries.
  • Improves reproducibility ahead of packaging and the SIST 1.0.0 release.
  • Does not intentionally change scientific calculations or command-line behaviour.

@harryswift01harryswift01 linked an issue Aug 13, 2026 that may be closed by this pull request
[Feature]: Clean repository for the SIST 1.0.0 release #33
Closed
jimboid
jimboid approved these changes Aug 13, 2026
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Looks like sensible changes taking account for removing previously and erroneously committed artifacts to history.

@harryswift01
harryswift01 merged commit e50f2d3 into mainAug 13, 2026
2 checks passed
@harryswift01
harryswift01 deleted the 33-feature-clean-repository branch August 13, 2026 14:23
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[Feature]: Clean repository for the SIST 1.0.0 release

2 participants

@harryswift01@jimboid
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release - #36
Merged
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Aug 13, 2026
Merged
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release#36
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Conversation
@harryswift01
@harryswift01harryswift01
commented
Aug 13, 2026

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Summary
This PR cleans up the SIST repository ahead of the 1.0.0 release by removing tracked build artefacts and ensuring generated files are ignored correctly.
The repository has also been rebuilt and tested after the cleanup to confirm that SIST can still be built from source without changing the established scientific results.
Changes
Repository cleanup:
  • Removed the tracked cmake-build-debug/ directory.
  • Removed tracked C++ object files from trans_three/ and trans_compete/.
  • Removed the tracked qsidd executables.
  • Removed generated depend files from version control.
  • Reviewed the existing files under example/ and retained them as intentional worked-example inputs and outputs.
Git ignore rules:
  • Added ignore rules for generated SIST qsidd executables.
  • Added ignore rules for generated dependency files.
  • Retained the existing rules for object files, build directories, documentation output, Python artefacts, and regression test output.
  • Left irf308.linux.exe unchanged pending the separate platform and dependency investigation.
Build and regression verification:
  • Rebuilt both trans_three and trans_compete successfully from source.
  • Confirmed regenerated build artefacts do not appear as untracked files.
  • Ran the full regression suite successfully after cleanup.
  • Confirmed the maintained scientific baseline remains unchanged.
Impact
  • Provides a cleaner and more maintainable source repository.
  • Prevents stale compiled artefacts from being accidentally used.
  • Ensures SIST executables are built from the maintained source rather than inherited binaries.
  • Improves reproducibility ahead of packaging and the SIST 1.0.0 release.
  • Does not intentionally change scientific calculations or command-line behaviour.
@harryswift01harryswift01
linked an issue
Aug 13, 2026
that may be
closed
by this pull request


[Feature]: Clean repository for the SIST 1.0.0 release
#33

Closed

jimboid
jimboid
approved these changes
Aug 13, 2026
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@jimboidjimboid
left a comment


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Looks like sensible changes taking account for removing previously and erroneously committed artifacts to history.
@harryswift01
harryswift01
merged commit e50f2d3
into
mainAug 13, 2026

2 checks passed

@harryswift01
harryswift01
deleted the

33-feature-clean-repository

branch
August 13, 2026 14:23
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[Feature]: Clean repository for the SIST 1.0.0 release


2 participants

@harryswift01@jimboid

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release - #36
Merged
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Aug 13, 2026
Merged
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release#36
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Conversation
@harryswift01
@harryswift01harryswift01
commented
Aug 13, 2026

Copy link


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Summary
This PR cleans up the SIST repository ahead of the 1.0.0 release by removing tracked build artefacts and ensuring generated files are ignored correctly.
The repository has also been rebuilt and tested after the cleanup to confirm that SIST can still be built from source without changing the established scientific results.
Changes
Repository cleanup:
  • Removed the tracked cmake-build-debug/ directory.
  • Removed tracked C++ object files from trans_three/ and trans_compete/.
  • Removed the tracked qsidd executables.
  • Removed generated depend files from version control.
  • Reviewed the existing files under example/ and retained them as intentional worked-example inputs and outputs.
Git ignore rules:
  • Added ignore rules for generated SIST qsidd executables.
  • Added ignore rules for generated dependency files.
  • Retained the existing rules for object files, build directories, documentation output, Python artefacts, and regression test output.
  • Left irf308.linux.exe unchanged pending the separate platform and dependency investigation.
Build and regression verification:
  • Rebuilt both trans_three and trans_compete successfully from source.
  • Confirmed regenerated build artefacts do not appear as untracked files.
  • Ran the full regression suite successfully after cleanup.
  • Confirmed the maintained scientific baseline remains unchanged.
Impact
  • Provides a cleaner and more maintainable source repository.
  • Prevents stale compiled artefacts from being accidentally used.
  • Ensures SIST executables are built from the maintained source rather than inherited binaries.
  • Improves reproducibility ahead of packaging and the SIST 1.0.0 release.
  • Does not intentionally change scientific calculations or command-line behaviour.
@harryswift01harryswift01
linked an issue
Aug 13, 2026
that may be
closed
by this pull request


[Feature]: Clean repository for the SIST 1.0.0 release
#33

Closed

jimboid
jimboid
approved these changes
Aug 13, 2026
View reviewed changes
@jimboidjimboid
left a comment


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Looks like sensible changes taking account for removing previously and erroneously committed artifacts to history.
@harryswift01
harryswift01
merged commit e50f2d3
into
mainAug 13, 2026

2 checks passed

@harryswift01
harryswift01
deleted the

33-feature-clean-repository

branch
August 13, 2026 14:23
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@jimboidjimboidjimboid approved these changes

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[Feature]: Clean repository for the SIST 1.0.0 release


2 participants

@harryswift01@jimboid

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release - #36
Merged
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Aug 13, 2026
Merged
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release#36
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Conversation
@harryswift01
@harryswift01harryswift01
commented
Aug 13, 2026

Copy link


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Summary
This PR cleans up the SIST repository ahead of the 1.0.0 release by removing tracked build artefacts and ensuring generated files are ignored correctly.
The repository has also been rebuilt and tested after the cleanup to confirm that SIST can still be built from source without changing the established scientific results.
Changes
Repository cleanup:
  • Removed the tracked cmake-build-debug/ directory.
  • Removed tracked C++ object files from trans_three/ and trans_compete/.
  • Removed the tracked qsidd executables.
  • Removed generated depend files from version control.
  • Reviewed the existing files under example/ and retained them as intentional worked-example inputs and outputs.
Git ignore rules:
  • Added ignore rules for generated SIST qsidd executables.
  • Added ignore rules for generated dependency files.
  • Retained the existing rules for object files, build directories, documentation output, Python artefacts, and regression test output.
  • Left irf308.linux.exe unchanged pending the separate platform and dependency investigation.
Build and regression verification:
  • Rebuilt both trans_three and trans_compete successfully from source.
  • Confirmed regenerated build artefacts do not appear as untracked files.
  • Ran the full regression suite successfully after cleanup.
  • Confirmed the maintained scientific baseline remains unchanged.
Impact
  • Provides a cleaner and more maintainable source repository.
  • Prevents stale compiled artefacts from being accidentally used.
  • Ensures SIST executables are built from the maintained source rather than inherited binaries.
  • Improves reproducibility ahead of packaging and the SIST 1.0.0 release.
  • Does not intentionally change scientific calculations or command-line behaviour.
@harryswift01harryswift01
linked an issue
Aug 13, 2026
that may be
closed
by this pull request


[Feature]: Clean repository for the SIST 1.0.0 release
#33

Closed

jimboid
jimboid
approved these changes
Aug 13, 2026
View reviewed changes
@jimboidjimboid
left a comment


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Looks like sensible changes taking account for removing previously and erroneously committed artifacts to history.
@harryswift01
harryswift01
merged commit e50f2d3
into
mainAug 13, 2026

2 checks passed

@harryswift01
harryswift01
deleted the

33-feature-clean-repository

branch
August 13, 2026 14:23
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@jimboidjimboidjimboid approved these changes

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Development

Successfully merging this pull request may close these issues.

[Feature]: Clean repository for the SIST 1.0.0 release


2 participants

@harryswift01@jimboid

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release - #36
Merged
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Aug 13, 2026
Merged
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release#36
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Conversation
@harryswift01
@harryswift01harryswift01
commented
Aug 13, 2026

Copy link


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Summary
This PR cleans up the SIST repository ahead of the 1.0.0 release by removing tracked build artefacts and ensuring generated files are ignored correctly.
The repository has also been rebuilt and tested after the cleanup to confirm that SIST can still be built from source without changing the established scientific results.
Changes
Repository cleanup:
  • Removed the tracked cmake-build-debug/ directory.
  • Removed tracked C++ object files from trans_three/ and trans_compete/.
  • Removed the tracked qsidd executables.
  • Removed generated depend files from version control.
  • Reviewed the existing files under example/ and retained them as intentional worked-example inputs and outputs.
Git ignore rules:
  • Added ignore rules for generated SIST qsidd executables.
  • Added ignore rules for generated dependency files.
  • Retained the existing rules for object files, build directories, documentation output, Python artefacts, and regression test output.
  • Left irf308.linux.exe unchanged pending the separate platform and dependency investigation.
Build and regression verification:
  • Rebuilt both trans_three and trans_compete successfully from source.
  • Confirmed regenerated build artefacts do not appear as untracked files.
  • Ran the full regression suite successfully after cleanup.
  • Confirmed the maintained scientific baseline remains unchanged.
Impact
  • Provides a cleaner and more maintainable source repository.
  • Prevents stale compiled artefacts from being accidentally used.
  • Ensures SIST executables are built from the maintained source rather than inherited binaries.
  • Improves reproducibility ahead of packaging and the SIST 1.0.0 release.
  • Does not intentionally change scientific calculations or command-line behaviour.
@harryswift01harryswift01
linked an issue
Aug 13, 2026
that may be
closed
by this pull request


[Feature]: Clean repository for the SIST 1.0.0 release
#33

Closed

jimboid
jimboid
approved these changes
Aug 13, 2026
View reviewed changes
@jimboidjimboid
left a comment


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Looks like sensible changes taking account for removing previously and erroneously committed artifacts to history.
@harryswift01
harryswift01
merged commit e50f2d3
into
mainAug 13, 2026

2 checks passed

@harryswift01
harryswift01
deleted the

33-feature-clean-repository

branch
August 13, 2026 14:23
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Development

Successfully merging this pull request may close these issues.

[Feature]: Clean repository for the SIST 1.0.0 release


2 participants

@harryswift01@jimboid

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release - #36
Merged
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Aug 13, 2026
Merged
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release#36
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Conversation
@harryswift01
@harryswift01harryswift01
commented
Aug 13, 2026

Copy link


Copy Markdown

Member
Summary
This PR cleans up the SIST repository ahead of the 1.0.0 release by removing tracked build artefacts and ensuring generated files are ignored correctly.
The repository has also been rebuilt and tested after the cleanup to confirm that SIST can still be built from source without changing the established scientific results.
Changes
Repository cleanup:
  • Removed the tracked cmake-build-debug/ directory.
  • Removed tracked C++ object files from trans_three/ and trans_compete/.
  • Removed the tracked qsidd executables.
  • Removed generated depend files from version control.
  • Reviewed the existing files under example/ and retained them as intentional worked-example inputs and outputs.
Git ignore rules:
  • Added ignore rules for generated SIST qsidd executables.
  • Added ignore rules for generated dependency files.
  • Retained the existing rules for object files, build directories, documentation output, Python artefacts, and regression test output.
  • Left irf308.linux.exe unchanged pending the separate platform and dependency investigation.
Build and regression verification:
  • Rebuilt both trans_three and trans_compete successfully from source.
  • Confirmed regenerated build artefacts do not appear as untracked files.
  • Ran the full regression suite successfully after cleanup.
  • Confirmed the maintained scientific baseline remains unchanged.
Impact
  • Provides a cleaner and more maintainable source repository.
  • Prevents stale compiled artefacts from being accidentally used.
  • Ensures SIST executables are built from the maintained source rather than inherited binaries.
  • Improves reproducibility ahead of packaging and the SIST 1.0.0 release.
  • Does not intentionally change scientific calculations or command-line behaviour.
@harryswift01harryswift01
linked an issue
Aug 13, 2026
that may be
closed
by this pull request


[Feature]: Clean repository for the SIST 1.0.0 release
#33

Closed

jimboid
jimboid
approved these changes
Aug 13, 2026
View reviewed changes
@jimboidjimboid
left a comment


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Looks like sensible changes taking account for removing previously and erroneously committed artifacts to history.
@harryswift01
harryswift01
merged commit e50f2d3
into
mainAug 13, 2026

2 checks passed

@harryswift01
harryswift01
deleted the

33-feature-clean-repository

branch
August 13, 2026 14:23
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@jimboidjimboidjimboid approved these changes

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Development

Successfully merging this pull request may close these issues.

[Feature]: Clean repository for the SIST 1.0.0 release


2 participants

@harryswift01@jimboid

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release - #36
Merged
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Aug 13, 2026
Merged
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release#36
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Conversation
@harryswift01
@harryswift01harryswift01
commented
Aug 13, 2026

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Summary
This PR cleans up the SIST repository ahead of the 1.0.0 release by removing tracked build artefacts and ensuring generated files are ignored correctly.
The repository has also been rebuilt and tested after the cleanup to confirm that SIST can still be built from source without changing the established scientific results.
Changes
Repository cleanup:
  • Removed the tracked cmake-build-debug/ directory.
  • Removed tracked C++ object files from trans_three/ and trans_compete/.
  • Removed the tracked qsidd executables.
  • Removed generated depend files from version control.
  • Reviewed the existing files under example/ and retained them as intentional worked-example inputs and outputs.
Git ignore rules:
  • Added ignore rules for generated SIST qsidd executables.
  • Added ignore rules for generated dependency files.
  • Retained the existing rules for object files, build directories, documentation output, Python artefacts, and regression test output.
  • Left irf308.linux.exe unchanged pending the separate platform and dependency investigation.
Build and regression verification:
  • Rebuilt both trans_three and trans_compete successfully from source.
  • Confirmed regenerated build artefacts do not appear as untracked files.
  • Ran the full regression suite successfully after cleanup.
  • Confirmed the maintained scientific baseline remains unchanged.
Impact
  • Provides a cleaner and more maintainable source repository.
  • Prevents stale compiled artefacts from being accidentally used.
  • Ensures SIST executables are built from the maintained source rather than inherited binaries.
  • Improves reproducibility ahead of packaging and the SIST 1.0.0 release.
  • Does not intentionally change scientific calculations or command-line behaviour.
@harryswift01harryswift01
linked an issue
Aug 13, 2026
that may be
closed
by this pull request


[Feature]: Clean repository for the SIST 1.0.0 release
#33

Closed

jimboid
jimboid
approved these changes
Aug 13, 2026
View reviewed changes
@jimboidjimboid
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Looks like sensible changes taking account for removing previously and erroneously committed artifacts to history.
@harryswift01
harryswift01
merged commit e50f2d3
into
mainAug 13, 2026

2 checks passed

@harryswift01
harryswift01
deleted the

33-feature-clean-repository

branch
August 13, 2026 14:23
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[Feature]: Clean repository for the SIST 1.0.0 release


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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release - #36
Merged
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Aug 13, 2026
Merged
Clean Up Tracked Build Artefacts for the SIST 1.0.0 Release#36
harryswift01 merged 4 commits into
mainfrom 
33-feature-clean-repository
Conversation
@harryswift01
@harryswift01harryswift01
commented
Aug 13, 2026

Copy link


Copy Markdown

Member
Summary
This PR cleans up the SIST repository ahead of the 1.0.0 release by removing tracked build artefacts and ensuring generated files are ignored correctly.
The repository has also been rebuilt and tested after the cleanup to confirm that SIST can still be built from source without changing the established scientific results.
Changes
Repository cleanup:
  • Removed the tracked cmake-build-debug/ directory.
  • Removed tracked C++ object files from trans_three/ and trans_compete/.
  • Removed the tracked qsidd executables.
  • Removed generated depend files from version control.
  • Reviewed the existing files under example/ and retained them as intentional worked-example inputs and outputs.
Git ignore rules:
  • Added ignore rules for generated SIST qsidd executables.
  • Added ignore rules for generated dependency files.
  • Retained the existing rules for object files, build directories, documentation output, Python artefacts, and regression test output.
  • Left irf308.linux.exe unchanged pending the separate platform and dependency investigation.
Build and regression verification:
  • Rebuilt both trans_three and trans_compete successfully from source.
  • Confirmed regenerated build artefacts do not appear as untracked files.
  • Ran the full regression suite successfully after cleanup.
  • Confirmed the maintained scientific baseline remains unchanged.
Impact
  • Provides a cleaner and more maintainable source repository.
  • Prevents stale compiled artefacts from being accidentally used.
  • Ensures SIST executables are built from the maintained source rather than inherited binaries.
  • Improves reproducibility ahead of packaging and the SIST 1.0.0 release.
  • Does not intentionally change scientific calculations or command-line behaviour.
@harryswift01harryswift01
linked an issue
Aug 13, 2026
that may be
closed
by this pull request


[Feature]: Clean repository for the SIST 1.0.0 release
#33

Closed

jimboid
jimboid
approved these changes
Aug 13, 2026
View reviewed changes
@jimboidjimboid
left a comment


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Looks like sensible changes taking account for removing previously and erroneously committed artifacts to history.
@harryswift01
harryswift01
merged commit e50f2d3
into
mainAug 13, 2026

2 checks passed

@harryswift01
harryswift01
deleted the

33-feature-clean-repository

branch
August 13, 2026 14:23
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Already have an account?
Sign in to comment

Reviewers

@jimboidjimboidjimboid approved these changes

Assignees


No one assigned


Labels


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Projects


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Milestone


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Development

Successfully merging this pull request may close these issues.

[Feature]: Clean repository for the SIST 1.0.0 release


2 participants

@harryswift01@jimboid