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Update metadata-schema.yaml - #15

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jrfaeder merged 9 commits into
RuleWorld:masterfrom
vcellmike:master
Jun 24, 2026
Merged

Update metadata-schema.yaml#15
jrfaeder merged 9 commits into
RuleWorld:masterfrom
vcellmike:master

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@vcellmike

@vcellmikevcellmike commented Jun 23, 2026

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Hello,

I've added some new keys to metadata, such as related to VCell and other rule-based tools.

Major changes to the existing schema:

  • category (which is now single value and includes such different terms as tutorial and immunology) is divided into two lists: one is biol_categories, one is comp_categories.
  • new keys in compatibility
  • features are added, where I collected existing (e.g. uses_energy) and added many more that affect other tools (such as uses_multiple_identical_sites).
  • uses_compartments is replaced with uses_cbngl_compartments, as I have also uses_vcell_compartments.

Minor changes:

  • added comments
  • added tested
  • added default_sim_command - the one that is actually in bngl

@jrfaeder

jrfaeder commented Jun 24, 2026

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Please address the file causing the validation to fail.

@vcellmike

vcellmike commented Jun 24, 2026

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The new .yaml examples file was an accident. Schema is updated with the year. Please use default values when updating all yaml files for the new schema:
rr_compatible: true
bnglviz_compatible: true
vcell_compatible: false
molclustpy_compatible: false

@jrfaeder

jrfaeder commented Jun 24, 2026

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Ok, it's still failing the CI check but maybe that's premature anyway since updating model data is a work in progress. I will go ahead and merge.

@jrfaeder
jrfaeder merged commit b84f0a7 into RuleWorld:masterJun 24, 2026
1 check failed
vcellmike pushed a commit to vcellmike/RuleHub that referenced this pull request Aug 10, 2026
@Psuedonerd
Merge pull requestRuleWorld#15from Psuedonerd/codex/inspect-model-f…
493d859
…olders-in-rulehub-repo-x1b29a
Add AI-generated model summaries and index (JSON + markdown files)
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@vcellmike@jrfaeder@NabilM35
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var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Update metadata-schema.yaml by vcellmike · Pull Request #15 · RuleWorld/RuleHub · GitHub
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Update metadata-schema.yaml - #15
Merged
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Jun 24, 2026
Merged
Update metadata-schema.yaml#15
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Conversation
@vcellmike
@vcellmikevcellmike
commented
Jun 23, 2026

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Hello,
I've added some new keys to metadata, such as related to VCell and other rule-based tools.
Major changes to the existing schema:
  • category (which is now single value and includes such different terms as tutorial and immunology) is divided into two lists: one is biol_categories, one is comp_categories.
  • new keys in compatibility
  • features are added, where I collected existing (e.g. uses_energy) and added many more that affect other tools (such as uses_multiple_identical_sites).
  • uses_compartments is replaced with uses_cbngl_compartments, as I have also uses_vcell_compartments.
Minor changes:
  • added comments
  • added tested
  • added default_sim_command - the one that is actually in bngl
@jrfaeder
jrfaeder
commented
Jun 24, 2026

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Please address the file causing the validation to fail.
@vcellmike
vcellmike
commented
Jun 24, 2026

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ContributorAuthor
The new .yaml examples file was an accident. Schema is updated with the year. Please use default values when updating all yaml files for the new schema:

rr_compatible: true

bnglviz_compatible: true

vcell_compatible: false

molclustpy_compatible: false
@jrfaeder
jrfaeder
commented
Jun 24, 2026

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Ok, it's still failing the CI check but maybe that's premature anyway since updating model data is a work in progress. I will go ahead and merge.
@jrfaeder
jrfaeder
merged commit b84f0a7
into
RuleWorld:masterJun 24, 2026

1 check failed

vcellmike pushed a commit
to vcellmike/RuleHub
that referenced
this pull request
Aug 10, 2026
@Psuedonerd
Merge pull requestRuleWorld#15from Psuedonerd/codex/inspect-model-f…
493d859
…olders-in-rulehub-repo-x1b29a
Add AI-generated model summaries and index (JSON + markdown files)
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@vcellmike@jrfaeder@NabilM35

, 'i');
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// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
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color-scheme: dark light;
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Update metadata-schema.yaml by vcellmike · Pull Request #15 · RuleWorld/RuleHub · GitHub
Skip to content
Update metadata-schema.yaml - #15
Merged
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Jun 24, 2026
Merged
Update metadata-schema.yaml#15
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Conversation
@vcellmike
@vcellmikevcellmike
commented
Jun 23, 2026

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Hello,
I've added some new keys to metadata, such as related to VCell and other rule-based tools.
Major changes to the existing schema:
  • category (which is now single value and includes such different terms as tutorial and immunology) is divided into two lists: one is biol_categories, one is comp_categories.
  • new keys in compatibility
  • features are added, where I collected existing (e.g. uses_energy) and added many more that affect other tools (such as uses_multiple_identical_sites).
  • uses_compartments is replaced with uses_cbngl_compartments, as I have also uses_vcell_compartments.
Minor changes:
  • added comments
  • added tested
  • added default_sim_command - the one that is actually in bngl
@jrfaeder
jrfaeder
commented
Jun 24, 2026

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Please address the file causing the validation to fail.
@vcellmike
vcellmike
commented
Jun 24, 2026

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ContributorAuthor
The new .yaml examples file was an accident. Schema is updated with the year. Please use default values when updating all yaml files for the new schema:

rr_compatible: true

bnglviz_compatible: true

vcell_compatible: false

molclustpy_compatible: false
@jrfaeder
jrfaeder
commented
Jun 24, 2026

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Contributor
Ok, it's still failing the CI check but maybe that's premature anyway since updating model data is a work in progress. I will go ahead and merge.
@jrfaeder
jrfaeder
merged commit b84f0a7
into
RuleWorld:masterJun 24, 2026

1 check failed

vcellmike pushed a commit
to vcellmike/RuleHub
that referenced
this pull request
Aug 10, 2026
@Psuedonerd
Merge pull requestRuleWorld#15from Psuedonerd/codex/inspect-model-f…
493d859
…olders-in-rulehub-repo-x1b29a
Add AI-generated model summaries and index (JSON + markdown files)
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3 participants

@vcellmike@jrfaeder@NabilM35

, 'i');
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// Highlight search terms from Google/DuckDuckGo/Bing referrer
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var ref = document.referrer;
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Update metadata-schema.yaml by vcellmike · Pull Request #15 · RuleWorld/RuleHub · GitHub
Skip to content
Update metadata-schema.yaml - #15
Merged
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Jun 24, 2026
Merged
Update metadata-schema.yaml#15
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Conversation
@vcellmike
@vcellmikevcellmike
commented
Jun 23, 2026

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Contributor
Hello,
I've added some new keys to metadata, such as related to VCell and other rule-based tools.
Major changes to the existing schema:
  • category (which is now single value and includes such different terms as tutorial and immunology) is divided into two lists: one is biol_categories, one is comp_categories.
  • new keys in compatibility
  • features are added, where I collected existing (e.g. uses_energy) and added many more that affect other tools (such as uses_multiple_identical_sites).
  • uses_compartments is replaced with uses_cbngl_compartments, as I have also uses_vcell_compartments.
Minor changes:
  • added comments
  • added tested
  • added default_sim_command - the one that is actually in bngl
@jrfaeder
jrfaeder
commented
Jun 24, 2026

Copy link


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Contributor
Please address the file causing the validation to fail.
@vcellmike
vcellmike
commented
Jun 24, 2026

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Copy Markdown

ContributorAuthor
The new .yaml examples file was an accident. Schema is updated with the year. Please use default values when updating all yaml files for the new schema:

rr_compatible: true

bnglviz_compatible: true

vcell_compatible: false

molclustpy_compatible: false
@jrfaeder
jrfaeder
commented
Jun 24, 2026

Copy link


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Contributor
Ok, it's still failing the CI check but maybe that's premature anyway since updating model data is a work in progress. I will go ahead and merge.
@jrfaeder
jrfaeder
merged commit b84f0a7
into
RuleWorld:masterJun 24, 2026

1 check failed

vcellmike pushed a commit
to vcellmike/RuleHub
that referenced
this pull request
Aug 10, 2026
@Psuedonerd
Merge pull requestRuleWorld#15from Psuedonerd/codex/inspect-model-f…
493d859
…olders-in-rulehub-repo-x1b29a
Add AI-generated model summaries and index (JSON + markdown files)
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3 participants

@vcellmike@jrfaeder@NabilM35

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
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return url;
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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Update metadata-schema.yaml by vcellmike · Pull Request #15 · RuleWorld/RuleHub · GitHub
Skip to content
Update metadata-schema.yaml - #15
Merged
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Jun 24, 2026
Merged
Update metadata-schema.yaml#15
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Conversation
@vcellmike
@vcellmikevcellmike
commented
Jun 23, 2026

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Contributor
Hello,
I've added some new keys to metadata, such as related to VCell and other rule-based tools.
Major changes to the existing schema:
  • category (which is now single value and includes such different terms as tutorial and immunology) is divided into two lists: one is biol_categories, one is comp_categories.
  • new keys in compatibility
  • features are added, where I collected existing (e.g. uses_energy) and added many more that affect other tools (such as uses_multiple_identical_sites).
  • uses_compartments is replaced with uses_cbngl_compartments, as I have also uses_vcell_compartments.
Minor changes:
  • added comments
  • added tested
  • added default_sim_command - the one that is actually in bngl
@jrfaeder
jrfaeder
commented
Jun 24, 2026

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Contributor
Please address the file causing the validation to fail.
@vcellmike
vcellmike
commented
Jun 24, 2026

Copy link


Copy Markdown

ContributorAuthor
The new .yaml examples file was an accident. Schema is updated with the year. Please use default values when updating all yaml files for the new schema:

rr_compatible: true

bnglviz_compatible: true

vcell_compatible: false

molclustpy_compatible: false
@jrfaeder
jrfaeder
commented
Jun 24, 2026

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Contributor
Ok, it's still failing the CI check but maybe that's premature anyway since updating model data is a work in progress. I will go ahead and merge.
@jrfaeder
jrfaeder
merged commit b84f0a7
into
RuleWorld:masterJun 24, 2026

1 check failed

vcellmike pushed a commit
to vcellmike/RuleHub
that referenced
this pull request
Aug 10, 2026
@Psuedonerd
Merge pull requestRuleWorld#15from Psuedonerd/codex/inspect-model-f…
493d859
…olders-in-rulehub-repo-x1b29a
Add AI-generated model summaries and index (JSON + markdown files)
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3 participants

@vcellmike@jrfaeder@NabilM35

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
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lastUrl = location.href;
setTimeout(tryTheater, 500);
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Update metadata-schema.yaml by vcellmike · Pull Request #15 · RuleWorld/RuleHub · GitHub
Skip to content
Update metadata-schema.yaml - #15
Merged
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Jun 24, 2026
Merged
Update metadata-schema.yaml#15
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Conversation
@vcellmike
@vcellmikevcellmike
commented
Jun 23, 2026

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Contributor
Hello,
I've added some new keys to metadata, such as related to VCell and other rule-based tools.
Major changes to the existing schema:
  • category (which is now single value and includes such different terms as tutorial and immunology) is divided into two lists: one is biol_categories, one is comp_categories.
  • new keys in compatibility
  • features are added, where I collected existing (e.g. uses_energy) and added many more that affect other tools (such as uses_multiple_identical_sites).
  • uses_compartments is replaced with uses_cbngl_compartments, as I have also uses_vcell_compartments.
Minor changes:
  • added comments
  • added tested
  • added default_sim_command - the one that is actually in bngl
@jrfaeder
jrfaeder
commented
Jun 24, 2026

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Contributor
Please address the file causing the validation to fail.
@vcellmike
vcellmike
commented
Jun 24, 2026

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Copy Markdown

ContributorAuthor
The new .yaml examples file was an accident. Schema is updated with the year. Please use default values when updating all yaml files for the new schema:

rr_compatible: true

bnglviz_compatible: true

vcell_compatible: false

molclustpy_compatible: false
@jrfaeder
jrfaeder
commented
Jun 24, 2026

Copy link


Copy Markdown

Contributor
Ok, it's still failing the CI check but maybe that's premature anyway since updating model data is a work in progress. I will go ahead and merge.
@jrfaeder
jrfaeder
merged commit b84f0a7
into
RuleWorld:masterJun 24, 2026

1 check failed

vcellmike pushed a commit
to vcellmike/RuleHub
that referenced
this pull request
Aug 10, 2026
@Psuedonerd
Merge pull requestRuleWorld#15from Psuedonerd/codex/inspect-model-f…
493d859
…olders-in-rulehub-repo-x1b29a
Add AI-generated model summaries and index (JSON + markdown files)
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3 participants

@vcellmike@jrfaeder@NabilM35

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
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function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
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el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
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unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Update metadata-schema.yaml by vcellmike · Pull Request #15 · RuleWorld/RuleHub · GitHub
Skip to content
Update metadata-schema.yaml - #15
Merged
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Jun 24, 2026
Merged
Update metadata-schema.yaml#15
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Conversation
@vcellmike
@vcellmikevcellmike
commented
Jun 23, 2026

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Contributor
Hello,
I've added some new keys to metadata, such as related to VCell and other rule-based tools.
Major changes to the existing schema:
  • category (which is now single value and includes such different terms as tutorial and immunology) is divided into two lists: one is biol_categories, one is comp_categories.
  • new keys in compatibility
  • features are added, where I collected existing (e.g. uses_energy) and added many more that affect other tools (such as uses_multiple_identical_sites).
  • uses_compartments is replaced with uses_cbngl_compartments, as I have also uses_vcell_compartments.
Minor changes:
  • added comments
  • added tested
  • added default_sim_command - the one that is actually in bngl
@jrfaeder
jrfaeder
commented
Jun 24, 2026

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Please address the file causing the validation to fail.
@vcellmike
vcellmike
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Jun 24, 2026

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The new .yaml examples file was an accident. Schema is updated with the year. Please use default values when updating all yaml files for the new schema:

rr_compatible: true

bnglviz_compatible: true

vcell_compatible: false

molclustpy_compatible: false
@jrfaeder
jrfaeder
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Jun 24, 2026

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Ok, it's still failing the CI check but maybe that's premature anyway since updating model data is a work in progress. I will go ahead and merge.
@jrfaeder
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merged commit b84f0a7
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RuleWorld:masterJun 24, 2026

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vcellmike pushed a commit
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Aug 10, 2026
@Psuedonerd
Merge pull requestRuleWorld#15from Psuedonerd/codex/inspect-model-f…
493d859
…olders-in-rulehub-repo-x1b29a
Add AI-generated model summaries and index (JSON + markdown files)
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Update metadata-schema.yaml by vcellmike · Pull Request #15 · RuleWorld/RuleHub · GitHub
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Update metadata-schema.yaml - #15
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jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
Jun 24, 2026
Merged
Update metadata-schema.yaml#15
jrfaeder merged 9 commits into
RuleWorld:masterfrom 
vcellmike:master
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@vcellmike
@vcellmikevcellmike
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Jun 23, 2026

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Hello,
I've added some new keys to metadata, such as related to VCell and other rule-based tools.
Major changes to the existing schema:
  • category (which is now single value and includes such different terms as tutorial and immunology) is divided into two lists: one is biol_categories, one is comp_categories.
  • new keys in compatibility
  • features are added, where I collected existing (e.g. uses_energy) and added many more that affect other tools (such as uses_multiple_identical_sites).
  • uses_compartments is replaced with uses_cbngl_compartments, as I have also uses_vcell_compartments.
Minor changes:
  • added comments
  • added tested
  • added default_sim_command - the one that is actually in bngl
@jrfaeder
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Jun 24, 2026

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Please address the file causing the validation to fail.
@vcellmike
vcellmike
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Jun 24, 2026

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The new .yaml examples file was an accident. Schema is updated with the year. Please use default values when updating all yaml files for the new schema:

rr_compatible: true

bnglviz_compatible: true

vcell_compatible: false

molclustpy_compatible: false
@jrfaeder
jrfaeder
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Jun 24, 2026

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Ok, it's still failing the CI check but maybe that's premature anyway since updating model data is a work in progress. I will go ahead and merge.
@jrfaeder
jrfaeder
merged commit b84f0a7
into
RuleWorld:masterJun 24, 2026

1 check failed

vcellmike pushed a commit
to vcellmike/RuleHub
that referenced
this pull request
Aug 10, 2026
@Psuedonerd
Merge pull requestRuleWorld#15from Psuedonerd/codex/inspect-model-f…
493d859
…olders-in-rulehub-repo-x1b29a
Add AI-generated model summaries and index (JSON + markdown files)
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