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Resolve BNG2.pl from $PATH via $BNGPATH env var #72

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Resolve BNG2.pl from $PATH via $BNGPATH env var#72

Description

@wshlavacek
wshlavacek
opened on May 9, 2026

Location:bionetgen/core/utils/utils.py:651

Original marker:

# TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route

test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.

What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.

Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.

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var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Resolve BNG2.pl from $PATH via $BNGPATH env var · Issue #72 · RuleWorld/PyBioNetGen · GitHub
      Skip to content
      Resolve BNG2.pl from $PATH via $BNGPATH env var #72
      Open
      Open
      Resolve BNG2.pl from $PATH via $BNGPATH env var#72
      Description
      @wshlavacek
      wshlavacek
      opened on May 9, 2026
      Location:bionetgen/core/utils/utils.py:651
      Original marker:
      # TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route

      test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.
      What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.
      Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
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var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
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document.head.appendChild(style);
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} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Resolve BNG2.pl from $PATH via $BNGPATH env var · Issue #72 · RuleWorld/PyBioNetGen · GitHub
          Skip to content
          Resolve BNG2.pl from $PATH via $BNGPATH env var #72
          Open
          Open
          Resolve BNG2.pl from $PATH via $BNGPATH env var#72
          Description
          @wshlavacek
          wshlavacek
          opened on May 9, 2026
          Location:bionetgen/core/utils/utils.py:651
          Original marker:
          # TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route

          test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.
          What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.
          Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.
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, 'i');
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var ref = document.referrer;
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observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Resolve BNG2.pl from $PATH via $BNGPATH env var · Issue #72 · RuleWorld/PyBioNetGen · GitHub
              Skip to content
              Resolve BNG2.pl from $PATH via $BNGPATH env var #72
              Open
              Open
              Resolve BNG2.pl from $PATH via $BNGPATH env var#72
              Description
              @wshlavacek
              wshlavacek
              opened on May 9, 2026
              Location:bionetgen/core/utils/utils.py:651
              Original marker:
              # TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route

              test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.
              What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.
              Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
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'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
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return url;
}
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if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Resolve BNG2.pl from $PATH via $BNGPATH env var · Issue #72 · RuleWorld/PyBioNetGen · GitHub
                  Skip to content
                  Resolve BNG2.pl from $PATH via $BNGPATH env var #72
                  Open
                  Open
                  Resolve BNG2.pl from $PATH via $BNGPATH env var#72
                  Description
                  @wshlavacek
                  wshlavacek
                  opened on May 9, 2026
                  Location:bionetgen/core/utils/utils.py:651
                  Original marker:
                  # TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route

                  test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.
                  What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.
                  Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
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function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
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observer.observe(document.body, { childList: true, subtree: true });
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Resolve BNG2.pl from $PATH via $BNGPATH env var · Issue #72 · RuleWorld/PyBioNetGen · GitHub
                      Skip to content
                      Resolve BNG2.pl from $PATH via $BNGPATH env var #72
                      Open
                      Open
                      Resolve BNG2.pl from $PATH via $BNGPATH env var#72
                      Description
                      @wshlavacek
                      wshlavacek
                      opened on May 9, 2026
                      Location:bionetgen/core/utils/utils.py:651
                      Original marker:
                      # TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route

                      test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.
                      What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.
                      Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.
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                          No branches or pull requests
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
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';
}
});
}
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('^' + ".*" + '
Resolve BNG2.pl from $PATH via $BNGPATH env var · Issue #72 · RuleWorld/PyBioNetGen · GitHub
                          Skip to content
                          Resolve BNG2.pl from $PATH via $BNGPATH env var #72
                          Open
                          Open
                          Resolve BNG2.pl from $PATH via $BNGPATH env var#72
                          Description
                          @wshlavacek
                          wshlavacek
                          opened on May 9, 2026
                          Location:bionetgen/core/utils/utils.py:651
                          Original marker:
                          # TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route

                          test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.
                          What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.
                          Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
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filter: none !important;
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filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
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::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
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::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
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var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Resolve BNG2.pl from $PATH via $BNGPATH env var · Issue #72 · RuleWorld/PyBioNetGen · GitHub
                              Skip to content
                              Resolve BNG2.pl from $PATH via $BNGPATH env var #72
                              Open
                              Open
                              Resolve BNG2.pl from $PATH via $BNGPATH env var#72
                              Description
                              @wshlavacek
                              wshlavacek
                              opened on May 9, 2026
                              Location:bionetgen/core/utils/utils.py:651
                              Original marker:
                              # TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route

                              test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.
                              What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.
                              Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.
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