Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories - #32

Merged
Rob-Welch merged 4 commits into
mainfrom
31-resolve-release-workflow-configuration
Jul 24, 2026
Merged

Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories#32
Rob-Welch merged 4 commits into
mainfrom
31-resolve-release-workflow-configuration

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@harryswift01

@harryswift01harryswift01 commented Jul 15, 2026

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Summary

This PR updates prepmd’s packaging and release setup to align more closely with the approach used by other CCPBioSim repos.

Changes

Package configuration

  • Switched the project build backend to Flit.
  • Added dynamic versioning using prepmd.__version__.
  • Simplified prepmd/__init__.py by removing eager imports of all submodules.
  • Retained the existing prepmd, runmd, and prep-license command-line entry points.

Conda packaging

  • Updated the Conda recipe to build the package using Flit.
  • Added the required prepmd runtime dependencies.
  • Kept openff-toolkit as a Conda runtime dependency.
  • Added import and command-line checks to the Conda package tests.
  • Configured dependency resolution through conda-forge.

Release workflow

  • Added automated version updates for prepmd/__init__.py and CITATION.cff.
  • Added automatic Git tagging and GitHub release creation.
  • Added automated Conda package building and publishing to Anaconda.org.
  • Kept the Conda recipe version as a placeholder that is replaced during the release workflow.

Impact

  • Makes prepmd’s packaging and release process more consistent with other CCPBioSim repos.
  • Avoids importing every prepmd module during a basic package import.
  • Reduces import failures caused by optional or heavyweight dependencies.
  • Provides a more consistent and repeatable Conda release process.

@harryswift01harryswift01 self-assigned this Jul 15, 2026
@harryswift01harryswift01 linked an issue Jul 15, 2026 that may be closed by this pull request
Resolve release workflow configuration #31
Closed
@harryswift01harryswift01 changed the title Align PrepMD Packaging and Release Workflow with Other CCPBioSim RepositoriesAlign prepmd Packaging and Release Workflow with Other CCPBioSim RepositoriesJul 16, 2026
@Rob-Welch
Rob-Welch merged commit 94117a3 into mainJul 24, 2026
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Resolve release workflow configuration

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, '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
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories - #32
Merged
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Jul 24, 2026
Merged
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories#32
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Conversation
@harryswift01
@harryswift01harryswift01
commented
Jul 15, 2026

Copy link


Copy Markdown

Member
Summary
This PR updates prepmd’s packaging and release setup to align more closely with the approach used by other CCPBioSim repos.
Changes
Package configuration
  • Switched the project build backend to Flit.
  • Added dynamic versioning using prepmd.__version__.
  • Simplified prepmd/__init__.py by removing eager imports of all submodules.
  • Retained the existing prepmd, runmd, and prep-license command-line entry points.
Conda packaging
  • Updated the Conda recipe to build the package using Flit.
  • Added the required prepmd runtime dependencies.
  • Kept openff-toolkit as a Conda runtime dependency.
  • Added import and command-line checks to the Conda package tests.
  • Configured dependency resolution through conda-forge.
Release workflow
  • Added automated version updates for prepmd/__init__.py and CITATION.cff.
  • Added automatic Git tagging and GitHub release creation.
  • Added automated Conda package building and publishing to Anaconda.org.
  • Kept the Conda recipe version as a placeholder that is replaced during the release workflow.
Impact
  • Makes prepmd’s packaging and release process more consistent with other CCPBioSim repos.
  • Avoids importing every prepmd module during a basic package import.
  • Reduces import failures caused by optional or heavyweight dependencies.
  • Provides a more consistent and repeatable Conda release process.
@harryswift01harryswift01
self-assigned this
Jul 15, 2026
@harryswift01harryswift01
linked an issue
Jul 15, 2026
that may be
closed
by this pull request


Resolve release workflow configuration
#31

Closed

@harryswift01harryswift01
changed the title
Align PrepMD Packaging and Release Workflow with Other CCPBioSim RepositoriesAlign prepmd Packaging and Release Workflow with Other CCPBioSim RepositoriesJul 16, 2026
@Rob-Welch
Rob-Welch
merged commit 94117a3
into
mainJul 24, 2026

3 of 5 checks passed

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@Rob-WelchRob-WelchAwaiting requested review from Rob-Welch

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Development

Successfully merging this pull request may close these issues.

Resolve release workflow configuration


2 participants

@harryswift01@Rob-Welch

, '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
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories - #32
Merged
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Jul 24, 2026
Merged
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories#32
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Conversation
@harryswift01
@harryswift01harryswift01
commented
Jul 15, 2026

Copy link


Copy Markdown

Member
Summary
This PR updates prepmd’s packaging and release setup to align more closely with the approach used by other CCPBioSim repos.
Changes
Package configuration
  • Switched the project build backend to Flit.
  • Added dynamic versioning using prepmd.__version__.
  • Simplified prepmd/__init__.py by removing eager imports of all submodules.
  • Retained the existing prepmd, runmd, and prep-license command-line entry points.
Conda packaging
  • Updated the Conda recipe to build the package using Flit.
  • Added the required prepmd runtime dependencies.
  • Kept openff-toolkit as a Conda runtime dependency.
  • Added import and command-line checks to the Conda package tests.
  • Configured dependency resolution through conda-forge.
Release workflow
  • Added automated version updates for prepmd/__init__.py and CITATION.cff.
  • Added automatic Git tagging and GitHub release creation.
  • Added automated Conda package building and publishing to Anaconda.org.
  • Kept the Conda recipe version as a placeholder that is replaced during the release workflow.
Impact
  • Makes prepmd’s packaging and release process more consistent with other CCPBioSim repos.
  • Avoids importing every prepmd module during a basic package import.
  • Reduces import failures caused by optional or heavyweight dependencies.
  • Provides a more consistent and repeatable Conda release process.
@harryswift01harryswift01
self-assigned this
Jul 15, 2026
@harryswift01harryswift01
linked an issue
Jul 15, 2026
that may be
closed
by this pull request


Resolve release workflow configuration
#31

Closed

@harryswift01harryswift01
changed the title
Align PrepMD Packaging and Release Workflow with Other CCPBioSim RepositoriesAlign prepmd Packaging and Release Workflow with Other CCPBioSim RepositoriesJul 16, 2026
@Rob-Welch
Rob-Welch
merged commit 94117a3
into
mainJul 24, 2026

3 of 5 checks passed

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@Rob-WelchRob-WelchAwaiting requested review from Rob-Welch

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Development

Successfully merging this pull request may close these issues.

Resolve release workflow configuration


2 participants

@harryswift01@Rob-Welch

, '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
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories - #32
Merged
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Jul 24, 2026
Merged
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories#32
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Conversation
@harryswift01
@harryswift01harryswift01
commented
Jul 15, 2026

Copy link


Copy Markdown

Member
Summary
This PR updates prepmd’s packaging and release setup to align more closely with the approach used by other CCPBioSim repos.
Changes
Package configuration
  • Switched the project build backend to Flit.
  • Added dynamic versioning using prepmd.__version__.
  • Simplified prepmd/__init__.py by removing eager imports of all submodules.
  • Retained the existing prepmd, runmd, and prep-license command-line entry points.
Conda packaging
  • Updated the Conda recipe to build the package using Flit.
  • Added the required prepmd runtime dependencies.
  • Kept openff-toolkit as a Conda runtime dependency.
  • Added import and command-line checks to the Conda package tests.
  • Configured dependency resolution through conda-forge.
Release workflow
  • Added automated version updates for prepmd/__init__.py and CITATION.cff.
  • Added automatic Git tagging and GitHub release creation.
  • Added automated Conda package building and publishing to Anaconda.org.
  • Kept the Conda recipe version as a placeholder that is replaced during the release workflow.
Impact
  • Makes prepmd’s packaging and release process more consistent with other CCPBioSim repos.
  • Avoids importing every prepmd module during a basic package import.
  • Reduces import failures caused by optional or heavyweight dependencies.
  • Provides a more consistent and repeatable Conda release process.
@harryswift01harryswift01
self-assigned this
Jul 15, 2026
@harryswift01harryswift01
linked an issue
Jul 15, 2026
that may be
closed
by this pull request


Resolve release workflow configuration
#31

Closed

@harryswift01harryswift01
changed the title
Align PrepMD Packaging and Release Workflow with Other CCPBioSim RepositoriesAlign prepmd Packaging and Release Workflow with Other CCPBioSim RepositoriesJul 16, 2026
@Rob-Welch
Rob-Welch
merged commit 94117a3
into
mainJul 24, 2026

3 of 5 checks passed

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Reviewers

@Rob-WelchRob-WelchAwaiting requested review from Rob-Welch

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Development

Successfully merging this pull request may close these issues.

Resolve release workflow configuration


2 participants

@harryswift01@Rob-Welch

, '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
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories - #32
Merged
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Jul 24, 2026
Merged
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories#32
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Conversation
@harryswift01
@harryswift01harryswift01
commented
Jul 15, 2026

Copy link


Copy Markdown

Member
Summary
This PR updates prepmd’s packaging and release setup to align more closely with the approach used by other CCPBioSim repos.
Changes
Package configuration
  • Switched the project build backend to Flit.
  • Added dynamic versioning using prepmd.__version__.
  • Simplified prepmd/__init__.py by removing eager imports of all submodules.
  • Retained the existing prepmd, runmd, and prep-license command-line entry points.
Conda packaging
  • Updated the Conda recipe to build the package using Flit.
  • Added the required prepmd runtime dependencies.
  • Kept openff-toolkit as a Conda runtime dependency.
  • Added import and command-line checks to the Conda package tests.
  • Configured dependency resolution through conda-forge.
Release workflow
  • Added automated version updates for prepmd/__init__.py and CITATION.cff.
  • Added automatic Git tagging and GitHub release creation.
  • Added automated Conda package building and publishing to Anaconda.org.
  • Kept the Conda recipe version as a placeholder that is replaced during the release workflow.
Impact
  • Makes prepmd’s packaging and release process more consistent with other CCPBioSim repos.
  • Avoids importing every prepmd module during a basic package import.
  • Reduces import failures caused by optional or heavyweight dependencies.
  • Provides a more consistent and repeatable Conda release process.
@harryswift01harryswift01
self-assigned this
Jul 15, 2026
@harryswift01harryswift01
linked an issue
Jul 15, 2026
that may be
closed
by this pull request


Resolve release workflow configuration
#31

Closed

@harryswift01harryswift01
changed the title
Align PrepMD Packaging and Release Workflow with Other CCPBioSim RepositoriesAlign prepmd Packaging and Release Workflow with Other CCPBioSim RepositoriesJul 16, 2026
@Rob-Welch
Rob-Welch
merged commit 94117a3
into
mainJul 24, 2026

3 of 5 checks passed

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@Rob-WelchRob-WelchAwaiting requested review from Rob-Welch

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Development

Successfully merging this pull request may close these issues.

Resolve release workflow configuration


2 participants

@harryswift01@Rob-Welch

, '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
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories - #32
Merged
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Jul 24, 2026
Merged
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories#32
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Conversation
@harryswift01
@harryswift01harryswift01
commented
Jul 15, 2026

Copy link


Copy Markdown

Member
Summary
This PR updates prepmd’s packaging and release setup to align more closely with the approach used by other CCPBioSim repos.
Changes
Package configuration
  • Switched the project build backend to Flit.
  • Added dynamic versioning using prepmd.__version__.
  • Simplified prepmd/__init__.py by removing eager imports of all submodules.
  • Retained the existing prepmd, runmd, and prep-license command-line entry points.
Conda packaging
  • Updated the Conda recipe to build the package using Flit.
  • Added the required prepmd runtime dependencies.
  • Kept openff-toolkit as a Conda runtime dependency.
  • Added import and command-line checks to the Conda package tests.
  • Configured dependency resolution through conda-forge.
Release workflow
  • Added automated version updates for prepmd/__init__.py and CITATION.cff.
  • Added automatic Git tagging and GitHub release creation.
  • Added automated Conda package building and publishing to Anaconda.org.
  • Kept the Conda recipe version as a placeholder that is replaced during the release workflow.
Impact
  • Makes prepmd’s packaging and release process more consistent with other CCPBioSim repos.
  • Avoids importing every prepmd module during a basic package import.
  • Reduces import failures caused by optional or heavyweight dependencies.
  • Provides a more consistent and repeatable Conda release process.
@harryswift01harryswift01
self-assigned this
Jul 15, 2026
@harryswift01harryswift01
linked an issue
Jul 15, 2026
that may be
closed
by this pull request


Resolve release workflow configuration
#31

Closed

@harryswift01harryswift01
changed the title
Align PrepMD Packaging and Release Workflow with Other CCPBioSim RepositoriesAlign prepmd Packaging and Release Workflow with Other CCPBioSim RepositoriesJul 16, 2026
@Rob-Welch
Rob-Welch
merged commit 94117a3
into
mainJul 24, 2026

3 of 5 checks passed

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Reviewers

@Rob-WelchRob-WelchAwaiting requested review from Rob-Welch

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No milestone


Development

Successfully merging this pull request may close these issues.

Resolve release workflow configuration


2 participants

@harryswift01@Rob-Welch

, '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('^' + ".*" + '

Skip to content
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories - #32
Merged
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Jul 24, 2026
Merged
Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories#32
Rob-Welch merged 4 commits into
mainfrom 
31-resolve-release-workflow-configuration
Conversation
@harryswift01
@harryswift01harryswift01
commented
Jul 15, 2026

Copy link


Copy Markdown

Member
Summary
This PR updates prepmd’s packaging and release setup to align more closely with the approach used by other CCPBioSim repos.
Changes
Package configuration
  • Switched the project build backend to Flit.
  • Added dynamic versioning using prepmd.__version__.
  • Simplified prepmd/__init__.py by removing eager imports of all submodules.
  • Retained the existing prepmd, runmd, and prep-license command-line entry points.
Conda packaging
  • Updated the Conda recipe to build the package using Flit.
  • Added the required prepmd runtime dependencies.
  • Kept openff-toolkit as a Conda runtime dependency.
  • Added import and command-line checks to the Conda package tests.
  • Configured dependency resolution through conda-forge.
Release workflow
  • Added automated version updates for prepmd/__init__.py and CITATION.cff.
  • Added automatic Git tagging and GitHub release creation.
  • Added automated Conda package building and publishing to Anaconda.org.
  • Kept the Conda recipe version as a placeholder that is replaced during the release workflow.
Impact
  • Makes prepmd’s packaging and release process more consistent with other CCPBioSim repos.
  • Avoids importing every prepmd module during a basic package import.
  • Reduces import failures caused by optional or heavyweight dependencies.
  • Provides a more consistent and repeatable Conda release process.
@harryswift01harryswift01
self-assigned this
Jul 15, 2026
@harryswift01harryswift01
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Jul 15, 2026
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Resolve release workflow configuration
#31

Closed

@harryswift01harryswift01
changed the title
Align PrepMD Packaging and Release Workflow with Other CCPBioSim RepositoriesAlign prepmd Packaging and Release Workflow with Other CCPBioSim RepositoriesJul 16, 2026
@Rob-Welch
Rob-Welch
merged commit 94117a3
into
mainJul 24, 2026

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Resolve release workflow configuration


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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); }
})();
})();

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Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories - #32
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Rob-Welch merged 4 commits into
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31-resolve-release-workflow-configuration
Jul 24, 2026
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Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories#32
Rob-Welch merged 4 commits into
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31-resolve-release-workflow-configuration
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Summary
This PR updates prepmd’s packaging and release setup to align more closely with the approach used by other CCPBioSim repos.
Changes
Package configuration
  • Switched the project build backend to Flit.
  • Added dynamic versioning using prepmd.__version__.
  • Simplified prepmd/__init__.py by removing eager imports of all submodules.
  • Retained the existing prepmd, runmd, and prep-license command-line entry points.
Conda packaging
  • Updated the Conda recipe to build the package using Flit.
  • Added the required prepmd runtime dependencies.
  • Kept openff-toolkit as a Conda runtime dependency.
  • Added import and command-line checks to the Conda package tests.
  • Configured dependency resolution through conda-forge.
Release workflow
  • Added automated version updates for prepmd/__init__.py and CITATION.cff.
  • Added automatic Git tagging and GitHub release creation.
  • Added automated Conda package building and publishing to Anaconda.org.
  • Kept the Conda recipe version as a placeholder that is replaced during the release workflow.
Impact
  • Makes prepmd’s packaging and release process more consistent with other CCPBioSim repos.
  • Avoids importing every prepmd module during a basic package import.
  • Reduces import failures caused by optional or heavyweight dependencies.
  • Provides a more consistent and repeatable Conda release process.
@harryswift01harryswift01
self-assigned this
Jul 15, 2026
@harryswift01harryswift01
linked an issue
Jul 15, 2026
that may be
closed
by this pull request


Resolve release workflow configuration
#31

Closed

@harryswift01harryswift01
changed the title
Align PrepMD Packaging and Release Workflow with Other CCPBioSim RepositoriesAlign prepmd Packaging and Release Workflow with Other CCPBioSim RepositoriesJul 16, 2026
@Rob-Welch
Rob-Welch
merged commit 94117a3
into
mainJul 24, 2026

3 of 5 checks passed

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Reviewers

@Rob-WelchRob-WelchAwaiting requested review from Rob-Welch

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@harryswift01harryswift01

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Development

Successfully merging this pull request may close these issues.

Resolve release workflow configuration


2 participants

@harryswift01@Rob-Welch