Update to Python 3.10, fix GitHub workflow and automated tests - #99

Merged
martinburchell merged 22 commits into
intermine:devfrom
ucam-department-of-psychiatry:python310-dev
Nov 21, 2025
Merged

Update to Python 3.10, fix GitHub workflow and automated tests#99
martinburchell merged 22 commits into
intermine:devfrom
ucam-department-of-psychiatry:python310-dev

Conversation

@martinburchell

@martinburchellmartinburchell commented Nov 18, 2025

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  • Update to Python 3.10, which is the oldest supported version
  • Update Python packages
  • Update Postgres in CI workflow to 14, which is the oldest supported version
  • Fix the CI scripts so they can be run locally
  • Don't try to support curl and wget as wget is assumed to be present elsewhere
  • Use Postgres over TCP not Unix socket as this is assumed elsewhere
  • Fix failing tests by replacing exact match XML comparison with checking specific nodes. There is scope for further optimisation here as there is a lot of duplication in the tests.

Note that the CI script is currently set up to work with the Intermine fork at https://github.com/ucam-department-of-psychiatry/intermine.git, build-workflows branch. We can update that once it is merged.

@martinburchell
Use later Postgres in GitHub test workflow
04f945d
@martinburchell
Use Python 3.10 in GitHub workflow
aa68843
Also use later versions of checkout and setup-python
@martinburchell
Better error handling in worflow
8dc7e3c
@martinburchell
Install python3-lxml build dependencies in workflow
771011c
@martinburchell
Try another way to install lxml dependencies
2c3c460
with apt-get build-dep we need a deb-src entry in sources.list. We can do that but I'd rather not.
@martinburchell
Use later setuptools
4746a5c
@martinburchell
python3-dev, not python-dev
3a538ea
@martinburchell
Upgrade all of the python packages
be72854
@martinburchell
Fix import errors
f056fc0
@martinburchell
Less noisy CI output
d48f766
@martinburchell
Make Solr initialisation runable locally
3b7a576
@martinburchell
Improvements to run workflow locally
5472ff2
@martinburchell
Set up Java in workflow
98ed65e
@martinburchell
Ignore Intermine directory
ec652e4
@martinburchell
Fix XML comparison tests
e054326
@martinburchell
Drop test databases in CI workflow
72f5643
@martinburchell
Replace removed base64.encodestring()
3bfe4fc
@martinburchell
Use Postgres 14 in workflow as 13 now EOL
0daca89
@martinburchell
Possible fix for GitHub workflow failure when fetching Java
84adc9d
Error: Unexpected HTTP status code '500' when retrieving versions from 'https://static.azul.com/zulu/bin/'. error code: 500
@martinburchell
Bump urllib3 to fixCVE-2025-50181andCVE-2025-50182
377d773
@martinburchell
Bump requests to fixCVE-2024-47081
1f18e95
@martinburchellmartinburchell mentioned this pull request Nov 19, 2025
Merged
7 tasks
@martinburchell
martinburchell merged commit 1e2ebfe into intermine:devNov 21, 2025
1 check failed
@martinburchell
martinburchell deleted the python310-dev branch November 21, 2025 18:19
@martinburchellmartinburchell mentioned this pull request Jan 11, 2026
Closed
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@martinburchell
, '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
Update to Python 3.10, fix GitHub workflow and automated tests - #99
Merged
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Nov 21, 2025
Merged
Update to Python 3.10, fix GitHub workflow and automated tests#99
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Conversation
@martinburchell
@martinburchellmartinburchell
commented
Nov 18, 2025

Copy link


Copy Markdown

Member
  • Update to Python 3.10, which is the oldest supported version
  • Update Python packages
  • Update Postgres in CI workflow to 14, which is the oldest supported version
  • Fix the CI scripts so they can be run locally
  • Don't try to support curl and wget as wget is assumed to be present elsewhere
  • Use Postgres over TCP not Unix socket as this is assumed elsewhere
  • Fix failing tests by replacing exact match XML comparison with checking specific nodes. There is scope for further optimisation here as there is a lot of duplication in the tests.
Note that the CI script is currently set up to work with the Intermine fork at https://github.com/ucam-department-of-psychiatry/intermine.git, build-workflows branch. We can update that once it is merged.
@martinburchell
Use later Postgres in GitHub test workflow
04f945d
@martinburchell
Use Python 3.10 in GitHub workflow
aa68843
Also use later versions of checkout and setup-python
@martinburchell
Better error handling in worflow
8dc7e3c
@martinburchell
Install python3-lxml build dependencies in workflow
771011c
@martinburchell
Try another way to install lxml dependencies
2c3c460
with apt-get build-dep we need a deb-src entry in sources.list. We can do that but I'd rather not.
@martinburchell
Use later setuptools
4746a5c
@martinburchell
python3-dev, not python-dev
3a538ea
@martinburchell
Upgrade all of the python packages
be72854
@martinburchell
Fix import errors
f056fc0
@martinburchell
Less noisy CI output
d48f766
@martinburchell
Make Solr initialisation runable locally
3b7a576
@martinburchell
Improvements to run workflow locally
5472ff2
@martinburchell
Set up Java in workflow
98ed65e
@martinburchell
Ignore Intermine directory
ec652e4
@martinburchell
Fix XML comparison tests
e054326
@martinburchell
Drop test databases in CI workflow
72f5643
@martinburchell
Replace removed base64.encodestring()
3bfe4fc
@martinburchell
Use Postgres 14 in workflow as 13 now EOL
0daca89
@martinburchell
Possible fix for GitHub workflow failure when fetching Java
84adc9d
Error: Unexpected HTTP status code '500' when retrieving versions from 'https://static.azul.com/zulu/bin/'. error code: 500
@martinburchell
Bump urllib3 to fixCVE-2025-50181andCVE-2025-50182
377d773
@martinburchell
Bump requests to fixCVE-2024-47081
1f18e95
@martinburchellmartinburchell
mentioned this pull request
Nov 19, 2025
 Merged

7 tasks
@martinburchell
martinburchell
merged commit 1e2ebfe
into
intermine:devNov 21, 2025

1 check failed

@martinburchell
martinburchell
deleted the

python310-dev

branch
November 21, 2025 18:19
@martinburchellmartinburchell
mentioned this pull request
Jan 11, 2026
 Closed

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1 participant

@martinburchell

, '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
Update to Python 3.10, fix GitHub workflow and automated tests - #99
Merged
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Nov 21, 2025
Merged
Update to Python 3.10, fix GitHub workflow and automated tests#99
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Conversation
@martinburchell
@martinburchellmartinburchell
commented
Nov 18, 2025

Copy link


Copy Markdown

Member
  • Update to Python 3.10, which is the oldest supported version
  • Update Python packages
  • Update Postgres in CI workflow to 14, which is the oldest supported version
  • Fix the CI scripts so they can be run locally
  • Don't try to support curl and wget as wget is assumed to be present elsewhere
  • Use Postgres over TCP not Unix socket as this is assumed elsewhere
  • Fix failing tests by replacing exact match XML comparison with checking specific nodes. There is scope for further optimisation here as there is a lot of duplication in the tests.
Note that the CI script is currently set up to work with the Intermine fork at https://github.com/ucam-department-of-psychiatry/intermine.git, build-workflows branch. We can update that once it is merged.
@martinburchell
Use later Postgres in GitHub test workflow
04f945d
@martinburchell
Use Python 3.10 in GitHub workflow
aa68843
Also use later versions of checkout and setup-python
@martinburchell
Better error handling in worflow
8dc7e3c
@martinburchell
Install python3-lxml build dependencies in workflow
771011c
@martinburchell
Try another way to install lxml dependencies
2c3c460
with apt-get build-dep we need a deb-src entry in sources.list. We can do that but I'd rather not.
@martinburchell
Use later setuptools
4746a5c
@martinburchell
python3-dev, not python-dev
3a538ea
@martinburchell
Upgrade all of the python packages
be72854
@martinburchell
Fix import errors
f056fc0
@martinburchell
Less noisy CI output
d48f766
@martinburchell
Make Solr initialisation runable locally
3b7a576
@martinburchell
Improvements to run workflow locally
5472ff2
@martinburchell
Set up Java in workflow
98ed65e
@martinburchell
Ignore Intermine directory
ec652e4
@martinburchell
Fix XML comparison tests
e054326
@martinburchell
Drop test databases in CI workflow
72f5643
@martinburchell
Replace removed base64.encodestring()
3bfe4fc
@martinburchell
Use Postgres 14 in workflow as 13 now EOL
0daca89
@martinburchell
Possible fix for GitHub workflow failure when fetching Java
84adc9d
Error: Unexpected HTTP status code '500' when retrieving versions from 'https://static.azul.com/zulu/bin/'. error code: 500
@martinburchell
Bump urllib3 to fixCVE-2025-50181andCVE-2025-50182
377d773
@martinburchell
Bump requests to fixCVE-2024-47081
1f18e95
@martinburchellmartinburchell
mentioned this pull request
Nov 19, 2025
 Merged

7 tasks
@martinburchell
martinburchell
merged commit 1e2ebfe
into
intermine:devNov 21, 2025

1 check failed

@martinburchell
martinburchell
deleted the

python310-dev

branch
November 21, 2025 18:19
@martinburchellmartinburchell
mentioned this pull request
Jan 11, 2026
 Closed

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1 participant

@martinburchell

, '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
Update to Python 3.10, fix GitHub workflow and automated tests - #99
Merged
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Nov 21, 2025
Merged
Update to Python 3.10, fix GitHub workflow and automated tests#99
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Conversation
@martinburchell
@martinburchellmartinburchell
commented
Nov 18, 2025

Copy link


Copy Markdown

Member
  • Update to Python 3.10, which is the oldest supported version
  • Update Python packages
  • Update Postgres in CI workflow to 14, which is the oldest supported version
  • Fix the CI scripts so they can be run locally
  • Don't try to support curl and wget as wget is assumed to be present elsewhere
  • Use Postgres over TCP not Unix socket as this is assumed elsewhere
  • Fix failing tests by replacing exact match XML comparison with checking specific nodes. There is scope for further optimisation here as there is a lot of duplication in the tests.
Note that the CI script is currently set up to work with the Intermine fork at https://github.com/ucam-department-of-psychiatry/intermine.git, build-workflows branch. We can update that once it is merged.
@martinburchell
Use later Postgres in GitHub test workflow
04f945d
@martinburchell
Use Python 3.10 in GitHub workflow
aa68843
Also use later versions of checkout and setup-python
@martinburchell
Better error handling in worflow
8dc7e3c
@martinburchell
Install python3-lxml build dependencies in workflow
771011c
@martinburchell
Try another way to install lxml dependencies
2c3c460
with apt-get build-dep we need a deb-src entry in sources.list. We can do that but I'd rather not.
@martinburchell
Use later setuptools
4746a5c
@martinburchell
python3-dev, not python-dev
3a538ea
@martinburchell
Upgrade all of the python packages
be72854
@martinburchell
Fix import errors
f056fc0
@martinburchell
Less noisy CI output
d48f766
@martinburchell
Make Solr initialisation runable locally
3b7a576
@martinburchell
Improvements to run workflow locally
5472ff2
@martinburchell
Set up Java in workflow
98ed65e
@martinburchell
Ignore Intermine directory
ec652e4
@martinburchell
Fix XML comparison tests
e054326
@martinburchell
Drop test databases in CI workflow
72f5643
@martinburchell
Replace removed base64.encodestring()
3bfe4fc
@martinburchell
Use Postgres 14 in workflow as 13 now EOL
0daca89
@martinburchell
Possible fix for GitHub workflow failure when fetching Java
84adc9d
Error: Unexpected HTTP status code '500' when retrieving versions from 'https://static.azul.com/zulu/bin/'. error code: 500
@martinburchell
Bump urllib3 to fixCVE-2025-50181andCVE-2025-50182
377d773
@martinburchell
Bump requests to fixCVE-2024-47081
1f18e95
@martinburchellmartinburchell
mentioned this pull request
Nov 19, 2025
 Merged

7 tasks
@martinburchell
martinburchell
merged commit 1e2ebfe
into
intermine:devNov 21, 2025

1 check failed

@martinburchell
martinburchell
deleted the

python310-dev

branch
November 21, 2025 18:19
@martinburchellmartinburchell
mentioned this pull request
Jan 11, 2026
 Closed

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No one assigned


Labels


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None yet


Milestone


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Development

Successfully merging this pull request may close these issues.

1 participant

@martinburchell

, '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
Update to Python 3.10, fix GitHub workflow and automated tests - #99
Merged
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Nov 21, 2025
Merged
Update to Python 3.10, fix GitHub workflow and automated tests#99
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Conversation
@martinburchell
@martinburchellmartinburchell
commented
Nov 18, 2025

Copy link


Copy Markdown

Member
  • Update to Python 3.10, which is the oldest supported version
  • Update Python packages
  • Update Postgres in CI workflow to 14, which is the oldest supported version
  • Fix the CI scripts so they can be run locally
  • Don't try to support curl and wget as wget is assumed to be present elsewhere
  • Use Postgres over TCP not Unix socket as this is assumed elsewhere
  • Fix failing tests by replacing exact match XML comparison with checking specific nodes. There is scope for further optimisation here as there is a lot of duplication in the tests.
Note that the CI script is currently set up to work with the Intermine fork at https://github.com/ucam-department-of-psychiatry/intermine.git, build-workflows branch. We can update that once it is merged.
@martinburchell
Use later Postgres in GitHub test workflow
04f945d
@martinburchell
Use Python 3.10 in GitHub workflow
aa68843
Also use later versions of checkout and setup-python
@martinburchell
Better error handling in worflow
8dc7e3c
@martinburchell
Install python3-lxml build dependencies in workflow
771011c
@martinburchell
Try another way to install lxml dependencies
2c3c460
with apt-get build-dep we need a deb-src entry in sources.list. We can do that but I'd rather not.
@martinburchell
Use later setuptools
4746a5c
@martinburchell
python3-dev, not python-dev
3a538ea
@martinburchell
Upgrade all of the python packages
be72854
@martinburchell
Fix import errors
f056fc0
@martinburchell
Less noisy CI output
d48f766
@martinburchell
Make Solr initialisation runable locally
3b7a576
@martinburchell
Improvements to run workflow locally
5472ff2
@martinburchell
Set up Java in workflow
98ed65e
@martinburchell
Ignore Intermine directory
ec652e4
@martinburchell
Fix XML comparison tests
e054326
@martinburchell
Drop test databases in CI workflow
72f5643
@martinburchell
Replace removed base64.encodestring()
3bfe4fc
@martinburchell
Use Postgres 14 in workflow as 13 now EOL
0daca89
@martinburchell
Possible fix for GitHub workflow failure when fetching Java
84adc9d
Error: Unexpected HTTP status code '500' when retrieving versions from 'https://static.azul.com/zulu/bin/'. error code: 500
@martinburchell
Bump urllib3 to fixCVE-2025-50181andCVE-2025-50182
377d773
@martinburchell
Bump requests to fixCVE-2024-47081
1f18e95
@martinburchellmartinburchell
mentioned this pull request
Nov 19, 2025
 Merged

7 tasks
@martinburchell
martinburchell
merged commit 1e2ebfe
into
intermine:devNov 21, 2025

1 check failed

@martinburchell
martinburchell
deleted the

python310-dev

branch
November 21, 2025 18:19
@martinburchellmartinburchell
mentioned this pull request
Jan 11, 2026
 Closed

Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone


No milestone


Development

Successfully merging this pull request may close these issues.

1 participant

@martinburchell

, '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
Update to Python 3.10, fix GitHub workflow and automated tests - #99
Merged
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Nov 21, 2025
Merged
Update to Python 3.10, fix GitHub workflow and automated tests#99
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Conversation
@martinburchell
@martinburchellmartinburchell
commented
Nov 18, 2025

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  • Update to Python 3.10, which is the oldest supported version
  • Update Python packages
  • Update Postgres in CI workflow to 14, which is the oldest supported version
  • Fix the CI scripts so they can be run locally
  • Don't try to support curl and wget as wget is assumed to be present elsewhere
  • Use Postgres over TCP not Unix socket as this is assumed elsewhere
  • Fix failing tests by replacing exact match XML comparison with checking specific nodes. There is scope for further optimisation here as there is a lot of duplication in the tests.
Note that the CI script is currently set up to work with the Intermine fork at https://github.com/ucam-department-of-psychiatry/intermine.git, build-workflows branch. We can update that once it is merged.
@martinburchell
Use later Postgres in GitHub test workflow
04f945d
@martinburchell
Use Python 3.10 in GitHub workflow
aa68843
Also use later versions of checkout and setup-python
@martinburchell
Better error handling in worflow
8dc7e3c
@martinburchell
Install python3-lxml build dependencies in workflow
771011c
@martinburchell
Try another way to install lxml dependencies
2c3c460
with apt-get build-dep we need a deb-src entry in sources.list. We can do that but I'd rather not.
@martinburchell
Use later setuptools
4746a5c
@martinburchell
python3-dev, not python-dev
3a538ea
@martinburchell
Upgrade all of the python packages
be72854
@martinburchell
Fix import errors
f056fc0
@martinburchell
Less noisy CI output
d48f766
@martinburchell
Make Solr initialisation runable locally
3b7a576
@martinburchell
Improvements to run workflow locally
5472ff2
@martinburchell
Set up Java in workflow
98ed65e
@martinburchell
Ignore Intermine directory
ec652e4
@martinburchell
Fix XML comparison tests
e054326
@martinburchell
Drop test databases in CI workflow
72f5643
@martinburchell
Replace removed base64.encodestring()
3bfe4fc
@martinburchell
Use Postgres 14 in workflow as 13 now EOL
0daca89
@martinburchell
Possible fix for GitHub workflow failure when fetching Java
84adc9d
Error: Unexpected HTTP status code '500' when retrieving versions from 'https://static.azul.com/zulu/bin/'. error code: 500
@martinburchell
Bump urllib3 to fixCVE-2025-50181andCVE-2025-50182
377d773
@martinburchell
Bump requests to fixCVE-2024-47081
1f18e95
@martinburchellmartinburchell
mentioned this pull request
Nov 19, 2025
 Merged

7 tasks
@martinburchell
martinburchell
merged commit 1e2ebfe
into
intermine:devNov 21, 2025

1 check failed

@martinburchell
martinburchell
deleted the

python310-dev

branch
November 21, 2025 18:19
@martinburchellmartinburchell
mentioned this pull request
Jan 11, 2026
 Closed

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, '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
Update to Python 3.10, fix GitHub workflow and automated tests - #99
Merged
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Nov 21, 2025
Merged
Update to Python 3.10, fix GitHub workflow and automated tests#99
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Conversation
@martinburchell
@martinburchellmartinburchell
commented
Nov 18, 2025

Copy link


Copy Markdown

Member
  • Update to Python 3.10, which is the oldest supported version
  • Update Python packages
  • Update Postgres in CI workflow to 14, which is the oldest supported version
  • Fix the CI scripts so they can be run locally
  • Don't try to support curl and wget as wget is assumed to be present elsewhere
  • Use Postgres over TCP not Unix socket as this is assumed elsewhere
  • Fix failing tests by replacing exact match XML comparison with checking specific nodes. There is scope for further optimisation here as there is a lot of duplication in the tests.
Note that the CI script is currently set up to work with the Intermine fork at https://github.com/ucam-department-of-psychiatry/intermine.git, build-workflows branch. We can update that once it is merged.
@martinburchell
Use later Postgres in GitHub test workflow
04f945d
@martinburchell
Use Python 3.10 in GitHub workflow
aa68843
Also use later versions of checkout and setup-python
@martinburchell
Better error handling in worflow
8dc7e3c
@martinburchell
Install python3-lxml build dependencies in workflow
771011c
@martinburchell
Try another way to install lxml dependencies
2c3c460
with apt-get build-dep we need a deb-src entry in sources.list. We can do that but I'd rather not.
@martinburchell
Use later setuptools
4746a5c
@martinburchell
python3-dev, not python-dev
3a538ea
@martinburchell
Upgrade all of the python packages
be72854
@martinburchell
Fix import errors
f056fc0
@martinburchell
Less noisy CI output
d48f766
@martinburchell
Make Solr initialisation runable locally
3b7a576
@martinburchell
Improvements to run workflow locally
5472ff2
@martinburchell
Set up Java in workflow
98ed65e
@martinburchell
Ignore Intermine directory
ec652e4
@martinburchell
Fix XML comparison tests
e054326
@martinburchell
Drop test databases in CI workflow
72f5643
@martinburchell
Replace removed base64.encodestring()
3bfe4fc
@martinburchell
Use Postgres 14 in workflow as 13 now EOL
0daca89
@martinburchell
Possible fix for GitHub workflow failure when fetching Java
84adc9d
Error: Unexpected HTTP status code '500' when retrieving versions from 'https://static.azul.com/zulu/bin/'. error code: 500
@martinburchell
Bump urllib3 to fixCVE-2025-50181andCVE-2025-50182
377d773
@martinburchell
Bump requests to fixCVE-2024-47081
1f18e95
@martinburchellmartinburchell
mentioned this pull request
Nov 19, 2025
 Merged

7 tasks
@martinburchell
martinburchell
merged commit 1e2ebfe
into
intermine:devNov 21, 2025

1 check failed

@martinburchell
martinburchell
deleted the

python310-dev

branch
November 21, 2025 18:19
@martinburchellmartinburchell
mentioned this pull request
Jan 11, 2026
 Closed

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1 participant

@martinburchell

, '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
Update to Python 3.10, fix GitHub workflow and automated tests - #99
Merged
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Nov 21, 2025
Merged
Update to Python 3.10, fix GitHub workflow and automated tests#99
martinburchell merged 22 commits into
intermine:devfrom 
ucam-department-of-psychiatry:python310-dev
Conversation
@martinburchell
@martinburchellmartinburchell
commented
Nov 18, 2025

Copy link


Copy Markdown

Member
  • Update to Python 3.10, which is the oldest supported version
  • Update Python packages
  • Update Postgres in CI workflow to 14, which is the oldest supported version
  • Fix the CI scripts so they can be run locally
  • Don't try to support curl and wget as wget is assumed to be present elsewhere
  • Use Postgres over TCP not Unix socket as this is assumed elsewhere
  • Fix failing tests by replacing exact match XML comparison with checking specific nodes. There is scope for further optimisation here as there is a lot of duplication in the tests.
Note that the CI script is currently set up to work with the Intermine fork at https://github.com/ucam-department-of-psychiatry/intermine.git, build-workflows branch. We can update that once it is merged.
@martinburchell
Use later Postgres in GitHub test workflow
04f945d
@martinburchell
Use Python 3.10 in GitHub workflow
aa68843
Also use later versions of checkout and setup-python
@martinburchell
Better error handling in worflow
8dc7e3c
@martinburchell
Install python3-lxml build dependencies in workflow
771011c
@martinburchell
Try another way to install lxml dependencies
2c3c460
with apt-get build-dep we need a deb-src entry in sources.list. We can do that but I'd rather not.
@martinburchell
Use later setuptools
4746a5c
@martinburchell
python3-dev, not python-dev
3a538ea
@martinburchell
Upgrade all of the python packages
be72854
@martinburchell
Fix import errors
f056fc0
@martinburchell
Less noisy CI output
d48f766
@martinburchell
Make Solr initialisation runable locally
3b7a576
@martinburchell
Improvements to run workflow locally
5472ff2
@martinburchell
Set up Java in workflow
98ed65e
@martinburchell
Ignore Intermine directory
ec652e4
@martinburchell
Fix XML comparison tests
e054326
@martinburchell
Drop test databases in CI workflow
72f5643
@martinburchell
Replace removed base64.encodestring()
3bfe4fc
@martinburchell
Use Postgres 14 in workflow as 13 now EOL
0daca89
@martinburchell
Possible fix for GitHub workflow failure when fetching Java
84adc9d
Error: Unexpected HTTP status code '500' when retrieving versions from 'https://static.azul.com/zulu/bin/'. error code: 500
@martinburchell
Bump urllib3 to fixCVE-2025-50181andCVE-2025-50182
377d773
@martinburchell
Bump requests to fixCVE-2024-47081
1f18e95
@martinburchellmartinburchell
mentioned this pull request
Nov 19, 2025
 Merged

7 tasks
@martinburchell
martinburchell
merged commit 1e2ebfe
into
intermine:devNov 21, 2025

1 check failed

@martinburchell
martinburchell
deleted the

python310-dev

branch
November 21, 2025 18:19
@martinburchellmartinburchell
mentioned this pull request
Jan 11, 2026
 Closed

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1 participant

@martinburchell