Support numpy >= 2.4 with backward-compatible fixes - #5

Merged
pmrv merged 2 commits into
masterfrom
claude/numpy-24-compat
Jul 16, 2026
Merged

Support numpy >= 2.4 with backward-compatible fixes#5
pmrv merged 2 commits into
masterfrom
claude/numpy-24-compat

Conversation

@pmrv

@pmrvpmrv commented Jul 16, 2026

Copy link
Copy Markdown
Owner

Pull Request Template

Description of Changes

Follow-up to #3: makes the code compatible with numpy ≥ 2.4 in a backward-compatible way and relaxes the requirement from numpy<2.4 to numpy<3.

Two numpy 2.4 breakages are fixed, both working identically on old and new numpy:

  1. Scalar energy output (src/pyace/asecalc.py). numpy 2.4 expired the "conversion of an array with ndim > 0 to a scalar" deprecation, so np.float64(energy.reshape(-1,)) started returning a shape-(1,) array instead of a scalar, and get_potential_energy() leaked an array of the total energy. The results dicts now use float() on the 0-d/scalar values (energy, free_energy, and the ensemble energy_std/energy_dev), which behaves identically on every numpy version, and .astype(np.float64) on per-atom arrays (energies_dev, forces_dev) — this also fixes those arrays silently degrading to scalars for single-atom structures on older numpy.
  2. np.trapz removal (src/pyace/radial.py). np.trapz was a deprecated alias of np.trapezoid from numpy 2.0 and was removed in 2.4. The module now picks np.trapezoid when it exists and falls back to np.trapz on numpy 1.x.

A regression assertion is added to tests/test_PyACECalculator.py so the energy coming back as an array would fail the tests.

Verification: built the package and ran tests/test_PyACECalculator.py (13 tests) against numpy 1.26.4 (exercises the np.trapz fallback), 2.3.5, and 2.4.6 — all pass on each. CI on this PR additionally covers the full test suite, which will now resolve numpy 2.4.x.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (full suite in CI; calculator tests locally against numpy 1.26.4 / 2.3.5 / 2.4.6)
  • Relevant documentation has been updated if necessary. (no docs reference the numpy pin)

License Agreement

By submitting this pull request, I agree that:

  • The code submitted in this pull request will be distributed under the Academic Software License (free for academic non-commercial use, not free for commercial use), see LICENSE.md for more details.
  • The copyright for the code, including the submitted code, remains with Ruhr University Bochum. Ruhr University Bochum retains the right to transfer or modify the copyright.

🤖 Generated with Claude Code

https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg

Generated by Claude Code

@claude
Support numpy >= 2.4 with backward-compatible fixes
08090c6
numpy 2.4 expired the ndim>0-to-scalar deprecation: np.float64(arr)
now returns an array for 1-element arrays instead of collapsing to a
scalar, so PyACECalculator's results['energy'] leaked out as a
shape-(1,) array from get_potential_energy(). Use float() on the 0-d
energy values instead, which behaves identically on all numpy versions,
and astype(np.float64) for per-atom arrays (also fixing energies_dev
degrading to a scalar for single-atom structures on older numpy).
numpy 2.4 also removed np.trapz (deprecated alias of np.trapezoid
since 2.0); pyace.radial now picks whichever exists.
Verified by building the package and running tests/test_PyACECalculator.py
against numpy 1.26.4, 2.3.5 and 2.4.6. Relax the numpy requirement to <3
accordingly.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
pmrv
pmrv commented Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py Outdated
pmrv
pmrv commented Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py Outdated
@claude
Drop review-flagged explanatory comments
ace21f4
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrv merged commit 2544d97 into masterJul 16, 2026
2 of 3 checks passed
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.

2 participants

@pmrv@claude
, '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
Support numpy >= 2.4 with backward-compatible fixes - #5
Merged
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Jul 16, 2026
Merged
Support numpy >= 2.4 with backward-compatible fixes#5
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Conversation
@pmrv
@pmrvpmrv
commented
Jul 16, 2026

Copy link


Copy Markdown

Owner
Pull Request Template
Description of Changes
Follow-up to #3: makes the code compatible with numpy ≥ 2.4 in a backward-compatible way and relaxes the requirement from numpy<2.4 to numpy<3.
Two numpy 2.4 breakages are fixed, both working identically on old and new numpy:
  1. Scalar energy output (src/pyace/asecalc.py). numpy 2.4 expired the "conversion of an array with ndim > 0 to a scalar" deprecation, so np.float64(energy.reshape(-1,)) started returning a shape-(1,) array instead of a scalar, and get_potential_energy() leaked an array of the total energy. The results dicts now use float() on the 0-d/scalar values (energy, free_energy, and the ensemble energy_std/energy_dev), which behaves identically on every numpy version, and .astype(np.float64) on per-atom arrays (energies_dev, forces_dev) — this also fixes those arrays silently degrading to scalars for single-atom structures on older numpy.
  2. np.trapz removal (src/pyace/radial.py). np.trapz was a deprecated alias of np.trapezoid from numpy 2.0 and was removed in 2.4. The module now picks np.trapezoid when it exists and falls back to np.trapz on numpy 1.x.
A regression assertion is added to tests/test_PyACECalculator.py so the energy coming back as an array would fail the tests.
Verification: built the package and ran tests/test_PyACECalculator.py (13 tests) against numpy 1.26.4 (exercises the np.trapz fallback), 2.3.5, and 2.4.6 — all pass on each. CI on this PR additionally covers the full test suite, which will now resolve numpy 2.4.x.
Checklist
  •  Code is well-documented.
  •  All tests have been run and passed. (full suite in CI; calculator tests locally against numpy 1.26.4 / 2.3.5 / 2.4.6)
  •  Relevant documentation has been updated if necessary. (no docs reference the numpy pin)
License Agreement
By submitting this pull request, I agree that:
  • The code submitted in this pull request will be distributed under the Academic Software License (free for academic non-commercial use, not free for commercial use), see LICENSE.md for more details.
  • The copyright for the code, including the submitted code, remains with Ruhr University Bochum. Ruhr University Bochum retains the right to transfer or modify the copyright.
🤖 Generated with Claude Code
https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
Generated by Claude Code
@claude
Support numpy >= 2.4 with backward-compatible fixes
08090c6
numpy 2.4 expired the ndim>0-to-scalar deprecation: np.float64(arr)
now returns an array for 1-element arrays instead of collapsing to a
scalar, so PyACECalculator's results['energy'] leaked out as a
shape-(1,) array from get_potential_energy(). Use float() on the 0-d
energy values instead, which behaves identically on all numpy versions,
and astype(np.float64) for per-atom arrays (also fixing energies_dev
degrading to a scalar for single-atom structures on older numpy).
numpy 2.4 also removed np.trapz (deprecated alias of np.trapezoid
since 2.0); pyace.radial now picks whichever exists.
Verified by building the package and running tests/test_PyACECalculator.py
against numpy 1.26.4, 2.3.5 and 2.4.6. Relax the numpy requirement to <3
accordingly.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

@claude
Drop review-flagged explanatory comments
ace21f4
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrv
merged commit 2544d97
into
masterJul 16, 2026

2 of 3 checks passed

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.

2 participants

@pmrv@claude

, '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
Support numpy >= 2.4 with backward-compatible fixes - #5
Merged
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Jul 16, 2026
Merged
Support numpy >= 2.4 with backward-compatible fixes#5
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Conversation
@pmrv
@pmrvpmrv
commented
Jul 16, 2026

Copy link


Copy Markdown

Owner
Pull Request Template
Description of Changes
Follow-up to #3: makes the code compatible with numpy ≥ 2.4 in a backward-compatible way and relaxes the requirement from numpy<2.4 to numpy<3.
Two numpy 2.4 breakages are fixed, both working identically on old and new numpy:
  1. Scalar energy output (src/pyace/asecalc.py). numpy 2.4 expired the "conversion of an array with ndim > 0 to a scalar" deprecation, so np.float64(energy.reshape(-1,)) started returning a shape-(1,) array instead of a scalar, and get_potential_energy() leaked an array of the total energy. The results dicts now use float() on the 0-d/scalar values (energy, free_energy, and the ensemble energy_std/energy_dev), which behaves identically on every numpy version, and .astype(np.float64) on per-atom arrays (energies_dev, forces_dev) — this also fixes those arrays silently degrading to scalars for single-atom structures on older numpy.
  2. np.trapz removal (src/pyace/radial.py). np.trapz was a deprecated alias of np.trapezoid from numpy 2.0 and was removed in 2.4. The module now picks np.trapezoid when it exists and falls back to np.trapz on numpy 1.x.
A regression assertion is added to tests/test_PyACECalculator.py so the energy coming back as an array would fail the tests.
Verification: built the package and ran tests/test_PyACECalculator.py (13 tests) against numpy 1.26.4 (exercises the np.trapz fallback), 2.3.5, and 2.4.6 — all pass on each. CI on this PR additionally covers the full test suite, which will now resolve numpy 2.4.x.
Checklist
  •  Code is well-documented.
  •  All tests have been run and passed. (full suite in CI; calculator tests locally against numpy 1.26.4 / 2.3.5 / 2.4.6)
  •  Relevant documentation has been updated if necessary. (no docs reference the numpy pin)
License Agreement
By submitting this pull request, I agree that:
  • The code submitted in this pull request will be distributed under the Academic Software License (free for academic non-commercial use, not free for commercial use), see LICENSE.md for more details.
  • The copyright for the code, including the submitted code, remains with Ruhr University Bochum. Ruhr University Bochum retains the right to transfer or modify the copyright.
🤖 Generated with Claude Code
https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
Generated by Claude Code
@claude
Support numpy >= 2.4 with backward-compatible fixes
08090c6
numpy 2.4 expired the ndim>0-to-scalar deprecation: np.float64(arr)
now returns an array for 1-element arrays instead of collapsing to a
scalar, so PyACECalculator's results['energy'] leaked out as a
shape-(1,) array from get_potential_energy(). Use float() on the 0-d
energy values instead, which behaves identically on all numpy versions,
and astype(np.float64) for per-atom arrays (also fixing energies_dev
degrading to a scalar for single-atom structures on older numpy).
numpy 2.4 also removed np.trapz (deprecated alias of np.trapezoid
since 2.0); pyace.radial now picks whichever exists.
Verified by building the package and running tests/test_PyACECalculator.py
against numpy 1.26.4, 2.3.5 and 2.4.6. Relax the numpy requirement to <3
accordingly.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

@claude
Drop review-flagged explanatory comments
ace21f4
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrv
merged commit 2544d97
into
masterJul 16, 2026

2 of 3 checks passed

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.

2 participants

@pmrv@claude

, '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
Support numpy >= 2.4 with backward-compatible fixes - #5
Merged
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Jul 16, 2026
Merged
Support numpy >= 2.4 with backward-compatible fixes#5
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Conversation
@pmrv
@pmrvpmrv
commented
Jul 16, 2026

Copy link


Copy Markdown

Owner
Pull Request Template
Description of Changes
Follow-up to #3: makes the code compatible with numpy ≥ 2.4 in a backward-compatible way and relaxes the requirement from numpy<2.4 to numpy<3.
Two numpy 2.4 breakages are fixed, both working identically on old and new numpy:
  1. Scalar energy output (src/pyace/asecalc.py). numpy 2.4 expired the "conversion of an array with ndim > 0 to a scalar" deprecation, so np.float64(energy.reshape(-1,)) started returning a shape-(1,) array instead of a scalar, and get_potential_energy() leaked an array of the total energy. The results dicts now use float() on the 0-d/scalar values (energy, free_energy, and the ensemble energy_std/energy_dev), which behaves identically on every numpy version, and .astype(np.float64) on per-atom arrays (energies_dev, forces_dev) — this also fixes those arrays silently degrading to scalars for single-atom structures on older numpy.
  2. np.trapz removal (src/pyace/radial.py). np.trapz was a deprecated alias of np.trapezoid from numpy 2.0 and was removed in 2.4. The module now picks np.trapezoid when it exists and falls back to np.trapz on numpy 1.x.
A regression assertion is added to tests/test_PyACECalculator.py so the energy coming back as an array would fail the tests.
Verification: built the package and ran tests/test_PyACECalculator.py (13 tests) against numpy 1.26.4 (exercises the np.trapz fallback), 2.3.5, and 2.4.6 — all pass on each. CI on this PR additionally covers the full test suite, which will now resolve numpy 2.4.x.
Checklist
  •  Code is well-documented.
  •  All tests have been run and passed. (full suite in CI; calculator tests locally against numpy 1.26.4 / 2.3.5 / 2.4.6)
  •  Relevant documentation has been updated if necessary. (no docs reference the numpy pin)
License Agreement
By submitting this pull request, I agree that:
  • The code submitted in this pull request will be distributed under the Academic Software License (free for academic non-commercial use, not free for commercial use), see LICENSE.md for more details.
  • The copyright for the code, including the submitted code, remains with Ruhr University Bochum. Ruhr University Bochum retains the right to transfer or modify the copyright.
🤖 Generated with Claude Code
https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
Generated by Claude Code
@claude
Support numpy >= 2.4 with backward-compatible fixes
08090c6
numpy 2.4 expired the ndim>0-to-scalar deprecation: np.float64(arr)
now returns an array for 1-element arrays instead of collapsing to a
scalar, so PyACECalculator's results['energy'] leaked out as a
shape-(1,) array from get_potential_energy(). Use float() on the 0-d
energy values instead, which behaves identically on all numpy versions,
and astype(np.float64) for per-atom arrays (also fixing energies_dev
degrading to a scalar for single-atom structures on older numpy).
numpy 2.4 also removed np.trapz (deprecated alias of np.trapezoid
since 2.0); pyace.radial now picks whichever exists.
Verified by building the package and running tests/test_PyACECalculator.py
against numpy 1.26.4, 2.3.5 and 2.4.6. Relax the numpy requirement to <3
accordingly.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

@claude
Drop review-flagged explanatory comments
ace21f4
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrv
merged commit 2544d97
into
masterJul 16, 2026

2 of 3 checks passed

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.

2 participants

@pmrv@claude

, '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
Support numpy >= 2.4 with backward-compatible fixes - #5
Merged
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Jul 16, 2026
Merged
Support numpy >= 2.4 with backward-compatible fixes#5
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Conversation
@pmrv
@pmrvpmrv
commented
Jul 16, 2026

Copy link


Copy Markdown

Owner
Pull Request Template
Description of Changes
Follow-up to #3: makes the code compatible with numpy ≥ 2.4 in a backward-compatible way and relaxes the requirement from numpy<2.4 to numpy<3.
Two numpy 2.4 breakages are fixed, both working identically on old and new numpy:
  1. Scalar energy output (src/pyace/asecalc.py). numpy 2.4 expired the "conversion of an array with ndim > 0 to a scalar" deprecation, so np.float64(energy.reshape(-1,)) started returning a shape-(1,) array instead of a scalar, and get_potential_energy() leaked an array of the total energy. The results dicts now use float() on the 0-d/scalar values (energy, free_energy, and the ensemble energy_std/energy_dev), which behaves identically on every numpy version, and .astype(np.float64) on per-atom arrays (energies_dev, forces_dev) — this also fixes those arrays silently degrading to scalars for single-atom structures on older numpy.
  2. np.trapz removal (src/pyace/radial.py). np.trapz was a deprecated alias of np.trapezoid from numpy 2.0 and was removed in 2.4. The module now picks np.trapezoid when it exists and falls back to np.trapz on numpy 1.x.
A regression assertion is added to tests/test_PyACECalculator.py so the energy coming back as an array would fail the tests.
Verification: built the package and ran tests/test_PyACECalculator.py (13 tests) against numpy 1.26.4 (exercises the np.trapz fallback), 2.3.5, and 2.4.6 — all pass on each. CI on this PR additionally covers the full test suite, which will now resolve numpy 2.4.x.
Checklist
  •  Code is well-documented.
  •  All tests have been run and passed. (full suite in CI; calculator tests locally against numpy 1.26.4 / 2.3.5 / 2.4.6)
  •  Relevant documentation has been updated if necessary. (no docs reference the numpy pin)
License Agreement
By submitting this pull request, I agree that:
  • The code submitted in this pull request will be distributed under the Academic Software License (free for academic non-commercial use, not free for commercial use), see LICENSE.md for more details.
  • The copyright for the code, including the submitted code, remains with Ruhr University Bochum. Ruhr University Bochum retains the right to transfer or modify the copyright.
🤖 Generated with Claude Code
https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
Generated by Claude Code
@claude
Support numpy >= 2.4 with backward-compatible fixes
08090c6
numpy 2.4 expired the ndim>0-to-scalar deprecation: np.float64(arr)
now returns an array for 1-element arrays instead of collapsing to a
scalar, so PyACECalculator's results['energy'] leaked out as a
shape-(1,) array from get_potential_energy(). Use float() on the 0-d
energy values instead, which behaves identically on all numpy versions,
and astype(np.float64) for per-atom arrays (also fixing energies_dev
degrading to a scalar for single-atom structures on older numpy).
numpy 2.4 also removed np.trapz (deprecated alias of np.trapezoid
since 2.0); pyace.radial now picks whichever exists.
Verified by building the package and running tests/test_PyACECalculator.py
against numpy 1.26.4, 2.3.5 and 2.4.6. Relax the numpy requirement to <3
accordingly.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

@claude
Drop review-flagged explanatory comments
ace21f4
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrv
merged commit 2544d97
into
masterJul 16, 2026

2 of 3 checks passed

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.

2 participants

@pmrv@claude

, '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
Support numpy >= 2.4 with backward-compatible fixes - #5
Merged
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Jul 16, 2026
Merged
Support numpy >= 2.4 with backward-compatible fixes#5
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Conversation
@pmrv
@pmrvpmrv
commented
Jul 16, 2026

Copy link


Copy Markdown

Owner
Pull Request Template
Description of Changes
Follow-up to #3: makes the code compatible with numpy ≥ 2.4 in a backward-compatible way and relaxes the requirement from numpy<2.4 to numpy<3.
Two numpy 2.4 breakages are fixed, both working identically on old and new numpy:
  1. Scalar energy output (src/pyace/asecalc.py). numpy 2.4 expired the "conversion of an array with ndim > 0 to a scalar" deprecation, so np.float64(energy.reshape(-1,)) started returning a shape-(1,) array instead of a scalar, and get_potential_energy() leaked an array of the total energy. The results dicts now use float() on the 0-d/scalar values (energy, free_energy, and the ensemble energy_std/energy_dev), which behaves identically on every numpy version, and .astype(np.float64) on per-atom arrays (energies_dev, forces_dev) — this also fixes those arrays silently degrading to scalars for single-atom structures on older numpy.
  2. np.trapz removal (src/pyace/radial.py). np.trapz was a deprecated alias of np.trapezoid from numpy 2.0 and was removed in 2.4. The module now picks np.trapezoid when it exists and falls back to np.trapz on numpy 1.x.
A regression assertion is added to tests/test_PyACECalculator.py so the energy coming back as an array would fail the tests.
Verification: built the package and ran tests/test_PyACECalculator.py (13 tests) against numpy 1.26.4 (exercises the np.trapz fallback), 2.3.5, and 2.4.6 — all pass on each. CI on this PR additionally covers the full test suite, which will now resolve numpy 2.4.x.
Checklist
  •  Code is well-documented.
  •  All tests have been run and passed. (full suite in CI; calculator tests locally against numpy 1.26.4 / 2.3.5 / 2.4.6)
  •  Relevant documentation has been updated if necessary. (no docs reference the numpy pin)
License Agreement
By submitting this pull request, I agree that:
  • The code submitted in this pull request will be distributed under the Academic Software License (free for academic non-commercial use, not free for commercial use), see LICENSE.md for more details.
  • The copyright for the code, including the submitted code, remains with Ruhr University Bochum. Ruhr University Bochum retains the right to transfer or modify the copyright.
🤖 Generated with Claude Code
https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
Generated by Claude Code
@claude
Support numpy >= 2.4 with backward-compatible fixes
08090c6
numpy 2.4 expired the ndim>0-to-scalar deprecation: np.float64(arr)
now returns an array for 1-element arrays instead of collapsing to a
scalar, so PyACECalculator's results['energy'] leaked out as a
shape-(1,) array from get_potential_energy(). Use float() on the 0-d
energy values instead, which behaves identically on all numpy versions,
and astype(np.float64) for per-atom arrays (also fixing energies_dev
degrading to a scalar for single-atom structures on older numpy).
numpy 2.4 also removed np.trapz (deprecated alias of np.trapezoid
since 2.0); pyace.radial now picks whichever exists.
Verified by building the package and running tests/test_PyACECalculator.py
against numpy 1.26.4, 2.3.5 and 2.4.6. Relax the numpy requirement to <3
accordingly.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

@claude
Drop review-flagged explanatory comments
ace21f4
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrv
merged commit 2544d97
into
masterJul 16, 2026

2 of 3 checks passed

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.

2 participants

@pmrv@claude

, '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
Support numpy >= 2.4 with backward-compatible fixes - #5
Merged
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Jul 16, 2026
Merged
Support numpy >= 2.4 with backward-compatible fixes#5
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Conversation
@pmrv
@pmrvpmrv
commented
Jul 16, 2026

Copy link


Copy Markdown

Owner
Pull Request Template
Description of Changes
Follow-up to #3: makes the code compatible with numpy ≥ 2.4 in a backward-compatible way and relaxes the requirement from numpy<2.4 to numpy<3.
Two numpy 2.4 breakages are fixed, both working identically on old and new numpy:
  1. Scalar energy output (src/pyace/asecalc.py). numpy 2.4 expired the "conversion of an array with ndim > 0 to a scalar" deprecation, so np.float64(energy.reshape(-1,)) started returning a shape-(1,) array instead of a scalar, and get_potential_energy() leaked an array of the total energy. The results dicts now use float() on the 0-d/scalar values (energy, free_energy, and the ensemble energy_std/energy_dev), which behaves identically on every numpy version, and .astype(np.float64) on per-atom arrays (energies_dev, forces_dev) — this also fixes those arrays silently degrading to scalars for single-atom structures on older numpy.
  2. np.trapz removal (src/pyace/radial.py). np.trapz was a deprecated alias of np.trapezoid from numpy 2.0 and was removed in 2.4. The module now picks np.trapezoid when it exists and falls back to np.trapz on numpy 1.x.
A regression assertion is added to tests/test_PyACECalculator.py so the energy coming back as an array would fail the tests.
Verification: built the package and ran tests/test_PyACECalculator.py (13 tests) against numpy 1.26.4 (exercises the np.trapz fallback), 2.3.5, and 2.4.6 — all pass on each. CI on this PR additionally covers the full test suite, which will now resolve numpy 2.4.x.
Checklist
  •  Code is well-documented.
  •  All tests have been run and passed. (full suite in CI; calculator tests locally against numpy 1.26.4 / 2.3.5 / 2.4.6)
  •  Relevant documentation has been updated if necessary. (no docs reference the numpy pin)
License Agreement
By submitting this pull request, I agree that:
  • The code submitted in this pull request will be distributed under the Academic Software License (free for academic non-commercial use, not free for commercial use), see LICENSE.md for more details.
  • The copyright for the code, including the submitted code, remains with Ruhr University Bochum. Ruhr University Bochum retains the right to transfer or modify the copyright.
🤖 Generated with Claude Code
https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
Generated by Claude Code
@claude
Support numpy >= 2.4 with backward-compatible fixes
08090c6
numpy 2.4 expired the ndim>0-to-scalar deprecation: np.float64(arr)
now returns an array for 1-element arrays instead of collapsing to a
scalar, so PyACECalculator's results['energy'] leaked out as a
shape-(1,) array from get_potential_energy(). Use float() on the 0-d
energy values instead, which behaves identically on all numpy versions,
and astype(np.float64) for per-atom arrays (also fixing energies_dev
degrading to a scalar for single-atom structures on older numpy).
numpy 2.4 also removed np.trapz (deprecated alias of np.trapezoid
since 2.0); pyace.radial now picks whichever exists.
Verified by building the package and running tests/test_PyACECalculator.py
against numpy 1.26.4, 2.3.5 and 2.4.6. Relax the numpy requirement to <3
accordingly.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

@claude
Drop review-flagged explanatory comments
ace21f4
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrv
merged commit 2544d97
into
masterJul 16, 2026

2 of 3 checks passed

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.

2 participants

@pmrv@claude

, '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
Support numpy >= 2.4 with backward-compatible fixes - #5
Merged
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Jul 16, 2026
Merged
Support numpy >= 2.4 with backward-compatible fixes#5
pmrv merged 2 commits into
masterfrom 
claude/numpy-24-compat
Conversation
@pmrv
@pmrvpmrv
commented
Jul 16, 2026

Copy link


Copy Markdown

Owner
Pull Request Template
Description of Changes
Follow-up to #3: makes the code compatible with numpy ≥ 2.4 in a backward-compatible way and relaxes the requirement from numpy<2.4 to numpy<3.
Two numpy 2.4 breakages are fixed, both working identically on old and new numpy:
  1. Scalar energy output (src/pyace/asecalc.py). numpy 2.4 expired the "conversion of an array with ndim > 0 to a scalar" deprecation, so np.float64(energy.reshape(-1,)) started returning a shape-(1,) array instead of a scalar, and get_potential_energy() leaked an array of the total energy. The results dicts now use float() on the 0-d/scalar values (energy, free_energy, and the ensemble energy_std/energy_dev), which behaves identically on every numpy version, and .astype(np.float64) on per-atom arrays (energies_dev, forces_dev) — this also fixes those arrays silently degrading to scalars for single-atom structures on older numpy.
  2. np.trapz removal (src/pyace/radial.py). np.trapz was a deprecated alias of np.trapezoid from numpy 2.0 and was removed in 2.4. The module now picks np.trapezoid when it exists and falls back to np.trapz on numpy 1.x.
A regression assertion is added to tests/test_PyACECalculator.py so the energy coming back as an array would fail the tests.
Verification: built the package and ran tests/test_PyACECalculator.py (13 tests) against numpy 1.26.4 (exercises the np.trapz fallback), 2.3.5, and 2.4.6 — all pass on each. CI on this PR additionally covers the full test suite, which will now resolve numpy 2.4.x.
Checklist
  •  Code is well-documented.
  •  All tests have been run and passed. (full suite in CI; calculator tests locally against numpy 1.26.4 / 2.3.5 / 2.4.6)
  •  Relevant documentation has been updated if necessary. (no docs reference the numpy pin)
License Agreement
By submitting this pull request, I agree that:
  • The code submitted in this pull request will be distributed under the Academic Software License (free for academic non-commercial use, not free for commercial use), see LICENSE.md for more details.
  • The copyright for the code, including the submitted code, remains with Ruhr University Bochum. Ruhr University Bochum retains the right to transfer or modify the copyright.
🤖 Generated with Claude Code
https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
Generated by Claude Code
@claude
Support numpy >= 2.4 with backward-compatible fixes
08090c6
numpy 2.4 expired the ndim>0-to-scalar deprecation: np.float64(arr)
now returns an array for 1-element arrays instead of collapsing to a
scalar, so PyACECalculator's results['energy'] leaked out as a
shape-(1,) array from get_potential_energy(). Use float() on the 0-d
energy values instead, which behaves identically on all numpy versions,
and astype(np.float64) for per-atom arrays (also fixing energies_dev
degrading to a scalar for single-atom structures on older numpy).
numpy 2.4 also removed np.trapz (deprecated alias of np.trapezoid
since 2.0); pyace.radial now picks whichever exists.
Verified by building the package and running tests/test_PyACECalculator.py
against numpy 1.26.4, 2.3.5 and 2.4.6. Relax the numpy requirement to <3
accordingly.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

pmrv
pmrv
commented
Jul 16, 2026
View reviewed changes
Comment threadsrc/pyace/asecalc.py
Outdated

@claude
Drop review-flagged explanatory comments
ace21f4
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrv
merged commit 2544d97
into
masterJul 16, 2026

2 of 3 checks passed

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.

2 participants

@pmrv@claude