Widen numpy constraint to <2.4 - #3

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pmrv merged 1 commit into
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Jul 16, 2026
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Widen numpy constraint to <2.4#3
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Pull Request Template

Description of Changes

Relaxes the numpy pin in setup.py from numpy<=1.26.4 to numpy<2.4. Versions up to 2.3.x are empirically known to work; 2.4 is excluded because it breaks pyace, with a full diagnosis below.

Diagnosis: why numpy ≥2.4 breaks the energy output

PyACECalculator.calculate() builds its ASE results dict like this (src/pyace/asecalc.py:167):

'energy': np.float64(self.energy.reshape(-1, )),

self.energy is a 0-d array wrapping the scalar total energy from the C++ evaluator, so .reshape(-1,) turns it into a shape-(1,) array, which is then passed through the np.float64constructor (not a cast of a Python float).

The behavior of that constructor changed in numpy 2.4:

  • numpy ≤2.3: np.float64(array_of_size_1) collapses the array to a scalar np.float64. Since numpy 1.25 this has emitted DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
  • numpy 2.4: that deprecation expired. Scalar constructors now behave like astype for ndim > 0 inputs and return an ndarray (numpy 2.4 release notes, "NumPy scalar constructor behaviour for arrays and 0-d inputs").

So on numpy 2.4, results['energy'] becomes array([E_total]) instead of a float, and atoms.get_potential_energy() returns a 1-element array of the total energy rather than a scalar — the observed symptom. Verified empirically:

numpy 2.3.5: np.float64(np.array(-123.456).reshape(-1,)) -> np.float64(-123.456) (scalar, ndim 0, + DeprecationWarning)
numpy 2.4.6: np.float64(np.array(-123.456).reshape(-1,)) -> array([-123.456]) (ndarray, ndim 1)

The same pattern affects free_energy on the same line pair, and energy / free_energy_std / energy_std in PyACEEnsembleCalculator (src/pyace/asecalc.py:308-315).

Second, independent numpy 2.4 breakage

pyace.radial.integrate() (src/pyace/radial.py:20) calls np.trapz, which numpy 2.0 kept only as a deprecated alias of np.trapezoid and numpy 2.4 removed outright — so radial-function integration raises AttributeError on 2.4 regardless of the energy issue.

Forward path (not in this PR)

Both are one-line fixes if support beyond 2.4 is wanted later: replace np.float64(self.energy.reshape(-1,)) with float(self.energy) (works on all versions and silences the existing DeprecationWarning), and np.trapz with np.trapezoid (available since numpy 2.0). Keeping this PR to the empirically validated <2.4 bound.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (dependency-pin change only; the C++ extension is not built in this environment — behavior difference verified against standalone numpy 2.3.5 vs 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

numpy releases up to 2.3.x work correctly; 2.4 breaks pyace in two ways:
1. np.float64(arr) on a 1-element array now returns an ndarray instead
of collapsing to a scalar (the ndim>0-to-scalar deprecation from
numpy 1.25 expired in 2.4), so PyACECalculator's results['energy']
becomes a shape-(1,) array and get_potential_energy() returns an
array of the total energy rather than a float.
2. np.trapz, used in pyace.radial, was removed in 2.4 (deprecated
alias for np.trapezoid since 2.0).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrvforce-pushed the claude/numpy-energy-output-bug-itm376 branch from c8c674a to 76adfe3CompareJuly 16, 2026 02:12

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lgtm.merge

@pmrv
pmrv merged commit 46db657 into masterJul 16, 2026
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
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Widen numpy constraint to <2.4 - #3

Merged
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376
Jul 16, 2026
Merged

Widen numpy constraint to <2.4#3
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376

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@pmrv

@pmrvpmrv commented Jul 15, 2026

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Pull Request Template

Description of Changes

Relaxes the numpy pin in setup.py from numpy<=1.26.4 to numpy<2.4. Versions up to 2.3.x are empirically known to work; 2.4 is excluded because it breaks pyace, with a full diagnosis below.

Diagnosis: why numpy ≥2.4 breaks the energy output

PyACECalculator.calculate() builds its ASE results dict like this (src/pyace/asecalc.py:167):

'energy': np.float64(self.energy.reshape(-1, )),

self.energy is a 0-d array wrapping the scalar total energy from the C++ evaluator, so .reshape(-1,) turns it into a shape-(1,) array, which is then passed through the np.float64constructor (not a cast of a Python float).

The behavior of that constructor changed in numpy 2.4:

  • numpy ≤2.3: np.float64(array_of_size_1) collapses the array to a scalar np.float64. Since numpy 1.25 this has emitted DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
  • numpy 2.4: that deprecation expired. Scalar constructors now behave like astype for ndim > 0 inputs and return an ndarray (numpy 2.4 release notes, "NumPy scalar constructor behaviour for arrays and 0-d inputs").

So on numpy 2.4, results['energy'] becomes array([E_total]) instead of a float, and atoms.get_potential_energy() returns a 1-element array of the total energy rather than a scalar — the observed symptom. Verified empirically:

numpy 2.3.5: np.float64(np.array(-123.456).reshape(-1,)) -> np.float64(-123.456) (scalar, ndim 0, + DeprecationWarning)
numpy 2.4.6: np.float64(np.array(-123.456).reshape(-1,)) -> array([-123.456]) (ndarray, ndim 1)

The same pattern affects free_energy on the same line pair, and energy / free_energy_std / energy_std in PyACEEnsembleCalculator (src/pyace/asecalc.py:308-315).

Second, independent numpy 2.4 breakage

pyace.radial.integrate() (src/pyace/radial.py:20) calls np.trapz, which numpy 2.0 kept only as a deprecated alias of np.trapezoid and numpy 2.4 removed outright — so radial-function integration raises AttributeError on 2.4 regardless of the energy issue.

Forward path (not in this PR)

Both are one-line fixes if support beyond 2.4 is wanted later: replace np.float64(self.energy.reshape(-1,)) with float(self.energy) (works on all versions and silences the existing DeprecationWarning), and np.trapz with np.trapezoid (available since numpy 2.0). Keeping this PR to the empirically validated <2.4 bound.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (dependency-pin change only; the C++ extension is not built in this environment — behavior difference verified against standalone numpy 2.3.5 vs 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

numpy releases up to 2.3.x work correctly; 2.4 breaks pyace in two ways:
1. np.float64(arr) on a 1-element array now returns an ndarray instead
of collapsing to a scalar (the ndim>0-to-scalar deprecation from
numpy 1.25 expired in 2.4), so PyACECalculator's results['energy']
becomes a shape-(1,) array and get_potential_energy() returns an
array of the total energy rather than a float.
2. np.trapz, used in pyace.radial, was removed in 2.4 (deprecated
alias for np.trapezoid since 2.0).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrvforce-pushed the claude/numpy-energy-output-bug-itm376 branch from c8c674a to 76adfe3CompareJuly 16, 2026 02:12

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lgtm.merge

@pmrv
pmrv merged commit 46db657 into masterJul 16, 2026
2 of 3 checks passed
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, '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('^' + ".*" + '
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Widen numpy constraint to <2.4 - #3

Merged
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376
Jul 16, 2026
Merged

Widen numpy constraint to <2.4#3
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376

Conversation

@pmrv

@pmrvpmrv commented Jul 15, 2026

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Pull Request Template

Description of Changes

Relaxes the numpy pin in setup.py from numpy<=1.26.4 to numpy<2.4. Versions up to 2.3.x are empirically known to work; 2.4 is excluded because it breaks pyace, with a full diagnosis below.

Diagnosis: why numpy ≥2.4 breaks the energy output

PyACECalculator.calculate() builds its ASE results dict like this (src/pyace/asecalc.py:167):

'energy': np.float64(self.energy.reshape(-1, )),

self.energy is a 0-d array wrapping the scalar total energy from the C++ evaluator, so .reshape(-1,) turns it into a shape-(1,) array, which is then passed through the np.float64constructor (not a cast of a Python float).

The behavior of that constructor changed in numpy 2.4:

  • numpy ≤2.3: np.float64(array_of_size_1) collapses the array to a scalar np.float64. Since numpy 1.25 this has emitted DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
  • numpy 2.4: that deprecation expired. Scalar constructors now behave like astype for ndim > 0 inputs and return an ndarray (numpy 2.4 release notes, "NumPy scalar constructor behaviour for arrays and 0-d inputs").

So on numpy 2.4, results['energy'] becomes array([E_total]) instead of a float, and atoms.get_potential_energy() returns a 1-element array of the total energy rather than a scalar — the observed symptom. Verified empirically:

numpy 2.3.5: np.float64(np.array(-123.456).reshape(-1,)) -> np.float64(-123.456) (scalar, ndim 0, + DeprecationWarning)
numpy 2.4.6: np.float64(np.array(-123.456).reshape(-1,)) -> array([-123.456]) (ndarray, ndim 1)

The same pattern affects free_energy on the same line pair, and energy / free_energy_std / energy_std in PyACEEnsembleCalculator (src/pyace/asecalc.py:308-315).

Second, independent numpy 2.4 breakage

pyace.radial.integrate() (src/pyace/radial.py:20) calls np.trapz, which numpy 2.0 kept only as a deprecated alias of np.trapezoid and numpy 2.4 removed outright — so radial-function integration raises AttributeError on 2.4 regardless of the energy issue.

Forward path (not in this PR)

Both are one-line fixes if support beyond 2.4 is wanted later: replace np.float64(self.energy.reshape(-1,)) with float(self.energy) (works on all versions and silences the existing DeprecationWarning), and np.trapz with np.trapezoid (available since numpy 2.0). Keeping this PR to the empirically validated <2.4 bound.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (dependency-pin change only; the C++ extension is not built in this environment — behavior difference verified against standalone numpy 2.3.5 vs 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

numpy releases up to 2.3.x work correctly; 2.4 breaks pyace in two ways:
1. np.float64(arr) on a 1-element array now returns an ndarray instead
of collapsing to a scalar (the ndim>0-to-scalar deprecation from
numpy 1.25 expired in 2.4), so PyACECalculator's results['energy']
becomes a shape-(1,) array and get_potential_energy() returns an
array of the total energy rather than a float.
2. np.trapz, used in pyace.radial, was removed in 2.4 (deprecated
alias for np.trapezoid since 2.0).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrvforce-pushed the claude/numpy-energy-output-bug-itm376 branch from c8c674a to 76adfe3CompareJuly 16, 2026 02:12

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lgtm.merge

@pmrv
pmrv merged commit 46db657 into masterJul 16, 2026
2 of 3 checks passed
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, '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('^' + ".*" + '
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Widen numpy constraint to <2.4 - #3

Merged
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376
Jul 16, 2026
Merged

Widen numpy constraint to <2.4#3
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376

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@pmrv

@pmrvpmrv commented Jul 15, 2026

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Pull Request Template

Description of Changes

Relaxes the numpy pin in setup.py from numpy<=1.26.4 to numpy<2.4. Versions up to 2.3.x are empirically known to work; 2.4 is excluded because it breaks pyace, with a full diagnosis below.

Diagnosis: why numpy ≥2.4 breaks the energy output

PyACECalculator.calculate() builds its ASE results dict like this (src/pyace/asecalc.py:167):

'energy': np.float64(self.energy.reshape(-1, )),

self.energy is a 0-d array wrapping the scalar total energy from the C++ evaluator, so .reshape(-1,) turns it into a shape-(1,) array, which is then passed through the np.float64constructor (not a cast of a Python float).

The behavior of that constructor changed in numpy 2.4:

  • numpy ≤2.3: np.float64(array_of_size_1) collapses the array to a scalar np.float64. Since numpy 1.25 this has emitted DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
  • numpy 2.4: that deprecation expired. Scalar constructors now behave like astype for ndim > 0 inputs and return an ndarray (numpy 2.4 release notes, "NumPy scalar constructor behaviour for arrays and 0-d inputs").

So on numpy 2.4, results['energy'] becomes array([E_total]) instead of a float, and atoms.get_potential_energy() returns a 1-element array of the total energy rather than a scalar — the observed symptom. Verified empirically:

numpy 2.3.5: np.float64(np.array(-123.456).reshape(-1,)) -> np.float64(-123.456) (scalar, ndim 0, + DeprecationWarning)
numpy 2.4.6: np.float64(np.array(-123.456).reshape(-1,)) -> array([-123.456]) (ndarray, ndim 1)

The same pattern affects free_energy on the same line pair, and energy / free_energy_std / energy_std in PyACEEnsembleCalculator (src/pyace/asecalc.py:308-315).

Second, independent numpy 2.4 breakage

pyace.radial.integrate() (src/pyace/radial.py:20) calls np.trapz, which numpy 2.0 kept only as a deprecated alias of np.trapezoid and numpy 2.4 removed outright — so radial-function integration raises AttributeError on 2.4 regardless of the energy issue.

Forward path (not in this PR)

Both are one-line fixes if support beyond 2.4 is wanted later: replace np.float64(self.energy.reshape(-1,)) with float(self.energy) (works on all versions and silences the existing DeprecationWarning), and np.trapz with np.trapezoid (available since numpy 2.0). Keeping this PR to the empirically validated <2.4 bound.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (dependency-pin change only; the C++ extension is not built in this environment — behavior difference verified against standalone numpy 2.3.5 vs 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

numpy releases up to 2.3.x work correctly; 2.4 breaks pyace in two ways:
1. np.float64(arr) on a 1-element array now returns an ndarray instead
of collapsing to a scalar (the ndim>0-to-scalar deprecation from
numpy 1.25 expired in 2.4), so PyACECalculator's results['energy']
becomes a shape-(1,) array and get_potential_energy() returns an
array of the total energy rather than a float.
2. np.trapz, used in pyace.radial, was removed in 2.4 (deprecated
alias for np.trapezoid since 2.0).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrvforce-pushed the claude/numpy-energy-output-bug-itm376 branch from c8c674a to 76adfe3CompareJuly 16, 2026 02:12

@pmrvpmrv left a comment

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lgtm.merge

@pmrv
pmrv merged commit 46db657 into masterJul 16, 2026
2 of 3 checks passed
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, '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" + '
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Widen numpy constraint to <2.4 - #3

Merged
pmrv merged 1 commit into
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Widen numpy constraint to <2.4#3
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Pull Request Template

Description of Changes

Relaxes the numpy pin in setup.py from numpy<=1.26.4 to numpy<2.4. Versions up to 2.3.x are empirically known to work; 2.4 is excluded because it breaks pyace, with a full diagnosis below.

Diagnosis: why numpy ≥2.4 breaks the energy output

PyACECalculator.calculate() builds its ASE results dict like this (src/pyace/asecalc.py:167):

'energy': np.float64(self.energy.reshape(-1, )),

self.energy is a 0-d array wrapping the scalar total energy from the C++ evaluator, so .reshape(-1,) turns it into a shape-(1,) array, which is then passed through the np.float64constructor (not a cast of a Python float).

The behavior of that constructor changed in numpy 2.4:

  • numpy ≤2.3: np.float64(array_of_size_1) collapses the array to a scalar np.float64. Since numpy 1.25 this has emitted DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
  • numpy 2.4: that deprecation expired. Scalar constructors now behave like astype for ndim > 0 inputs and return an ndarray (numpy 2.4 release notes, "NumPy scalar constructor behaviour for arrays and 0-d inputs").

So on numpy 2.4, results['energy'] becomes array([E_total]) instead of a float, and atoms.get_potential_energy() returns a 1-element array of the total energy rather than a scalar — the observed symptom. Verified empirically:

numpy 2.3.5: np.float64(np.array(-123.456).reshape(-1,)) -> np.float64(-123.456) (scalar, ndim 0, + DeprecationWarning)
numpy 2.4.6: np.float64(np.array(-123.456).reshape(-1,)) -> array([-123.456]) (ndarray, ndim 1)

The same pattern affects free_energy on the same line pair, and energy / free_energy_std / energy_std in PyACEEnsembleCalculator (src/pyace/asecalc.py:308-315).

Second, independent numpy 2.4 breakage

pyace.radial.integrate() (src/pyace/radial.py:20) calls np.trapz, which numpy 2.0 kept only as a deprecated alias of np.trapezoid and numpy 2.4 removed outright — so radial-function integration raises AttributeError on 2.4 regardless of the energy issue.

Forward path (not in this PR)

Both are one-line fixes if support beyond 2.4 is wanted later: replace np.float64(self.energy.reshape(-1,)) with float(self.energy) (works on all versions and silences the existing DeprecationWarning), and np.trapz with np.trapezoid (available since numpy 2.0). Keeping this PR to the empirically validated <2.4 bound.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (dependency-pin change only; the C++ extension is not built in this environment — behavior difference verified against standalone numpy 2.3.5 vs 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

numpy releases up to 2.3.x work correctly; 2.4 breaks pyace in two ways:
1. np.float64(arr) on a 1-element array now returns an ndarray instead
of collapsing to a scalar (the ndim>0-to-scalar deprecation from
numpy 1.25 expired in 2.4), so PyACECalculator's results['energy']
becomes a shape-(1,) array and get_potential_energy() returns an
array of the total energy rather than a float.
2. np.trapz, used in pyace.radial, was removed in 2.4 (deprecated
alias for np.trapezoid since 2.0).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrvforce-pushed the claude/numpy-energy-output-bug-itm376 branch from c8c674a to 76adfe3CompareJuly 16, 2026 02:12

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lgtm.merge

@pmrv
pmrv merged commit 46db657 into masterJul 16, 2026
2 of 3 checks passed
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, '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

Widen numpy constraint to <2.4 - #3

Merged
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376
Jul 16, 2026
Merged

Widen numpy constraint to <2.4#3
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376

Conversation

@pmrv

@pmrvpmrv commented Jul 15, 2026

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Pull Request Template

Description of Changes

Relaxes the numpy pin in setup.py from numpy<=1.26.4 to numpy<2.4. Versions up to 2.3.x are empirically known to work; 2.4 is excluded because it breaks pyace, with a full diagnosis below.

Diagnosis: why numpy ≥2.4 breaks the energy output

PyACECalculator.calculate() builds its ASE results dict like this (src/pyace/asecalc.py:167):

'energy': np.float64(self.energy.reshape(-1, )),

self.energy is a 0-d array wrapping the scalar total energy from the C++ evaluator, so .reshape(-1,) turns it into a shape-(1,) array, which is then passed through the np.float64constructor (not a cast of a Python float).

The behavior of that constructor changed in numpy 2.4:

  • numpy ≤2.3: np.float64(array_of_size_1) collapses the array to a scalar np.float64. Since numpy 1.25 this has emitted DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
  • numpy 2.4: that deprecation expired. Scalar constructors now behave like astype for ndim > 0 inputs and return an ndarray (numpy 2.4 release notes, "NumPy scalar constructor behaviour for arrays and 0-d inputs").

So on numpy 2.4, results['energy'] becomes array([E_total]) instead of a float, and atoms.get_potential_energy() returns a 1-element array of the total energy rather than a scalar — the observed symptom. Verified empirically:

numpy 2.3.5: np.float64(np.array(-123.456).reshape(-1,)) -> np.float64(-123.456) (scalar, ndim 0, + DeprecationWarning)
numpy 2.4.6: np.float64(np.array(-123.456).reshape(-1,)) -> array([-123.456]) (ndarray, ndim 1)

The same pattern affects free_energy on the same line pair, and energy / free_energy_std / energy_std in PyACEEnsembleCalculator (src/pyace/asecalc.py:308-315).

Second, independent numpy 2.4 breakage

pyace.radial.integrate() (src/pyace/radial.py:20) calls np.trapz, which numpy 2.0 kept only as a deprecated alias of np.trapezoid and numpy 2.4 removed outright — so radial-function integration raises AttributeError on 2.4 regardless of the energy issue.

Forward path (not in this PR)

Both are one-line fixes if support beyond 2.4 is wanted later: replace np.float64(self.energy.reshape(-1,)) with float(self.energy) (works on all versions and silences the existing DeprecationWarning), and np.trapz with np.trapezoid (available since numpy 2.0). Keeping this PR to the empirically validated <2.4 bound.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (dependency-pin change only; the C++ extension is not built in this environment — behavior difference verified against standalone numpy 2.3.5 vs 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

numpy releases up to 2.3.x work correctly; 2.4 breaks pyace in two ways:
1. np.float64(arr) on a 1-element array now returns an ndarray instead
of collapsing to a scalar (the ndim>0-to-scalar deprecation from
numpy 1.25 expired in 2.4), so PyACECalculator's results['energy']
becomes a shape-(1,) array and get_potential_energy() returns an
array of the total energy rather than a float.
2. np.trapz, used in pyace.radial, was removed in 2.4 (deprecated
alias for np.trapezoid since 2.0).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrvforce-pushed the claude/numpy-energy-output-bug-itm376 branch from c8c674a to 76adfe3CompareJuly 16, 2026 02:12

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lgtm.merge

@pmrv
pmrv merged commit 46db657 into masterJul 16, 2026
2 of 3 checks passed
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@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

Widen numpy constraint to <2.4 - #3

Merged
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376
Jul 16, 2026
Merged

Widen numpy constraint to <2.4#3
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376

Conversation

@pmrv

@pmrvpmrv commented Jul 15, 2026

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Pull Request Template

Description of Changes

Relaxes the numpy pin in setup.py from numpy<=1.26.4 to numpy<2.4. Versions up to 2.3.x are empirically known to work; 2.4 is excluded because it breaks pyace, with a full diagnosis below.

Diagnosis: why numpy ≥2.4 breaks the energy output

PyACECalculator.calculate() builds its ASE results dict like this (src/pyace/asecalc.py:167):

'energy': np.float64(self.energy.reshape(-1, )),

self.energy is a 0-d array wrapping the scalar total energy from the C++ evaluator, so .reshape(-1,) turns it into a shape-(1,) array, which is then passed through the np.float64constructor (not a cast of a Python float).

The behavior of that constructor changed in numpy 2.4:

  • numpy ≤2.3: np.float64(array_of_size_1) collapses the array to a scalar np.float64. Since numpy 1.25 this has emitted DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
  • numpy 2.4: that deprecation expired. Scalar constructors now behave like astype for ndim > 0 inputs and return an ndarray (numpy 2.4 release notes, "NumPy scalar constructor behaviour for arrays and 0-d inputs").

So on numpy 2.4, results['energy'] becomes array([E_total]) instead of a float, and atoms.get_potential_energy() returns a 1-element array of the total energy rather than a scalar — the observed symptom. Verified empirically:

numpy 2.3.5: np.float64(np.array(-123.456).reshape(-1,)) -> np.float64(-123.456) (scalar, ndim 0, + DeprecationWarning)
numpy 2.4.6: np.float64(np.array(-123.456).reshape(-1,)) -> array([-123.456]) (ndarray, ndim 1)

The same pattern affects free_energy on the same line pair, and energy / free_energy_std / energy_std in PyACEEnsembleCalculator (src/pyace/asecalc.py:308-315).

Second, independent numpy 2.4 breakage

pyace.radial.integrate() (src/pyace/radial.py:20) calls np.trapz, which numpy 2.0 kept only as a deprecated alias of np.trapezoid and numpy 2.4 removed outright — so radial-function integration raises AttributeError on 2.4 regardless of the energy issue.

Forward path (not in this PR)

Both are one-line fixes if support beyond 2.4 is wanted later: replace np.float64(self.energy.reshape(-1,)) with float(self.energy) (works on all versions and silences the existing DeprecationWarning), and np.trapz with np.trapezoid (available since numpy 2.0). Keeping this PR to the empirically validated <2.4 bound.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (dependency-pin change only; the C++ extension is not built in this environment — behavior difference verified against standalone numpy 2.3.5 vs 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

numpy releases up to 2.3.x work correctly; 2.4 breaks pyace in two ways:
1. np.float64(arr) on a 1-element array now returns an ndarray instead
of collapsing to a scalar (the ndim>0-to-scalar deprecation from
numpy 1.25 expired in 2.4), so PyACECalculator's results['energy']
becomes a shape-(1,) array and get_potential_energy() returns an
array of the total energy rather than a float.
2. np.trapz, used in pyace.radial, was removed in 2.4 (deprecated
alias for np.trapezoid since 2.0).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrvforce-pushed the claude/numpy-energy-output-bug-itm376 branch from c8c674a to 76adfe3CompareJuly 16, 2026 02:12

@pmrvpmrv left a comment

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lgtm.merge

@pmrv
pmrv merged commit 46db657 into masterJul 16, 2026
2 of 3 checks passed
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@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

Widen numpy constraint to <2.4 - #3

Merged
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376
Jul 16, 2026
Merged

Widen numpy constraint to <2.4#3
pmrv merged 1 commit into
masterfrom
claude/numpy-energy-output-bug-itm376

Conversation

@pmrv

@pmrvpmrv commented Jul 15, 2026

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Pull Request Template

Description of Changes

Relaxes the numpy pin in setup.py from numpy<=1.26.4 to numpy<2.4. Versions up to 2.3.x are empirically known to work; 2.4 is excluded because it breaks pyace, with a full diagnosis below.

Diagnosis: why numpy ≥2.4 breaks the energy output

PyACECalculator.calculate() builds its ASE results dict like this (src/pyace/asecalc.py:167):

'energy': np.float64(self.energy.reshape(-1, )),

self.energy is a 0-d array wrapping the scalar total energy from the C++ evaluator, so .reshape(-1,) turns it into a shape-(1,) array, which is then passed through the np.float64constructor (not a cast of a Python float).

The behavior of that constructor changed in numpy 2.4:

  • numpy ≤2.3: np.float64(array_of_size_1) collapses the array to a scalar np.float64. Since numpy 1.25 this has emitted DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future.
  • numpy 2.4: that deprecation expired. Scalar constructors now behave like astype for ndim > 0 inputs and return an ndarray (numpy 2.4 release notes, "NumPy scalar constructor behaviour for arrays and 0-d inputs").

So on numpy 2.4, results['energy'] becomes array([E_total]) instead of a float, and atoms.get_potential_energy() returns a 1-element array of the total energy rather than a scalar — the observed symptom. Verified empirically:

numpy 2.3.5: np.float64(np.array(-123.456).reshape(-1,)) -> np.float64(-123.456) (scalar, ndim 0, + DeprecationWarning)
numpy 2.4.6: np.float64(np.array(-123.456).reshape(-1,)) -> array([-123.456]) (ndarray, ndim 1)

The same pattern affects free_energy on the same line pair, and energy / free_energy_std / energy_std in PyACEEnsembleCalculator (src/pyace/asecalc.py:308-315).

Second, independent numpy 2.4 breakage

pyace.radial.integrate() (src/pyace/radial.py:20) calls np.trapz, which numpy 2.0 kept only as a deprecated alias of np.trapezoid and numpy 2.4 removed outright — so radial-function integration raises AttributeError on 2.4 regardless of the energy issue.

Forward path (not in this PR)

Both are one-line fixes if support beyond 2.4 is wanted later: replace np.float64(self.energy.reshape(-1,)) with float(self.energy) (works on all versions and silences the existing DeprecationWarning), and np.trapz with np.trapezoid (available since numpy 2.0). Keeping this PR to the empirically validated <2.4 bound.

Checklist

  • Code is well-documented.
  • All tests have been run and passed. (dependency-pin change only; the C++ extension is not built in this environment — behavior difference verified against standalone numpy 2.3.5 vs 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

numpy releases up to 2.3.x work correctly; 2.4 breaks pyace in two ways:
1. np.float64(arr) on a 1-element array now returns an ndarray instead
of collapsing to a scalar (the ndim>0-to-scalar deprecation from
numpy 1.25 expired in 2.4), so PyACECalculator's results['energy']
becomes a shape-(1,) array and get_potential_energy() returns an
array of the total energy rather than a float.
2. np.trapz, used in pyace.radial, was removed in 2.4 (deprecated
alias for np.trapezoid since 2.0).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015Ui6Drmop9gZXo1fgn8yVg
@pmrv
pmrvforce-pushed the claude/numpy-energy-output-bug-itm376 branch from c8c674a to 76adfe3CompareJuly 16, 2026 02:12

@pmrvpmrv left a comment

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lgtm.merge

@pmrv
pmrv merged commit 46db657 into masterJul 16, 2026
2 of 3 checks passed
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2 participants

@pmrv@claude