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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Andrius Merkys pushed to branch upstream at <a href="https://salsa.debian.org/java-team/openchemlib">Debian Java Maintainers / openchemlib</a>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b2f028bc03f295344678f12b7301477253a60cf0">b2f028bc</a></strong>
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<span> by Andrius Merkys </span> <i> at 2025-04-11T02:32:51-04:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2025.4.0+dfsg</pre>
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