reapxdev/zenodo-scraper huggingface dataset:
One Edge, Unbounded Instability: Lean Formalization and Reproducible Artifacts
Authors: Künzi, Anton
Type: Software
Published: 2026-08-03
Keywords: multiparameter persistence, persistent homology, Hilbert decomposition signed measures, formal verification, Lean 4

Lean 4 formalization and independent finite checks for counterexamples to proposed dimension-only stability bounds for Hilbert decomposition signed measures in multiparameter persistence.
BrainLesion/preprocessing: v0.6.12
Authors: neuronflow, marcel rosier, Sarthak Pati, Ph.D., Isra Mekki, nicmuenster, Muhammad Nabi Yasinzai, Utku Turkbey, Joshua Scarsbrook, Eva Oswald, Mahyar Valizadeh
Type: Software
Published: 2026-08-02

<h2>What's Changed</h2>
<ul>
<li>Fix CLI output directory type by @Vbitz in https://github.com/BrainLesion/preprocessing/pull/182</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@Vbitz made their first contribution in https://github.com/BrainLesion/preprocessing/pull/182</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/BrainLesion/preprocessing/compare/v0.6.11...v0.6.12</p>
Mycelium: Procedural Urban Morphology Generation for Rhino and Grasshopper
Authors: Karadag, Ilker, Kastner, Patrick
Type: Software
Published: 2026-08-03
Keywords: procedural urban modeling, synthetic data, urban morphology, environmental simulation, Grasshopper

<h3>Added</h3>
<ul>
<li>Urban morphology indicators from the Massing Generator: plan area density (<code>lambda_p</code>), open-space and park ratios, direction-dependent gross frontal area density (<code>lambda_f</code>), and building-height mean, standard deviation, minimum, median, 90th percentile, and maximum.</li>
<li>Optional <code>AnalysisDirection</code> input for directional frontal-area calculations. The vector is normalized in the XY plane and falls back to world X when it is zero or vertical.</li>
<li>Schema-versioned <code>CaseManifest</code> JSON output containing a deterministic SHA-256 case ID, random seed, installed plug-in version, model units, network family and subtype, effective generator inputs, geometry counts, development metrics, and morphology metrics.</li>
<li>Published JSON Schema for the case manifest at <code>docs/case-manifest.schema.json</code>.</li>
<li><code>CITATION.cff</code> metadata for GitHub and Zenodo software citations.</li>
<li>Dataset-export example in Mycelium-Templates, with morphology metrics and JSON manifest outputs wired to panels for inspection and file streaming.</li>
</ul>
<h3>Changed</h3>
<ul>
<li>Massing Generator retains its existing GUID and parameter order; the analysis-direction input and new outputs are appended for compatibility with existing Grasshopper definitions.</li>
<li>Repository metadata now uses the canonical <code>MyceliumGH-Dev</code> organization URL after the GitHub organization rename.</li>
<li>Mycelium Templates now fetches version-matched examples from <code>MyceliumGH-Dev/Mycelium-Templates</code> after the repository transfer.</li>
</ul>
<p>Install with Rhino's Package Manager, or <code>yak install Mycelium 0.1.0.4</code>.</p>
morloc-project/morloc: v0.96.0
Authors: Zebulun Arendsee, melody!, Zach1031, Jennifer Chang, Wang Rui
Type: Software
Published: 2026-08-02

<p><strong>Full Changelog</strong>: https://github.com/morloc-project/morloc/compare/v0.95.0...v0.96.0</p>
KoopmanGraph: Topology-Aware Koopman Autoencoders for Networked Dynamics
Authors: Kessler, Travis
Type: Software
Published: 2026-08-02
Keywords: Koopman operator, graph neural networks, PyTorch Geometric, spatiotemporal dynamics, dynamical systems

A PyTorch Geometric library for topology-aware Koopman autoencoders on graphs: GNN lifting and decoding with a learned linear latent operator for forecasting and analyzing networked dynamical systems.
Culsma: Public Reference Implementation
Authors: Chen, Yang
Type: Software
Published: 2026-08-02
Keywords: laboratory protocols, formal language, execution semantics, workflow automation, reproducibility, Culsma

Public reference implementation of the Culsma language and execution stack, including parser, semantic validation, type and unit checking, plan lowering, runtime execution, driver interfaces, standard-library source, runnable examples, tests, and a command-line interface.
research-core
Authors: Càllisto, Mario
Type: Software
Published: 2026-08-02
Keywords: tilings, tessellations, Delaney-Dress symbols, exact arithmetic, formal verification, Scala

Shared substrate for the scala-tessella research programme on tilings: exact rational and cyclotomic arithmetic, the Delaney-Dress symbol engine, the exact angle/moduli layer, exported algebraic rank witnesses, the U(z) class machinery, and a SAT/DRAT certification harness. No theorems live here; individual results live in their own verification repositories and depend on a pinned release.
PROTEUS framework and data used in figures of BO paper
Authors: Nicholls, Harrison, Lichtenberg, Tim
Type: Software
Published: 2026-08-02

<p>PROTEUS is an open-source framework that couples models of planetary interiors, atmospheres, chemistry, and orbital dynamics to simulate how rocky planets evolve from molten beginnings to potentially habitable worlds. </p>
<p>The zip file contains the the version of PROTEUS used for the paper "Constraining the lives and times of exoplanets through evolutionary Bayesian retrievals" submitted to ApJ.</p>
<p>The tar files contain simulation outputs from PROTEUS used to make the figures.</p>
convex-uniform-honeycombs: machine-checked companion to "The 28 convex uniform honeycombs: a completeness theorem"
Authors: Càllisto, Mario
Type: Software
Published: 2026-08-02
Keywords: honeycombs, uniform honeycombs, convex uniform polyhedra, tilings of 3-space, vertex-transitive, Andreini, Grunbaum, Barlow packings, Delaney-Dress symbols, interval arithmetic, exact arithmetic, computer-assisted proof, reproducibility, Scala

The verification artifact for the paper's claims: the Alphabet Theorem (only 13 cells can occur in any face-to-face unit-edge honeycomb by convex uniform polyhedra) via an interval-certified corona fixpoint, two exact identities over Q(sqrt 5), closed forms and an interleaving lemma closing the prism and antiprism tails with no cap anywhere, and lifted odd-face walks killing the nine exotic prism families; the species table of exactly 34 vertex stars, enumerated as edge-to-edge tilings of the sphere of directions, with the Barlow fcc/hcp dichotomy as a corollary; the mono-species shell filter cutting 34 to 26; the transitive pattern enumeration landing on exactly 28 fingerprint classes, including the collision that shows local consistency does not imply developability; the completeness audit (periodization, coherence, separation, cap closure); the re-verification of all 34 star models and 28 periodization certificates in exact arithmetic over Q(sqrt 2, sqrt 3); the identification against the classical list of Grunbaum and Deza-Shtogrin; and the appendix's independent Delaney-Dress symbol census, which reproduces the count 28 sharing only the species table with the proof. The whole artifact re-derives from scratch in about a minute; all shared machinery is the pinned research-core library.
Mascope
Authors: Kausiala, Oskari, Chernonog, Philip, Tumashevich, Konstantin, Shenhav, Matan Bendix, Upornikov, Alexei
Type: Software
Published: 2026-08-02

Mascope is a platform for analysing and storing high-resolution mass spectrometry data: import instrument files, process, run targeted matching, and explore results in a web application or from Python.
BridgeDb
Authors: Awasthi, Manas, Basaric, Helena, Conklin, Bruce R., Evelo, Chris T., Gao, Jianjiong, Gray, Alasdair, Hanspers, Kristina, Isaac, Ho, Kelder, Thomas, Kerber, Randy, Kutmon, Martina, Mélius, Jonathan, Nunes, Nuno, Pico, Alexander R., Riutta, Anders, Slenter, Denise, Soiland-Reyes, Stian, Van Iersel, Martijn P., Willighagen, Egon L.
Type: Software
Published: 2026-08-02
Keywords: identifier mapping, Genes, Proteins, Metabolites, Biological data

<p>This release add three new species and updates to Guava 33.6.</p>
<p><strong>Full Changelog</strong>: https://github.com/bridgedb/BridgeDb/compare/release_3.0.30...release_3.0.31</p>
<p>The below examples assume you need just <code>org.bridgedb.bio</code>, and you can use it as template and modify to add other modules.</p>
<p>For <a href="https://maven.apache.org/">Maven</a>:</p>
<pre><code class="language-xml"><dependencies>
    <dependency>
        <groupId>org.bridgedb</groupId>
        <artifactId>org.bridgedb.bio</artifactId>
        <version>3.0.31</version>
    </dependency>
</dependencies>
</code></pre>
<p>For <a href="https://gradle.org/">Gradle</a>:</p>
<pre><code class="language-gradle">compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.31'
</code></pre>
<p>For <a href="http://ant.apache.org/ivy/">Ivy</a>:</p>
<pre><code class="language-xml"><dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.0.31"/>
</code></pre>
<p>For <a href="https://buildr.apache.org/">Buildr</a>:</p>
<pre><code class="language-buildr">'org.bridgedb:org.bridgedb.bio:jar:3.0.31'
</code></pre>
<p>For Python:</p>
<pre><code class="language-python">from scyjava import config, jimport
config.set_java_constraints(fetch=True, vendor='zulu', version='21')

config.add_repositories({'sonatype': 'https://central.sonatype.com'})
config.endpoints.append('bridgedb:org.bridgedb.bio:3.0.31')
</code></pre>
TabPFN-MCFF: An Implementation of the Multi-modal Cognitive Fusion Framework
Authors: null
Type: Software
Published: 2026-08-02

<div>
<div>This repository contains the official open-source implementation of the Multi-modal Cognitive Fusion Framework (MCFF), as described in our publication. As our work builds upon and extends the TabPFN architecture, this implementation is named **TabPFN-MCFF** in accordance with its license requirements.</div>
</div>
PyEarthTools: Machine learning for Earth system science
Authors: Leeuwenburg, Tennessee, Cook, Harrison, Rio, Maxime, Hobeichi, Sanaa, Yang, Edward, Miller, Joel, Mason, Gemma, Ramanathan, Nikeeth, Pill, John, Haddad, Stephen, Stassen, Christian, de Burgh-Day, Catherine, Holmes, Ryan, Potokina, Margarita, Bogacheva, Jenya, James, Matthew, Sullivan, Ben, Hoffmann, Luke, Pegios, Michael
Type: Software
Published: 2026-08-02
Keywords: modelling, geoscience, earth system science

<p><strong>PyEarthTools:</strong></p>
<ul class="simple">
<li>
<p>is a Python framework that supports the develoment of machine learning models, big and small, for Earth system science</p>
</li>
<li>
<p>is suitable for students and newcomers, as well as for domain specialists and scientists</p>
</li>
<li>
<p>runs effectively on HPC (supercomputers), cloud, workstations and laptops</p>
</li>
<li>
<p>is suitable for use with megabytes to petabytes of data</p>
</li>
</ul>
<p> </p>
<p>Source Code: <a class="reference external" href="https://github.com/ACCESS-Community-Hub/PyEarthTools">github.com/ACCESS-Community-Hub/PyEarthTools</a></p>
<p>Documentation: <a class="reference external" href="https://pyearthtools.readthedocs.io/">pyearthtools.readthedocs.io</a></p>
<p>Tutorial Gallery: <a class="reference internal" href="https://pyearthtools.readthedocs.io/en/latest/notebooks/Gallery.html"><span class="doc std std-doc">available here</span></a></p>
<p>New Users Guide: <a class="reference internal" href="https://pyearthtools.readthedocs.io/en/latest/newuser.html"><span class="std std-doc">available here</span></a></p>
<p> </p>
<p><strong>If you use <code class="docutils literal notranslate"><span class="pre">PyEarthTools</span></code> for your work or a publication, <a class="reference external" href="https://pyearthtools.readthedocs.io/en/latest/#citing-pyearthtools">please cite our work</a>.</strong></p>
<h2> </h2>
<h2>What's Changed</h2>
<ul>
<li>Add SimpleModel and expand tutorials by @tennlee in https://github.com/ACCESS-Community-Hub/PyEarthTools/pull/272</li>
<li>Added significant new tutorial content for upcoming workshops</li>
<li>Various minor bugfixes</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/ACCESS-Community-Hub/PyEarthTools/compare/0.6.1...0.6.2</p>
Datasets for "Great earthquake behaviour unlikely to be controlled by subduction interface roughness"
Authors: Yang, Xiaodong, Bell, Rebecca, Whittaker, Alexander, Xu, Haobo, Han, Xinze, Knowlson, Angela, Locher, Valerie
Type: Dataset
Published: 2026-08-02

<p>This repository contains the datasets supporting the study “Great earthquake behaviour unlikely to be controlled by subduction interface roughness”. The dataset includes reconstructed subduction interface geometry, along-strike variations in megathrust topography, quantified interface roughness metrics, interplate coupling characteristics, and associated great earthquake rupture parameters compiled across global subduction zones. These datasets were used to evaluate the relationships between subduction interface roughness, plate coupling, and great earthquake behaviour. The repository provides the processed datasets and calculated parameters underlying the analyses and figures presented in the manuscript.</p>
biodatageeks/polars-bio: Release 0.33.1
Authors: Marek Wiewiórka, zkeram, Drew T. Doering, Vincent Gao, Wojciech Sitek
Type: Software
Published: 2026-08-02

<h3><a href="https://github.com/biodatageeks/polars-bio/compare/0.33.0...0.33.1">0.33.1</a> (2026-08-02)</h3>
<h3>Bug Fixes</h3>
<ul>
<li><strong>cram:</strong> read CRAM files that use Huffman coding for the bases series (<a href="https://github.com/biodatageeks/polars-bio/issues/429">#429</a>) (<a href="https://github.com/biodatageeks/polars-bio/issues/431">#431</a>) (<a href="https://github.com/biodatageeks/polars-bio/commit/5a8e80adb98dc2b3043b95845058c9ec6a9d25e3">5a8e80a</a>), closes <a href="https://github.com/biodatageeks/datafusion-bio-formats/issues/225">biodatageeks/datafusion-bio-formats#225</a> <a href="https://github.com/zaeleus/noodles/issues/393">zaeleus/noodles#393</a> <a href="https://github.com/biodatageeks/datafusion-bio-formats/issues/225">biodatageeks/datafusion-bio-formats#225</a> <a href="https://github.com/biodatageeks/datafusion-bio-formats/issues/225">biodatageeks/datafusion-bio-formats#225</a> <a href="https://github.com/biodatageeks/polars-bio/issues/225">#225</a></li>
<li><strong>depth:</strong> 0-based output is half-open, not closed (<a href="https://github.com/biodatageeks/polars-bio/issues/427">#427</a>) (<a href="https://github.com/biodatageeks/polars-bio/issues/430">#430</a>) (<a href="https://github.com/biodatageeks/polars-bio/commit/7aedba8e01fd4e65db06280737d7ac86cfdc4ae4">7aedba8</a>), closes <a href="https://github.com/biodatageeks/datafusion-bio-functions/issues/205">biodatageeks/datafusion-bio-functions#205</a> <a href="https://github.com/biodatageeks/datafusion-bio-functions/issues/205">biodatageeks/datafusion-bio-functions#205</a></li>
</ul>
<h3>Documentation</h3>
<ul>
<li>explain how to suppress progress output (<a href="https://github.com/biodatageeks/polars-bio/issues/432">#432</a>) (<a href="https://github.com/biodatageeks/polars-bio/commit/10941ae9ffbda8b32102a002d7bcbfcfe96622b8">10941ae</a>)</li>
</ul>
NeoGeographyToolkit/StereoPipeline: 2026-08-02-daily-build
Authors: Oleg Alexandrov, ScottMcMichael, Michael Broxton, Mike Lundy, Ross Beyer, Kyle Husmann, Larry Edwards, Ara Nefian, SmithB, David Shean, Trey Smith, mstyer, Dr. Andrew Annex, Garion Milazzo, Ben Purinton, Stefano Bertone, drpeachboy, Amaury Dehecq, Giacomo Nodjoumi, Aleksandr Aravkin, Shashank Bhushan, Zack Moratto, Joachim Meyer, PicoJr, Jay Laura
Type: Software
Published: 2026-08-02

<p>Recent additions log: https://stereopipeline.readthedocs.io/en/latest/news.html</p>
SidSin0809/doi-citation-compiler: v1.2
Authors: Siddharth Singh
Type: Software
Published: 2026-08-02

<h1>Changelog</h1>
<h2>1.2.0</h2>
<h3>Compatibility and field integrity</h3>
<ul>
<li>Preserved the functional 1.1.0 implementation unchanged as <code>doi_citation_compiler_core.py</code>.</li>
<li>Added Zotero 7/8/9 document-preference metadata using chunked <code>ZOTERO_PREF_n</code> custom properties and XML data version 3.</li>
<li>Added deterministic occurrence-unique citation IDs; repeated DOI groups no longer reuse the same <code>citationID</code>.</li>
<li>Added validation of custom-property relationships/content types, complex-field balance, citation-ID uniqueness, field-code size, XML, ZIP integrity, and residual DOI text.</li>
<li>Kept native Word complex fields (<code>w:fldChar</code> begin/separate/end plus chunked <code>w:instrText</code>).</li>
</ul>
<h3>DOI scanner</h3>
<ul>
<li>Added conservative safe-repair mode for Unicode/full-width punctuation, spaces around DOI punctuation, line breaks, tabs, soft hyphens, and zero-width characters.</li>
<li>Added incomplete-candidate reporting with context; incomplete strings are never silently invented.</li>
<li>Added field-aware paragraph scanning: existing managed fields are protected, while uncited DOI text later in the same paragraph remains eligible.</li>
<li>Added optional scanning of headers, footers, comments, glossary/building blocks, text boxes, footnotes, and endnotes.</li>
<li>Added formatting-context preservation and removal of residual hyperlink styling from visible citation results.</li>
</ul>
<h3>Workflow and reliability</h3>
<ul>
<li>Added metadata retry/backoff controls while retaining deterministic sequential resolution and caching.</li>
<li>Added rerun-safe generated-bibliography bookmarks and bibliography policies (<code>reuse</code>, <code>replace</code>, <code>none</code>).</li>
<li>Added profiles, GUI, multi-file batch runner, validation runner, environment checker, and optional Windows Explorer context-menu extension.</li>
<li>Added installable Python project metadata and console commands.</li>
<li>Expanded tests from 4 to 13, including end-to-end DOCX construction, line-break repair, existing-field protection, Zotero preferences, and repeated-citation IDs.</li>
</ul>
<h2>1.1.0</h2>
<ul>
<li>Replaced Microsoft Word COM automation with a cross-platform OOXML backend.</li>
<li>Correctly detected all 295 citation groups in the supplied manuscript instead of 44.</li>
<li>Wrote complex Word fields with <code>w:fldChar</code> and chunked <code>w:instrText</code> nodes.</li>
<li>Added transactional DOCX validation and residual-DOI checks.</li>
<li>Added separate Zotero, Mendeley legacy-migration, and portable outputs.</li>
<li>Removed the <code>Fields.Add()</code> dependency and <code>pywin32</code> requirement.</li>
</ul>