reapxdev/zenodo-scraper huggingface dataset:
OPARI2 OpenMP instrumenter
Authors: Mohr, Bernd, Wylie, Brian, Wolf, Felix, Geimer, Markus, Feld, Christian, Lorenz, Daniel, Schmidl, Dirk, Philippen, Peter, Jiang, Jie, Wesarg, Bert, Reuter, Jan André
Type: Software
Published: 2026-07-30
Keywords: OPARI2, source-to-source, instrumentation, OpenMP

<p>OPARI2 is a source-to-source instrumentation tool designed for OpenMP and hybrid codes. It wraps OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. As a user of OPARI2, you either need to implement the POMP2 interface yourself, or use a tool that does so. The most convenient way to use it is via <a href="https://score-p.org/">Score-P</a> measurement infrastructure.</p>
<p>OPARI2 is available under the 3-clause BSD Open Source license.</p>
<p>Version 2.0.10 is a bugfix release for version 2.0.</p>
City2Graph: A Python Library for Heterogeneous Graph Neural Networks and Spatial Analysis in Urban Systems
Authors: Sato, Yuta
Type: Software
Published: 2026-08-01
Keywords: GeoAI, Graph Neural Networks, GNN, PyTorch Geometric, Geospatial Analysis, Urban Analytics, Spatial Data Science, Urban Mobility, Transportation Networks, Spatial Knowledge Graphs, Spatiotemporal Analysis, Geospatial Foundation Models, Digital Twin, Urban Informatics, Geographic Data Science, Graph Representation Learning, Urban Planning and Design

City2Graph is a Python library that provides an integrated interface of geospatial datasets from multiple domains converting into graph representations. It facilitates the one-stop data pipeline for spatial network analysis and Graph Neaural Networks (GNNs)  for GeoAI applications.
cgohlke/tifffile: v2026.7.31
Authors: Christoph Gohlke
Type: Software
Published: 2026-08-01

<h2>Read and write TIFF files</h2>
<p>Tifffile is a comprehensive Python library to</p>
<ol>
<li>store NumPy arrays in TIFF (Tagged Image File Format) files, and</li>
<li>read image and metadata from TIFF-like files used in bioimaging.</li>
</ol>
<p>Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, GeoTIFF, Adobe DNG, ZIF (Zoomable Image File Format), MetaMorph STK, Zeiss LSM, ImageJ hyperstack, Micro-Manager MMStack and NDTiff, SGI, NIHImage, FLIMage, Olympus FluoView and SIS, ScanImage, Molecular Dynamics GEL, Huron TIFF, Aperio SVS, Leica SCN, Roche BIF, PerkinElmer QPTIFF (QPI, PKI), Hamamatsu NDPI, Argos AVS, Philips DP, DICOM-TIFF, and ThermoFisher EER formatted files.</p>
<p>Image data can be read as NumPy arrays or Zarr arrays/groups from strips, tiles, pages (IFDs), SubIFDs, higher order series, and pyramidal levels.</p>
<p>Image data can be written to TIFF, BigTIFF, OME-TIFF, and ImageJ hyperstack compatible files in multi-page, volumetric, pyramidal, memory-mappable, tiled, predicted, or compressed form.</p>
<p>Many compression and predictor schemes are supported via the imagecodecs library, including LZW, PackBits, Deflate, CCITT, PIXTIFF, LZMA, LERC, Zstd, JPEG (8 and 12-bit, lossless), JPEG 2000, JPEG XR, JPEG XL, WebP, PNG, EER, Jetraw, 24-bit floating-point, and horizontal differencing.</p>
<p>Tifffile can also be used to inspect TIFF structures, read image data from multi-dimensional file sequences, write fsspec ReferenceFileSystem for TIFF files and image file sequences, patch TIFF tag values, and parse many proprietary metadata formats.</p>
<h2>Changes</h2>
<ul>
<li>Fsspec v3 stores using big-endian floatpred are incompatible with zarr>=3.3.</li>
<li>Specify bytes codec endian configuration in ZarrFileSequenceStore.</li>
<li>Add additional NDPI tags from specification (#331).</li>
</ul>
conda: A system-level, binary package and environment manager running on all major operating systems and platforms.
Authors: conda contributors
Type: Software
Published: 2026-08-01

Conda is a cross-platform, language-agnostic binary package manager. It is the package manager used by Anaconda installations, but it may be used for other systems as well. Conda makes environments first-class citizens, making it easy to create independent environments even for C libraries. Conda is written entirely in Python, and is BSD licensed open source.
expecto: a Python package for querying PHOENIX model spectra
Authors: Morris, Brett
Type: Software
Published: 2024-04-28

<p>Pure Python package for retrieving <a href="https://phoenix.astro.physik.uni-goettingen.de/?" rel="nofollow">PHOENIX model stellar spectra</a> via FTP. Spectra are returned as <a href="https://specutils.readthedocs.io/en/stable/api/specutils.Spectrum1D.html#specutils.Spectrum1D" rel="nofollow">specutils.Spectrum1D</a> objects.</p>
OpenChemistry/tomviz: Tomviz 3.0.0
Authors: Marcus D. Hanwell, Chris Harris, Patrick Avery, Shawn Waldon, Cory Quammen, Alessandro Genova, Yi Jiang, Robert Hovden, Utkarsh Ayachit, Jonathan Schwartz, Brianna Major, Sebastien Jourdain (Kitware), Dan Lipsa, alvaro, Wei (Celia) Xu, Matt McCormick, jepietryga, T.J. Corona, Elliot Padgett, Ben Boeckel, Dan Allan, Padraic Shafer, Christian Clauss, Julien Nabet, Barnaby Levin, Janne Blomqvist, sukhsung, Zhuokai Zhao
Type: Software
Published: 2026-07-31

<h1>Tomviz 3.0</h1>
<p><strong>Redesigned node-based pipeline.</strong> A graph of nodes with typed input/output ports instead of a single linear chain. Branch, merge, and insert nodes; one output can feed many inputs. Pause, stop, and resume execution, set breakpoints on any transform, and cache intermediate results so downstream changes don't force a full re-run. Operators are now Transforms, Modules are Sinks, Workflows are Sources.</p>
<p><strong>Run any transform in any conda environment.</strong> Pick an environment per node in the transform dialog's Execution tab. Heavy or conflicting dependencies stay out of Tomviz.</p>
<p><strong>AI segmentation.</strong> SAM 2 propagates a segmentation through the volume from a single seeded slice. SAM 3 segments from a text prompt with no seed, labeling connected components as separate instances. Both run locally (CUDA, Apple Silicon, or CPU) or against a facility-hosted service.</p>
<p><strong>Faster reconstruction.</strong> New SIRT, ART, and TV minimization transforms, a generalized TomoPy transform with optional CUDA acceleration, and an interactive rotation-center tool with live previews.</p>
<p><strong>Native multi-array support.</strong> Datasets carry many scalar arrays (for example, one per element in an XRF map). Transforms apply to any subset; visualizations color by any array.</p>
<p><strong>Synchrotron workflows.</strong> Built-in PyXRF and ptychography sources developed with the HXN beamline at NSLS-II, including correlative phase + XRF loading.</p>
<p><strong>Better alignment.</strong> New PyStackReg transform, improved cross-correlation and tilt-axis alignment, and shifts that can be saved and reloaded.</p>
<p><strong>Interactive plotting.</strong> Nodes can output tables, rendered as line charts with CSV export. Ships with Fourier Shell Correlation, Power Spectral Density, and a two-input Similarity Metrics transform.</p>
<p><strong>Usability.</strong> Reorganized menus with a search dialog (<code>Ctrl+Space</code>), drag-and-drop file loading, <code>.npy</code>/<code>.mat</code> reading, an MRC writer, enhanced DICOM, a cylindrical crop widget, and data generators.</p>
<p><strong>Modernized foundation.</strong> Qt 6, ParaView 6.1, pybind11 3.0, recent Python versions, conda-forge packages for all three platforms, CI on Linux/macOS/Windows, and many stability and memory-leak fixes.</p>
<h2>Downloads</h2>
<p>conda-forge packages, plus DMG, MSI, and Linux installers.</p>
ICB-DCM/pyABC: pyABC v0.13.0
Authors: Yannik Schaelte, Stephan Grein, Jonas Arruda, drickert, Emad Alamoudi, Daniel Weindl, Fabian Rost, Felipe, Pariksheet Nanda, Patrick Laub
Type: Software
Published: 2026-07-31

<p>General:</p>
<ul>
<li>Add support for python3.14</li>
<li>Add execution time profiling to the ABC-SMC run, reporting pure simulation
time, parallel-pipeline setup time, and in-between-iteration time,
including population-size calculation and distance-function adaptation.
The timings are also returned by <code>run_generation</code>. Resolves #325.</li>
<li>Minor bug fixes and improved typesetting.</li>
</ul>
<p>Visualization:</p>
<ul>
<li><code>plot_walltime</code> and <code>plot_total_walltime</code> now report the actual
per-generation walltimes and no longer include the idle time that passed
between a stored analysis and a later resumed run. Resolves #667.</li>
</ul>
<p>Storage (breaking):</p>
<ul>
<li>Store the per-generation walltime in the database (new <code>wall_time</code> column,
database version 2). Databases created with older pyABC versions must be
migrated via <code>abc-migrate</code> before they can be resumed; for such databases
the walltime plots fall back to the previous, end-time-based behavior.</li>
<li>Particle weights are now stored using the global normalization (weights sum
to 1 across all particles of all models, matching the in-memory
<code>Population</code> representation). This is bundled into database version 2 and
handled by <code>abc-migrate</code> for existing databases. Resolves #47.</li>
</ul>
easyscience/core: easyscience 2.5.1
Authors: Piotr Rozyczko, Andreas Pedersen, Christian Dam Vedel, Andrew Sazonov, Henrik Jacobsen, Ales Kutsepau, Eric Lindgren
Type: Software
Published: 2026-07-31

<h2>Changed</h2>
<ul>
<li>Fix release workflow by committing updated Pixi lock state (#286)</li>
</ul>
refnx/refnx: v0.1.66
Authors: Andrew Nelson, ACNS-Sample-Environment, Stuart Prescott, Oliver, DLCortie, dcortie, Isaac Gresham, James Durant
Type: Software
Published: 2026-07-29

<h2>What's Changed</h2>
<ul>
<li>MAINT: different way of retrieving components by @andyfaff in https://github.com/refnx/refnx/pull/903</li>
<li>ENH: monkeypatch LipidLeafletGuest for jax by @andyfaff in https://github.com/refnx/refnx/pull/904</li>
<li>MAINT: PaddedSlabSpec by @andyfaff in https://github.com/refnx/refnx/pull/905</li>
<li>MAINT: jax_funcify by @andyfaff in https://github.com/refnx/refnx/pull/906</li>
<li>MAINT: process_trace by @andyfaff in https://github.com/refnx/refnx/pull/907</li>
<li>Jabeles by @andyfaff in https://github.com/refnx/refnx/pull/908</li>
<li>MAINT: update INSTALL_CONTRIBUTE.md by @andyfaff in https://github.com/refnx/refnx/pull/909</li>
<li>ENH: add CompiledObjective.generative by @andyfaff in https://github.com/refnx/refnx/pull/910</li>
<li>MAINT: pm.Deterministic by @andyfaff in https://github.com/refnx/refnx/pull/911</li>
<li>MAINT: speed up jax compiled functions by @andyfaff in https://github.com/refnx/refnx/pull/912</li>
<li>CI: scope GITHUB_TOKEN permissions in release workflow by @andyfaff in https://github.com/refnx/refnx/pull/913</li>
<li>MAINT: add a compile_global_objective test by @andyfaff in https://github.com/refnx/refnx/pull/914</li>
<li>Doc by @andyfaff in https://github.com/refnx/refnx/pull/915</li>
<li>MAINT: much wider tests on jax operations by @andyfaff in https://github.com/refnx/refnx/pull/916</li>
<li>MAINT: adjust parameterisation of LipidLeaflet in test by @andyfaff in https://github.com/refnx/refnx/pull/917</li>
<li>ENH: improved plotting of confidence bands from MCMC sampling by @andyfaff in https://github.com/refnx/refnx/pull/918</li>
<li>MAINT: enhanced plotting of confidence intervals by @andyfaff in https://github.com/refnx/refnx/pull/919</li>
<li>DOC: pymc + lipid example by @andyfaff in https://github.com/refnx/refnx/pull/920</li>
<li>REL: v0.1.66 by @andyfaff in https://github.com/refnx/refnx/pull/921</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/refnx/refnx/compare/v0.1.65...v0.1.66</p>
cgohlke/oirfile: v2026.7.28
Authors: Christoph Gohlke
Type: Software
Published: 2026-07-29

<h2>Read Olympus/Evident OIR and POIR files</h2>
<p>Oirfile is a Python library to read images and metadata from OIR (Olympus Image Format Raw) files and POIR archives (ZIP collections of OIR files) produced by Olympus/Evident FluoView fluorescence microscopy software.</p>
<h2>Changes</h2>
<ul>
<li>Fix spatial and time coordinates.</li>
<li>Add OirFile.timestamps, scanner, and is_linescan properties.</li>
</ul>
molssi-seamm/gaussian_step: Energy of formation via seamm_thermochemistry; initial checkpoint job:// support
Authors: Paul Saxe, seamm
Type: Software
Published: 2026-07-28

<ul>
<li>The energy of formation is now computed via the shared <code>seamm_thermochemistry</code> library: a 0 K, ZPE-free energy of formation referenced to the elements, computed for every job with an electronic energy rather than only the subset with a full harmonic thermochemistry calculation. Part of unifying the atomic reference-energy handling across steps.</li>
<li><strong>Initial checkpoint</strong> (on the Energy and Wavefunction Stability steps) can now reference another job's checkpoint file, via <code>job://<job number>/<name></code> (SEAMM's <code>Node.file_path</code> gained read-only cross-job references) -- useful for seeding from a checkpoint computed in a different job.</li>
</ul>
molssi-seamm/control_parameters_step: File-typed control parameters can reference another job
Authors: Paul Saxe, seamm
Type: Software
Published: 2026-07-28

<ul>
<li>A control parameter of type "file" can now reference another job's file, via <code>job://<job number>/<name></code> (SEAMM's <code>Node.file_path</code> gained read-only cross-job references) -- useful for pulling in a file produced by an earlier, separate job.</li>
</ul>
sdss/sdssdb: sdssdb 1.1.2
Authors: José Sánchez-Gallego, Pramod Gupta, Brian Cherinka, John Donor, Conor Sayres, Tom Dwelly, Ilija Medan, Joel Brownstein, Kevin Covey, Sean Morrison, Andy Casey, Felipe Santana Rojas, jonathantrump
Type: Software
Published: 2026-07-28

Central SDSS product for database management
napari-ome-zarr
Authors: Moore, Josh, Moore, Will, Besson, Sébastien, Doncila Pop, Draga
Type: Software
Published: 2026-07-31

<h2>What's Changed</h2>
<ul>
<li>Forward NGFF axis names and units into napari layer metadata by @hinderling in https://github.com/ome/napari-ome-zarr/pull/149</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@hinderling made their first contribution in https://github.com/ome/napari-ome-zarr/pull/149</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/ome/napari-ome-zarr/compare/0.9.1...0.10.0</p>
michen00/invisible-squiggles: v0.4.0
Authors: Michael I Chen, Parvati Jayakumar, Sneha Joshi, Madhur Dixit
Type: Software
Published: 2026-07-31

<p><!-- Release notes generated using configuration in .github/release.yml at v0.4.0 --></p>
<h2>What's Changed</h2>
<ul>
<li>docs: add badges by @michen00 in https://github.com/michen00/invisible-squiggles/pull/91</li>
<li>test: robustify readme prep by @michen00 in https://github.com/michen00/invisible-squiggles/pull/92</li>
<li>chore: update boilerplate by @michen00 in https://github.com/michen00/invisible-squiggles/pull/104</li>
<li>fix: fix state management by @michen00 in https://github.com/michen00/invisible-squiggles/pull/103</li>
<li>feat: enable starting with hidden squiggles by @michen00 in https://github.com/michen00/invisible-squiggles/pull/107</li>
<li>ci: greet only genuine newcomers by @michen00 in https://github.com/michen00/invisible-squiggles/pull/195</li>
<li>ci: publish and attest releases, fix packaging by @michen00 in https://github.com/michen00/invisible-squiggles/pull/228</li>
<li>ci: package the vsix on every PR by @michen00 in https://github.com/michen00/invisible-squiggles/pull/229</li>
<li>ci: harden bot auto-merge against actor drift by @michen00 in https://github.com/michen00/invisible-squiggles/pull/233</li>
<li>ci: gate majors on ecosystem, not file paths by @michen00 in https://github.com/michen00/invisible-squiggles/pull/235</li>
<li>ci: unhold actions majors CI actually runs by @michen00 in https://github.com/michen00/invisible-squiggles/pull/236</li>
<li>docs: remove manual line breaks from prose by @michen00 in https://github.com/michen00/invisible-squiggles/pull/237</li>
<li>chore: release v0.4.0 by @michen00 in https://github.com/michen00/invisible-squiggles/pull/232</li>
<li>build(deps-dev): clear seven dev-tree advisories by @michen00 in https://github.com/michen00/invisible-squiggles/pull/238</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@github-actions[bot] made their first contribution in https://github.com/michen00/invisible-squiggles/pull/102</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/michen00/invisible-squiggles/compare/v0.3.1...v0.4.0</p>
eidolon (formerly rusty-neat): a Rust toolkit for simulating NGS read data, including tumor/normal cancer sequencing
Authors: Allen, Joshua, Kowalik, Mikolaj, NEAT Contributors
Type: Software
Published: 2026-07-31
Keywords: bioinformatics, ngs-simulation, cancer-genomics, structural-variants, variant-calling, fastq, vcf, rust

eidolon is a Rust port and extension of NEAT that generates simulated next-generation sequencing data in FASTQ and VCF formats with the statistical properties of real datasets, along with a golden BAM/VCF truth set of inserted variants and ideal alignments. It adds structural-variant simulation (CNV, BND, INV, INS, and others) and an end-to-end tumor/normal cancer workflow (gen-cancer-reads) that merges two read passes at a configurable purity and emits an origin-tagged truth VCF for benchmarking somatic and structural-variant callers, with an emphasis on low memory use and short CPU time.