19:40 Yuri Victorovich (yuri) 

science/zx: Remove

    5d28f86

10:23 Po-Chuan Hsieh (sunpoet) 

science/py-pysal: Add py-pysal 25.7

PySAL, the Python spatial analysis library, is an open source cross-platform
library for geospatial data science with an emphasis on geospatial vector data
written in Python. It supports the development of high level applications for
spatial analysis, such as
- detection of spatial clusters, hot-spots, and outliers
- construction of graphs from spatial data
- spatial regression and statistical modeling on geographically embedded
  networks
- spatial econometrics
- exploratory spatio-temporal data analysis

    2c0c0ef

12:56 Älven (alven) 

science/cpcmx: [NEW PORT] Extended conductor-like polarizable continuum
solvation model

This is an fully Free Software solvation model, based on the original
conductor like screening model for realistic solvation (COSMO-RS)
model by Klamt et al. in combination with the universal solvation
model based on solute electron density (SMD): by Marenich, Cramer and
Truhlar.

WWW: https://github.com/grimme-lab/CPCM-X/

Reviewed by:		diizzy@
Approved by:		yuri@ (Mentor)
Differential Revision:	https://reviews.freebsd.org/D53531

    34452b5

12:53 Älven (alven) 

science/numsa: [NEW PORT] Solvent accessible surface area calculation

Numerical surface area integrator for molecular inputs. This project
is based on routines from xtb and dftb+.

WWW: https://github.com/grimme-lab/numsa/

Reviewed by:		diizzy@
Approved by:		yuri@ (Mentor)
Differential Revision:	https://reviews.freebsd.org/D53529

    b885b76

03:42 Yuri Victorovich (yuri) 

science/py-hiphive: Move to py-hiPhive; update 1.2 → 1.5

    a976366

23:14 Yuri Victorovich (yuri) 

science/py-corner: New port: Make some beautiful corner plots

    b2599bac8

15:46 Yuri Victorovich (yuri) 

science/py-cirq-web: New port: Cirq module to run on pasqal quantum computers

    567f4fd

15:17 Yuri Victorovich (yuri) 

science/py-cirq-rigetti: Remove: Deprecated by the upstream

    e612156

08:25 Yuri Victorovich (yuri) 

science/py-pynrrd: New port: Pure Python module for reading and writing NRRD
files

    73fca48

08:25 Yuri Victorovich (yuri) 

science/py-neo: New port: Package for representing electrophysiology data in
Python

    fb77695

08:25 Yuri Victorovich (yuri) 

science/py-mne: New port: Python project for MEG and EEG data analysis

    dd82f40

01:38 Yuri Victorovich (yuri) 

science/py-dwave-gate: New port: DWave: Gate model library

    c493324

14:26 Rene Ladan (rene) 

science/R-cran-eco: Remove expired port

2025-06-14 science/R-cran-eco: Unsupported upstream

Event:	Kitchener-Waterloo Hackathon 202506

    4dd59ae

22:00 Rene Ladan (rene) 

science/py-pysal: Remove expired port

2025-06-04 science/py-pysal: Depends on expired math/py-spvcm

    e40e6e6

19:01 Rene Ladan (rene) 

science/py-DendroPy: Remove expired port

2025-03-31 science/py-DendroPy: Depends on expired devel/py-pytest-runner

    8e5f53e

17:40 Rene Ladan (rene) 

Revert: "science/pastix: Remove expired port"

This reverts commit 05c6f4b9240f9d4432cd718463c9ae71c54216cc.

lang/julia is no longer expired

    520b713

17:04 Rene Ladan (rene) 

science/dvc: Remove expired port

2025-06-01 science/dvc: Depends on expired math/py-grandalf

    0d9608a

17:03 Rene Ladan (rene) 

science/pastix: Remove expired port

2025-06-01 science/pastix: Depends on expired lang/julia

    05c6f4b

11:45 Rene Ladan (rene) 

science/gtamsanalyzer: Remove expired port

2025-05-04 science/gtamsanalyzer: Upstream unmaintained as last release was in
2004

    2a56410

06:45 Wen Heping (wen) 

science/py-qiskit: Resurrect and Update to 2.0.0

    bc25741

14:25 Rene Ladan (rene) 

science/py-moltemplate: Remove expired port

2025-03-31 science/py-moltemplate: Depends on expired devel/py-pytest-runner

    d036634

12:37 Gleb Popov (arrowd)  Author: Alexey Donskov

science/linux-ai-ml-env: Linux Python environment for running AI and ML stuff

Sponsored by:	Future Crew, LLC
Pull Request:	https://github.com/freebsd/freebsd-ports/pull/361

    8f28236

11:15 Yuri Victorovich (yuri) 

science/py-h5netcdf: New port: netCDF4 via h5py

    6913450

07:47 Wen Heping (wen) 

science/p5-Chemistry-OpenSMILES: New port

Chemistry::OpenSMILES provides support for SMILES chemical
identifiers conforming to OpenSMILES v1.0 specification
(http://opensmiles.org/opensmiles.html).

    2169ecb

15:50 Po-Chuan Hsieh (sunpoet) 

science/sz3: Add sz3 3.2.1

SZ is a modular parametrizable lossy compressor framework for scientific data
(floating point and integers). It has applications in simulations, AI and
instruments. It is a production quality software and a research platform for
lossy compression. SZ is open and transparent. Open because all interested
researchers and students can study or contribute to it. Transparent because all
performance improvements are detailed in publications.

SZ can be used for classic use-cases: visualization, accelerating I/O, reducing
memory and storage footprint and more advanced use-cases like compression of DNN
models and training sets, acceleration of computation, checkpoint/restart,
reducing streaming intensity and running efficiently large problems that cannot
fit in memory. Other use-cases will augment this list as users find new
opportunities to benefit from lossy compression of scientific data.

SZ has implementations on CPU, GPU, and FPGA and is integrated in the main I/O
libraries: HFD5, ADIOS, PnetCDF.

    9a01009

17:04 Po-Chuan Hsieh (sunpoet) 

science/py-pnetcdf: Add py-pnetcdf 1.0.0

PnetCDF-Python is a Python interface to PnetCDF, a high-performance I/O library
for accessing NetCDF files in parallel. It can provide MPI-based parallel python
programs to achieve a scalable I/O performance.

    9e122cc

01:42 Yuri Victorovich (yuri) 

science/py-icet: New port: Pythonic approach to alloy cluster expansions

    0813890

01:42 Yuri Victorovich (yuri) 

science/py-seekpath: New port: Obtain, visualize k-vector coefficients in
crystal Brillouin zone

    fec524c

22:36 Yuri Victorovich (yuri) 

science/acados: New port: Fast and embedded solvers for nonlinear optimal
control

    79112d3d

10:59 Rene Ladan (rene) 

science/py-nilearn: Remove expired port

2024-12-31 science/py-nilearn: Depends on expired devel/py-codecov

    dd41e11

16:35 Rene Ladan (rene) 

science/grib_api: Remove expired port

2024-11-30 science/grib_api: Deprecated by upstream. Use science/eccodes instead

    312c78d

09:20 Yuri Victorovich (yuri) 

science/py-symfc: New port: Generate symmetrized force constants

    8228fb6

20:34 Yuri Victorovich (yuri) 

science/seacas: New port: Sandia Engineering Analysis Code Access System
(SEACAS)

    4f142c6c

05:51 Yuri Victorovich (yuri) 

science/py-pyphot: New port: Library for computing photometry from spectra

    680659e

20:43 Yuri Victorovich (yuri) 

science/parthenon: New port: Portable block-structured Adaptive Mesh Refinement
(AMR) framework

    abee57d

06:11 Po-Chuan Hsieh (sunpoet) 

science/py-sarpy: Add py-sarpy 1.3.58

SarPy is a basic Python library to read, write, and do simple processing of
complex SAR data using the NGA SICD format (standards linked below). It has been
released by NGA to encourage the use of SAR data standards throughout the
international SAR community. SarPy complements the SIX library (C++) and the
MATLAB SAR Toolbox, which are implemented in other languages but have similar
goals.

    db94842

07:54 Yuri Victorovich (yuri) 

science/libpsml: New port: Library to handle pseudopotentials in PSML format

    ddb5a45

07:11 Yuri Victorovich (yuri) 

science/py-openEMS: New port: Electromagnetic field solver using the EC-FDTD
method

    cf6edc8

17:13 Po-Chuan Hsieh (sunpoet) 

science/py-mercantile: Move science/mercantile to science/py-mercantile

- Change MASTER_SITES from GitHub to PYPI
- Add LICENSE_FILE
- Fix version requirement of RUN_DEPENDS
- Convert to USE_PYTHON=pep517
- Bump PORTREVISION for package change
- Take maintainership

    1608be4

07:19 Yuri Victorovich (yuri) 

science/py-dwave-optimization: New port: DWave: Nonlinear models for industrial
optimization problems

    af92280

13:02 Thierry Thomas (thierry) 

science/Makefile: connect mmg

    dae95f9

12:58 Thierry Thomas (thierry) 

science/linearelasticity: new port, Elas, a solver for linear elasticity

Required by Mmg.

    298551c

10:54 Yuri Victorovich (yuri) 

science/py-mplhep-data: New port: Font (Data) sub-package for mplhep

    ca06520

10:54 Yuri Victorovich (yuri) 

science/py-mplhep: New port: Matplotlib styles for HEP

    788eadd

17:16 Yuri Victorovich (yuri) 

science/py-periodictable: New port: Extensible periodic table of the elements
pre-populated with data

    9b01d7f

19:28 Yuri Victorovich (yuri) 

science/py-HofstadterTools: New port: Package for analyzing the Hofstadter model
of particles in the lattice

    1fc3054

19:55 Rene Ladan (rene) 

science/svmlight: Remove expired port

2024-04-14 science/svmlight: Unmaintained, last upstream release in 2008 and
there are more modern alternatives

    1ec3fe7

19:54 Rene Ladan (rene) 

science/p5-Algorithm-SVMLight: Remove expired port

2024-04-14 science/p5-Algorithm-SVMLight: Depends on DEPRECATED science/svmlight

    287d278

18:37 Yuri Victorovich (yuri) 

science/py-h5pyd: New port: h5py compatible client lib for HDF REST API

    e06cdb8

13:47 Antoine Brodin (antoine) 

py-qiskit: remove and unbreak the ports tree

    30cfa1e

21:49 Yuri Victorovich (yuri) 

science/py-qiskit-terra: Removed until ported again

The upstream gutted the previous project and replaced it with an
unrelated repository under the same name.
The new project should be ported as new.
It was failing for a while in poudriere.

    b601591

14:44 Rene Ladan (rene) 

science/py-asdf-unit-schemas: Remove expired port

2024-03-31 science/py-asdf-unit-schemas: This package is decommissioned and no
longer provides any ASDF schemas. The schemas provided by the package were
duplicates of the schemas provided by asdf-standard. Use
science/py-asdf-standard instead

    5a2db3a

16:37 Thierry Thomas (thierry) 

science/optench: new port, a virtual optical bench

    2558582

11:32 Rene Ladan (rene) 

science/libtensorflow1: Remove expired port

2024-01-15 science/libtensorflow1: Broken for more than a year

    36babc4

19:01 Yuri Victorovich (yuri) 

science/py-trx-python: New port: Experiments with new file format for
tractography

    f47c470

13:40 Rene Ladan (rene) 

science/libgeodecomp: Remove expired port

2023-11-30 science/libgeodecomp: BROKEN for more than an year

    f19cf1d

05:43 Yuri Victorovich (yuri) 

science/mcpl: New port: Monte Carlo Particle Lists library

    0db904a

22:05 Yuri Victorovich (yuri) 

science/py-ncrystal: New port: Library for thermal neutron transport in crystals
and other materials

    46b9279

03:56 Yuri Victorovich (yuri) 

science/ncrystal: New port: Library for thermal neutron transport in crystals
and other materials

    88fff07

06:33 Yuri Victorovich (yuri) 

science/mutationpp: New port: MUlticomponent Thermodynamic And Transport library
for IONized gases

    d093257

21:26 Jason E. Hale (jhale) 

science/qt6-quick3dphysics: New port

Qt Quick 3D Physics provides a high-level API for physics simulation. It
supports simulating interactive rigid bodies as well as static meshes and
non-colliding bodies used for detecting overlaps. Every simulated body
can have its own physical properties like mass, density and friction.

https://doc.qt.io/qt-6/qtquick3dphysics-index.html

    594a399

02:22 Muhammad Moinur Rahman (bofh) 

science/crf++: Remove expired port

2023-09-30 science/crf++: Last upstream activity was in 2015

    e58795c

18:49 Yuri Victorovich (yuri) 

science/gcp: New port: Geometrical Counter-Poise Correction

    7f1f24a

07:02 Yuri Victorovich (yuri) 

science/py-dftd4: New port: Python API of the DFT-D4 project

    6db35e2

09:43 Yuri Victorovich (yuri) 

science/py-nglview: New port: IPython widget to view molecular structures and
trajectories

    a275c86

09:30 Yuri Victorovich (yuri) 

science/salome-configuration: New port: Salome Project: Multi-physics
simulations: Configuration

    bdbeacf

09:30 Yuri Victorovich (yuri) 

science/salome-kernel: New port: Salome Project: Multi-physics simulations:
Kernel

    5411099

17:48 Yuri Victorovich (yuri) 

science/py-emmet-core: New port: Materials API Toolkit for the Materials Project

    3992794

17:48 Yuri Victorovich (yuri) 

science/py-mp-api: New port: API for server for the Materials Project

    cf910b4

05:49 Yuri Victorovich (yuri) 

science/py-mpcontribs-client: New port: Client library for MPContribs API on
contribs-api.materialsproject.org

    baef140

16:39 Yuri Victorovich (yuri) 

science/py-pymatgen-analysis-alloys: New port: PyMatgen add-on library with
classes useful for describing alloys

    7d7d929

20:30 Yuri Victorovich (yuri) 

science/py-dftbplus: New port: DFTB+: Package for performing fast atomistic
simulations

    602af4b

16:24 Yuri Victorovich (yuri) 

science/py-signac: New port: Manage large and heterogeneous data spaces on the
file system

    f207625

18:57 Rene Ladan (rene) 

cleanup: Remove expired ports related to cdcl:

2023-04-21 science/cdcl: Broken since 2021
2023-04-21 science/rubygem-ruby-dcl: requires deprecated science/cdcl

    04c7d1e

08:47 Yuri Victorovich (yuri) 

science/py-HepMC3: New port: Event record for High Energy Physics Monte Carlo
generators/simulation

    0e14eaf

23:00 Yuri Victorovich (yuri) 

science/py-qiskit-dynamics: New port: Qiskit ODE solver

    e052de5

15:12 Yuri Victorovich (yuri) 

science/InsightToolkit521: Retire if favor of science/InsightToolkit

    173807a

00:01 Muhammad Moinur Rahman (bofh) 

science/dcl: Remove expired port:

2023-03-21 science/dcl: Broken since 2021

    38c1f38

00:01 Muhammad Moinur Rahman (bofh) 

science/fisicalab: Remove expired port:

2023-03-21 science/fisicalab: Broken since 2021

    09654bc

15:47 Po-Chuan Hsieh (sunpoet) 

science/py-cfgrib: Add py-cfgrib 0.9.10.3

cfgrib provides a Python interface to map GRIB files to the Unidata's Common
Data Model v4 following the CF Conventions. The high level API is designed to
support a GRIB engine for xarray and it is inspired by netCDF4-python and
h5netcdf. Low level access and decoding is performed via the ECMWF ecCodes
library and the eccodes python package.

    5660adf

12:58 Po-Chuan Hsieh (sunpoet) 

science/py-asdf-unit-schemas: Add py-asdf-unit-schemas 0.1.0

asdf-unit-schemas provides ASDF schemas for validating unit tags. Users should
not need to install this directly; instead, install an implementation package
such as asdf-astropy, which includes asdf-unit-schemas as a dependency.

    3de7714

23:05 Yuri Victorovich (yuri) 

science/py-vedo: New port: Python module for scientific analysis and
visualization of 3D objects

    de6c547

03:24 Yuri Victorovich (yuri) 

science/py-ipygany: New port: 3-D scientific visualization in Jupyter Notebooks

    85d1c98

09:04 Po-Chuan Hsieh (sunpoet) 

science/p5-Geo-Coordinates-Transform: Add p5-Geo-Coordinates-Transform 0.10

There are several formats used to present geographic coordinates.

Geo::Coordinates::Transform converts a list of provided latitude and longitude
coordinates in any of the three formats above (mixed input is ok) and converts
to the desired format. Note that special characters or non-numerical characters
such as " will throw an warning and return NaN for that list item.

In addition, the input does not interpert N,S,W,E designators but expects
coordinates to be in positive or negative representation.

Format of the output can be controlled via input arguments in the constructor.
The arguments are expected to be in the form of a hash reference.

    a6a8beb

21:00 Yuri Victorovich (yuri) 

science/py-arch: New port: Autoregressive Conditional Heteroskedasticity (ARCH)
models

    cc2dc10

15:04 Thierry Thomas (thierry)  Author: Erik Jensen

science/geant4: adding Geant4, a TK for the simulation of the passage of
particles through matter

PR:		268300
Reported by:	erik (at) tenku.dk

    3f600a7

01:22 Yuri Victorovich (yuri) 

science/bout++-merging-filaments: New port: Simulation of reconnection during
merging of current filaments

    5d3cbf5

01:22 Yuri Victorovich (yuri) 

science/py-xbout: New port: Collect data from BOUT++ runs in python using xarray

    e39b702

11:31 Yuri Victorovich (yuri) 

science/py-boutdata: New port: Python package for collecting BOUT++ data

    5f09224

11:06 Yuri Victorovich (yuri) 

science/py-boututils: New port: Python package containing BOUT++ utils

    4f2941a

11:06 Yuri Victorovich (yuri) 

science/bout++: New port: Plasma fluid finite-difference simulation code

    50bbd0a

20:41 Yuri Victorovich (yuri) 

science/openmodelica: New port: Modelica-based modeling and simulation
environment

    a51acec

00:44 Yuri Victorovich (yuri) 

science/spheral: New port: Environment for hydrodynamical & gravitational
numerical simulations

    762ba39

09:51 Yuri Victorovich (yuri) 

science/m-aneos: New port: M-ANEOS: program for construction of thermodynamic
equations of state

    1a68a9e

11:11 Yuri Victorovich (yuri) 

science/dftd3: New port: S. Grimme's dispersion correction for DFT, Hartree-Fock
methods

    4924d81

11:11 Yuri Victorovich (yuri) 

science/py-optking: New port: Python version of the PSI4 geometry optimization
program by R.A. King

    b6381ec

12:04 Yuri Victorovich (yuri) 

science/mp2d: New port: Program for calculating the MP2D dispersion energy

    7a26105

09:47 Yuri Victorovich (yuri) 

science/polytope: New port: Library for generating Voronoi and Voronoi-like
tessellations

    27ca116

10:12 Yuri Victorovich (yuri) 

science/py-arbor: New port: Multi-compartment neural network simulation library

    8feba41

10:12 Yuri Victorovich (yuri) 

science/arbor: New port: Multi-compartment neural network simulation library

    2647f3e