11:04 Yuri Victorovich (yuri) 

science/libint2-psi4: New port: Evaluate the integrals in modern atomic and
molecular theory (psi4)

    aa9c528

11:04 Yuri Victorovich (yuri) 

science/psi4: New port: Open-source suite of ab initio quantum chemistry
programs

    c492d0d

12:37 Wen Heping (wen) 

science/p5-Geo-Calc: Add new port

Geo::Calc implements a variety of calculations for latitude/longitude points.

All these formulare are for calculations on the basis of a spherical earth
(ignoring ellipsoidal effects) which is accurate enough* for most purposes.

    26024f6

21:50 Yuri Victorovich (yuri) 

science/py-openbabel: New port: Chemical toolbox designed to speak the many
languages of chemical data

    8eb5a64

16:35 Thierry Thomas (thierry) 

science/py-sdf: add a simple SDF mesh generator

    68756d9

16:35 Thierry Thomas (thierry) 

science/py-meshio: add a program to handle I/O for mesh files

    57b0181

02:05 Yuri Victorovich (yuri) 

science/InsightToolkit521: New port: Fork of science/InsightToolkit

for graphics/elastix

    fa8a770

10:42 Yuri Victorovich (yuri) 

science/InsightToolkit: Update 5.0.1 -> 5.2.1

Also fork InsightToolkit to InsightToolkit501 for graphics/vv.

    4c3fb7e

07:33 Yuri Victorovich (yuri) 

graphics/sciplot: Move to science/sciplot

PR:		267692
Reported by:	Franco Fichtner <franco@opnsense.org>; philip@

    2763db8

03:06 Yuri Victorovich (yuri) 

science/py-mrchem: New port: MultiResolution Chemistry

    cd3d8ed

03:06 Yuri Victorovich (yuri) 

science/mrchem: New port: MultiResolution Chemistry

    297ec91

22:44 Yuri Victorovich (yuri) 

science/mrcpp: New port: MultiResolution Computation Program Package

    dc8b8c3

11:59 Thierry Thomas (thierry) 

science/py-earthpy: adding a tool to plot and manipulate spatial data in Python

    8a197ac

05:31 Yuri Victorovich (yuri) 

science/ttk: New port: Topology ToolKit: Topological data analysis and
visualization

    32231b9

16:22 Yuri Victorovich (yuri) 

science/zx: New port: MQT ZX: A library for working with ZX-diagrams

    9959a6a

16:22 Yuri Victorovich (yuri) 

science/dd_package: New port: MQT decision diagram package tailored to quantum
computing

    1040fd3

17:13 Yuri Victorovich (yuri) 

science/feff10: New port: Ab initio scattering calculations of X-ray absorption
fine structure

    8221bc4

16:11 Yuri Victorovich (yuri) 

science/ocean: New port: BSE code for core spectroscopy

    b242240

18:36 Yuri Victorovich (yuri) 

science/py-kimpy: New port: Python interface to the KIM-API

    7fa243e

04:06 Yuri Victorovich (yuri) 

science/py-atomium: New port: Molecular modeller and file parser

    c8a9968

02:40 Yuri Victorovich (yuri) 

science/dssp: New port: Application to assign secondary structure to proteins

    fdff0a7

02:40 Yuri Victorovich (yuri) 

science/libcifpp: New port: Library to manipulate mmCIF and PDB files

    16f9822

02:40 Yuri Victorovich (yuri) 

science/cif-tools: New port: Suite of programs to manipulate and examine mmCIF
files

    610c83b

01:35 Yuri Victorovich (yuri) 

science/{,py-}gemmi: New ports: Macromolecular crystallography library and
utilities

    8a36560

01:35 Yuri Victorovich (yuri) 

science/py-mmcif: New port: mmCIF Core Access Library

    742c1c0

21:43 Rene Ladan (rene) 

cleanup: Remove expired ports:

2022-09-12 science/R-cran-AMORE: Upstream no longer maintained

    3c9bb28

17:50 Alexander Nedotsukov (bland) 

science/mercantile: Add mercantile, a spherical mercator coordinate and tile
utilities

    32bbc9b

08:15 Yuri Victorovich (yuri) 

science/serac: New port: High order nonlinear thermomechanical simulation code

    565a8a4

02:35 Yuri Victorovich (yuri) 

science/dwave-preprocessing: New port: DWave: Preprocessing tools to aid in
solving binary quadratic models

    999d53d

04:52 Yuri Victorovich (yuri) 

science/dimod: New port: DWave: Shared API for QUBO/Ising samplers

    6ed61c3

04:25 Yuri Victorovich (yuri) 

science/sirius: New port: Domain specific library for electronic structure
calculations

    45cc1f7

00:11 Yuri Victorovich (yuri) 

science/nlcglib: New port: Nonlinear CG methods for wave-function optimization
in DFT

    6b4f2fe

20:32 Yuri Victorovich (yuri) 

science/cardioid: New port: Cardiac simulation toolkit

    0b9278e

22:16 Yuri Victorovich (yuri) 

science/py-qiskit-finance: New port: Quantum Finance module from the Qiskit
quantum computing framework

    a44d4da

02:58 Yuri Victorovich (yuri) 

science/py-dwave-hybrid: New port: DWave: Hybrid asynchronous decomposition
sampler prototype framework

    efafc68

02:58 Yuri Victorovich (yuri) 

science/py-dwave-ocean-sdk: New port: DWave: Meta-package for D-Wave's Ocean
tools

    0751869

23:48 Yuri Victorovich (yuri) 

science/py-dwavebinarycsp: New port: DWave: Map CSP with binary variables to
binary quadratic models

    ee99418

23:48 Yuri Victorovich (yuri) 

science/py-dwave-inspector: New port: DWave: Problem Inspector

    0943bfd

21:12 Yuri Victorovich (yuri) 

science/py-pyqubo: New port: DWave: Python DSL for constructing QUBOs from
mathematical expressions

    dcbef54

23:00 Yuri Victorovich (yuri) 

science/py-penaltymodel: New port: DWave: Utilities and interfaces for using
penalty models

    6310de6

21:36 Yuri Victorovich (yuri) 

science/py-dwave-greedy: New port: DWave: Greedy binary quadratic model solvers

    ad61700

21:36 Yuri Victorovich (yuri) 

science/py-dwave-system: New port: DWave: API for incorporating the D-Wave
system as a sampler

    d68f3b7

18:37 Yuri Victorovich (yuri) 

science/py-dwave-cloud-client: New port: DWave: REST interface to communicate
with D-Wave Solver API servers

    cf5e965

18:37 Yuri Victorovich (yuri) 

science/py-dwave-preprocessing: New port: DWave: Preprocessing tools to aid in
solving binary quadratic models

    b4c4494

08:22 Yuri Victorovich (yuri) 

science/py-dwave-networkx: New port: DWave: Extension of the NetworkX Python
package for graphs

    d092c6e

06:01 Yuri Victorovich (yuri) 

science/py-dwave-tabu: New port: DWave: Tabu solver for QUBO/Ising problems

    68abc57

05:41 Yuri Victorovich (yuri) 

science/py-dwave-neal: New port: DWave: Simulated annealing sampler for general
Ising model graphs

    06ac78b

05:13 Yuri Victorovich (yuri) 

science/Makefile: Remove accidentally added directory

    dc6e8a1

05:12 Yuri Victorovich (yuri) 

science/py-dimod: New port: DWave: Shared API for QUBO/Ising samplers

    29ad935

05:12 Yuri Victorovich (yuri) 

science/py-dwave-samplers: New port: DWave: Classical algorithms for solving
binary quadratic models

    8d3f328

00:11 Yuri Victorovich (yuri) 

science/py-OpenFermion-PySCF: New port: Interface between OpenFermion and PySCF

    ed417e4

22:52 Yuri Victorovich (yuri) 

science/py-OpenFermion-Dirac: New port: Interface between OpenFermion and Dirac

    f5225f9

07:46 Yuri Victorovich (yuri) 

science/dirac: New port: Program for atomic & molecular relativistic
all-electron calculations

    f9e5eb0

04:17 Yuri Victorovich (yuri) 

science/py-qiskit-experiments: New port: Experiments submodule for Quiskit
framework for quantum computing

    846dbcc

21:53 Yuri Victorovich (yuri) 

science/py-qiskit-ibm-experiment: New port: IBM Experiment submodule for Quiskit
framework for quantum computing

    6d61cb9

21:24 Yuri Victorovich (yuri) 

science/py-qiskit-nature: New port: Natural science submodule for Quiskit
framework for quantum computing

    713541e

07:15 Yuri Victorovich (yuri) 

science/py-qiskit-ibmq-provider: New port: Qiskit Provider for accessing IBM
quantum devices and simulators

    3e94e59

07:15 Yuri Victorovich (yuri) 

science/py-qiskit: New port: Qiskit meta-package: SDK for working with quantum
computers

    56b9fce

07:15 Yuri Victorovich (yuri) 

science/py-qiskit-aer: New port:  Aer submodule of the Quiskit framework for
quantum computing

    b6f3955

07:15 Yuri Victorovich (yuri) 

science/py-qiskit-optimization: New port: Optimization submodule of the Quiskit
framework for quantum computing

    52f50ba

03:28 Yuri Victorovich (yuri) 

science/py-qiskit-ibm-provider: New port: Qiskit Provider for accessing IBM
quantum devices and simulators

    cab2866

22:17 Yuri Victorovich (yuri) 

science/py-qiskit-terra: New port: Terra submodule of the Quiskit framework for
quantum computing

    9cc5069

06:44 Yuri Victorovich (yuri) 

science/openkim: Remove in favor of science/openkim-models

science/openkim-models and science/kim-api are packages
distributed by the OpenKIM project.

PR:		246144
Approved by:	jwb@ (maintainer)

    7be8373

03:37 Yuri Victorovich (yuri) 

science/py-tweedledum: New port: Library for analysis, compilation, synthesis of
quantum circuits

    b6b4009

03:35 Yuri Victorovich (yuri) 

science/tweedledum: New port: Library for analysis, compilation, synthesis of
quantum circuits

    bd91788

17:52 Yuri Victorovich (yuri) 

science/py-pymbd: New port: Many-body dispersion library

    9e90ff1

06:57 Yuri Victorovich (yuri) 

science/meep: Re-add port: Finite-difference time-domain software for
electromagnetic simulations

    2a165c4

12:50 Po-Chuan Hsieh (sunpoet) 

science/hdf5-110: Add hd5-110 1.10.9 (copied from hdf5)

- Add PKGNAMESUFFIX
- Install files with suffix:
  - Install binary executables with -110 suffix
  - Install include files to hdf5-110 sub-directory
  - Install examples to EXAMPLESDIR with -110 suffix
- Add PORTSCOUT

PR:		265152
Exp-run by:	antoine

    1bc7803

06:28 Yuri Victorovich (yuri) 

science/kplib: New port: Library for finding optimal Generalized Monkhorst-Pack
k-points grid

    4a9dc80

06:28 Yuri Victorovich (yuri) 

science/py-kpLib: New port: Library for finding optimal Generalized
Monkhorst-Pack k-points grid

    f3cca09

07:19 Yuri Victorovich (yuri) 

devel/ChipmunkPhysics: Move to science/ChipmunkPhysics

    fa189d5

16:30 Yuri Victorovich (yuri) 

science/trilinos: New port: Solver for multi-physics engineering and scientific
problems

    ee1edf9

01:55 Yuri Victorovich (yuri) 

science/py-cirq-rigetti: New port: Cirq module to run on Rigetti quantum
computers

    670b8e4

17:58 Yuri Victorovich (yuri) 

science/libgetar: New port: Library to read and write GEneric Trajectory
ARchives

    e5b105c

17:58 Yuri Victorovich (yuri) 

science/py-libgetar: New port: Library to read and write GEneric Trajectory
ARchives

    f0fd466

16:53 Yuri Victorovich (yuri) 

science/py-pyprecice: New port: Coupling library for partitioned multi-physics
simulations

    2281a1c

16:53 Yuri Victorovich (yuri) 

science/precice: New port: Coupling library for partitioned multi-physics
simulations

    672f96d

10:01 Yuri Victorovich (yuri) 

science/py-asap3: New port: Classical potentials for MD with ASE

    30c83a1

07:52 Yuri Victorovich (yuri) 

biology/mopac: Move to science/mopac; Add TIMESTAMP to distinfo; Take
maintainership

    db283c3

15:13 Po-Chuan Hsieh (sunpoet) 

science/szip: Remove obsoleted port

Use science/libaec instead.

    3110404

20:56 Yuri Victorovich (yuri) 

science/py-py3Dmol: New port: IPython interface for embedding 3Dmol.js views

    19cdfb0

19:04 Chris Rees (crees)  Author: Paul Armstrong

science/libtensorflow1: Add new port

C API for TensorFlow, an open source platform for machine learning

TensorFlow is an end-to-end open source platform for machine learning.
It has a comprehensive, flexible ecosystem of tools, libraries, and
community resources that lets researchers push the state-of-the-art in
ML and developers easily build and deploy ML-powered applications.
The TensorFlow C API is typically a requirement of TensorFlow APIs in
other languages such as Go and Rust.

This is version 1 of the API, which is deprecated but still widely used.

PR:		ports/260694
Improved by:	delphij

    67d31a5

03:42 Yuri Victorovich (yuri) 

science/py-thewalrus: New port: Open source library for hafnian calculation

    c391721

20:02 Yuri Victorovich (yuri) 

science/quantum-jet: New port: Cross-platform header-only library for simulating
quantum circuits

    522ac45

20:04 Thierry Thomas (thierry) 

science/paraview: resurrect

It has been removed in r548980 because it used a deprecated version of
Python, but this is fixed now.

    d976ae7

02:06 Yuri Victorovich (yuri) 

science/ukrmol+: New port: Code to compute electron and positron scattering from
molecules

    f4b7787

00:02 Yuri Victorovich (yuri) 

science/gbtolib: New port: High-performance library for evaluation of molecular
integrals

    b9c18e8

19:51 Yuri Victorovich (yuri) 

science/openmolcas: New port: Quantum chemistry software package

OpenMolcas has issues: it doesn't respect UNIX file path
conventions, it expects the installation directory to be writable.

Currently it needs to be either run as root, or after chown,
or after copying the entire tree to the home directory.

Hopefully they will resolve these issues.

    3079ad1

01:54 Yuri Victorovich (yuri) 

science/q: New port: Molecular Dynamics (MD) tools

    861dc05

15:32 Thierry Thomas (thierry) 

science/R-cran-ks: adding a R library for Kernel Smoothing

    b9186746

16:41 Thierry Thomas (thierry) 

science/pastix: adding PaStiX, a sparse direct solver

Requested by:	pfg

    09d8821

12:41 Mikael Urankar (mikael) 

science/zotero: Add new port

Zotero is a reference management software to manage bibliographic data and
related research materials.

WWW: https://www.zotero.org/

    ed17235

20:14 Yuri Victorovich (yuri) 

science/py-trainstation: New port: Convenient training of linear models

    4d18055

18:10 Po-Chuan Hsieh (sunpoet) 

science/py-asdf-standard: Add py-asdf-standard 1.0.1

ASDF standard

This document describes the Advanced Scientific Data Format (ASDF), pronounced
AZ-diff.

WWW: https://github.com/asdf-format/asdf-standard

    5d805bd

18:10 Po-Chuan Hsieh (sunpoet) 

science/py-asdf-transform-schemas: Add py-asdf-transform-schemas 0.2.2

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

WWW: https://github.com/asdf-format/asdf-transform-schemas

    f6656e1

23:26 Po-Chuan Hsieh (sunpoet) 

science/py-sklearn-pandas: Add py-sklearn-pandas 2.2.0

This module provides a bridge between Scikit-Learn's machine learning methods
and pandas-style Data Frames. In particular, it provides a way to map DataFrame
columns to transformations, which are later recombined into features.

WWW: https://github.com/scikit-learn-contrib/sklearn-pandas

    c6f3b6e

17:13 Yuri Victorovich (yuri) 

science/py-fresnel: New port: Publication quality path tracing in real time

    3054f22

10:00 Yuri Victorovich (yuri) 

science/py-hoomd-blue: New port: Molecular dynamics and Monte Carlo soft matter
simulation

    ccfa03a

07:05 Yuri Victorovich (yuri) 

science/chimes-calculator: New port: Chebyshev Interaction Model for Efficient
Simulation

    090ecb7

18:42 Yuri Victorovich (yuri) 

science/chemicalfun: New port: C++ library for working with chemical reactions
and formulas

    499a8f4