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

02:42 Yuri Victorovich (yuri) 

science/simple-dftd3: New port: Reimplementation of the DFT-D3 program

    8c3413a

02:42 Yuri Victorovich (yuri) 

science/tblite: New port: Light-weight tight-binding framework

    a6c7c85

05:15 Yuri Victorovich (yuri) 

science/libnegf: New port: Non Equilibrium Green's Functions library

    b0b0f2a

05:15 Yuri Victorovich (yuri) 

science/libmbd: New port: Many-body dispersion library

    9d5d7aa

09:40 Yuri Victorovich (yuri) 

science/fleur: Re-add port: FLAPW code for atomic computations in quantum
chemistry and physics

    9ff296b

20:26 Yuri Victorovich (yuri) 

science/multicharge: New port: Electronegativity equilibration model for atomic
partial charges

    912aa55

20:23 Yuri Victorovich (yuri) 

science/dftd4: New port: Atomic-charge dependent london dispersion correction
computation

    646aaca

19:54 Yuri Victorovich (yuri) 

science/mstore: New port: Molecular structure store for testing

    299c87d

19:36 Yuri Victorovich (yuri) 

science/mctc-lib: New port: Computation tool chain library to work with
molecular structure data

    d40ba16

16:20 Mateusz Piotrowski (0mp) 

science/linux-zotero: Add new port

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

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

MFH:		2021Q4

    8c6cd1e

15:57 Po-Chuan Hsieh (sunpoet) 

*/Makefile: Sort SUBDIRs

    70b8183

23:56 Yuri Victorovich (yuri) 

science/py-pyberny: New port: Optimizer of molecular geometries with respect to
the total energy

    b57cde2

15:51 Yuri Victorovich (yuri) 

science/py-OpenMC: New port: Monte Carlo neutron and photon transport simulation
code (Python)

    2944d20

03:56 Yuri Victorovich (yuri) 

science/openmc: New port: Monte Carlo neutron and photon transport simulation
code

    eb26b25

05:21 Yuri Victorovich (yuri) 

science/py-PyNE: New port: PyNE: The Nuclear Engineering Toolkit

    7c0a02b

16:46 Yuri Victorovich (yuri) 

science/ascent: New port: Visualization and analysis runtime for multi-physics
HPC simulations

    91e83b6

09:24 Yuri Victorovich (yuri) 

science/helfem: New port: Finite element methods for electronic structure
calculations

    94d91d8

07:13 Yuri Victorovich (yuri) 

science/py-pyked: New port: Package for manipulating Chemical Kinetics
Experimental Data files

    dfc0238

18:50 Yuri Victorovich (yuri) 

science/cantera: New port: Chemical kinetics, thermodynamics, and transport tool
suite

    af1b8fd

01:25 Yuri Victorovich (yuri) 

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

    f389fab

07:33 Yuri Victorovich (yuri) 

science/openmx: Re-add port: Nanoscale material simulations using density
functional theories (DFT)

It isn't unfetchable.

    54e006a

08:56 Yuri Victorovich (yuri) 

science/dynare: Re-add port: Software platform for handling a wide class of
economic models

    5f4d541

22:51 Yuri Victorovich (yuri) 

science/siconos: New port: Simulation framework for nonsmooth dynamical systems

    3270400

08:26 Guangyuan Yang (ygy)  Author: Frank Scholl

science/orthanc-dicomweb: Revive port

Plugin to bring support of the DICOMweb standard into Orthanc.

PR:		242547
Reviewed by:	lwhsu

    27ff93b

21:40 Guangyuan Yang (ygy)  Author: Frank Scholl

science/orthanc-postgresql: Revive port

Orthanc plugin to use PostgreSQL for indexing or storage.

PR:		242548

    b660b9f

21:26 Guangyuan Yang (ygy)  Author: Frank Scholl

science/orthanc-mysql: New port

Orthanc plugin to use MySQL/MariaDB for indexing or storage.

PR:		242552

    fd66760

13:31 Guangyuan Yang (ygy)  Author: Frank Scholl

science/orthanc-webviewer: Revive port

Plugin to extend Orthanc with a Web viewer of medical images.

PR:		242549

    0b34ae6

16:51 Yuri Victorovich (yuri) 

science/phonopy: New port: Package for phonon calculations at harmonic and
quasi-harmonic levels

    3401e54

16:51 Yuri Victorovich (yuri) 

science/py-hiphive: New port: High-order force constants for the masses

    16c1136

17:13 Yuri Victorovich (yuri) 

science/py-cirq-{aqt,ionq,pasqal}: New ports: Modules for the Cirq quantum
computing framework

    f792513

13:16 Yuri Victorovich (yuri) 

science/py-PubChemPy: New port: Simple Python wrapper around the PubChem PUG
REST API

    e74986e

22:36 Yuri Victorovich (yuri) 

science/py-{core,google}: New ports: Writing, manipulating, and optimizing
quantum circuits and running them against quantum computers and simulators

    e1f12f9

21:28 Jason W. Bacon (jwb) 

science/csvtk: Cross-platform and ultrafast toolkit for CSV/TSV processing

CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics
and data science.

People usually use spreadsheet software like MS Excel to process table data.
However this is all by clicking and typing, which is not automated and is
time-consuming to repeat, especially when you want to apply similar operations
with different datasets or purposes.

csvtk is convenient for rapid data investigation and also easy to integrate
into analysis pipelines. It could save you lots of time in (not) writing
Python/R scripts.

    98807e0

18:20 Guangyuan Yang (ygy) 

science/orthanc: Hook to the build

PR:		242546
Fixes:		d0359493ee0443e596be74b336ea12e6db936a01
Approved by:	lwhsu (mentor, implicit), portmgr (fix build)

    e7091be

20:01 Yuri Victorovich (yuri) 

science/xcfun: New port: Exchange-correlation functionals with arbitrary-order
derivatives

    05a1e2c

20:01 Yuri Victorovich (yuri) 

science/py-pyscf: New port: Python module for quantum chemistry

    f97053f

10:17 Thierry Thomas (thierry) 

science/frontistr adding FrontISTR

This is an Open-Source Large-Scale Parallel FEM Program for Nonlinear
Structural Analysis.

    fc6c793

20:35 Po-Chuan Hsieh (sunpoet) 

science/py-skrebate: Add py-skrebate 0.62

This package includes a scikit-learn-compatible Python implementation of ReBATE,
a suite of Relief-based feature selection algorithms for Machine Learning. These
Relief-Based algorithms (RBAs) are designed for feature weighting/selection as
part of a machine learning pipeline (supervised learning). Presently this
includes the following core RBAs: ReliefF, SURF, SURF*, MultiSURF*, and
MultiSURF. Additionally, an implementation of the iterative TuRF mechanism and
VLSRelief is included.

WWW: https://github.com/EpistasisLab/scikit-rebate

    a15ff33

08:09 Mathieu Arnold (mat) 

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

    cf118cc