On 04/14/17 12:14, Alistair Crooks
wrote:
In the past, we've said that we need to get a critical mass of
packages in a certain (notional) category before we made that new
category, and left the stipulation of critical mass until a later
date. Which has kinda worked well, and has prevented us from some
churn, which a lot of people dislike.
So firstly, what packages specifically are you thinking of for this
new category?
And, probably more importantly, "science" is too generic a name for
me. Computing science, for instance, bears little relation to fluid
dynamics, or molecular modeling, or forensic science, or anything
else. Would you care to refine your category suggestion a bit, please?
Thirdly, who actually cares about the category? If ever I want to find
a package, then a search with pkgsrc.se is what I'll use, and that
usually forgives typos and case sensitivity.
Best,
Alistair
On 14 April 2017 at 08:05, Jason Bacon <bacon4000%gmail.com@localhost> wrote:
I would like to request the addition of a science category to pkgsrc.
We have developed and are developing a number of scientific packages that do
not fit well into math, biology, or geography.
They include things like computational fluid dynamics and molecular
modeling, which are used across multiple disciplines such as engineering,
physics, and chemistry.
Trying to create more specific categories would result in a large number of
categories with very few packages in each, as well as arguments about where
specific packages belong.
I think a science category would provide a good home for many packages until
the day arrives that there is justification to create more specific
categories for some of them.
Thanks,
Jason
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Responding to your items out-of-order...
2) I already addressed this in my initial post. Again, there
are many scientific packages that are not specific to one domain
and many areas of science that will not generate enough packages
to warrant their own category. I don't think this means they
should be misclassified as "math" or "biology" or "devel". As an
example, FreeBSD ports has separate categories for astro and
biology, but everything else is under science.
3) If we don't care about categories, why do we have them at
all? Searching is fine if you're looking for a specific package
by name. Other times, people might not care about specific tools,
but may want to browse
http://cdn.netbsd.org/pub/pkgsrc/current/pkgsrc/README.html and
see what's currently available to suit their purpose.
1) Below are packages that we've developed so far, some of
which are in wip. The rest will get there after a bit of clean
up. There will be many more coming, as we are now committed to
using pkgsrc for our research computing support. I also provided
a small sample of packages that I would argue are misclassified.
I won't argue for moving them: that's up to their maintainers.
But it illustrates the reality of the problem for people browsing
the collection. Last is a list of packages in the FreeBSD ports
science category. You can also see the potential for a science
category in https://packages.debian.org/jessie/science/.
Packages in wip that should be in science category:
antlr
dlpoly-classic
espresso
fsom
fvcom2
gwyddion
meep
mpb
openmx-openmpi
Packages in our local collection
(https://github.com/outpaddling/uwm-pkgsrc-wip) that should be in
science
category (these will be transferred to pkgsrc-wip after some
clean-up):
angora
dlpoly
espresso
flann
fvcom2
fvcom3
glerl-lib
klustakwik
kwiklib
lammps
liblemon
nco
ncview
openmx
pomgl
py-h5py
py-klustakwik2
py-klustaviewa
py-kwiklib
py-spikedetekt2
siesta
spikedetekt2
trilinos
Packages currently in biology that aren't really biology-specific:
bodr
chemical-mime-data
chemtool
Gabedit
GChemPaint
GROMACS
MOPAC
mpqc
py-mol
There are also scientific packages currently listed in devel and
math. Here's
a small sample:
hdf5
netcdf
h5py
classias
...
FreeBSD ports science category (candidates for conversion to
pkgsrc using
wip/fbsd2pkg, which is now fairly mature):
2d-rewriter
InsightToolkit
R-cran-AMORE
R-cran-DCluster
R-cran-Epi
R-cran-bayesm
R-cran-cmprsk
R-cran-e1071
R-cran-eco
R-cran-epicalc
R-cran-etm
R-cran-snow
R-cran-som
afni
avogadro
bddsolve
bft
bodr
brian
buddy
cdcl
cdf
cdo
cgnslib
cgribex
checkmol
chemtool-devel
clhep
colt
crf++
dcl
devisor
dlpoly-classic
ecs
epte
fastcap
fasthenry
fisicalab
fvcom
fvcom-mpi
fvm
gchemutils
getdp
ghemical
ghmm
gnudatalanguage
gramps
grib_api
gsmc
gtamsanalyzer
gwyddion
h5utils
harminv
hdf
hdf5
hdf5-18
hs-bio
isaac-cfd
jstrack
kalzium
kst2
lamprop
libaec
libctl
libgeodecomp
libghemical
libint
libkml
liblinear
liboglappth
libquantum
libsvm
libsvm-python
libxc
linsmith
massxpert
mbdyn
mcstas
mcstas-comps
medit
meep
mei
metaf2xml
minc2
mol2ps
mpb
mpqc-mpich
ncs
netcdf
netcdf-cxx
netcdf-fortran
nifticlib
openbabel
openkim
orthanc
orthanc-dicomweb
orthanc-postgresql
orthanc-webviewer
p5-Algorithm-SVMLight
p5-Chemistry-3DBuilder
p5-Chemistry-Bond-Find
p5-Chemistry-Canonicalize
p5-Chemistry-Elements
p5-Chemistry-File-MDLMol
p5-Chemistry-File-Mopac
p5-Chemistry-File-PDB
p5-Chemistry-File-SLN
p5-Chemistry-File-SMARTS
p5-Chemistry-File-SMILES
p5-Chemistry-File-VRML
p5-Chemistry-File-XYZ
p5-Chemistry-FormulaPattern
p5-Chemistry-InternalCoords
p5-Chemistry-Isotope
p5-Chemistry-MacroMol
p5-Chemistry-MidasPattern
p5-Chemistry-Mok
p5-Chemistry-Mol
p5-Chemistry-Pattern
p5-Chemistry-Reaction
p5-Chemistry-Ring
p5-Geo-BUFR
p5-Geo-Coordinates-Converter
p5-Geo-Coordinates-Converter-iArea
p5-Geo-ReadGRIB
p5-Geo-WebService-Elevation-USGS
p5-Mcstas-Tools
p5-PerlMol
p5-Physics-Unit
paje
paraview
pnetcdf
psychopy
pulseview
py-DendroPy
py-cdo
py-coards
py-h5py
py-hcluster
py-mdp
py-mlpy
py-netCDF4
py-obspy
py-paida
py-pupynere
py-pyaixi
py-pydicom
py-pysal
py-pyteomics
py-pyteomics.biolccc
py-scikit-fuzzy
py-scikit-learn
py-scikit-sparse
py-scimath
py-scipy
py-ws2300
pybrain
pycdf
pynn
qcl
qtresistors
rubygem-ai4r
rubygem-cdo
rubygem-ruby-dcl
rubygem-ruby-netcdf
sigrok-cli
sigrok-firmware
sigrok-firmware-fx2lafw
sigrok-firmware-utils
silo
simlib
simsmith
step
svmlight
szip
tfel
udunits
v_sim
veusz
vmd
voro++
xfce4-equake-plugin
xmakemol
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