tech-pkg archive

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]

Re: categories of science: math biology geography … and?

On 7/28/22 08:40, Greg Troxel wrote:

[pmc hat off]

Jason Bacon <> writes:

We discussed this a few years back and I think the consensus was it
would be OK to add a science category, but then my work priorities
changed and it fell off the radar.  I have some things in wip that
would go under science.

I think the key question is how many packages would end up there,
   - things not in pkgsrc that should be added
   - things that properly would be moved, but NB we do not move as a
     cleanup process because
     * VCS does not yet support history across moves
     * upgrade tooling does not all cope with PKGPATH changing
     and therefore the churn is worse for users and developers than it

I can see that there are things that would fit, but if it's only going
to be 10, that's what misc is for.   It seems that if it is 50 somebody
could easily post a list and establish this.  With that established I
don't have a problem with someone creating a science category.

There are some things already poorly categoried due to the lack of a
science category like biology/gromacs, maybe biology/chemtool,
math/py-scipy, etc.  I'm not suggesting they should all be moved, but
it would be nice to stop adding to the confusion (for those of us who
care about categories).

Are you suggesting that biology/* be moved to science, in a future world
where moving doesn't hurt?  I am guessing not.

FWIW I see scipy as squarely belonging in math even if there is science
despite the name, just from reading DESCR.  The nature of math is that
it's generally useful, and lots of what is in scipy is reasonably usable
in engineering, rather than being specialist software for a particular
research discipline within science, and not usable in an engineering

Math is the best category we have for scipy, but I think science would
be a better fit, since it's not 100% math and all the math in it is
scientific in nature, not, e.g. theoretical math, business math, math
education, ...  This would help unclutter the math category, which is
huge in part because it's sometimes used as a catch-all.

No, I'm not suggesting moving everything from biology.  I'm just saying
that a few packages in that category might be better classified under
science or chemistry.

I'm not a proponent of creating a lot of specific scientific categories.
 There are too many disciplines and subdisciplines and most would have
very few packages.  Maybe chemistry and physics could be justified,
since there is a lot of software for these fields and a more general
science category has the potential to become very large.  FreeBSD has
astro, which I think could be rolled into physics if such a category

Counts for FreeBSD ports in science-related categories:

astro        136
biology      227
cad          142
math        1140
science      426
Total       2071

FreeBSD moray.acadix  bacon ~/Teach/458/Lecture 1005: ls /usr/ports/science/
2d-rewriter/                        p5-Chemistry-File-MDLMol/
ALPSCore/                           p5-Chemistry-File-Mopac/
ChipmunkPhysics/                    p5-Chemistry-File-PDB/
InsightToolkit/                     p5-Chemistry-File-SLN/
Makefile                            p5-Chemistry-File-SMARTS/
PETSc/                              p5-Chemistry-File-SMILES/
R-cran-AMORE/                       p5-Chemistry-File-VRML/
R-cran-DCluster/                    p5-Chemistry-File-XYZ/
R-cran-Epi/                         p5-Chemistry-FormulaPattern/
R-cran-FAdist/                      p5-Chemistry-InternalCoords/
R-cran-bayesm/                      p5-Chemistry-Isotope/
R-cran-cmprsk/                      p5-Chemistry-MacroMol/
R-cran-e1071/                       p5-Chemistry-MidasPattern/
R-cran-eco/                         p5-Chemistry-Mok/
R-cran-epicalc/                     p5-Chemistry-Mol/
R-cran-etm/                         p5-Chemistry-Pattern/
R-cran-fastICA/                     p5-Chemistry-Reaction/
R-cran-kernlab/                     p5-Chemistry-Ring/
R-cran-ks/                          p5-Geo-BUFR/
R-cran-snow/                        p5-Geo-Coordinates-Converter/
R-cran-som/                         p5-Geo-Coordinates-Converter-iArea/
R-cran-udunits2/                    p5-Geo-WebService-Elevation-USGS/
abinit/                             p5-Mcstas-Tools/
afni/                               p5-PerlMol/
agrum/                              p5-Physics-Unit/
aircraft-datcom/                    packmol/
antioch/                            pagmo2/
apbs/                               paje/
ascent/                             paraview/
atompaw/                            pastix/
avogadro2/                          pcmsolver/
avogadrolibs/                       phonopy/
axom/                               plumed/
bagel/                              pnetcdf/
bddsolve/                           precice/
berkeleygw/                         pulseview/
bodr/                               py-DendroPy/
buddy/                              py-GPy/
cantera/                            py-GPyOpt/
cdcl/                               py-MDAnalysis/
cdf/                                py-MDAnalysisTests/
cdk/                                py-OpenFermion/
cdo/                                py-OpenMC/
cgnslib/                            py-PubChemPy/
cgribex/                            py-PyFR/
checkmol/                           py-PyNE/
chemical-mime-data/                 py-SimpleSpectral/
chemicalfun/                        py-abipy/
chemps2/                            py-access/
chemtool/                           py-asap3/
chemtool-devel/                     py-asdf/
chimes-calculator/                  py-asdf-standard/
chrono/                             py-asdf-transform-schemas/
clhep/                              py-ase/
clipper/                            py-avogadrolibs/
code_saturne/                       py-cdo/
colt/                               py-chainer/
conduit/                            py-chainer-chemistry/
coordgenlibs/                       py-chempy/
cp2k/                               py-cirq-aqt/
cp2k-data/                          py-cirq-core/
crf++/                              py-cirq-google/
csvtk/                              py-cirq-ionq/
dakota/                             py-cirq-pasqal/
dalton/                             py-cirq-rigetti/
dcl/                                py-coards/
devisor/                            py-dipy/
dftbplus/                           py-dlib/
dftd4/                              py-eccodes/
dkh/                                py-esda/
dlib-cpp/                           py-fresnel/
drawxtl/                            py-geolinks/
dvc/                                py-geomet/
dynare/                             py-geometer/
eccodes/                            py-geometric/
elk/                                py-gpaw/
elmerfem/                           py-gsd/
epte/                               py-h5json/
erd/                                py-h5py/
ergo/                               py-hiphive/
erkale/                             py-hoomd-blue/
erkale-pseudopotentials/            py-inequality/
fastcap/                            py-jupyter_jsmol/
fasthenry/                          py-kim-query/
fastjet/                            py-kinematics/
fisicalab/                          py-kliff/
fleur/                              py-kpLib/
frontistr/                          py-liac-arff/
fsom/                               py-libgetar/
fvcom/                              py-libpysal/
fvcom-mpi/                          py-lifelines/
gabedit/                            py-mdp/
gamess-us/                          py-mmtf-python/
gbtolib/                            py-molmod/
gchemutils/                         py-moltemplate/
gdma/                               py-netCDF4/
getdp/                              py-netcdf-flattener/
ghemical/                           py-nibabel/
ghmm/                               py-nilearn/
gnudatalanguage/                    py-obspy/
gpaw-setups/                        py-oddt/
gramps/                             py-openpiv/
grib_api/                           py-paida/
gromacs/                            py-paramz/
gsmc/                               py-phono3py/
gtamsanalyzer/                      py-phonopy/
h5utils/                            py-pupynere/
h5z-zfp/                            py-py3Dmol/
harminv/                            py-pyaixi/
hdf/                                py-pyberny/
hdf5/                               py-pycsw/
hdf5-110/                           py-pydicom/
hdf5-18/                            py-pygeodesy/
healpix/                            py-pygeometa/
helfem/                             py-pygmo2/
hepmc3/                             py-pyked/
highfive/                           py-pymatgen/
hypre/                              py-pymol/
iboview/                            py-pyosf/
isaac-cfd/                          py-pyprecice/
jdftx/                              py-pysal/
jmol/                               py-pyscf/
jstrack/                            py-pyteomics/
kalzium/                            py-qcelemental/
kim-api/                            py-qcengine/
kplib/                              py-qspin/
kst2/                               py-quantities/
lammps/                             py-rmf/
lamprop/                            py-rmsd/
latte/                              py-ruffus/
libaec/                             py-scikit-fuzzy/
libccp4/                            py-scikit-learn/
libcint/                            py-scikit-optimize/
libctl/                             py-scikit-sparse/
libecpint/                          py-scimath/
libefp/                             py-scipy/
libgeodecomp/                       py-scoria/
libgetar/                           py-segregation/
libghemical/                        py-segyio/
libgridxc/                          py-sklearn-pandas/
libint/                             py-skrebate/
libint2/                            py-spaghetti/
libkml/                             py-spglib/
liblinear/                          py-tensorflow/
libmbd/                             py-thewalrus/
libmsym/                            py-tobler/
libnegf/                            py-trainstation/
liboglappth/                        py-veusz/
libquantum/                         pybrain/
libssm/                             pynn/
libsvm/                             q/
libsvm-python/                      qbox/
libtensorflow1/                     qcl/
libvdwxc/                           qiskit-aer/
libxc/                              qmcpack/
liggghts/                           quantum-espresso/
linux-zotero/                       quantum-espresso-pseudopotentials/
luscus/                             quantum-jet/
madness/                            qwalk/
maeparser/                          rdkit/
massxpert/                          rmf/
mbdyn/                              rubygem-ai4r/
mcstas/                             rubygem-cdo/
mcstas-comps/                       rubygem-rgeo/
mctc-lib/                           rubygem-rgeo-geojson/
mcxtrace/                           rubygem-rgeo-proj4/
mcxtrace-comps/                     rubygem-rgeo-shapefile/
mdynamix/                           rubygem-ruby-dcl/
medit/                              rubygem-ruby-netcdf/
meep/                               scidavis/
metaphysicl/                        segyio/
minc2/                              shelxle/
mmdb2/                              siconos/
mmtf-cpp/                           siesta/
mol2ps/                             sigrok-cli/
molgif/                             sigrok-firmware/
molscript/                          sigrok-firmware-fx2lafw/
molsketch/                          sigrok-firmware-utils/
mopac/                              silo/
mpb/                                simbody/
mpqc/                               simgrid/
msms/                               simint/
mstore/                             simlib/
multicharge/                        simple-dftd3/
multiwfn/                           simsmith/
namd/                               smoldyn/
nest/                               sparta/
netcdf/                             spglib/
netcdf-cxx/                         step/
netcdf-fortran/                     svmlight/
nifticlib/                          tblite/
nwchem/                             teem/
nwchem-data/                        tfel/
octopus/                            tfel-edf/
openbabel/                          thermofun/
openems/                            tinker/
openkim/                            trilinos/
openkim-models/                     udunits/
openmc/                             ukrmol+/
openmolcas/                         v_sim/
openmx/                             vipster/
opensim-core/                       vmd/
opensph/                            voro++/
opsin/                              votca/
orthanc/                            wannier90/
orthanc-dicomweb/                   wwplot/
orthanc-mysql/                      wxmacmolplt/
orthanc-postgresql/                 xcfun/
orthanc-webviewer/                  xcrysden/
p5-Algorithm-SVMLight/              xdrawchem/
p5-Chemistry-3DBuilder/             xtb/
p5-Chemistry-Bond-Find/             yoda/
p5-Chemistry-Canonicalize/          zotero/

Home | Main Index | Thread Index | Old Index