On 7/28/22 08:40, Greg Troxel wrote:
[pmc hat off] Jason Bacon <jtocino%gmx.com@localhost> 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, between: - 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 helps. 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 context.
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 existed. 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/ p5-Chemistry-Elements/