mirror of
https://git.FreeBSD.org/ports.git
synced 2025-01-25 09:34:11 +00:00
science/{,py-}gemmi: New ports: Macromolecular crystallography library and utilities
This commit is contained in:
Yuri Victorovich
parent
742c1c0610
commit
8a36560387
@ -98,6 +98,7 @@
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SUBDIR += gbtolib
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SUBDIR += gchemutils
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SUBDIR += gdma
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SUBDIR += gemmi
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SUBDIR += getdp
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SUBDIR += ghemical
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SUBDIR += ghmm
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@ -303,6 +304,7 @@
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SUBDIR += py-eccodes
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SUBDIR += py-esda
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SUBDIR += py-fresnel
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SUBDIR += py-gemmi
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SUBDIR += py-geolinks
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SUBDIR += py-geomet
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SUBDIR += py-geometer
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24
science/gemmi/Makefile
Normal file
24
science/gemmi/Makefile
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@ -0,0 +1,24 @@
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PORTNAME= gemmi
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DISTVERSIONPREFIX= v
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DISTVERSION= 0.5.7
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CATEGORIES= science
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MAINTAINER= yuri@FreeBSD.org
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COMMENT= Macromolecular crystallography library and utilities
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WWW= https://gemmi.readthedocs.io/en/latest/
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LICENSE= MPL20
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LICENSE_FILE= ${WRKSRC}/LICENSE.txt
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USES= cmake:testing compiler:c++17-lang # tests don't run, see https://github.com/project-gemmi/gemmi/issues/231
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USE_GITHUB= yes
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GH_ACCOUNT= project-gemmi
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OPTIONS_DEFINE= FORTRAN
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FORTRAN_USES= fortran
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FORTRAN_CMAKE_BOOL= USE_FORTRAN
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FORTRAN_BROKEN= project option doesn't do anything, see https://github.com/project-gemmi/gemmi/issues/232
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.include <bsd.port.mk>
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3
science/gemmi/distinfo
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3
science/gemmi/distinfo
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@ -0,0 +1,3 @@
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TIMESTAMP = 1664834213
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SHA256 (project-gemmi-gemmi-v0.5.7_GH0.tar.gz) = dede98c52920dac4a86dd77f38daa20bc8a1449ce16833815f5b563f4e8384a0
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SIZE (project-gemmi-gemmi-v0.5.7_GH0.tar.gz) = 1677695
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7
science/gemmi/pkg-descr
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7
science/gemmi/pkg-descr
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@ -0,0 +1,7 @@
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Gemmi is a library, accompanied by a set of programs, developed primarily for
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use in macromolecular crystallography (MX). For working with:
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* macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
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* refinement restraints (CIF files),
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* reflection data (MTZ and mmCIF formats),
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* data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
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* crystallographic symmetry.
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231
science/gemmi/pkg-plist
Normal file
231
science/gemmi/pkg-plist
Normal file
@ -0,0 +1,231 @@
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bin/gemmi
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include/gemmi/addends.hpp
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include/gemmi/align.hpp
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include/gemmi/assembly.hpp
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include/gemmi/asudata.hpp
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include/gemmi/asumask.hpp
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include/gemmi/atof.hpp
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include/gemmi/atox.hpp
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include/gemmi/bessel.hpp
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include/gemmi/binner.hpp
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include/gemmi/blob.hpp
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include/gemmi/c4322.hpp
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include/gemmi/calculate.hpp
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include/gemmi/ccp4.hpp
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include/gemmi/cellred.hpp
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include/gemmi/chemcomp.hpp
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include/gemmi/chemcomp_xyz.hpp
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include/gemmi/cif.hpp
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include/gemmi/cif2mtz.hpp
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include/gemmi/cifdoc.hpp
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include/gemmi/contact.hpp
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include/gemmi/crd.hpp
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include/gemmi/dencalc.hpp
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include/gemmi/dirwalk.hpp
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include/gemmi/eig3.hpp
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include/gemmi/elem.hpp
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include/gemmi/enumstr.hpp
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include/gemmi/fail.hpp
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include/gemmi/fileutil.hpp
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include/gemmi/floodfill.hpp
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include/gemmi/formfact.hpp
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include/gemmi/fourier.hpp
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include/gemmi/fprime.hpp
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include/gemmi/fstream.hpp
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include/gemmi/grid.hpp
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include/gemmi/gz.hpp
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include/gemmi/input.hpp
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include/gemmi/interop.hpp
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include/gemmi/it92.hpp
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include/gemmi/iterator.hpp
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include/gemmi/json.hpp
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include/gemmi/levmar.hpp
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include/gemmi/linkhunt.hpp
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include/gemmi/math.hpp
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include/gemmi/merge.hpp
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include/gemmi/metadata.hpp
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include/gemmi/mmcif.hpp
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include/gemmi/mmcif_impl.hpp
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include/gemmi/mmread.hpp
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include/gemmi/model.hpp
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include/gemmi/modify.hpp
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include/gemmi/monlib.hpp
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include/gemmi/mtz.hpp
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include/gemmi/mtz2cif.hpp
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include/gemmi/neighbor.hpp
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include/gemmi/neutron92.hpp
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include/gemmi/numb.hpp
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include/gemmi/pdb.hpp
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include/gemmi/pirfasta.hpp
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include/gemmi/placeh.hpp
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include/gemmi/polyheur.hpp
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include/gemmi/qcp.hpp
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include/gemmi/read_cif.hpp
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include/gemmi/read_coor.hpp
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include/gemmi/read_map.hpp
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include/gemmi/recgrid.hpp
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include/gemmi/reciproc.hpp
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include/gemmi/refln.hpp
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include/gemmi/reindex.hpp
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include/gemmi/remarks.hpp
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include/gemmi/resinfo.hpp
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include/gemmi/scaling.hpp
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include/gemmi/select.hpp
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include/gemmi/seqalign.hpp
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include/gemmi/seqid.hpp
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include/gemmi/sfcalc.hpp
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include/gemmi/small.hpp
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include/gemmi/smcif.hpp
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include/gemmi/solmask.hpp
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include/gemmi/span.hpp
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include/gemmi/sprintf.hpp
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include/gemmi/symmetry.hpp
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include/gemmi/third_party/fast_float.h
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include/gemmi/third_party/pocketfft_hdronly.h
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include/gemmi/third_party/sajson.h
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include/gemmi/third_party/stb_sprintf.h
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include/gemmi/third_party/tao/LICENSE
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include/gemmi/third_party/tao/NOTES
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include/gemmi/third_party/tao/pegtl.hpp
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include/gemmi/third_party/tao/pegtl/analysis/analyze_cycles.hpp
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include/gemmi/third_party/tao/pegtl/analysis/counted.hpp
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include/gemmi/third_party/tao/pegtl/analysis/generic.hpp
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include/gemmi/third_party/tao/pegtl/analysis/grammar_info.hpp
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include/gemmi/third_party/tao/pegtl/analysis/insert_guard.hpp
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include/gemmi/third_party/tao/pegtl/analysis/insert_rules.hpp
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include/gemmi/third_party/tao/pegtl/analysis/rule_info.hpp
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include/gemmi/third_party/tao/pegtl/analysis/rule_type.hpp
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include/gemmi/third_party/tao/pegtl/analyze.hpp
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include/gemmi/third_party/tao/pegtl/apply_mode.hpp
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include/gemmi/third_party/tao/pegtl/argv_input.hpp
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include/gemmi/third_party/tao/pegtl/ascii.hpp
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include/gemmi/third_party/tao/pegtl/buffer_input.hpp
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include/gemmi/third_party/tao/pegtl/config.hpp
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include/gemmi/third_party/tao/pegtl/cstream_input.hpp
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include/gemmi/third_party/tao/pegtl/eol.hpp
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include/gemmi/third_party/tao/pegtl/eol_pair.hpp
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include/gemmi/third_party/tao/pegtl/file_input.hpp
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include/gemmi/third_party/tao/pegtl/input_error.hpp
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include/gemmi/third_party/tao/pegtl/internal/action.hpp
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include/gemmi/third_party/tao/pegtl/internal/action_input.hpp
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include/gemmi/third_party/tao/pegtl/internal/alnum.hpp
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include/gemmi/third_party/tao/pegtl/internal/alpha.hpp
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include/gemmi/third_party/tao/pegtl/internal/any.hpp
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include/gemmi/third_party/tao/pegtl/internal/apply.hpp
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include/gemmi/third_party/tao/pegtl/internal/apply0.hpp
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include/gemmi/third_party/tao/pegtl/internal/apply0_single.hpp
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include/gemmi/third_party/tao/pegtl/internal/apply_single.hpp
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include/gemmi/third_party/tao/pegtl/internal/at.hpp
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include/gemmi/third_party/tao/pegtl/internal/bof.hpp
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include/gemmi/third_party/tao/pegtl/internal/bol.hpp
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include/gemmi/third_party/tao/pegtl/internal/bump_help.hpp
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include/gemmi/third_party/tao/pegtl/internal/bump_impl.hpp
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include/gemmi/third_party/tao/pegtl/internal/bytes.hpp
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include/gemmi/third_party/tao/pegtl/internal/control.hpp
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include/gemmi/third_party/tao/pegtl/internal/cr_crlf_eol.hpp
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include/gemmi/third_party/tao/pegtl/internal/cr_eol.hpp
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include/gemmi/third_party/tao/pegtl/internal/crlf_eol.hpp
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include/gemmi/third_party/tao/pegtl/internal/cstream_reader.hpp
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include/gemmi/third_party/tao/pegtl/internal/cstring_reader.hpp
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include/gemmi/third_party/tao/pegtl/internal/demangle.hpp
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include/gemmi/third_party/tao/pegtl/internal/demangle_cxxabi.hpp
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include/gemmi/third_party/tao/pegtl/internal/demangle_nop.hpp
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include/gemmi/third_party/tao/pegtl/internal/demangle_sanitise.hpp
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include/gemmi/third_party/tao/pegtl/internal/disable.hpp
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include/gemmi/third_party/tao/pegtl/internal/discard.hpp
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include/gemmi/third_party/tao/pegtl/internal/dusel_mode.hpp
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include/gemmi/third_party/tao/pegtl/internal/duseltronik.hpp
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include/gemmi/third_party/tao/pegtl/internal/enable.hpp
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include/gemmi/third_party/tao/pegtl/internal/endian.hpp
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include/gemmi/third_party/tao/pegtl/internal/endian_gcc.hpp
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include/gemmi/third_party/tao/pegtl/internal/endian_win.hpp
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include/gemmi/third_party/tao/pegtl/internal/eof.hpp
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include/gemmi/third_party/tao/pegtl/internal/eol.hpp
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include/gemmi/third_party/tao/pegtl/internal/eolf.hpp
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include/gemmi/third_party/tao/pegtl/internal/file_mapper.hpp
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include/gemmi/third_party/tao/pegtl/internal/file_opener.hpp
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include/gemmi/third_party/tao/pegtl/internal/file_reader.hpp
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include/gemmi/third_party/tao/pegtl/internal/has_apply.hpp
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include/gemmi/third_party/tao/pegtl/internal/has_apply0.hpp
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include/gemmi/third_party/tao/pegtl/internal/identifier.hpp
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include/gemmi/third_party/tao/pegtl/internal/if_apply.hpp
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include/gemmi/third_party/tao/pegtl/internal/if_must.hpp
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include/gemmi/third_party/tao/pegtl/internal/if_must_else.hpp
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include/gemmi/third_party/tao/pegtl/internal/if_then_else.hpp
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include/gemmi/third_party/tao/pegtl/internal/input_pair.hpp
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include/gemmi/third_party/tao/pegtl/internal/integer_sequence.hpp
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include/gemmi/third_party/tao/pegtl/internal/istream_reader.hpp
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include/gemmi/third_party/tao/pegtl/internal/istring.hpp
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include/gemmi/third_party/tao/pegtl/internal/iterator.hpp
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include/gemmi/third_party/tao/pegtl/internal/lf_crlf_eol.hpp
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include/gemmi/third_party/tao/pegtl/internal/lf_eol.hpp
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include/gemmi/third_party/tao/pegtl/internal/list.hpp
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include/gemmi/third_party/tao/pegtl/internal/list_must.hpp
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include/gemmi/third_party/tao/pegtl/internal/list_tail.hpp
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include/gemmi/third_party/tao/pegtl/internal/list_tail_pad.hpp
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include/gemmi/third_party/tao/pegtl/internal/marker.hpp
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include/gemmi/third_party/tao/pegtl/internal/minus.hpp
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include/gemmi/third_party/tao/pegtl/internal/must.hpp
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include/gemmi/third_party/tao/pegtl/internal/not_at.hpp
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include/gemmi/third_party/tao/pegtl/internal/one.hpp
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include/gemmi/third_party/tao/pegtl/internal/opt.hpp
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include/gemmi/third_party/tao/pegtl/internal/pad.hpp
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include/gemmi/third_party/tao/pegtl/internal/pad_opt.hpp
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include/gemmi/third_party/tao/pegtl/internal/peek_char.hpp
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include/gemmi/third_party/tao/pegtl/internal/peek_utf16.hpp
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include/gemmi/third_party/tao/pegtl/internal/peek_utf32.hpp
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include/gemmi/third_party/tao/pegtl/internal/peek_utf8.hpp
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include/gemmi/third_party/tao/pegtl/internal/pegtl_string.hpp
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include/gemmi/third_party/tao/pegtl/internal/plus.hpp
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include/gemmi/third_party/tao/pegtl/internal/raise.hpp
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include/gemmi/third_party/tao/pegtl/internal/range.hpp
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include/gemmi/third_party/tao/pegtl/internal/ranges.hpp
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include/gemmi/third_party/tao/pegtl/internal/rep.hpp
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include/gemmi/third_party/tao/pegtl/internal/rep_min.hpp
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include/gemmi/third_party/tao/pegtl/internal/rep_min_max.hpp
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include/gemmi/third_party/tao/pegtl/internal/rep_opt.hpp
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include/gemmi/third_party/tao/pegtl/internal/require.hpp
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include/gemmi/third_party/tao/pegtl/internal/result_on_found.hpp
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include/gemmi/third_party/tao/pegtl/internal/rule_conjunction.hpp
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include/gemmi/third_party/tao/pegtl/internal/rules.hpp
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include/gemmi/third_party/tao/pegtl/internal/seq.hpp
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include/gemmi/third_party/tao/pegtl/internal/skip_control.hpp
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include/gemmi/third_party/tao/pegtl/internal/sor.hpp
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include/gemmi/third_party/tao/pegtl/internal/star.hpp
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include/gemmi/third_party/tao/pegtl/internal/star_must.hpp
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include/gemmi/third_party/tao/pegtl/internal/state.hpp
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include/gemmi/third_party/tao/pegtl/internal/string.hpp
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include/gemmi/third_party/tao/pegtl/internal/trivial.hpp
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include/gemmi/third_party/tao/pegtl/internal/try_catch_type.hpp
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include/gemmi/third_party/tao/pegtl/internal/until.hpp
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include/gemmi/third_party/tao/pegtl/istream_input.hpp
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include/gemmi/third_party/tao/pegtl/memory_input.hpp
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include/gemmi/third_party/tao/pegtl/mmap_input.hpp
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include/gemmi/third_party/tao/pegtl/normal.hpp
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include/gemmi/third_party/tao/pegtl/nothing.hpp
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include/gemmi/third_party/tao/pegtl/parse.hpp
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include/gemmi/third_party/tao/pegtl/parse_error.hpp
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include/gemmi/third_party/tao/pegtl/position.hpp
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include/gemmi/third_party/tao/pegtl/read_input.hpp
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include/gemmi/third_party/tao/pegtl/rewind_mode.hpp
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include/gemmi/third_party/tao/pegtl/rules.hpp
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include/gemmi/third_party/tao/pegtl/string_input.hpp
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include/gemmi/third_party/tao/pegtl/tracking_mode.hpp
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include/gemmi/third_party/tao/pegtl/utf16.hpp
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include/gemmi/third_party/tao/pegtl/utf32.hpp
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include/gemmi/third_party/tao/pegtl/utf8.hpp
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include/gemmi/third_party/tao/pegtl/version.hpp
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include/gemmi/third_party/tinydir.h
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include/gemmi/to_chemcomp.hpp
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include/gemmi/to_cif.hpp
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include/gemmi/to_json.hpp
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include/gemmi/to_mmcif.hpp
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include/gemmi/to_mmdb.hpp
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include/gemmi/to_pdb.hpp
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include/gemmi/topo.hpp
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include/gemmi/twin.hpp
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include/gemmi/unitcell.hpp
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include/gemmi/utf.hpp
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include/gemmi/util.hpp
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include/gemmi/version.hpp
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include/gemmi/xds_ascii.hpp
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29
science/py-gemmi/Makefile
Normal file
29
science/py-gemmi/Makefile
Normal file
@ -0,0 +1,29 @@
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PORTNAME= gemmi
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DISTVERSIONPREFIX= v
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DISTVERSION= 0.5.7
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CATEGORIES= science
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PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
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MAINTAINER= yuri@FreeBSD.org
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COMMENT= Macromolecular crystallography library and utilities
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WWW= https://gemmi.readthedocs.io/en/latest/
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LICENSE= MPL20
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LICENSE_FILE= ${WRKSRC}/LICENSE.txt
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BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \
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pybind11>=2.6:devel/pybind11
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USES= cmake compiler:c++17-lang python
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USE_GITHUB= yes
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GH_ACCOUNT= project-gemmi
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CMAKE_ON= USE_PYTHON
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PLIST_FILES= ${PYTHON_SITELIBDIR}/gemmi${PYTHON_EXT_SUFFIX}.so
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do-test:
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@cd ${WRKSRC} && ${PYTHON_CMD} -m unittest discover -v tests/
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.include <bsd.port.mk>
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3
science/py-gemmi/distinfo
Normal file
3
science/py-gemmi/distinfo
Normal file
@ -0,0 +1,3 @@
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TIMESTAMP = 1664834213
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SHA256 (project-gemmi-gemmi-v0.5.7_GH0.tar.gz) = dede98c52920dac4a86dd77f38daa20bc8a1449ce16833815f5b563f4e8384a0
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SIZE (project-gemmi-gemmi-v0.5.7_GH0.tar.gz) = 1677695
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46
science/py-gemmi/files/patch-CMakeLists.txt
Normal file
46
science/py-gemmi/files/patch-CMakeLists.txt
Normal file
@ -0,0 +1,46 @@
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--- CMakeLists.txt.orig 2022-09-21 17:17:09 UTC
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+++ CMakeLists.txt
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@@ -274,6 +274,7 @@ add_executable(gemmi-wcn EXCLUDE_FROM_ALL $<TARGET_OBJ
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src/wcn.cpp $<TARGET_OBJECTS:input>)
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support_gz(gemmi-wcn)
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+if (FALSE)
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add_executable(program
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src/align.cpp src/blobs.cpp
|
||||
src/cif2mtz.cpp src/cif2json.cpp src/contact.cpp
|
||||
@@ -290,15 +291,16 @@ add_executable(program
|
||||
$<TARGET_OBJECTS:options>)
|
||||
support_gz(program)
|
||||
target_compile_definitions(program PRIVATE GEMMI_ALL_IN_ONE=1)
|
||||
-set_target_properties(program PROPERTIES OUTPUT_NAME gemmi)
|
||||
+#set_target_properties(program PROPERTIES OUTPUT_NAME gemmi)
|
||||
if (WIN32 AND USE_WMAIN)
|
||||
# _UNICODE=1 is now set globally
|
||||
- #target_compile_definitions(program PRIVATE _UNICODE=1)
|
||||
+ target_compile_definitions(program PRIVATE _UNICODE=1)
|
||||
if(MINGW)
|
||||
# target_link_options were added in cmake 3.13
|
||||
set_target_properties(program PROPERTIES LINK_FLAGS "-municode")
|
||||
endif()
|
||||
endif()
|
||||
+endif()
|
||||
|
||||
### tests and examples ###
|
||||
|
||||
@@ -416,12 +418,12 @@ else()
|
||||
message(STATUS "Skipping Python module. Add -D USE_PYTHON=1 to build it.")
|
||||
endif()
|
||||
|
||||
-install(TARGETS program DESTINATION bin)
|
||||
-install(DIRECTORY include/gemmi DESTINATION include)
|
||||
+#install(TARGETS program DESTINATION bin)
|
||||
+#install(DIRECTORY include/gemmi DESTINATION include)
|
||||
if (USE_PYTHON AND DEFINED PYTHON_INSTALL_DIR)
|
||||
install(TARGETS py DESTINATION ${PYTHON_INSTALL_DIR})
|
||||
- install(DIRECTORY examples/ DESTINATION ${PYTHON_INSTALL_DIR}/gemmi-examples
|
||||
- FILES_MATCHING PATTERN "*.py")
|
||||
+ #install(DIRECTORY examples/ DESTINATION ${PYTHON_INSTALL_DIR}/gemmi-examples
|
||||
+ # FILES_MATCHING PATTERN "*.py")
|
||||
if (INSTALL_EGG_INFO)
|
||||
install(CODE
|
||||
"execute_process(COMMAND \"${PYTHON_EXECUTABLE}\" setup.py install_egg_info --install-dir \"\$ENV{DESTDIR}${PYTHON_INSTALL_DIR}\"
|
||||
7
science/py-gemmi/pkg-descr
Normal file
7
science/py-gemmi/pkg-descr
Normal file
@ -0,0 +1,7 @@
|
||||
Gemmi is a library, accompanied by a set of programs, developed primarily for
|
||||
use in macromolecular crystallography (MX). For working with:
|
||||
* macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
|
||||
* refinement restraints (CIF files),
|
||||
* reflection data (MTZ and mmCIF formats),
|
||||
* data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
|
||||
* crystallographic symmetry.
|
||||
Loading…
Reference in New Issue
Block a user