Details about package oxdna-cuda
Name: | oxdna-cuda |
---|---|
Uploader: | Constantine Evans <const@costi.eu> (Debian QA page) |
Description: | oxdna-cuda - simulator for DNA, RNA and more python3-oxpy - Python interface to oxDNA simulator python3-oxdna-analysis-tools - Python and CLI analysis tools for oxDNA simulator |
Package uploads
Upload #3
Information
Version: | 3.4.2-1 |
---|---|
Uploaded: | 2022-09-17 18:21 |
Source package: | oxdna-cuda_3.4.2-1.dsc |
Distribution: | unstable |
Section: | science |
Priority: | optional |
Homepage: | https://github.com/lorenzo-rovigatti/oxDNA |
Vcs-Browser: | https://github.com/cgevans/oxdna-cuda-debian |
Vcs-Git: | https://github.com/debian/oxdna-cuda-debian.git |
Closes bugs: | #1019890 |
Changelog
oxdna-cuda (3.4.2-1) unstable; urgency=medium . * Initial release (Closes: #1019890) * Patched to use system pybind11-dev and nhlohmann-json3-dev. * Still uses embedded copies of exprtk and fast_double_parsen in src/extern. Both these are single headers, and are similarly embedded in other Debian packages. * Uses RPATH for a private shared library. This is set during cmake installation of binaries, and by a bit of a roundabout method for the oxpy Python package, 'installing' it and then moving it back into the build directory to be installed during the oxpy Python package installation. * CUDA compilation should support architures 5.0, 5.2, 6.0, 6.1, 7.0, and 7.5. * Man pages added, though they mostly point to html documentation. * html documentation links javascript, and tries to avoid external mathjax use. One external iframe, to oxView, remains.
QA information
-
–
Package uses debhelper-compatDebhelper compatibility level 13
-
–
Package is the latest upstream version
Local: 3.4.2 Upstream: 3.4.2 Url: https://github.com/lorenzo-rovigatti/oxDNA/archive/refs/tags/v3.4.2.tar.gz -
–
Package is not native
Format: 3.0 (quilt) -
–
"Maintainer" email is the same as the uploader
-
–
Package has lintian pedantic tagsoxdna-cuda source
-
P
maintainer-manual-page
- [debian/DNAnalysis.1]
- [debian/confGenerator.1]
- [debian/oat.1]
- [debian/oxDNA.1]
-
P
very-long-line-length-in-source-file
- 1106 > 512 [examples/FFS_example/FFS_CUDA/README:90]
- 1223 > 512 [docs/source/umbrella_sampling.md:96]
- 1271 > 512 [docs/source/ffs.md:5]
- 1298 > 512 [examples/PERSISTENCE_LENGTH/readme.pdf:410]
- 130676 > 512 [docs/source/images/oxView_frame/devs.json:1]
- 1318 > 512 [examples/HAIRPIN/DOCS/histo_MD.pdf:67]
- 13850 > 512 [examples/NEW_RELAX_PROCEDURE/caca.json:1]
- 1474 > 512 [examples/HAIRPIN/DOCS/histo_MD_seq_dep.pdf:91]
- 1802 > 512 [examples/HAIRPIN/DOCS/hairpin.pdf:2586]
- 24081 > 512 [examples/CADNANO_INTERFACE/sq_rectangle_origami.json:1]
- 3707 > 512 [examples/METADYNAMICS/SINGLE_HELIX_BENDING/analysis.ipynb:54]
- 39107 > 512 [examples/CADNANO_INTERFACE/he_template.json:1]
- 4083 > 512 [examples/CADNANO_INTERFACE/TILE/tile.json:1]
- 516 > 512 [examples/MAJOR_MINOR_GROOVING/README:7]
- 525 > 512 [src/Interactions/PatchyInteractionDan.cpp:504]
- 540 > 512 [analysis/paper_examples/README.md:1]
- 543 > 512 [analysis/paper_examples/svd_mean/README.md:19]
- 551 > 512 [src/Backends/Thermostats/ThermostatFactory.h:18]
- 578 > 512 [legacy/UTILS/process_data/Makefile:7]
- 605 > 512 [src/Observables/Contacts.h:25]
- 606 > 512 [examples/METADYNAMICS/README.md:22]
- 615 > 512 [docs/source/observables.md:289]
- 628 > 512 [test/howto.md:24]
- 658 > 512 [src/Observables/HBList.h:18]
- 675 > 512 [docs/source/relaxation.md:3]
- 694 > 512 [src/Observables/MeanVectorCosine.cpp:152]
- 702 > 512 [analysis/paper_examples/h_bonds/README.md:1]
- 703 > 512 [src/extern/nlohmann/detail/macro_scope.hpp:333]
- 710 > 512 [oxpy/pybind11/docs/faq.rst:212]
- 719 > 512 [docs/source/index.md:5]
- 733 > 512 [docs/source/install.md:63]
- 767 > 512 [analysis/README.md:122]
- 767 > 512 [docs/source/input.md:186]
- 767 > 512 [src/Interactions/PatchyInteractionDan.h:333]
- 782 > 512 [analysis/paper_examples/clustering/README.md:1]
- 786 > 512 [breaking_changes.md:17]
- 802 > 512 [analysis/paper_examples/distances/README.md:3]
- 818 > 512 [analysis/paper_examples/mds_mean/README.md:1]
- 837 > 512 [src/CUDA/Backends/FFS_MD_CUDAMixedBackend.h:151]
- 851 > 512 [examples/HAIRPIN/DOCS/hairpin.tex:77]
- 877 > 512 [legacy/UTILS/traj2chimera.py:27]
- 895 > 512 [examples/HAIRPIN/DOCS/histo_TRAP.pdf:31]
-
X
debian-watch-does-not-check-gpg-signature
- [debian/watch]
-
X
prefer-uscan-symlink
- filenamemangle s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%oxdna-cuda-$1.tar.gz% [debian/watch:5]
-
X
upstream-metadata-file-is-missing
-
P
maintainer-manual-page
-
–
Package closes ITP bug
-
oxdna-cuda:
- #1019890 (Wishlist, ITP): ITP: oxdna-cuda -- coarse-grained simulation software for DNA, RNA, and related systems
-
oxdna-cuda:
-
–
Package is not in Debian
-
–
d/copyright is in DEP5 format
Author: Lorenzo Rovigatti <lorenzo.rovigatti@gmail.com> Licenses: BSD-3-Clause, MIT, Apache-2.0, GPL-3+
Comments
No comments
Upload #2
Information
Version: | 3.4.2-1 |
---|---|
Uploaded: | 2022-09-16 18:51 |
Source package: | oxdna-cuda_3.4.2-1.dsc |
Distribution: | unstable |
Section: | science |
Priority: | optional |
Homepage: | https://github.com/lorenzo-rovigatti/oxDNA |
Vcs-Browser: | https://github.com/cgevans/oxdna-cuda-debian |
Vcs-Git: | https://github.com/debian/oxdna-cuda-debian.git |
Closes bugs: | #1019890 |
Changelog
oxdna-cuda (3.4.2-1) unstable; urgency=medium . * Initial release (Closes: #1019890) * Patched to use system pybind11-dev and nhlohmann-json3-dev. * Still uses embedded copies of exprtk and fast_double_parsen in src/extern. Both these are single headers, and are similarly embedded in other Debian packages. * Uses RPATH for a private shared library. This is set during cmake installation of binaries, and by a bit of a roundabout method for the oxpy Python package, 'installing' it and then moving it back into the build directory to be installed during the oxpy Python package installation. * CUDA compilation should support architures 5.0, 5.2, 6.0, 6.1, 7.0, and 7.5. * Man pages added, though they mostly point to html documentation. * html documentation links javascript, and tries to avoid external mathjax use. One external iframe, to oxView, remains.
QA information
-
–
Package uses debhelper-compatDebhelper compatibility level 13
-
–
Package is the latest upstream version
Local: 3.4.2 Upstream: 3.4.2 Url: https://github.com/lorenzo-rovigatti/oxDNA/archive/refs/tags/v3.4.2.tar.gz -
–
Package is not native
Format: 3.0 (quilt) -
–
"Maintainer" email is the same as the uploader
-
–
Package has lintian informational tagsoxdna-cuda source
-
I
debian-watch-contains-dh_make-template
- <project> [debian/watch]
-
I
patch-not-forwarded-upstream
- [debian/patches/000-install-cmake.patch]
- [debian/patches/010-overwrite-rpath-in-place-oxpy.patch]
- [debian/patches/020-use-system-pybind11.patch]
- [debian/patches/025-fix-pybind11-includes.patch]
-
P
maintainer-manual-page
- [debian/DNAnalysis.1]
- [debian/confGenerator.1]
- [debian/oat.1]
- [debian/oxDNA.1]
-
P
trailing-whitespace
- [debian/changelog:10]
- [debian/changelog:11]
- [debian/changelog:5]
-
P
very-long-line-length-in-source-file
- 1106 > 512 [examples/FFS_example/FFS_CUDA/README:90]
- 1223 > 512 [docs/source/umbrella_sampling.md:96]
- 1271 > 512 [docs/source/ffs.md:5]
- 1298 > 512 [examples/PERSISTENCE_LENGTH/readme.pdf:410]
- 130676 > 512 [docs/source/images/oxView_frame/devs.json:1]
- 1318 > 512 [examples/HAIRPIN/DOCS/histo_MD.pdf:67]
- 13850 > 512 [examples/NEW_RELAX_PROCEDURE/caca.json:1]
- 1474 > 512 [examples/HAIRPIN/DOCS/histo_MD_seq_dep.pdf:91]
- 1802 > 512 [examples/HAIRPIN/DOCS/hairpin.pdf:2586]
- 24081 > 512 [examples/CADNANO_INTERFACE/sq_rectangle_origami.json:1]
- 3707 > 512 [examples/METADYNAMICS/SINGLE_HELIX_BENDING/analysis.ipynb:54]
- 39107 > 512 [examples/CADNANO_INTERFACE/he_template.json:1]
- 4083 > 512 [examples/CADNANO_INTERFACE/TILE/tile.json:1]
- 516 > 512 [examples/MAJOR_MINOR_GROOVING/README:7]
- 525 > 512 [src/Interactions/PatchyInteractionDan.cpp:504]
- 540 > 512 [analysis/paper_examples/README.md:1]
- 543 > 512 [analysis/paper_examples/svd_mean/README.md:19]
- 551 > 512 [src/Backends/Thermostats/ThermostatFactory.h:18]
- 578 > 512 [legacy/UTILS/process_data/Makefile:7]
- 605 > 512 [src/Observables/Contacts.h:25]
- 606 > 512 [examples/METADYNAMICS/README.md:22]
- 615 > 512 [docs/source/observables.md:289]
- 628 > 512 [test/howto.md:24]
- 658 > 512 [src/Observables/HBList.h:18]
- 675 > 512 [docs/source/relaxation.md:3]
- 694 > 512 [src/Observables/MeanVectorCosine.cpp:152]
- 702 > 512 [analysis/paper_examples/h_bonds/README.md:1]
- 703 > 512 [src/extern/nlohmann/detail/macro_scope.hpp:333]
- 710 > 512 [oxpy/pybind11/docs/faq.rst:212]
- 719 > 512 [docs/source/index.md:5]
- 733 > 512 [docs/source/install.md:63]
- 767 > 512 [analysis/README.md:122]
- 767 > 512 [docs/source/input.md:186]
- 767 > 512 [src/Interactions/PatchyInteractionDan.h:333]
- 782 > 512 [analysis/paper_examples/clustering/README.md:1]
- 786 > 512 [breaking_changes.md:17]
- 802 > 512 [analysis/paper_examples/distances/README.md:3]
- 818 > 512 [analysis/paper_examples/mds_mean/README.md:1]
- 837 > 512 [src/CUDA/Backends/FFS_MD_CUDAMixedBackend.h:151]
- 851 > 512 [examples/HAIRPIN/DOCS/hairpin.tex:77]
- 877 > 512 [legacy/UTILS/traj2chimera.py:27]
- 895 > 512 [examples/HAIRPIN/DOCS/histo_TRAP.pdf:31]
-
X
debian-watch-does-not-check-gpg-signature
- [debian/watch]
-
X
prefer-uscan-symlink
- filenamemangle s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%<project>-$1.tar.gz% [debian/watch:5]
-
X
upstream-metadata-file-is-missing
-
I
debian-watch-contains-dh_make-template
-
–
Package closes ITP bug
-
oxdna-cuda:
- #1019890 (Wishlist, ITP): ITP: oxdna-cuda -- coarse-grained simulation software for DNA, RNA, and related systems
-
oxdna-cuda:
-
–
Package is not in Debian
-
–
d/copyright is in DEP5 format
Author: Lorenzo Rovigatti <lorenzo.rovigatti@gmail.com> Licenses: BSD-3-Clause, MIT, Apache-2.0, GPL-3+
Comments
No comments
Upload #1
Information
Version: | 3.4.2-1 |
---|---|
Uploaded: | 2022-09-16 18:21 |
Source package: | oxdna-cuda_3.4.2-1.dsc |
Distribution: | unstable |
Section: | science |
Priority: | optional |
Homepage: | https://github.com/lorenzo-rovigatti/oxDNA |
Vcs-Browser: | https://github.com/cgevans/oxdna-cuda-debian |
Vcs-Git: | https://github.com/debian/oxdna-cuda-debian.git |
Closes bugs: | #1019890 |
Changelog
oxdna-cuda (3.4.2-1) unstable; urgency=medium . * Initial release (Closes: #1019890)
QA information
-
–
Package uses debhelper-compatDebhelper compatibility level 13
-
–
Package is the latest upstream version
Local: 3.4.2 Upstream: 3.4.2 Url: https://github.com/lorenzo-rovigatti/oxDNA/archive/refs/tags/v3.4.2.tar.gz -
–
Package is not native
Format: 3.0 (quilt) -
–
"Maintainer" email is the same as the uploader
-
–
Package has lintian informational tagsoxdna-cuda source
-
I
debian-watch-contains-dh_make-template
- <project> [debian/watch]
-
I
patch-not-forwarded-upstream
- [debian/patches/000-install-cmake.patch]
- [debian/patches/010-overwrite-rpath-in-place-oxpy.patch]
- [debian/patches/020-use-system-pybind11.patch]
- [debian/patches/025-fix-pybind11-includes.patch]
-
P
maintainer-manual-page
- [debian/DNAnalysis.1]
- [debian/confGenerator.1]
- [debian/oat.1]
- [debian/oxDNA.1]
-
P
very-long-line-length-in-source-file
- 1106 > 512 [examples/FFS_example/FFS_CUDA/README:90]
- 1223 > 512 [docs/source/umbrella_sampling.md:96]
- 1271 > 512 [docs/source/ffs.md:5]
- 1298 > 512 [examples/PERSISTENCE_LENGTH/readme.pdf:410]
- 130676 > 512 [docs/source/images/oxView_frame/devs.json:1]
- 1318 > 512 [examples/HAIRPIN/DOCS/histo_MD.pdf:67]
- 13850 > 512 [examples/NEW_RELAX_PROCEDURE/caca.json:1]
- 1474 > 512 [examples/HAIRPIN/DOCS/histo_MD_seq_dep.pdf:91]
- 1802 > 512 [examples/HAIRPIN/DOCS/hairpin.pdf:2586]
- 24081 > 512 [examples/CADNANO_INTERFACE/sq_rectangle_origami.json:1]
- 3707 > 512 [examples/METADYNAMICS/SINGLE_HELIX_BENDING/analysis.ipynb:54]
- 39107 > 512 [examples/CADNANO_INTERFACE/he_template.json:1]
- 4083 > 512 [examples/CADNANO_INTERFACE/TILE/tile.json:1]
- 516 > 512 [examples/MAJOR_MINOR_GROOVING/README:7]
- 525 > 512 [src/Interactions/PatchyInteractionDan.cpp:504]
- 540 > 512 [analysis/paper_examples/README.md:1]
- 543 > 512 [analysis/paper_examples/svd_mean/README.md:19]
- 551 > 512 [src/Backends/Thermostats/ThermostatFactory.h:18]
- 578 > 512 [legacy/UTILS/process_data/Makefile:7]
- 605 > 512 [src/Observables/Contacts.h:25]
- 606 > 512 [examples/METADYNAMICS/README.md:22]
- 615 > 512 [docs/source/observables.md:289]
- 628 > 512 [test/howto.md:24]
- 658 > 512 [src/Observables/HBList.h:18]
- 675 > 512 [docs/source/relaxation.md:3]
- 694 > 512 [src/Observables/MeanVectorCosine.cpp:152]
- 702 > 512 [analysis/paper_examples/h_bonds/README.md:1]
- 703 > 512 [src/extern/nlohmann/detail/macro_scope.hpp:333]
- 710 > 512 [oxpy/pybind11/docs/faq.rst:212]
- 719 > 512 [docs/source/index.md:5]
- 733 > 512 [docs/source/install.md:63]
- 767 > 512 [analysis/README.md:122]
- 767 > 512 [docs/source/input.md:186]
- 767 > 512 [src/Interactions/PatchyInteractionDan.h:333]
- 782 > 512 [analysis/paper_examples/clustering/README.md:1]
- 786 > 512 [breaking_changes.md:17]
- 802 > 512 [analysis/paper_examples/distances/README.md:3]
- 818 > 512 [analysis/paper_examples/mds_mean/README.md:1]
- 837 > 512 [src/CUDA/Backends/FFS_MD_CUDAMixedBackend.h:151]
- 851 > 512 [examples/HAIRPIN/DOCS/hairpin.tex:77]
- 877 > 512 [legacy/UTILS/traj2chimera.py:27]
- 895 > 512 [examples/HAIRPIN/DOCS/histo_TRAP.pdf:31]
-
X
debian-watch-does-not-check-gpg-signature
- [debian/watch]
-
X
prefer-uscan-symlink
- filenamemangle s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%<project>-$1.tar.gz% [debian/watch:5]
-
X
upstream-metadata-file-is-missing
-
I
debian-watch-contains-dh_make-template
-
–
Package closes ITP bug
-
oxdna-cuda:
- #1019890 (Wishlist, ITP): ITP: oxdna-cuda -- coarse-grained simulation software for DNA, RNA, and related systems
-
oxdna-cuda:
-
–
Package is not in Debian
-
–
d/copyright is in DEP5 format
Author: Lorenzo Rovigatti <lorenzo.rovigatti@gmail.com> Licenses: BSD-3-Clause, MIT, Apache-2.0, GPL-3+
Comments
No comments