sci-chemistry / mdtraj

Read, write and analyze MD trajectories with only a few lines of Python code

Official package sites : https://mdtraj.org ·

v1.9.7 :: 0 :: gentoo

Modified
License
LGPL-2.1+
Keywords
~amd64 ~amd64-linux ~x86 ~x86-linux
USE flags
test

General

test
Enable dependencies and/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)

python_targets

python3_10
Build with Python 3.10
python3_11
Build with Python 3.11

dev-python / astor : Read/rewrite/write Python ASTs

dev-python / astunparse : Astun parser for python

dev-python / ipykernel : IPython Kernel for Jupyter

dev-python / jupyter-client : Jupyter protocol implementation and client libraries

dev-python / nbformat : Reference implementation of the Jupyter Notebook format

dev-python / networkx : Python tools to manipulate graphs and complex networks

dev-python / numpy : Fast array and numerical python library

dev-python / pandas : Powerful data structures for data analysis and statistics

dev-python / pyparsing : Easy-to-use Python module for text parsing

dev-python / pytables : Hierarchical datasets for Python

dev-python / scipy : Scientific algorithms library for Python

sci-libs / scikit-learn : Machine learning library for Python

dev-lang / python : An interpreted, interactive, object-oriented programming language

dev-python / astor : Read/rewrite/write Python ASTs

dev-python / astunparse : Astun parser for python

dev-python / networkx : Python tools to manipulate graphs and complex networks

dev-python / numpy : Fast array and numerical python library

dev-python / pandas : Powerful data structures for data analysis and statistics

dev-python / pyparsing : Easy-to-use Python module for text parsing

dev-python / pytables : Hierarchical datasets for Python

dev-python / scipy : Scientific algorithms library for Python

net-mail / isync : MailDir mailbox synchronizer

741320
sci-chemistry/mdtraj-1.9.7 fails to link with LLD because of /usr/lib in the link command line
836859
sci-chemistry/mdtraj-1.9.7 fails tests on MUSL
862387
sci-chemistry/mdtraj-1.9.7 fails to compile (lto): trr_header.h:28:5: error: type of do_trnheader does not match original declaration [-Werror=lto-type-mismatch]
886105
sci-chemistry/mdtraj-1.9.7 fails to compile (CLANG-STRICTER-SYSTEM): tng_io.c:1064:57: error: incompatible function pointer types assigning to tng_function_status ()(const tng_trajectory_t, int32_t ) (aka tng_function_status ()(struct tng_trajectory cons
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Pacho Ramos · gentoo
sci-chemistry/mdtraj: BDEPEND on cython
Closes: https://bugs.gentoo.org/905782 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Pacho Ramos · gentoo
sci-chemistry/mdtraj: enable py3.11
Closes: https://bugs.gentoo.org/897198 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Sam James · gentoo
sci-chemistry/mdtraj: drop 1.9.4
Signed-off-by: Sam James <sam@gentoo.org>
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Michał Górny · gentoo
Rename dev-python/{jupyter_client → jupyter-client}
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Michał Górny · gentoo
sci-chemistry/mdtraj: Use pypi.eclass
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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David Seifert · gentoo
*/*: remove py3.8 from PYTHON_COMPAT
Signed-off-by: David Seifert <soap@gentoo.org>
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Michael Mair-Keimberger · gentoo
sci-chemistry/mdtraj: use HTTPS, fix LICENSE
Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at> Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
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Andrew Ammerlaan · gentoo
sci-chemistry/mdtraj: add missing test dep
Closes: https://bugs.gentoo.org/830174 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
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Andrew Ammerlaan · gentoo
sci-chemistry/mdtraj: add version 1.9.7, enable py3.10, fix tests
Bug: https://bugs.gentoo.org/809770 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
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Jakov Smolić · gentoo
sci-chemistry/mdtraj: Fix DISTUTILS_USE_SETUPTOOLS
Closes: https://bugs.gentoo.org/809767 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
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Michał Górny · gentoo
*/*: Remove obsolete values from PYTHON_COMPAT
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Michał Górny · gentoo
sci-chemistry/mdtraj: Remove old (py3.6)
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/mdtraj: Works with py39
Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
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Michał Górny · gentoo
Move {sci-libs → dev-python}/scipy
Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Pacho Ramos · gentoo
sci-chemistry/mdtraj: Bump to 1.9.4
Closes: https://bugs.gentoo.org/711696 Closes: https://bugs.gentoo.org/718478 Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Pacho Ramos <pacho@gentoo.org>
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Michał Górny · gentoo
*/*: Clean PYTHON_COMPAT of obsolete impls
Closes: https://github.com/gentoo/gentoo/pull/14246 Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Andreas Sturmlechner · gentoo
sci-chemistry/mdtraj: Drop python2_7
Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
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Michał Górny · gentoo
*/*: [QA] Fix trivial cases of MissingTestRestrict
The result was achieved via the following pipeline: pkgcheck scan -c RestrictTestCheck -R FormatReporter \ --format '{category}/{package}/{package}-{version}.ebuild' | xargs -n32 grep -L RESTRICT | xargs -n32 sed -i -e '/^IUSE=.*test/aRESTRICT="!test? ( test )"' The resulting metadata was compared before and after the change. Few Go ebuilds had to be fixed manually due to implicit RESTRICT=strip added by the eclass. Two ebuilds have to be fixed because of multiline IUSE. Suggested-by: Robin H. Johnson <robbat2@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/13942 Signed-off-by: Michał Górny <mgorny@gentoo.org>
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Alexey Shvetsov · gentoo
sci-chemistry/mdtraj: Fix newline
Package-Manager: Portage-2.3.40, Repoman-2.3.9
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Alexey Shvetsov · gentoo
sci-chemistry/mdtraj: Initial import
Package-Manager: Portage-2.3.41, Repoman-2.3.9