* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2019-12-29 13:23 Andreas Sturmlechner
0 siblings, 0 replies; 16+ messages in thread
From: Andreas Sturmlechner @ 2019-12-29 13:23 UTC (permalink / raw
To: gentoo-commits
commit: 9e4de76951dc4716b59a653647271cb430e9aded
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 28 16:45:30 2019 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Dec 29 13:22:56 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9e4de769
sci-chemistry/mdtraj: Drop python2_7
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
index 889d5e8e0b2..bf00532bf74 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
@@ -3,8 +3,7 @@
EAPI=6
-PYTHON_COMPAT=( python{2_7,3_5,3_6} )
-
+PYTHON_COMPAT=( python3_{5,6} )
inherit distutils-r1
DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2023-08-13 1:09 Sam James
0 siblings, 0 replies; 16+ messages in thread
From: Sam James @ 2023-08-13 1:09 UTC (permalink / raw
To: gentoo-commits
commit: bd539f89b5aa658654fd717864e6210913d05942
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 13 00:51:37 2023 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sun Aug 13 00:51:37 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bd539f89
sci-chemistry/mdtraj: depend on <cython-3
Bug: https://bugs.gentoo.org/911646
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
index 71b43cfef3f3..8a6aa966e865 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
@@ -31,8 +31,9 @@ DEPEND="${RDEPEND}
sci-libs/scikit-learn[${PYTHON_USEDEP}]
)
"
+# <cython-3 for bug #911646
BDEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
+ <dev-python/cython-3[${PYTHON_USEDEP}]
"
distutils_enable_tests --install pytest
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2023-05-06 14:35 Pacho Ramos
0 siblings, 0 replies; 16+ messages in thread
From: Pacho Ramos @ 2023-05-06 14:35 UTC (permalink / raw
To: gentoo-commits
commit: f0a4231911fe8556404dd8fc8d061c2dbba69a09
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sat May 6 14:34:12 2023 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sat May 6 14:34:12 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f0a42319
sci-chemistry/mdtraj: BDEPEND on cython
Closes: https://bugs.gentoo.org/905782
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild | 3 +++
1 file changed, 3 insertions(+)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
index f1d744000147..71b43cfef3f3 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
@@ -31,6 +31,9 @@ DEPEND="${RDEPEND}
sci-libs/scikit-learn[${PYTHON_USEDEP}]
)
"
+BDEPEND="
+ dev-python/cython[${PYTHON_USEDEP}]
+"
distutils_enable_tests --install pytest
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2023-05-01 12:52 Sam James
0 siblings, 0 replies; 16+ messages in thread
From: Sam James @ 2023-05-01 12:52 UTC (permalink / raw
To: gentoo-commits
commit: 4c3ab76085d7018c8238d44b51f4d4b1d6ecbc95
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Mon May 1 12:52:22 2023 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Mon May 1 12:52:22 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4c3ab760
sci-chemistry/mdtraj: add pypi upstream metadata
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-chemistry/mdtraj/metadata.xml | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-chemistry/mdtraj/metadata.xml b/sci-chemistry/mdtraj/metadata.xml
index 950fb315228b..b91aca7d360a 100644
--- a/sci-chemistry/mdtraj/metadata.xml
+++ b/sci-chemistry/mdtraj/metadata.xml
@@ -7,5 +7,6 @@
</maintainer>
<upstream>
<remote-id type="github">mdtraj/mdtraj</remote-id>
+ <remote-id type="pypi">mdtraj</remote-id>
</upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2023-05-01 12:49 Sam James
0 siblings, 0 replies; 16+ messages in thread
From: Sam James @ 2023-05-01 12:49 UTC (permalink / raw
To: gentoo-commits
commit: 6c8ded23facd1c4667e5684413de953b03c59684
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Mon May 1 12:44:12 2023 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Mon May 1 12:48:56 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6c8ded23
sci-chemistry/mdtraj: drop 1.9.4
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-chemistry/mdtraj/Manifest | 1 -
sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild | 42 --------------------------------
2 files changed, 43 deletions(-)
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
index 353f6958a591..8fa7ae2e758e 100644
--- a/sci-chemistry/mdtraj/Manifest
+++ b/sci-chemistry/mdtraj/Manifest
@@ -1,2 +1 @@
-DIST mdtraj-1.9.4.tar.gz 2133297 BLAKE2B c1507246bf0c8d7f6753f3d505f940e6f2f001361e42f10c9775647a7e6b58edf2d3953a8e48932f6bf9ad90b27e1baf30df6a7c1a590e49a860175822a25360 SHA512 55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee11110894d2a89e5504e20d200ca38
DIST mdtraj-1.9.7.tar.gz 2087085 BLAKE2B 430b42eddee0be8beba47994efd16515727970ac7acb36007c9b153cdb474551e5ea228f78a194fa9672d5b169753a9db3c090412bf749b3f1e9323bad9f52de SHA512 5dc9d474909a160e0b1d7989325e8190d1c593087f0130854094eb9c49bc00fd631ea19142d396d49aa7a3dadddaf535b5e811f7574ffff36f0cd22f14691067
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
deleted file mode 100644
index 374b682ad264..000000000000
--- a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_9 )
-
-inherit distutils-r1
-
-DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
-HOMEPAGE="https://mdtraj.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="LGPL-2.1+"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
- dev-python/astor[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/pytables[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}
- test? (
- dev-python/jupyter-client[${PYTHON_USEDEP}]
- dev-python/nbformat[${PYTHON_USEDEP}]
- )
-"
-
-distutils_enable_tests pytest
-
-# Tests fail (in previous ebuild versions they weren't even run
-RESTRICT="test"
-
-python_prepare() {
- sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
- -i basesetup.py || die
- distutils-r1_python_prepare_all
-}
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2023-03-16 18:52 Michał Górny
0 siblings, 0 replies; 16+ messages in thread
From: Michał Górny @ 2023-03-16 18:52 UTC (permalink / raw
To: gentoo-commits
commit: 3be144a49f3324a6c2bf2ba744e7544a45c75679
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 16 16:04:07 2023 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu Mar 16 18:50:26 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3be144a4
sci-chemistry/mdtraj: Use pypi.eclass
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
index c662120a72f3..70487c3185ac 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
@@ -4,11 +4,10 @@
EAPI=8
PYTHON_COMPAT=( python3_{9..10} )
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
HOMEPAGE="https://mdtraj.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
LICENSE="LGPL-2.1+"
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2022-11-19 11:41 Andrew Ammerlaan
0 siblings, 0 replies; 16+ messages in thread
From: Andrew Ammerlaan @ 2022-11-19 11:41 UTC (permalink / raw
To: gentoo-commits
commit: 1e684c51a65cd1739398c8d4fc8d343dd2dc176b
Author: Michael Mair-Keimberger <mmk <AT> levelnine <DOT> at>
AuthorDate: Sat Nov 19 08:54:49 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Nov 19 11:39:21 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1e684c51
sci-chemistry/mdtraj: use HTTPS, fix LICENSE
Signed-off-by: Michael Mair-Keimberger <mmk <AT> levelnine.at>
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild | 6 +++---
sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
index f618155f1397..c04aad519faf 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,11 +7,11 @@ PYTHON_COMPAT=( python3_{7,8,9} )
inherit distutils-r1
DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
-HOMEPAGE="http://mdtraj.org"
+HOMEPAGE="https://mdtraj.org"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
-LICENSE="GPL-2"
+LICENSE="LGPL-2.1+"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
index 0dcd8ceb970c..7b47f97e00d4 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -7,11 +7,11 @@ PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
-HOMEPAGE="http://mdtraj.org"
+HOMEPAGE="https://mdtraj.org"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
SLOT="0"
-LICENSE="GPL-2"
+LICENSE="LGPL-2.1+"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
RDEPEND="
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2022-07-30 23:32 Sam James
0 siblings, 0 replies; 16+ messages in thread
From: Sam James @ 2022-07-30 23:32 UTC (permalink / raw
To: gentoo-commits
commit: 20b14d2b308e1da612fed515befb35835fc105a9
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 30 21:30:57 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jul 30 22:19:11 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20b14d2b
sci-chemistry/mdtraj: add github upstream metadata
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-chemistry/mdtraj/metadata.xml | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/sci-chemistry/mdtraj/metadata.xml b/sci-chemistry/mdtraj/metadata.xml
index 7d3acaf5d252..950fb315228b 100644
--- a/sci-chemistry/mdtraj/metadata.xml
+++ b/sci-chemistry/mdtraj/metadata.xml
@@ -1,8 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">mdtraj/mdtraj</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2021-12-29 12:02 Andrew Ammerlaan
0 siblings, 0 replies; 16+ messages in thread
From: Andrew Ammerlaan @ 2021-12-29 12:02 UTC (permalink / raw
To: gentoo-commits
commit: 44c139783e28d1fa9180e10dae9a1ceff073f9f0
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 29 12:01:40 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Dec 29 12:02:39 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=44c13978
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 <AT> gentoo.org>
sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
index b069f9456270..0dcd8ceb970c 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
@@ -26,6 +26,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}
test? (
+ dev-python/ipykernel[${PYTHON_USEDEP}]
dev-python/jupyter_client[${PYTHON_USEDEP}]
dev-python/nbformat[${PYTHON_USEDEP}]
sci-libs/scikit-learn[${PYTHON_USEDEP}]
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2021-12-28 14:15 Andrew Ammerlaan
0 siblings, 0 replies; 16+ messages in thread
From: Andrew Ammerlaan @ 2021-12-28 14:15 UTC (permalink / raw
To: gentoo-commits
commit: 42c276a1602f6ddf7f1725e7b81115a1aa4ecc0e
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 28 14:14:48 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Dec 28 14:15:02 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=42c276a1
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 <AT> gentoo.org>
sci-chemistry/mdtraj/Manifest | 1 +
sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild | 41 ++++++++++++++++++++++++++++++++
2 files changed, 42 insertions(+)
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
index 369fb48765ab..353f6958a591 100644
--- a/sci-chemistry/mdtraj/Manifest
+++ b/sci-chemistry/mdtraj/Manifest
@@ -1 +1,2 @@
DIST mdtraj-1.9.4.tar.gz 2133297 BLAKE2B c1507246bf0c8d7f6753f3d505f940e6f2f001361e42f10c9775647a7e6b58edf2d3953a8e48932f6bf9ad90b27e1baf30df6a7c1a590e49a860175822a25360 SHA512 55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee11110894d2a89e5504e20d200ca38
+DIST mdtraj-1.9.7.tar.gz 2087085 BLAKE2B 430b42eddee0be8beba47994efd16515727970ac7acb36007c9b153cdb474551e5ea228f78a194fa9672d5b169753a9db3c090412bf749b3f1e9323bad9f52de SHA512 5dc9d474909a160e0b1d7989325e8190d1c593087f0130854094eb9c49bc00fd631ea19142d396d49aa7a3dadddaf535b5e811f7574ffff36f0cd22f14691067
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
new file mode 100644
index 000000000000..b069f9456270
--- /dev/null
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
+HOMEPAGE="http://mdtraj.org"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+ dev-python/astunparse[${PYTHON_USEDEP}]
+ dev-python/astor[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/pytables[${PYTHON_USEDEP}]
+ dev-python/pyparsing[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}
+ test? (
+ dev-python/jupyter_client[${PYTHON_USEDEP}]
+ dev-python/nbformat[${PYTHON_USEDEP}]
+ sci-libs/scikit-learn[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests --install pytest
+
+python_prepare_all() {
+ sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
+ -i basesetup.py || die
+ distutils-r1_python_prepare_all
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2021-09-13 18:10 Jakov Smolić
0 siblings, 0 replies; 16+ messages in thread
From: Jakov Smolić @ 2021-09-13 18:10 UTC (permalink / raw
To: gentoo-commits
commit: 03f5761951b58157b161cd65fb35b7cd6bd4be92
Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 13 18:03:39 2021 +0000
Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
CommitDate: Mon Sep 13 18:03:39 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=03f57619
sci-chemistry/mdtraj: Fix DISTUTILS_USE_SETUPTOOLS
Closes: https://bugs.gentoo.org/809767
Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org>
sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
index 229f664042a..f618155f139 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
@@ -1,9 +1,8 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2021-01-01 1:50 Michał Górny
0 siblings, 0 replies; 16+ messages in thread
From: Michał Górny @ 2021-01-01 1:50 UTC (permalink / raw
To: gentoo-commits
commit: f2aba2b456b54511128bb4427fdd492500ca360b
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 1 01:47:57 2021 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Fri Jan 1 01:50:42 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f2aba2b4
sci-chemistry/mdtraj: Remove old (py3.6)
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-chemistry/mdtraj/Manifest | 1 -
sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild | 34 --------------------------------
2 files changed, 35 deletions(-)
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
index 8e63d1026da..369fb48765a 100644
--- a/sci-chemistry/mdtraj/Manifest
+++ b/sci-chemistry/mdtraj/Manifest
@@ -1,2 +1 @@
-DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76
DIST mdtraj-1.9.4.tar.gz 2133297 BLAKE2B c1507246bf0c8d7f6753f3d505f940e6f2f001361e42f10c9775647a7e6b58edf2d3953a8e48932f6bf9ad90b27e1baf30df6a7c1a590e49a860175822a25360 SHA512 55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee11110894d2a89e5504e20d200ca38
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
deleted file mode 100644
index cdf5b949625..00000000000
--- a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_6 )
-inherit distutils-r1
-
-DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
-HOMEPAGE="http://mdtraj.org"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/pytables[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}
- test? ( dev-python/nose[${PYTHON_USEDEP}] )"
-
-python_prepare() {
- sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
- -i basesetup.py || die
- distutils-r1_python_prepare_all
-}
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2020-10-13 20:08 Alexey Shvetsov
0 siblings, 0 replies; 16+ messages in thread
From: Alexey Shvetsov @ 2020-10-13 20:08 UTC (permalink / raw
To: gentoo-commits
commit: c958bb24e3101d9a6286259d248a926d2f757dea
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Oct 13 20:08:04 2020 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Oct 13 20:08:04 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c958bb24
sci-chemistry/mdtraj: Works with py39
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
index fba1fb10eed..b2c7bf93d80 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2020-06-13 17:42 Pacho Ramos
0 siblings, 0 replies; 16+ messages in thread
From: Pacho Ramos @ 2020-06-13 17:42 UTC (permalink / raw
To: gentoo-commits
commit: 4b72e59ed9b1fcdb1ab88ede59c9a863549c5295
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 13 17:41:10 2020 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sat Jun 13 17:41:48 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4b72e59e
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 <AT> gentoo.org>
sci-chemistry/mdtraj/Manifest | 1 +
sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild | 43 ++++++++++++++++++++++++++++++++
2 files changed, 44 insertions(+)
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
index 982cdea3569..8e63d1026da 100644
--- a/sci-chemistry/mdtraj/Manifest
+++ b/sci-chemistry/mdtraj/Manifest
@@ -1 +1,2 @@
DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76
+DIST mdtraj-1.9.4.tar.gz 2133297 BLAKE2B c1507246bf0c8d7f6753f3d505f940e6f2f001361e42f10c9775647a7e6b58edf2d3953a8e48932f6bf9ad90b27e1baf30df6a7c1a590e49a860175822a25360 SHA512 55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee11110894d2a89e5504e20d200ca38
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
new file mode 100644
index 00000000000..5537daa6a53
--- /dev/null
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python3_{6,7} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+
+inherit distutils-r1
+
+DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
+HOMEPAGE="http://mdtraj.org"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ dev-python/astor[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/pytables[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ sci-libs/scipy[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}
+ test? (
+ dev-python/jupyter_client[${PYTHON_USEDEP}]
+ dev-python/nbformat[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+# Tests fail (in previous ebuild versions they weren't even run
+RESTRICT="test"
+
+python_prepare() {
+ sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
+ -i basesetup.py || die
+ distutils-r1_python_prepare_all
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2018-06-29 12:36 Alexey Shvetsov
0 siblings, 0 replies; 16+ messages in thread
From: Alexey Shvetsov @ 2018-06-29 12:36 UTC (permalink / raw
To: gentoo-commits
commit: 70a94bd23269b813b22981b69c4b5a23718d73d8
Author: Alexey Shvetsov <alexxy <AT> omrb <DOT> pnpi <DOT> spb <DOT> ru>
AuthorDate: Fri Jun 29 12:36:01 2018 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Jun 29 12:36:01 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=70a94bd2
sci-chemistry/mdtraj: Fix newline
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
index 20033bd3da6..2ac95db2c57 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
@@ -31,4 +31,4 @@ python_prepare() {
sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
-i basesetup.py || die
distutils-r1_python_prepare_all
-}
\ No newline at end of file
+}
^ permalink raw reply related [flat|nested] 16+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/
@ 2018-06-28 21:28 Alexey Shvetsov
0 siblings, 0 replies; 16+ messages in thread
From: Alexey Shvetsov @ 2018-06-28 21:28 UTC (permalink / raw
To: gentoo-commits
commit: 37d77f4d6250277c494aa6353f3cebe49db2e900
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 28 21:28:09 2018 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Jun 28 21:28:09 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=37d77f4d
sci-chemistry/mdtraj: Initial import
Package-Manager: Portage-2.3.41, Repoman-2.3.9
sci-chemistry/mdtraj/Manifest | 1 +
sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild | 34 ++++++++++++++++++++++++++++++++
sci-chemistry/mdtraj/metadata.xml | 8 ++++++++
3 files changed, 43 insertions(+)
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
new file mode 100644
index 00000000000..982cdea3569
--- /dev/null
+++ b/sci-chemistry/mdtraj/Manifest
@@ -0,0 +1 @@
+DIST mdtraj-1.9.1.tar.gz 1985711 BLAKE2B 625b7c1da998bd46732604dcc93c76f970f3c79f10e81aa9f4b3051ee45101efea8afd803d539ba1831dac3e7ed208d7c3773f74189a3887063cbff2b4d79df6 SHA512 015d9d1e258a7a207ac3b7e7a81b87c308e8684ee0a173ae9b722a90910e95e7f2ee18158c163212fae39d093b0cf397293d6e713538acb1fd20a7b70f2adc76
diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
new file mode 100644
index 00000000000..20033bd3da6
--- /dev/null
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
+HOMEPAGE="http://mdtraj.org"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+ dev-python/setuptools[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ sci-libs/scipy[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/pytables[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}
+ test? ( dev-python/nose[${PYTHON_USEDEP}] )"
+
+python_prepare() {
+ sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
+ -i basesetup.py || die
+ distutils-r1_python_prepare_all
+}
\ No newline at end of file
diff --git a/sci-chemistry/mdtraj/metadata.xml b/sci-chemistry/mdtraj/metadata.xml
new file mode 100644
index 00000000000..8425c0d53cb
--- /dev/null
+++ b/sci-chemistry/mdtraj/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 16+ messages in thread
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2019-12-29 13:23 [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/ Andreas Sturmlechner
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2023-08-13 1:09 Sam James
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