[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2023-08-12 Thread Sam James 
commit: bd539f89b5aa658654fd717864e6210913d05942
Author: Sam James  gentoo  org>
AuthorDate: Sun Aug 13 00:51:37 2023 +
Commit: Sam James  gentoo  org>
CommitDate: Sun Aug 13 00:51:37 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bd539f89

sci-chemistry/mdtraj: depend on https://bugs.gentoo.org/911646
Signed-off-by: Sam James  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}]
)
 "
+#

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2023-05-06 Thread Pacho Ramos 
commit: f0a4231911fe8556404dd8fc8d061c2dbba69a09
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sat May  6 14:34:12 2023 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sat May  6 14:34:12 2023 +
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  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

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/files/, sci-chemistry/mdtraj/

2023-05-05 Thread Pacho Ramos 
commit: a51915fb410cf715cd1610b3539830321e6867d2
Author: Pacho Ramos  gentoo  org>
AuthorDate: Fri May  5 14:25:18 2023 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Fri May  5 14:25:42 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a51915fb

sci-chemistry/mdtraj: enable py3.11

Closes: https://bugs.gentoo.org/897198
Signed-off-by: Pacho Ramos  gentoo.org>

 sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch | 16 
 sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild|  6 +-
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch 
b/sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch
new file mode 100644
index ..303c819aaee4
--- /dev/null
+++ b/sci-chemistry/mdtraj/files/mdtraj-1.9.7-python311.patch
@@ -0,0 +1,16 @@
+Index: mdtraj/setup.py
+===
+--- mdtraj.orig/setup.py   2023-01-18 15:26:51.424826255 +0100
 mdtraj/setup.py2023-01-18 15:26:51.420826223 +0100
+@@ -298,6 +298,10 @@
+ 
+ for e in extensions:
+ e.include_dirs.append(np.get_include())
+-metadata['ext_modules'] = cythonize(extensions, 
language_level=sys.version_info[0])
++metadata['ext_modules'] = cythonize(
++extensions,
++language_level=sys.version_info[0],
++force=True,
++)
+ 
+ setup(**metadata)

diff --git a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild 
b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
index 997dacaa72dd..f1d744000147 100644
--- a/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
+++ b/sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
-PYTHON_COMPAT=( python3_{9..10} )
+PYTHON_COMPAT=( python3_{9..11} )
 
 inherit distutils-r1 pypi
 
@@ -34,6 +34,10 @@ DEPEND="${RDEPEND}
 
 distutils_enable_tests --install pytest
 
+PATCHES=(
+   "${FILESDIR}/${P}-python311.patch"
+)
+
 python_prepare_all() {
sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
-i basesetup.py || die

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2023-05-01 Thread Sam James 
commit: 4c3ab76085d7018c8238d44b51f4d4b1d6ecbc95
Author: Sam James  gentoo  org>
AuthorDate: Mon May  1 12:52:22 2023 +
Commit: Sam James  gentoo  org>
CommitDate: Mon May  1 12:52:22 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4c3ab760

sci-chemistry/mdtraj: add pypi upstream metadata

Signed-off-by: Sam James  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 @@


mdtraj/mdtraj
+   mdtraj

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2023-05-01 Thread Sam James 
commit: 6c8ded23facd1c4667e5684413de953b03c59684
Author: Sam James  gentoo  org>
AuthorDate: Mon May  1 12:44:12 2023 +
Commit: Sam James  gentoo  org>
CommitDate: Mon May  1 12:48:56 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6c8ded23

sci-chemistry/mdtraj: drop 1.9.4

Signed-off-by: Sam James  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 
55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee0894d2a89e5504e20d200ca38
 DIST mdtraj-1.9.7.tar.gz 2087085 BLAKE2B 
430b42eddee0be8beba47994efd16515727970ac7acb36007c9b153cdb474551e5ea228f78a194fa9672d5b169753a9db3c090412bf749b3f1e9323bad9f52de
 SHA512 
5dc9d474909a160e0b1d7989325e8190d1c593087f0130854094eb9c49bc00fd631ea19142d396d49aa7a3dadddaf535b5e811f757436f0cd22f14691067

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..
--- 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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/, dev-python/spyder-kernels/, dev-python/octave_kernel/, ...

2023-04-14 Thread Michał Górny 
commit: 9492595553aa0ab558c84c8aa4f002e931274e38
Author: Michał Górny  gentoo  org>
AuthorDate: Fri Apr 14 13:19:22 2023 +
Commit: Michał Górny  gentoo  org>
CommitDate: Fri Apr 14 13:19:22 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=94925955

Rename dev-python/{jupyter_client → jupyter-client}

Signed-off-by: Michał Górny  gentoo.org>

 dev-python/ipykernel/ipykernel-6.20.2.ebuild  | 2 +-
 dev-python/ipykernel/ipykernel-6.21.2.ebuild  | 2 +-
 dev-python/ipykernel/ipykernel-6.21.3.ebuild  | 2 +-
 dev-python/ipykernel/ipykernel-6.22.0.ebuild  | 2 +-
 dev-python/ipyparallel/ipyparallel-8.4.1.ebuild   | 2 +-
 dev-python/ipyparallel/ipyparallel-8.5.1.ebuild   | 2 +-
 dev-python/ipyparallel/ipyparallel-8.6.0.ebuild   | 2 +-
 dev-python/{jupyter_client => jupyter-client}/Manifest| 0
 .../jupyter-client-8.0.3.ebuild}  | 0
 .../jupyter-client-8.1.0.ebuild}  | 0
 .../jupyter-client-8.2.0.ebuild}  | 0
 dev-python/{jupyter_client => jupyter-client}/metadata.xml| 0
 dev-python/jupyter-server/jupyter-server-2.4.0.ebuild | 2 +-
 dev-python/jupyter-server/jupyter-server-2.5.0.ebuild | 2 +-
 dev-python/jupyter_console/jupyter_console-6.6.3.ebuild   | 2 +-
 dev-python/jupyter_kernel_test/jupyter_kernel_test-0.5.0.ebuild   | 2 +-
 dev-python/nbclassic/nbclassic-0.5.5.ebuild   | 2 +-
 dev-python/nbclient/nbclient-0.7.2.ebuild | 2 +-
 dev-python/nbclient/nbclient-0.7.3.ebuild | 2 +-
 dev-python/nbval/nbval-0.10.0-r1.ebuild   | 2 +-
 dev-python/nbval/nbval-0.10.0.ebuild  | 2 +-
 dev-python/nbval/nbval-0.9.6.ebuild   | 2 +-
 dev-python/notebook/notebook-6.4.12.ebuild| 2 +-
 dev-python/notebook/notebook-6.5.3.ebuild | 2 +-
 dev-python/notebook/notebook-6.5.4.ebuild | 2 +-
 dev-python/octave_kernel/octave_kernel-0.34.2.ebuild  | 2 +-
 dev-python/pytest-jupyter/pytest-jupyter-0.6.2.ebuild | 2 +-
 dev-python/pytest-jupyter/pytest-jupyter-0.7.0.ebuild | 2 +-
 dev-python/qtconsole/qtconsole-5.4.0.ebuild   | 2 +-
 dev-python/qtconsole/qtconsole-5.4.1.ebuild   | 2 +-
 dev-python/qtconsole/qtconsole-5.4.2.ebuild   | 2 +-
 dev-python/spyder-kernels/spyder-kernels-2.4.3.ebuild | 4 ++--
 dev-python/statsmodels/statsmodels-0.13.2.ebuild  | 2 +-
 dev-python/statsmodels/statsmodels-0.13.5.ebuild  | 2 +-
 profiles/updates/2Q-2023  | 1 +
 sci-chemistry/mdtraj/mdtraj-1.9.4.ebuild  | 2 +-
 sci-chemistry/mdtraj/mdtraj-1.9.7.ebuild  | 2 +-
 37 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/dev-python/ipykernel/ipykernel-6.20.2.ebuild 
b/dev-python/ipykernel/ipykernel-6.20.2.ebuild
index 56f087335f41..1e5e1e1e4721 100644
--- a/dev-python/ipykernel/ipykernel-6.20.2.ebuild
+++ b/dev-python/ipykernel/ipykernel-6.20.2.ebuild
@@ -24,7 +24,7 @@ RDEPEND="
>=dev-python/comm-0.1.1[${PYTHON_USEDEP}]
>=dev-python/debugpy-1.0[${PYTHON_USEDEP}]
>=dev-python/ipython-7.23.1[${PYTHON_USEDEP}]
-   >=dev-python/jupyter_client-6.1.12[${PYTHON_USEDEP}]
+   >=dev-python/jupyter-client-6.1.12[${PYTHON_USEDEP}]
>=dev-python/matplotlib-inline-0.1[${PYTHON_USEDEP}]
dev-python/nest_asyncio[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]

diff --git a/dev-python/ipykernel/ipykernel-6.21.2.ebuild 
b/dev-python/ipykernel/ipykernel-6.21.2.ebuild
index ccf7082b4a62..b00e6b2f724f 100644
--- a/dev-python/ipykernel/ipykernel-6.21.2.ebuild
+++ b/dev-python/ipykernel/ipykernel-6.21.2.ebuild
@@ -23,7 +23,7 @@ RDEPEND="
>=dev-python/comm-0.1.1[${PYTHON_USEDEP}]
>=dev-python/debugpy-1.6.5[${PYTHON_USEDEP}]
>=dev-python/ipython-7.23.1[${PYTHON_USEDEP}]
-   >=dev-python/jupyter_client-8[${PYTHON_USEDEP}]
+   >=dev-python/jupyter-client-8[${PYTHON_USEDEP}]
>=dev-python/jupyter-core-4.12[${PYTHON_USEDEP}]
>=dev-python/matplotlib-inline-0.1[${PYTHON_USEDEP}]
dev-python/nest_asyncio[${PYTHON_USEDEP}]

diff --git a/dev-python/ipykernel/ipykernel-6.21.3.ebuild 
b/dev-python/ipykernel/ipykernel-6.21.3.ebuild
index fa49750494e9..233dc4730f18 100644
--- a/dev-python/ipykernel/ipykernel-6.21.3.ebuild
+++ b/dev-python/ipykernel/ipykernel-6.21.3.ebuild
@@ -23,7

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2023-03-16 Thread Michał Górny 
commit: 3be144a49f3324a6c2bf2ba744e7544a45c75679
Author: Michał Górny  gentoo  org>
AuthorDate: Thu Mar 16 16:04:07 2023 +
Commit: Michał Górny  gentoo  org>
CommitDate: Thu Mar 16 18:50:26 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3be144a4

sci-chemistry/mdtraj: Use pypi.eclass

Signed-off-by: Michał Górny  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+"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2022-11-19 Thread Andrew Ammerlaan 
commit: 1e684c51a65cd1739398c8d4fc8d343dd2dc176b
Author: Michael Mair-Keimberger  levelnine  at>
AuthorDate: Sat Nov 19 08:54:49 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Sat Nov 19 11:39:21 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1e684c51

sci-chemistry/mdtraj: use HTTPS, fix LICENSE

Signed-off-by: Michael Mair-Keimberger  levelnine.at>
Signed-off-by: Andrew Ammerlaan  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="

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2022-07-30 Thread Sam James 
commit: 20b14d2b308e1da612fed515befb35835fc105a9
Author: Sam James  gentoo  org>
AuthorDate: Sat Jul 30 21:30:57 2022 +
Commit: Sam James  gentoo  org>
CommitDate: Sat Jul 30 22:19:11 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20b14d2b

sci-chemistry/mdtraj: add github upstream metadata

Signed-off-by: Sam James  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 @@
 
 https://www.gentoo.org/dtd/metadata.dtd;>
 
-  
-s...@gentoo.org
-Gentoo Science Project
-  
+   
+   s...@gentoo.org
+   Gentoo Science Project
+   
+   
+   mdtraj/mdtraj
+

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2021-12-29 Thread Andrew Ammerlaan 
commit: 44c139783e28d1fa9180e10dae9a1ceff073f9f0
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Wed Dec 29 12:01:40 2021 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Wed Dec 29 12:02:39 2021 +
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  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}]

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2021-12-28 Thread Andrew Ammerlaan 
commit: 42c276a1602f6ddf7f1725e7b81115a1aa4ecc0e
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Tue Dec 28 14:14:48 2021 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue Dec 28 14:15:02 2021 +
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  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 
55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee0894d2a89e5504e20d200ca38
+DIST mdtraj-1.9.7.tar.gz 2087085 BLAKE2B 
430b42eddee0be8beba47994efd16515727970ac7acb36007c9b153cdb474551e5ea228f78a194fa9672d5b169753a9db3c090412bf749b3f1e9323bad9f52de
 SHA512 
5dc9d474909a160e0b1d7989325e8190d1c593087f0130854094eb9c49bc00fd631ea19142d396d49aa7a3dadddaf535b5e811f757436f0cd22f14691067

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 ..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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2021-09-13 Thread Jakov Smolić 
commit: 03f5761951b58157b161cd65fb35b7cd6bd4be92
Author: Jakov Smolić  gentoo  org>
AuthorDate: Mon Sep 13 18:03:39 2021 +
Commit: Jakov Smolić  gentoo  org>
CommitDate: Mon Sep 13 18:03:39 2021 +
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  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

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2020-12-31 Thread Michał Górny 
commit: f2aba2b456b54511128bb4427fdd492500ca360b
Author: Michał Górny  gentoo  org>
AuthorDate: Fri Jan  1 01:47:57 2021 +
Commit: Michał Górny  gentoo  org>
CommitDate: Fri Jan  1 01:50:42 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f2aba2b4

sci-chemistry/mdtraj: Remove old (py3.6)

Signed-off-by: Michał Górny  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 
55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee0894d2a89e5504e20d200ca38

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..000
--- 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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2020-10-13 Thread Alexey Shvetsov 
commit: c958bb24e3101d9a6286259d248a926d2f757dea
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Tue Oct 13 20:08:04 2020 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Tue Oct 13 20:08:04 2020 +
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  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

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2020-06-13 Thread Pacho Ramos 
commit: 4b72e59ed9b1fcdb1ab88ede59c9a863549c5295
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sat Jun 13 17:41:10 2020 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sat Jun 13 17:41:48 2020 +
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  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 
55f67546db20ce63da3af2231df459e9983e15a65da960784613f746dcce820fe6b0deffbb21b528e93fc6cf674dc7a25ee0894d2a89e5504e20d200ca38

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 000..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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2019-12-29 Thread Andreas Sturmlechner 
commit: 9e4de76951dc4716b59a653647271cb430e9aded
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sat Dec 28 16:45:30 2019 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun Dec 29 13:22:56 2019 +
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  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"

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2018-06-29 Thread Alexey Shvetsov 
commit: 70a94bd23269b813b22981b69c4b5a23718d73d8
Author: Alexey Shvetsov  omrb  pnpi  spb  ru>
AuthorDate: Fri Jun 29 12:36:01 2018 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Fri Jun 29 12:36:01 2018 +
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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mdtraj/

2018-06-28 Thread Alexey Shvetsov 
commit: 37d77f4d6250277c494aa6353f3cebe49db2e900
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Thu Jun 28 21:28:09 2018 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Thu Jun 28 21:28:09 2018 +
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 000..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 000..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 000..8425c0d53cb
--- /dev/null
+++ b/sci-chemistry/mdtraj/metadata.xml
@@ -0,0 +1,8 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+  
+s...@gentoo.org
+Gentoo Science Project
+  
+