[gentoo-commits] proj/sci:master commit in: profiles/
commit: 633f65383dbc7bcc1178b2e2caeaa6929bb79c5b Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jul 18 11:28:40 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jul 18 11:28:40 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=633f6538 profiles: mask sci-biology/BBmap Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 1b622a85b..c184ca27b 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,5 +30,6 @@ #--- END OF EXAMPLES --- -# Andrew Ammerlaan (2024-04-24) -# reverse deps +# Andrew Ammerlaan (2024-07-18) +# Requires java openmpi bindings, no longer packaged. +sci-biology/BBmap
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 670b006885dabe96503628a52ddfc6d9a6635c57 Author: Horea Christian chymera eu> AuthorDate: Thu May 9 22:51:59 2024 + Commit: Horea Christian gmail com> CommitDate: Thu May 9 22:51:59 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=670b0068 profiles: unmasked nipype Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 2 -- 1 file changed, 2 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index efc64be51..09429792d 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -35,8 +35,6 @@ sci-biology/multiqc # Andrew Ammerlaan (2024-04-24) -# Dependencies dev-python/prov removed -sci-libs/nipype # reverse deps sci-biology/samri sci-biology/samri_bidsdata
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 1b90823136a7aa189484deb0f3769daf58d3c040 Author: Horea Christian chymera eu> AuthorDate: Thu May 9 23:02:28 2024 + Commit: Horea Christian gmail com> CommitDate: Thu May 9 23:02:28 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1b908231 profiles: unmasked samri, heudiconv Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 4 1 file changed, 4 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 09429792d..48068ccf9 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -36,7 +36,3 @@ sci-biology/multiqc # Andrew Ammerlaan (2024-04-24) # reverse deps -sci-biology/samri -sci-biology/samri_bidsdata -sci-biology/samri_bindata -dev-python/heudiconv
[gentoo-commits] proj/sci:master commit in: profiles/
commit: ca51d5147ba4ef27db118dffc07302eaac1bc7b9 Author: Andrew Ammerlaan gentoo org> AuthorDate: Wed Apr 24 09:34:43 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Wed Apr 24 09:34:43 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca51d514 package.mask: mask multiqc and nipype Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 13 + 1 file changed, 13 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..efc64be51 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,16 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (2024-04-24) +# Dependencies dev-python/future removed +sci-biology/multiqc + +# Andrew Ammerlaan (2024-04-24) +# Dependencies dev-python/prov removed +sci-libs/nipype +# reverse deps +sci-biology/samri +sci-biology/samri_bidsdata +sci-biology/samri_bindata +dev-python/heudiconv
[gentoo-commits] proj/sci:master commit in: profiles/
commit: e3c9b1be480b74fa4b9d1b84002f8a2d261c6163 Author: Horea Christian chymera eu> AuthorDate: Fri Mar 22 21:19:03 2024 + Commit: Horea Christian gmail com> CommitDate: Fri Mar 22 21:19:03 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3c9b1be profiles: unmasked packages with formerly missing deps Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 7 --- 1 file changed, 7 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 464a4005a..d39812beb 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,10 +29,3 @@ ## app-misc/some-package #--- END OF EXAMPLES --- - -# Andrew Ammerlaan (2024-03-15) -# Depends on unkeyworded dev-libs/libpthread-stubs -sci-biology/afni -sci-biology/samri -sci-biology/samri_bidsdata -sci-biology/samri_bindata
[gentoo-commits] proj/sci:master commit in: profiles/
commit: b846f5dfcb198edc40f2061b2e8bbf2cd3f555ad Author: Horea Christian chymera eu> AuthorDate: Thu Mar 21 22:11:32 2024 + Commit: Horea Christian gmail com> CommitDate: Thu Mar 21 22:15:29 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b846f5df profiles: unmasked packages with formerly missing deps Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 4 1 file changed, 4 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index b908c0a3e..464a4005a 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -31,10 +31,6 @@ #--- END OF EXAMPLES --- # Andrew Ammerlaan (2024-03-15) -# Depends on removed dev-python/pydantic -dev-python/dandi-schema -dev-vcs/dandi-cli -sci-biology/neuroconv # Depends on unkeyworded dev-libs/libpthread-stubs sci-biology/afni sci-biology/samri
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 481cfc5b24936c3b6d9216861e6a438a8db9c7c6 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Mar 15 11:28:27 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Mar 15 11:28:27 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=481cfc5b mask packs with incomp deps Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 3 +++ 1 file changed, 3 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 9384fafc7..b908c0a3e 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -37,3 +37,6 @@ dev-vcs/dandi-cli sci-biology/neuroconv # Depends on unkeyworded dev-libs/libpthread-stubs sci-biology/afni +sci-biology/samri +sci-biology/samri_bidsdata +sci-biology/samri_bindata
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 557d3b57a23fc54c993f0296b1935a06bc99bf8e Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Mar 15 11:25:41 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Mar 15 11:25:41 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=557d3b57 mask packs with incomp deps Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 8 1 file changed, 8 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..9384fafc7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,11 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (2024-03-15) +# Depends on removed dev-python/pydantic +dev-python/dandi-schema +dev-vcs/dandi-cli +sci-biology/neuroconv +# Depends on unkeyworded dev-libs/libpthread-stubs +sci-biology/afni
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/pytorch-lightning/
commit: a6dbed04be114775959f5c09e3230a148e9605f8
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Mar 8 16:42:02 2024 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Mar 8 16:42:02 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6dbed04
dev-python/pytorch-lightning: treeclean
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/pytorch-lightning/metadata.xml | 12 -
.../pytorch-lightning-1.8.6.ebuild | 31 --
profiles/package.mask | 4 ---
3 files changed, 47 deletions(-)
diff --git a/dev-python/pytorch-lightning/metadata.xml
b/dev-python/pytorch-lightning/metadata.xml
deleted file mode 100644
index df24db4ac..0
--- a/dev-python/pytorch-lightning/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- s...@gentoo.org
- Science Project
-
-
- Lightning-AI/lightning
- pytorch-lightning
-
-
diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
b/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
deleted file mode 100644
index a775be3bf..0
--- a/dev-python/pytorch-lightning/pytorch-lightning-1.8.6.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_PEP517=setuptools
-DISTUTILS_SINGLE_IMPL=1
-PYPI_NO_NORMALIZE=1
-inherit distutils-r1 pypi
-
-DESCRIPTION="Lightweight PyTorch wrapper for ML researchers"
-HOMEPAGE="https://github.com/Lightning-AI/lightning;
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
- $(python_gen_cond_dep '
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/pyyaml[${PYTHON_USEDEP}]
- dev-python/fsspec[${PYTHON_USEDEP}]
- sci-visualization/tensorboard[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- dev-python/typing-extensions[${PYTHON_USEDEP}]
- dev-python/ratelimit[${PYTHON_USEDEP}]
- ')
-"
diff --git a/profiles/package.mask b/profiles/package.mask
index adc653878..527c834e4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,10 +30,6 @@
#--- END OF EXAMPLES ---
-# Andrew Ammerlaan (27-02-2024)
-# Depends on removed sci-visualization/tensorboard
-dev-python/pytorch-lightning
-
# Andrew Ammerlaan (29 Dec 2023)
# Depends on removed llvm:14, at the time of writing no llvm:15
# update available.
[gentoo-commits] proj/sci:master commit in: profiles/desc/, sci-physics/lhapdf-sets/
commit: d21400c2bb5b7d9f213047df109b7d40fde8e8a8
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Tue Feb 27 14:14:36 2024 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Tue Feb 27 15:29:14 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d21400c2
sci-physics/lhapdf-sets: Add more PDFs
Closes: https://github.com/gentoo/sci/pull/1248
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
profiles/desc/lhapdf_sets.desc | 4 +++-
sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild | 6 +-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/profiles/desc/lhapdf_sets.desc b/profiles/desc/lhapdf_sets.desc
index 7270fbee7..66da0763c 100644
--- a/profiles/desc/lhapdf_sets.desc
+++ b/profiles/desc/lhapdf_sets.desc
@@ -14,4 +14,6 @@ nnpdf23_nlo_as_0119_qed_mc - NNPDF23_nlo_as_0119_qed_mc
LHAPDF grid
nnpdf23_nnlo_as_0119_qed_mc - NNPDF23_nnlo_as_0119_qed_mc LHAPDF grid
cteq66 - CTEQ66 LHAPDF grid
cteq6l1 - CTEQ6L1 LHAPDF grid
-mrst2004qed - MRST2004qed LHAPDF grid
\ No newline at end of file
+mrst2004qed - MRST2004qed LHAPDF grid
+nnpdf23_nlo_as_0118 - nnpdf23_nlo_as_0118 grid
+nnpdf31_nnlo_as_0118 - nnpdf31_nnlo_as_0118 grid
\ No newline at end of file
diff --git a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
index edd3639d2..784d94f97 100644
--- a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
+++ b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
@@ -17,6 +17,8 @@ IUSE_LHAPDF_SETS="
lhapdf_sets_cteq66
lhapdf_sets_cteq6l1
lhapdf_sets_mrst2004qed
+ lhapdf_sets_nnpdf23_nlo_as_0118
+ lhapdf_sets_nnpdf31_nnlo_as_0118
"
COMMON_URI="https://lhapdfsets.web.cern.ch/lhapdfsets/current;
@@ -36,7 +38,9 @@ SRC_URI="
lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc? (
${COMMON_URI}/NNPDF23_nnlo_as_0119_qed_mc.tar.gz )
lhapdf_sets_cteq66? ( ${COMMON_URI}/cteq66.tar.gz
)
lhapdf_sets_cteq6l1? ( ${COMMON_URI}/cteq6l1.tar.gz
)
- lhapdf_sets_mrst2004qed? (
${HEPFORGE_URI}/MRST2004qed.tar.gz )
+ lhapdf_sets_mrst2004qed? (
${HEPFORGE_URI}/MRST2004qed.tar.gz )
+ lhapdf_sets_nnpdf23_nlo_as_0118? (
${COMMON_URI}/NNPDF23_nlo_as_0118.tar.gz )
+ lhapdf_sets_nnpdf31_nnlo_as_0118?(
${COMMON_URI}/NNPDF31_nnlo_as_0118.tar.gz)
"
MY_PV=$(ver_cut 1-3)
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 392b8a17389643a9f9b5b467b0c0aacb11c1f38a Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Feb 27 14:40:14 2024 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Feb 27 14:40:14 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=392b8a17 profiles: mask dev-python/pytorch-lightning Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 4 1 file changed, 4 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 527c834e4..adc653878 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,10 @@ #--- END OF EXAMPLES --- +# Andrew Ammerlaan (27-02-2024) +# Depends on removed sci-visualization/tensorboard +dev-python/pytorch-lightning + # Andrew Ammerlaan (29 Dec 2023) # Depends on removed llvm:14, at the time of writing no llvm:15 # update available.
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 41349a88222444a77180a5b55e43c1d5a2ec92d7 Author: Horea Christian chymera eu> AuthorDate: Mon Jan 22 14:41:36 2024 + Commit: Horea Christian gmail com> CommitDate: Mon Jan 22 14:41:36 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=41349a88 profiles: heudiconv package no longer affected by dropped dependency Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 4 1 file changed, 4 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 60e453d16..527c834e4 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -41,10 +41,6 @@ dev-python/pynndescent dev-python/tridesclous dev-python/umap-learn -# Andrew Ammerlaan (16 Dec 2023) -# Depends on removed dev-python/pydotplus -dev-python/heudiconv - # Andrew Ammerlaan (26 Jun 2023) # Depends on removed dev-python/toml. # Alternatives are tomli or tomlkit
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 5c3158f9fbd0a76cfea2663ffbb197baf371e864 Author: Horea Christian chymera eu> AuthorDate: Mon Jan 22 14:39:39 2024 + Commit: Horea Christian gmail com> CommitDate: Mon Jan 22 14:39:39 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c3158f9 profiles: removed old package version with dropped dependency Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 78a8b2480..56bf41059 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -43,7 +43,6 @@ dev-python/umap-learn # Andrew Ammerlaan (16 Dec 2023) # Depends on removed dev-python/pydotplus -sci-libs/nipype dev-python/heudiconv sci-biology/samri
[gentoo-commits] proj/sci:master commit in: profiles/
commit: f9d3a76bb758353dcb4eefd37bd8159c5b369eb7 Author: Horea Christian chymera eu> AuthorDate: Mon Jan 22 14:40:35 2024 + Commit: Horea Christian gmail com> CommitDate: Mon Jan 22 14:40:35 2024 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9d3a76b profiles: samri package no longer affected by deprecated dependency Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 56bf41059..60e453d16 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -44,7 +44,6 @@ dev-python/umap-learn # Andrew Ammerlaan (16 Dec 2023) # Depends on removed dev-python/pydotplus dev-python/heudiconv -sci-biology/samri # Andrew Ammerlaan (26 Jun 2023) # Depends on removed dev-python/toml.
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 88304a8f232c2d6576e174655b05bfa66d605621 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Dec 29 10:05:25 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Dec 29 10:05:25 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=88304a8f profiles: mask reverse deps of numba Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 4 1 file changed, 4 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 1bcec67dc..78a8b2480 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -36,6 +36,10 @@ dev-python/llvmlite dev-python/numba dev-python/numba-dpex +dev-python/pynndescent +# Reverse dep of numba +dev-python/tridesclous +dev-python/umap-learn # Andrew Ammerlaan (16 Dec 2023) # Depends on removed dev-python/pydotplus
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 4495bb4fb18a789d54ccacea7f9bf1973f846ef8 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Dec 29 09:54:40 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Dec 29 09:54:40 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4495bb4f profiles: mask llvmlite Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 7 +++ 1 file changed, 7 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index b51a8ddcc..1bcec67dc 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,13 @@ #--- END OF EXAMPLES --- +# Andrew Ammerlaan (29 Dec 2023) +# Depends on removed llvm:14, at the time of writing no llvm:15 +# update available. +dev-python/llvmlite +dev-python/numba +dev-python/numba-dpex + # Andrew Ammerlaan (16 Dec 2023) # Depends on removed dev-python/pydotplus sci-libs/nipype
[gentoo-commits] proj/sci:master commit in: profiles/
commit: c79afc63534d2ba48f22fb857c4139d10d400fab Author: Andrew Ammerlaan gentoo org> AuthorDate: Mon Dec 18 15:33:12 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Mon Dec 18 15:33:12 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c79afc63 profiles: mask sci-libs/nipype Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 6 ++ 1 file changed, 6 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 9f3b8e7f5..b51a8ddcc 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,12 @@ #--- END OF EXAMPLES --- +# Andrew Ammerlaan (16 Dec 2023) +# Depends on removed dev-python/pydotplus +sci-libs/nipype +dev-python/heudiconv +sci-biology/samri + # Andrew Ammerlaan (26 Jun 2023) # Depends on removed dev-python/toml. # Alternatives are tomli or tomlkit
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 6912b6bbc31088b709dbcfb775b60b5ef419a8a5 Author: Horea Christian chymera eu> AuthorDate: Fri Dec 1 15:04:29 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Dec 1 15:04:29 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6912b6bb profiles: nptyping reinstated Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 5 - 1 file changed, 5 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 3aac93f31..9f3b8e7f5 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,11 +30,6 @@ #--- END OF EXAMPLES --- -# Andrew Ammerlaan (24 Oct 2023) -# Depends on removed dev-python/nptyping -dev-python/pynrrd -dev-python/typish - # Andrew Ammerlaan (26 Jun 2023) # Depends on removed dev-python/toml. # Alternatives are tomli or tomlkit
[gentoo-commits] proj/sci:master commit in: profiles/desc/, profiles/, sci-physics/lhapdf-sets/
commit: 2e22079da1c948701180f3665c5a5730f55f18f5
Author: Alexander Puck Neuwirth neuwirth-informatik
de>
AuthorDate: Mon Oct 23 18:37:10 2023 +
Commit: Alexander Puck Neuwirth neuwirth-informatik
de>
CommitDate: Sat Oct 28 10:03:49 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e22079d
sci-physics/lhapdf-sets: new package, add 0
Closes: https://github.com/gentoo/sci/pull/1219
Signed-off-by: Alexander Puck Neuwirth neuwirth-informatik.de>
profiles/desc/lhapdf_sets.desc | 17 +++
profiles/make.defaults | 1 +
sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild | 66
sci-physics/lhapdf-sets/metadata.xml | 12 +
4 files changed, 96 insertions(+)
diff --git a/profiles/desc/lhapdf_sets.desc b/profiles/desc/lhapdf_sets.desc
new file mode 100644
index 0..7270fbee7
--- /dev/null
+++ b/profiles/desc/lhapdf_sets.desc
@@ -0,0 +1,17 @@
+# Copyright 2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+# This file contains descriptions of LHAPDF_SETS USE_EXPAND flags.
+
+nnpdf31_nnlo_as_0118_luxqed - NNPDF31_nnlo_as_0118_luxqed LHAPDF grid
+pdf4lhc15_nlo_asvar - PDF4LHC15_nlo_asvar LHAPDF grid
+ct14qed_proton - CT14qed_proton LHAPDF grid
+ct14lo - CT14lo LHAPDF grid
+ct14nlo - CT14nlo LHAPDF grid
+ct10 - CT10 LHAPDF grid
+mrst2007lomod - MRST2007lomod LHAPDF grid
+nnpdf23_nlo_as_0119_qed_mc - NNPDF23_nlo_as_0119_qed_mc LHAPDF grid
+nnpdf23_nnlo_as_0119_qed_mc - NNPDF23_nnlo_as_0119_qed_mc LHAPDF grid
+cteq66 - CTEQ66 LHAPDF grid
+cteq6l1 - CTEQ6L1 LHAPDF grid
+mrst2004qed - MRST2004qed LHAPDF grid
\ No newline at end of file
diff --git a/profiles/make.defaults b/profiles/make.defaults
new file mode 100644
index 0..88d3fe603
--- /dev/null
+++ b/profiles/make.defaults
@@ -0,0 +1 @@
+USE_EXPAND="LHAPDF_SETS"
\ No newline at end of file
diff --git a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
new file mode 100644
index 0..edd3639d2
--- /dev/null
+++ b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+LHA_VER="6.2.1"
+
+IUSE_LHAPDF_SETS="
+ lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed
+ lhapdf_sets_pdf4lhc15_nlo_asvar
+ lhapdf_sets_ct14qed_proton
+ lhapdf_sets_ct14lo
+ lhapdf_sets_ct14nlo
+ lhapdf_sets_ct10
+ lhapdf_sets_mrst2007lomod
+ lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc
+ lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc
+ lhapdf_sets_cteq66
+ lhapdf_sets_cteq6l1
+ lhapdf_sets_mrst2004qed
+"
+
+COMMON_URI="https://lhapdfsets.web.cern.ch/lhapdfsets/current;
+HEPFORGE_URI="https://www.hepforge.org/downloads/lhapdf/pdfsets/v6.backup/${LHA_VER};
+# Alternatively to fetching them here already the user can install them by
lhapdf install,
+# BUT some codes need them during test and even compile (Herwig) stage.
+# Also since it belongs to LHAPDF it is better to fetch them here.
+SRC_URI="
+ lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed? (
${COMMON_URI}/NNPDF31_nnlo_as_0118_luxqed.tar.gz )
+ lhapdf_sets_pdf4lhc15_nlo_asvar? (
${COMMON_URI}/PDF4LHC15_nlo_asvar.tar.gz )
+ lhapdf_sets_ct14qed_proton? (
${COMMON_URI}/CT14qed_proton.tar.gz )
+ lhapdf_sets_ct14lo? ( ${COMMON_URI}/CT14lo.tar.gz
)
+ lhapdf_sets_ct14nlo? ( ${COMMON_URI}/CT14nlo.tar.gz
)
+ lhapdf_sets_ct10?( ${COMMON_URI}/CT10.tar.gz
)
+ lhapdf_sets_mrst2007lomod? (
${COMMON_URI}/MRST2007lomod.tar.gz )
+ lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc? (
${COMMON_URI}/NNPDF23_nlo_as_0119_qed_mc.tar.gz )
+ lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc? (
${COMMON_URI}/NNPDF23_nnlo_as_0119_qed_mc.tar.gz )
+ lhapdf_sets_cteq66? ( ${COMMON_URI}/cteq66.tar.gz
)
+ lhapdf_sets_cteq6l1? ( ${COMMON_URI}/cteq6l1.tar.gz
)
+ lhapdf_sets_mrst2004qed? (
${HEPFORGE_URI}/MRST2004qed.tar.gz )
+"
+
+MY_PV=$(ver_cut 1-3)
+MY_PF=LHAPDF-${MY_PV}
+
+DESCRIPTION="LHAPDF data grids"
+HOMEPAGE="https://lhapdf.hepforge.org/;
+KEYWORDS="~amd64 ~x86"
+S="${WORKDIR}"
+
+LICENSE="public-domain"
+SLOT="0"
+IUSE="${IUSE_LHAPDF_SETS}"
+SLOT="0"
+RDEPEND="sci-physics/lhapdf"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+ # unpack in destination only to avoid copy
+ return
+}
+
+src_install() {
+ dodir /usr/share/LHAPDF/
+ cd "${ED}/usr/share/LHAPDF/" || die
+ unpack ${A}
+}
diff --git a/sci-physics/lhapdf-sets/metadata.xml
b/sci-physics/lhapdf-sets/metadata.xml
new file mode 100644
index
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 1d7cb19d427b664d94b8c8db416b9820a8242090 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Oct 24 07:52:45 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Oct 24 07:52:45 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d7cb19d profiles: mask nptyping revdeps Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 5 + 1 file changed, 5 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 9f3b8e7f5..3aac93f31 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,11 @@ #--- END OF EXAMPLES --- +# Andrew Ammerlaan (24 Oct 2023) +# Depends on removed dev-python/nptyping +dev-python/pynrrd +dev-python/typish + # Andrew Ammerlaan (26 Jun 2023) # Depends on removed dev-python/toml. # Alternatives are tomli or tomlkit
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 8a77f2837b8cc397a0703983e7d6ea7f22305c47 Author: Andrew Ammerlaan gentoo org> AuthorDate: Mon Jun 26 17:54:19 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Mon Jun 26 17:54:19 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a77f283 profiles: mask dev-python/cadquery* Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 7 +++ 1 file changed, 7 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..9f3b8e7f5 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,10 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (26 Jun 2023) +# Depends on removed dev-python/toml. +# Alternatives are tomli or tomlkit +dev-python/cadquery +dev-python/cadquery-ocp +dev-python/cadquery-pywrap
[gentoo-commits] proj/sci:master commit in: profiles/
commit: f63436394c638f7c5f002a692b7e45ebc949521a Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue May 2 12:35:12 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue May 2 12:35:12 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f6343639 profiles: cleanup old entries Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.use.mask | 4 1 file changed, 4 deletions(-) diff --git a/profiles/package.use.mask b/profiles/package.use.mask index 79c0fcb5c..39a6df0b7 100644 --- a/profiles/package.use.mask +++ b/profiles/package.use.mask @@ -18,7 +18,3 @@ # Andrew Ammerlaan (23 Aug 2022) # vtk<9 no longer available in ::gentoo sci-libs/gdcm python - -# Christoph Junghans (05 Nov 2013) -# gui sandbox error -dev-lang/conceptual gui
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/trans-abyss/
commit: eb11c042a4a47b6b4ba249ab1e41e4117e51e21d
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Apr 25 11:30:38 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Apr 25 11:30:38 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=eb11c042
sci-biology/trans-abyss: treeclean
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask| 1 -
sci-biology/trans-abyss/metadata.xml | 15 --
sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild | 35
3 files changed, 51 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index a8da49349..20d20abc8 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -33,4 +33,3 @@
# Andrew Ammerlaan
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- bcgsc/transabyss
-
-
diff --git a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild
b/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild
deleted file mode 100644
index cf10dd3b9..0
--- a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit python-r1
-
-DESCRIPTION="Analyze and combine multiple assemblies from abyss"
-HOMEPAGE="https://www.bcgsc.ca/resources/software/trans-abyss;
-SRC_URI="https://github.com/bcgsc/transabyss/archive/${PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
- dev-lang/perl
- dev-python/python-igraph[${PYTHON_USEDEP}]
- sci-biology/abyss
- sci-biology/blat
-"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/transabyss-${PV}"
-
-src_install() {
- einstalldocs
- python_foreach_impl python_domodule utilities
- dobin transabyss
- dobin transabyss-merge
-}
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/chiron/
commit: 797241ba80bff8d62325714f8770582a11484d87
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Apr 25 11:31:16 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Apr 25 11:31:16 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=797241ba
sci-biology/chiron: treeclean
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask| 4
sci-biology/chiron/chiron-0.6.1.1.ebuild | 29 -
sci-biology/chiron/metadata.xml | 12
3 files changed, 45 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 20d20abc8..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,7 +29,3 @@
## app-misc/some-package
#--- END OF EXAMPLES ---
-
-# Andrew Ammerlaan https://github.com/haotianteng/chiron
- https://www.biorxiv.org/content/early/2017/09/12/179531;
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MPL-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- dev-python/h5py[${PYTHON_USEDEP}]
- sci-biology/mappy[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- sci-biology/biopython[${PYTHON_USEDEP}]
- dev-python/packaging[${PYTHON_USEDEP}]
- sci-libs/tensorflow[${PYTHON_USEDEP}]
-"
diff --git a/sci-biology/chiron/metadata.xml b/sci-biology/chiron/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/chiron/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
[gentoo-commits] proj/sci:master commit in: profiles/, sci-chemistry/ligplot+/
commit: 99bb0d558f8f42fd8a39f3341213e379eabf7a79
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Apr 25 11:26:36 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Apr 25 11:26:36 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=99bb0d55
sci-chemistry/ligplot+: treeclean
Bug: https://bugs.gentoo.org/902383
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 1 -
sci-chemistry/ligplot+/ligplot+-1.4.ebuild | 42 --
sci-chemistry/ligplot+/metadata.xml| 8 --
3 files changed, 51 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 15acd8546..0600eed4c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -41,6 +41,5 @@ sci-biology/RSeQC
# Andrew Ammerlaan https://www.ebi.ac.uk/thornton-srv/software/LigPlus/;
-SRC_URI="LigPlus.zip"
-
-SLOT="0"
-LICENSE="ligplot+"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="virtual/jre:*"
-DEPEND="app-arch/unzip"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/LigPlus"
-
-QA_PREBUILT="opt/${PN}/.*"
-
-pkg_nofetch() {
- elog "Please visit"
- elog
"http://www.ebi.ac.uk/thornton-srv/software/LigPlus/applicence.html;
- elog "download ${A}"
- elog "and save into your DISTDIR folder"
-}
-
-src_prepare() {
- default
- rm -rf lib/*{win,mac} || die
-}
-
-src_install() {
- insinto /opt/${PN}
- doins -r lib LigPlus.jar
-
- make_wrapper ${PN} "java -jar \"${EPREFIX}/opt/${PN}/LigPlus.jar\""
-}
diff --git a/sci-chemistry/ligplot+/metadata.xml
b/sci-chemistry/ligplot+/metadata.xml
deleted file mode 100644
index da36ecbfc..0
--- a/sci-chemistry/ligplot+/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- sci-chemis...@gentoo.org
- Gentoo Chemistry Project
-
-
[gentoo-commits] proj/sci:master commit in: profiles/, dev-lang/pgi/files/, dev-lang/pgi/
commit: a60ef457ab7c7039a22d9dd04268748bd5e35c8f Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Apr 25 11:24:28 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Apr 25 11:24:28 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a60ef457 dev-lang/pgi: treeclean Bug: https://bugs.gentoo.org/902383 Signed-off-by: Andrew Ammerlaan gentoo.org> dev-lang/pgi/files/pgi-13.5-glibc.patch| 31 - dev-lang/pgi/files/pgi-13.5-terminal.patch | 39 --- dev-lang/pgi/metadata.xml | 15 - dev-lang/pgi/pgi-13.5.ebuild | 105 - profiles/package.mask | 1 - 5 files changed, 191 deletions(-) diff --git a/dev-lang/pgi/files/pgi-13.5-glibc.patch b/dev-lang/pgi/files/pgi-13.5-glibc.patch deleted file mode 100644 index 434f12cb5..0 --- a/dev-lang/pgi/files/pgi-13.5-glibc.patch +++ /dev/null @@ -1,31 +0,0 @@ -diff -ru opt/pgi/linux86/13.5/include/bits/types.h opt/pgi-b/linux86/13.5/include/bits/types.h opt/pgi/linux86/13.5/include/bits/types.h 2013-05-07 21:45:39.0 +0200 -+++ opt/pgi-b/linux86/13.5/include/bits/types.h2013-06-02 01:24:19.0 +0200 -@@ -136,6 +136,7 @@ - #include/* Defines __*_T_TYPE macros. */ - - -+__STD_TYPE __SQUAD_TYPE __syscall_slong_t; - __STD_TYPE __DEV_T_TYPE __dev_t; /* Type of device numbers. */ - __STD_TYPE __UID_T_TYPE __uid_t; /* Type of user identifications. */ - __STD_TYPE __GID_T_TYPE __gid_t; /* Type of group identifications. */ -diff -ru opt/pgi/linux86-64/13.5/include/bits/types.h opt/pgi-b/linux86-64/13.5/include/bits/types.h opt/pgi/linux86-64/13.5/include/bits/types.h 2013-05-07 21:45:39.0 +0200 -+++ opt/pgi-b/linux86-64/13.5/include/bits/types.h 2013-06-02 01:23:51.0 +0200 -@@ -135,7 +135,7 @@ - #endif - #include/* Defines __*_T_TYPE macros. */ - -- -+__STD_TYPE __SQUAD_TYPE __syscall_slong_t; - __STD_TYPE __DEV_T_TYPE __dev_t; /* Type of device numbers. */ - __STD_TYPE __UID_T_TYPE __uid_t; /* Type of user identifications. */ - __STD_TYPE __GID_T_TYPE __gid_t; /* Type of group identifications. */ -@@ -156,7 +156,6 @@ - __STD_TYPE __SUSECONDS_T_TYPE __suseconds_t; /* Signed count of microseconds. */ - - __STD_TYPE __DADDR_T_TYPE __daddr_t; /* The type of a disk address. */ --__STD_TYPE __SWBLK_T_TYPE __swblk_t; /* Type of a swap block maybe? */ - __STD_TYPE __KEY_T_TYPE __key_t; /* Type of an IPC key. */ - - /* Clock ID used in clock and timer functions. */ diff --git a/dev-lang/pgi/files/pgi-13.5-terminal.patch b/dev-lang/pgi/files/pgi-13.5-terminal.patch deleted file mode 100644 index 9b5b67474..0 --- a/dev-lang/pgi/files/pgi-13.5-terminal.patch +++ /dev/null @@ -1,39 +0,0 @@ -diff -ru pgi-a/install pgi/install pgi-a/install 2013-06-01 01:24:11.522714654 +0200 -+++ pgi/install2013-06-01 01:27:36.372713265 +0200 -@@ -83,7 +83,7 @@ - else - licensefile=$SRC/common/BETA_LICENSE - fi --more $licensefile -+#more $licensefile - echo - echo -n 'Do you accept these terms? (accept,decline) ' - read x -@@ -296,7 +296,7 @@ - echo - echo 'In order to install the ACML software, please read and accept the' - echo 'following license.' -- more $SRC/common/LICENSE_ACML.txt -+ #more $SRC/common/LICENSE_ACML.txt - echo - echo -n 'Do you accept these terms? (accept,decline) ' - read x -@@ -342,7 +342,7 @@ - echo - echo 'In order to install the CUDA software, please read and accept the' - echo 'following license.' -- more $SRC/common/LICENSE_NVIDIA_CUDA.txt -+ #more $SRC/common/LICENSE_NVIDIA_CUDA.txt - echo - echo -n 'Do you accept these terms? (accept,decline) ' - read x -@@ -398,7 +398,7 @@ - echo - echo 'In order to install the JAVA software, please read and accept the' - echo 'following license.' -- more $SRC/common/LICENSE_JRE_6U21.txt -+ #more $SRC/common/LICENSE_JRE_6U21.txt - echo - echo -n 'Do you accept these terms? (accept,decline) ' - read x diff --git a/dev-lang/pgi/metadata.xml b/dev-lang/pgi/metadata.xml deleted file mode 100644 index b9e493f21..0 --- a/dev-lang/pgi/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ - -http://www.gentoo.org/dtd/metadata.dtd;> - - - gent...@gmx.de - - - clus...@gentoo.org - Gentoo Cluster Project - - - Install a PGI-tuned JRE. - Install PGI's CUDA components (e.g. for OpenACC) - - diff --git a/dev-lang/pgi/pgi-13.5.ebuild b/dev-lang/pgi/pgi-13.5.ebuild deleted file mode 100644 index 19ec7445b..0 --- a/dev-lang/pgi/pgi-13.5.ebuild +++ /dev/null @@ -1,105 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="PGI compiler suite" -HOMEPAGE="https://www.pgroup.com;
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/signalp/
commit: df1b752e2d45731e3ed75840ec6b2e04e314bd64
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Apr 25 11:25:25 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Apr 25 11:25:25 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=df1b752e
sci-biology/signalp: treeclean
Bug: https://bugs.gentoo.org/902383
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 1 -
sci-biology/signalp/metadata.xml | 8 --
sci-biology/signalp/signalp-3.0.ebuild | 46 --
3 files changed, 55 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index ba856cb7f..51da8d80c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -41,7 +41,6 @@ sci-biology/RSeQC
# Andrew Ammerlaan
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
diff --git a/sci-biology/signalp/signalp-3.0.ebuild
b/sci-biology/signalp/signalp-3.0.ebuild
deleted file mode 100644
index dcd83d920..0
--- a/sci-biology/signalp/signalp-3.0.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Prediction of signal peptide cleavage sites in amino acid
sequences"
-HOMEPAGE="http://www.cbs.dtu.dk/services/SignalP/;
-SRC_URI="${P}.Linux.tar.Z"
-
-LICENSE="signalp"
-SLOT="0"
-IUSE="gnuplot"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND="gnuplot? (
- sci-visualization/gnuplot
- media-libs/netpbm )"
-
-RESTRICT="fetch strip"
-
-pkg_nofetch() {
- einfo "Please visit ${HOMEPAGE} and obtain the file"
- einfo "\"${SRC_URI}\", then place it into your DISTDIR folder"
-}
-
-src_prepare() {
- default
- sed -i -e '/SIGNALP=/ s/\/usr//' \
- -e '/TMPDIR=/ s/$SIGNALP//' "${S}/signalp" || die
- sed -i 's/nawk/gawk/' "${S}"/bin/* || die
-}
-
-src_install() {
- dobin signalp
- insinto /opt/${P}
- doins -r bin hmm how mod syn* test
- exeinto /opt/${P}/bin
- doexe bin/*
- exeinto /opt/${P}/hmm
- doexe hmm/*
- exeinto /opt/${P}/how
- doexe how/*
- doman signalp.1
- dodoc *readme
-}
[gentoo-commits] proj/sci:master commit in: profiles/
commit: ce13899e857dfed9f0f50a32819ae487ce659887 Author: Horea Christian chymera eu> AuthorDate: Wed Mar 29 05:04:36 2023 + Commit: Horea Christian gmail com> CommitDate: Wed Mar 29 05:04:36 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ce13899e profiles: providing full dependency stack Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 7 --- 1 file changed, 7 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index d6599c66f..80bd60014 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,13 +30,6 @@ #--- END OF EXAMPLES --- -# Andrew Ammerlaan (17 Mar 2023) -# Needs bump to support vtk-9.2 (vtk-9.1 removed). This likely -# requires bumping the version which would also require bumping -# sci-libs/itk -# revdep of above -sci-biology/samri - # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 1eafc176027de6359599c9d1e54bd0374891b7b0 Author: Horea Christian chymera eu> AuthorDate: Wed Mar 29 04:05:56 2023 + Commit: Horea Christian gmail com> CommitDate: Wed Mar 29 04:08:02 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1eafc176 profiles: providing required dependencies Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 147869ad2..d6599c66f 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -34,7 +34,6 @@ # Needs bump to support vtk-9.2 (vtk-9.1 removed). This likely # requires bumping the version which would also require bumping # sci-libs/itk -sci-biology/ants # revdep of above sci-biology/samri
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 10c79dc12eeb0e5052f7de8608bd34a78ab09f43 Author: Horea Christian chymera eu> AuthorDate: Sat Mar 25 05:16:45 2023 + Commit: Horea Christian gmail com> CommitDate: Sat Mar 25 05:16:45 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=10c79dc1 profiles: package issues resolved Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 2 -- 1 file changed, 2 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 4c649adb9..147869ad2 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -40,13 +40,11 @@ sci-biology/samri # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: d14ba1e4c57bcd0b12488eed12d82facb664c0bc Author: Horea Christian chymera eu> AuthorDate: Sat Mar 25 04:45:37 2023 + Commit: Horea Christian gmail com> CommitDate: Sat Mar 25 04:45:37 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d14ba1e4 profiles: packages issues addressed Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 37e5273d0..4c649adb9 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -46,7 +46,6 @@ sci-biology/trans-abyss # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: da33e05fe0b36a64bc5b8524b65d6978135de844 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Mar 17 14:06:32 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Mar 17 14:06:32 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=da33e05f profiles: also maks sci-biology/samri Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 2 ++ 1 file changed, 2 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index f95f8e28c..37e5273d0 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -35,6 +35,8 @@ # requires bumping the version which would also require bumping # sci-libs/itk sci-biology/ants +# revdep of above +sci-biology/samri # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 0a40e11ac4f93df6cc97e53b24706c34863a04f9 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Mar 17 14:02:57 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Mar 17 14:02:57 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a40e11a profiles: mask sci-biology/ants Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 6 ++ 1 file changed, 6 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 188bab233..f95f8e28c 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,12 @@ #--- END OF EXAMPLES --- +# Andrew Ammerlaan (17 Mar 2023) +# Needs bump to support vtk-9.2 (vtk-9.1 removed). This likely +# requires bumping the version which would also require bumping +# sci-libs/itk +sci-biology/ants + # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: ead757b56b3a7e38e95251371cb4206eace80626 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Feb 10 13:35:52 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Feb 10 13:35:52 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ead757b5 profiles: mask packages with missing checksums Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 9 + 1 file changed, 9 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 25e3558f8..188bab233 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -41,3 +41,12 @@ sci-biology/trans-abyss sci-biology/pyfaidx sci-biology/gffutils sci-biology/RSeQC + +# Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: dc733d93060b7b01c10867bbc02c4208d7d79ff0 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Feb 10 13:29:32 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Feb 10 13:29:32 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc733d93 profiles: mask sci-biology/trans-abyss Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 1 + 1 file changed, 1 insertion(+) diff --git a/profiles/package.mask b/profiles/package.mask index 0596e0782..25e3558f8 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -34,6 +34,7 @@ # Needs bump of PYTHON_COMPAT to at least python3_10 sci-biology/gffutils sci-biology/chiron +sci-biology/trans-abyss # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/transforms3d/
commit: 4d9bff206d659f20fd22107b818fb424fe8f6fb8
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Feb 10 13:26:42 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Feb 10 13:26:42 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d9bff20
dev-python/transforms3d: add 0.4.1, remove 0.3.1
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/transforms3d/transforms3d-0.3.1.ebuild | 23 ---
dev-python/transforms3d/transforms3d-0.4.1.ebuild | 22 ++
profiles/package.mask | 1 -
3 files changed, 22 insertions(+), 24 deletions(-)
diff --git a/dev-python/transforms3d/transforms3d-0.3.1.ebuild
b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
deleted file mode 100644
index fe3dedf84..0
--- a/dev-python/transforms3d/transforms3d-0.3.1.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_10 )
-DISTUTILS_USE_SETUPTOOLS=no
-
-inherit distutils-r1
-
-DESCRIPTION="Functions for 3D coordinate transformations"
-HOMEPAGE="https://matthew-brett.github.io/transforms3d;
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="BSD-2"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-BDEPEND="test? ( dev-python/numpy[${PYTHON_USEDEP}] )"
-RDEPEND=">=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests nose
diff --git a/dev-python/transforms3d/transforms3d-0.4.1.ebuild
b/dev-python/transforms3d/transforms3d-0.4.1.ebuild
new file mode 100644
index 0..661d78acb
--- /dev/null
+++ b/dev-python/transforms3d/transforms3d-0.4.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Functions for 3D coordinate transformations"
+HOMEPAGE="https://matthew-brett.github.io/transforms3d/;
+
+LICENSE="BSD-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+RDEPEND="
+ >=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
diff --git a/profiles/package.mask b/profiles/package.mask
index dd619ffdf..0596e0782 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -40,4 +40,3 @@ sci-biology/chiron
sci-biology/pyfaidx
sci-biology/gffutils
sci-biology/RSeQC
-dev-python/transforms3d
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/ripser/
commit: d34f7e8b0d5d5f65c7fb41b707bb25d01d434c93
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Feb 10 13:19:01 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Feb 10 13:19:21 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d34f7e8b
dev-python/ripser: add 0.6.4, drop 0.6.0
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/ripser/metadata.xml| 3 +++
.../ripser/{ripser-0.6.0.ebuild => ripser-0.6.4.ebuild} | 11 +--
profiles/package.mask | 2 --
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/dev-python/ripser/metadata.xml b/dev-python/ripser/metadata.xml
index 2f2c0b51c..f983c3d4c 100644
--- a/dev-python/ripser/metadata.xml
+++ b/dev-python/ripser/metadata.xml
@@ -9,4 +9,7 @@
s...@gentoo.org
Gentoo Science Project
+
+ripser
+
diff --git a/dev-python/ripser/ripser-0.6.0.ebuild
b/dev-python/ripser/ripser-0.6.4.ebuild
similarity index 76%
rename from dev-python/ripser/ripser-0.6.0.ebuild
rename to dev-python/ripser/ripser-0.6.4.ebuild
index 5317a7208..e0ea6f24b 100644
--- a/dev-python/ripser/ripser-0.6.0.ebuild
+++ b/dev-python/ripser/ripser-0.6.4.ebuild
@@ -1,22 +1,21 @@
# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="python frontend for the fast ripser tda tool"
HOMEPAGE="https://ripser.scikit-tda.org/;
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-RDEPEND="${PYTHON_DEPS}
+RDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/persim[${PYTHON_USEDEP}]
diff --git a/profiles/package.mask b/profiles/package.mask
index 95899c9f4..fc1374a30 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,8 +34,6 @@
# Needs bump of PYTHON_COMPAT to at least python3_10
sci-biology/gffutils
sci-biology/chiron
-# Reverse deps of above
-dev-python/ripser
# Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/kmapper/
commit: 1c4359fa901dcaa31ad4836366d12c05d3186658
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Feb 10 13:09:28 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Feb 10 13:09:28 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c4359fa
dev-python/kmapper: enable py3.11, pep517
Signed-off-by: Andrew Ammerlaan gentoo.org>
.../kmapper/{kmapper-2.0.1.ebuild => kmapper-2.0.1-r1.ebuild} | 7 ---
dev-python/kmapper/metadata.xml| 1 +
profiles/package.mask | 1 -
3 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/dev-python/kmapper/kmapper-2.0.1.ebuild
b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
similarity index 89%
rename from dev-python/kmapper/kmapper-2.0.1.ebuild
rename to dev-python/kmapper/kmapper-2.0.1-r1.ebuild
index 2099fa4db..c8bdf2b00 100644
--- a/dev-python/kmapper/kmapper-2.0.1.ebuild
+++ b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild
@@ -1,15 +1,16 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1
DESCRIPTION="Python implementation of Mapper algorithm for Topological Data
Analysis"
HOMEPAGE="https://kepler-mapper.scikit-tda.org;
-SRC_URI="https://github.com/scikit-tda/kepler-mapper/archive/refs/tags/v${PV}.tar.gz
-> ${P}.tar.gz"
+SRC_URI="https://github.com/scikit-tda/kepler-mapper/archive/refs/tags/v${PV}.tar.gz
-> ${P}.gh.tar.gz"
S="${WORKDIR}"/kepler-mapper-${PV}
LICENSE="MIT"
diff --git a/dev-python/kmapper/metadata.xml b/dev-python/kmapper/metadata.xml
index 006b418f5..4dee7702f 100644
--- a/dev-python/kmapper/metadata.xml
+++ b/dev-python/kmapper/metadata.xml
@@ -11,5 +11,6 @@
scikit-tda/kepler-mapper
+ kmapper
diff --git a/profiles/package.mask b/profiles/package.mask
index 2ce61c946..95899c9f4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -34,7 +34,6 @@
# Needs bump of PYTHON_COMPAT to at least python3_10
sci-biology/gffutils
sci-biology/chiron
-dev-python/kmapper
# Reverse deps of above
dev-python/ripser
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/gammapy/
commit: 0edcd19bed0b8c849894282bd0de04813d20c8a4
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Feb 10 12:03:30 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Feb 10 12:03:30 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0edcd19b
dev-python/gammapy: add 1.0, drop 0.18.2
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/gammapy/{gammapy-0.18.2.ebuild => gammapy-1.0.ebuild} | 9 -
dev-python/gammapy/metadata.xml | 1 +
profiles/package.mask| 1 -
3 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/dev-python/gammapy/gammapy-0.18.2.ebuild
b/dev-python/gammapy/gammapy-1.0.ebuild
similarity index 90%
rename from dev-python/gammapy/gammapy-0.18.2.ebuild
rename to dev-python/gammapy/gammapy-1.0.ebuild
index c26732aed..ab50e7a85 100644
--- a/dev-python/gammapy/gammapy-0.18.2.ebuild
+++ b/dev-python/gammapy/gammapy-1.0.ebuild
@@ -1,16 +1,15 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1 optfeature
+inherit distutils-r1 pypi optfeature
DESCRIPTION="A Python package for gamma-ray astronomy"
HOMEPAGE="https://github.com/gammapy/gammapy;
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/gammapy/metadata.xml b/dev-python/gammapy/metadata.xml
index a9f88e7d8..f4a01e639 100644
--- a/dev-python/gammapy/metadata.xml
+++ b/dev-python/gammapy/metadata.xml
@@ -12,5 +12,6 @@ H.E.S.S, and CTA in primarily Galactic plane survey studies.
gammapy/gammapy
+ gammapy
diff --git a/profiles/package.mask b/profiles/package.mask
index dd4b0d343..f2d821d2b 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -36,7 +36,6 @@ sci-biology/gffutils
sci-biology/chiron
dev-python/snakemake
dev-python/specutils
-dev-python/regions
dev-python/kmapper
# Reverse deps of above
dev-python/ripser
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/regions/
commit: bb240eb9f8928308cf654e5ae12d46fbe524cb57
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Feb 10 12:02:16 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Feb 10 12:02:16 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bb240eb9
dev-python/regions: add 0.7, drop 0.4
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/regions/metadata.xml | 1 +
dev-python/regions/{regions-0.4.ebuild => regions-0.7.ebuild} | 9 -
profiles/package.mask | 1 -
3 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/dev-python/regions/metadata.xml b/dev-python/regions/metadata.xml
index a9f88e7d8..b0d9fd489 100644
--- a/dev-python/regions/metadata.xml
+++ b/dev-python/regions/metadata.xml
@@ -12,5 +12,6 @@ H.E.S.S, and CTA in primarily Galactic plane survey studies.
gammapy/gammapy
+ regions
diff --git a/dev-python/regions/regions-0.4.ebuild
b/dev-python/regions/regions-0.7.ebuild
similarity index 82%
rename from dev-python/regions/regions-0.4.ebuild
rename to dev-python/regions/regions-0.7.ebuild
index eccec0eda..ef412a153 100644
--- a/dev-python/regions/regions-0.4.ebuild
+++ b/dev-python/regions/regions-0.7.ebuild
@@ -1,16 +1,15 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="Astropy affilated package for region handling"
HOMEPAGE="https://github.com/astropy/regions;
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
diff --git a/profiles/package.mask b/profiles/package.mask
index 9b2d80619..dd4b0d343 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,7 +38,6 @@ dev-python/snakemake
dev-python/specutils
dev-python/regions
dev-python/kmapper
-dev-python/gammapy
# Reverse deps of above
dev-python/ripser
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/astroquery/
commit: 5753bff49179a4659a4e0644087cfaba5d7c421f
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Feb 10 11:42:04 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Feb 10 11:42:04 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5753bff4
dev-python/astroquery: add 0.4.6, drop 0.4.1
Signed-off-by: Andrew Ammerlaan gentoo.org>
.../{astroquery-0.4.1.ebuild => astroquery-0.4.6.ebuild} | 10 +-
dev-python/astroquery/metadata.xml | 1 +
profiles/package.mask | 2 --
3 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/dev-python/astroquery/astroquery-0.4.1.ebuild
b/dev-python/astroquery/astroquery-0.4.6.ebuild
similarity index 86%
rename from dev-python/astroquery/astroquery-0.4.1.ebuild
rename to dev-python/astroquery/astroquery-0.4.6.ebuild
index a7884eb1d..3e140280c 100644
--- a/dev-python/astroquery/astroquery-0.4.1.ebuild
+++ b/dev-python/astroquery/astroquery-0.4.6.ebuild
@@ -1,15 +1,15 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
-inherit distutils-r1
+inherit distutils-r1 pypi
DESCRIPTION="A collection of packages to access online astronomical resources"
-HOMEPAGE="https://www.astropy.org/astroquery/;
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+HOMEPAGE="https://astroquery.readthedocs.io/;
LICENSE="BSD"
SLOT="0"
diff --git a/dev-python/astroquery/metadata.xml
b/dev-python/astroquery/metadata.xml
index bb6a20b51..b70564de2 100644
--- a/dev-python/astroquery/metadata.xml
+++ b/dev-python/astroquery/metadata.xml
@@ -12,5 +12,6 @@ to support many services with a uniform API.
astropy/astroquery
+ astroquery
diff --git a/profiles/package.mask b/profiles/package.mask
index 7f28675b3..9b2d80619 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -38,9 +38,7 @@ dev-python/snakemake
dev-python/specutils
dev-python/regions
dev-python/kmapper
-dev-python/photutils
dev-python/gammapy
-dev-python/astroquery
# Reverse deps of above
dev-python/ripser
[gentoo-commits] proj/sci:master commit in: profiles/, dev-python/pyzo/
commit: 81c03a41d2f096a2f5c9b5dcd3f1ed01e4799bbb
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Feb 10 11:05:40 2023 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Feb 10 11:05:51 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=81c03a41
dev-python/pyzo: add 4.12.7, drop 4.11.2
Signed-off-by: Andrew Ammerlaan gentoo.org>
dev-python/pyzo/{pyzo-4.11.2.ebuild => pyzo-4.12.7.ebuild} | 11 +++
profiles/package.mask | 1 -
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/dev-python/pyzo/pyzo-4.11.2.ebuild
b/dev-python/pyzo/pyzo-4.12.7.ebuild
similarity index 87%
rename from dev-python/pyzo/pyzo-4.11.2.ebuild
rename to dev-python/pyzo/pyzo-4.12.7.ebuild
index 772793be5..f65ebcc7d 100644
--- a/dev-python/pyzo/pyzo-4.11.2.ebuild
+++ b/dev-python/pyzo/pyzo-4.12.7.ebuild
@@ -3,13 +3,14 @@
EAPI=8
-PYTHON_COMPAT=( python3_{8..9} )
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 virtualx desktop xdg
DESCRIPTION="The Python IDE for scientific computing"
HOMEPAGE="https://pyzo.org/;
-SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/v${PV}.tar.gz ->
${P}.tar.gz"
+SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/v${PV}.tar.gz ->
${P}.gh.tar.gz"
LICENSE="BSD-2"
SLOT="0"
@@ -17,12 +18,14 @@ KEYWORDS="~amd64"
# For some reason this requires network access
# Qt: Session management error: Could not open network socket
+PROPERTIES="test_network"
RESTRICT="test"
RDEPEND="
dev-python/QtPy[${PYTHON_USEDEP}]
"
BDEPEND="
+ dev-python/packaging[${PYTHON_USEDEP}]
test? (
dev-python/visvis[${PYTHON_USEDEP}]
)
@@ -42,8 +45,8 @@ python_prepare_all() {
distutils-r1_python_prepare_all
}
-src_test() {
- virtx python_foreach_impl python_test
+python_test() {
+ virtx epytest
}
python_install() {
diff --git a/profiles/package.mask b/profiles/package.mask
index a0d859d7f..7f28675b3 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -37,7 +37,6 @@ sci-biology/chiron
dev-python/snakemake
dev-python/specutils
dev-python/regions
-dev-python/pyzo
dev-python/kmapper
dev-python/photutils
dev-python/gammapy
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 78b2c0f8dd5b888739b7a97003efe103a3524d02 Author: Horea Christian chymera eu> AuthorDate: Mon Jan 16 00:46:13 2023 + Commit: Horea Christian gmail com> CommitDate: Mon Jan 16 00:46:13 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=78b2c0f8 profiles: sci-biology/longstitch dep stack cleared Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index ef1fd73f3..a0d859d7f 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -44,7 +44,6 @@ dev-python/gammapy dev-python/astroquery # Reverse deps of above dev-python/ripser -sci-biology/longstitch # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 3eb1934fb17a153026d22daa9a53a41aa104cde8 Author: Horea Christian chymera eu> AuthorDate: Sun Jan 15 20:23:54 2023 + Commit: Horea Christian gmail com> CommitDate: Sun Jan 15 20:23:54 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3eb1934f profiles: sci-biology/arcs dep stack cleared Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 3f6a655f3..ef1fd73f3 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -44,7 +44,6 @@ dev-python/gammapy dev-python/astroquery # Reverse deps of above dev-python/ripser -sci-biology/arcs sci-biology/longstitch # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 1ec270f5e4257488b39886e0ade87563a0fcecde Author: Horea Christian chymera eu> AuthorDate: Sun Jan 15 17:51:34 2023 + Commit: Horea Christian gmail com> CommitDate: Sun Jan 15 17:51:34 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ec270f5 profiles: py3.10 available for holoviews stack Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 2 -- 1 file changed, 2 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 1942944f6..3f6a655f3 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -38,13 +38,11 @@ dev-python/snakemake dev-python/specutils dev-python/regions dev-python/pyzo -dev-python/panel dev-python/kmapper dev-python/photutils dev-python/gammapy dev-python/astroquery # Reverse deps of above -dev-python/holoviews dev-python/ripser sci-biology/arcs sci-biology/longstitch
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 6ed21e5b1191124b2119e83f1e32d44394b5a195 Author: Horea Christian chymera eu> AuthorDate: Sat Jan 14 11:51:40 2023 + Commit: Horea Christian gmail com> CommitDate: Sat Jan 14 11:51:40 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ed21e5b profiles: sci-biology/Fastaq issues solved Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 765ddcbc7..1942944f6 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -54,7 +54,6 @@ sci-biology/longstitch sci-biology/pyfaidx sci-biology/gffutils sci-biology/RSeQC -sci-biology/Fastaq dev-python/hdf5storage dev-python/transforms3d dev-python/pysolar
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 3a53d23ac91246de0d682d35b06030eaaf9dc043 Author: Horea Christian chymera eu> AuthorDate: Sat Jan 14 10:31:50 2023 + Commit: Horea Christian gmail com> CommitDate: Sat Jan 14 10:31:50 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a53d23a profiles: dev-python/persim no longer fails Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 6a88b2fa9..765ddcbc7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -38,7 +38,6 @@ dev-python/snakemake dev-python/specutils dev-python/regions dev-python/pyzo -dev-python/persim dev-python/panel dev-python/kmapper dev-python/photutils
[gentoo-commits] proj/sci:master commit in: profiles/
commit: e58e6b9d616219399fdb07940aac3b9b305beedf Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 23:34:17 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 23:34:17 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e58e6b9d profiles: pyvista no longer breaks the depgraph Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 9d0e2fe50..6a88b2fa9 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -35,7 +35,6 @@ sci-biology/gffutils sci-biology/chiron dev-python/snakemake -dev-python/pyvista dev-python/specutils dev-python/regions dev-python/pyzo
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 2e3e22579110e476e1f549ba59f741612f778401 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 22:00:22 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 22:00:22 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e3e2257 profiles: dev-python/asdf issues solved Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index b152090c5..9d0e2fe50 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -44,7 +44,6 @@ dev-python/panel dev-python/kmapper dev-python/photutils dev-python/gammapy -dev-python/asdf dev-python/astroquery # Reverse deps of above dev-python/holoviews
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 84ed01ae78910b4424cd2270241720cea897e0b8 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 20:22:31 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 20:22:31 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=84ed01ae profiles: gwcs updated Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index cacd3491c..b152090c5 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -43,7 +43,6 @@ dev-python/persim dev-python/panel dev-python/kmapper dev-python/photutils -dev-python/gwcs dev-python/gammapy dev-python/asdf dev-python/astroquery
[gentoo-commits] proj/sci:master commit in: profiles/
commit: a1b726e22a8ae9d77f915e75d0e39a99400a24a1 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 19:28:53 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 19:28:53 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1b726e2 profiles: fixed PYTHON_COMPAt Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 986f9acc7..cacd3491c 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -32,7 +32,6 @@ # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/default/linux/amd64/17.0/x32/
commit: 2035f1b0631394455c187c42f35aad09576b6f79 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 09:00:33 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 09:00:33 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2035f1b0 profiles/default/linux/amd64/17.0/x32: removed unused profile dirs Signed-off-by: Horea Christian chymera.eu> profiles/default/linux/amd64/17.0/x32/package.mask | 3 --- 1 file changed, 3 deletions(-) diff --git a/profiles/default/linux/amd64/17.0/x32/package.mask b/profiles/default/linux/amd64/17.0/x32/package.mask deleted file mode 100644 index 4f9228f91..0 --- a/profiles/default/linux/amd64/17.0/x32/package.mask +++ /dev/null @@ -1,3 +0,0 @@ -# Cecil Curry (2021-10-07) -# Panel requires Node.js, which fails to support the x32 ABI. -dev-python/panel
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 7e46d4bd9c621fcac1aabf1da862b5b770ce5ae7 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 08:58:47 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 08:58:47 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7e46d4bd profiles: package no longer errors Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 2 -- 1 file changed, 2 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index d67ffb203..986f9acc7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -32,7 +32,6 @@ # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: e2726eb31b1c3644ddee6168fa5f77bae5b10693 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 07:42:46 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 07:42:46 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e2726eb3 profiles: sci-biology/tigmint PYTHON_COMPAT updated Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 32408cfdf..d67ffb203 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -32,7 +32,6 @@ # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: a13cad7fa16533ca21e20bb7f39642602896f618 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 07:03:21 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 07:03:21 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a13cad7f profiles: dependencies unmasked Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 4 1 file changed, 4 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 3d1ba947e..32408cfdf 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -66,7 +66,3 @@ sci-biology/deeptools dev-python/hdf5storage dev-python/transforms3d dev-python/pysolar -# Reverse deps of above -dev-vcs/datalad -sci-biology/samri -sci-libs/nipype
[gentoo-commits] proj/sci:master commit in: profiles/
commit: cfadcb30f5f733326cf70fba3b39ddad24f10a17 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 07:00:49 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 07:00:49 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cfadcb30 profiles: sci-biology/nitime python compatibility fixed Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index cd56346bf..3d1ba947e 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -33,7 +33,6 @@ # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: a55baa11cf375d05f43d38042b9078a7e7aac8b5 Author: Horea Christian chymera eu> AuthorDate: Fri Jan 13 06:20:37 2023 + Commit: Horea Christian gmail com> CommitDate: Fri Jan 13 06:20:37 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a55baa11 profiles: dev-python/annexremote causes no errors Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 9798c0df7..cd56346bf 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -66,7 +66,6 @@ sci-biology/Fastaq sci-biology/deeptools dev-python/hdf5storage dev-python/transforms3d -dev-python/annexremote dev-python/pysolar # Reverse deps of above dev-vcs/datalad
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 58d24cfc469084887cb5e65346cfbe2dc0741fdb Author: Horea Christian chymera eu> AuthorDate: Thu Jan 12 23:51:43 2023 + Commit: Horea Christian gmail com> CommitDate: Thu Jan 12 23:51:43 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=58d24cfc profiles: no error for package Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index 922b70f3e..9798c0df7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -64,7 +64,6 @@ sci-biology/gffutils sci-biology/RSeQC sci-biology/Fastaq sci-biology/deeptools -dev-python/traits dev-python/hdf5storage dev-python/transforms3d dev-python/annexremote
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 9360858627cb06129382d31f5d49e935d0c816dd Author: Horea Christian chymera eu> AuthorDate: Thu Jan 12 22:18:38 2023 + Commit: Horea Christian gmail com> CommitDate: Thu Jan 12 22:18:38 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=93608586 profiles: is test restricted Signed-off-by: Horea Christian chymera.eu> profiles/package.mask | 1 - 1 file changed, 1 deletion(-) diff --git a/profiles/package.mask b/profiles/package.mask index dc9da2ce5..922b70f3e 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -59,7 +59,6 @@ sci-biology/longstitch # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: f6063ad6adbbfd4386ac163670b6c7bf91692927 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 12 12:20:42 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 12 12:20:42 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f6063ad6 profiles: mask more revdeps Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 2 ++ 1 file changed, 2 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 50b538443..dc9da2ce5 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -72,3 +72,5 @@ dev-python/annexremote dev-python/pysolar # Reverse deps of above dev-vcs/datalad +sci-biology/samri +sci-libs/nipype
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 2fb7b4e4079686b89ca696ac7837cfcb10c26695 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 12 12:16:05 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 12 12:16:05 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2fb7b4e4 profiles: mask packages still depending on nose Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 14 ++ 1 file changed, 14 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 69343d5b7..bccc7a16d 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -56,3 +56,17 @@ dev-python/holoviews dev-python/ripser sci-biology/arcs sci-biology/longstitch + +# Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: dae6ebe82dfe6f98de3238d98066b00a5d4d6a66 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 12 12:17:40 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 12 12:17:40 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dae6ebe8 profiles: mask packages still depending on nose Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 2 ++ 1 file changed, 2 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index bccc7a16d..50b538443 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -70,3 +70,5 @@ dev-python/hdf5storage dev-python/transforms3d dev-python/annexremote dev-python/pysolar +# Reverse deps of above +dev-vcs/datalad
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 986193d5c7ae9b79963c5320b5362115aef88c06 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 12 11:57:32 2023 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 12 11:59:01 2023 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=986193d5 profiles: mask packages that need bump to py3.10+ Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 27 +++ 1 file changed, 27 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..69343d5b7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,30 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: d3d63c165da3d4f3782ef06f718996126f68b8f6 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Dec 1 21:56:43 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Dec 1 21:56:43 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d3d63c16 profiles: cleanup entry for non-existent package Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.use.mask | 4 1 file changed, 4 deletions(-) diff --git a/profiles/package.use.mask b/profiles/package.use.mask index b4116bd86..79c0fcb5c 100644 --- a/profiles/package.use.mask +++ b/profiles/package.use.mask @@ -19,10 +19,6 @@ # vtk<9 no longer available in ::gentoo sci-libs/gdcm python -# Andrew Savchenko (02 Jun 2016) -# doesn't link with plotutils-2.6 -sci-physics/qcl plotutils - # Christoph Junghans (05 Nov 2013) # gui sandbox error dev-lang/conceptual gui
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/estscan/
commit: 9c80f0ef473bca66c7cbd29c41a7330958f8d820
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Thu Dec 1 21:55:13 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Thu Dec 1 21:55:50 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c80f0ef
sci-biology/estscan: treeclean
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.use.mask| 4 -
sci-biology/estscan/estscan-3.0.3.ebuild | 124 ---
sci-biology/estscan/metadata.xml | 19 -
3 files changed, 147 deletions(-)
diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 8aff1df94..b4116bd86 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -23,10 +23,6 @@ sci-libs/gdcm python
# doesn't link with plotutils-2.6
sci-physics/qcl plotutils
-# Christoph Junghans (12 Sep 2014)
-# icc and ifc don't work on no-multilib
-sci-biology/estscan icc ifc
-
# Christoph Junghans (05 Nov 2013)
# gui sandbox error
dev-lang/conceptual gui
diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild
b/sci-biology/estscan/estscan-3.0.3.ebuild
deleted file mode 100644
index a0992b76b..0
--- a/sci-biology/estscan/estscan-3.0.3.ebuild
+++ /dev/null
@@ -1,124 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit fortran-2 perl-module toolchain-funcs
-
-DESCRIPTION="Prediction of coding regions in DNA/RNA sequences"
-HOMEPAGE="https://sourceforge.net/projects/estscan/;
-SRC_URI="
- https://downloads.sourceforge.net/${PN}/${P}.tar.gz
- https://downloads.sourceforge.net/${PN}/At.smat.gz
- https://downloads.sourceforge.net/${PN}/Dm.smat.gz
- https://downloads.sourceforge.net/${PN}/Dr.smat.gz
- https://downloads.sourceforge.net/${PN}/Hs.smat.gz
- https://downloads.sourceforge.net/${PN}/Mm.smat.gz
- https://downloads.sourceforge.net/${PN}/Rn.smat.gz
- https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf
- https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz;
-
-SLOT="0"
-LICENSE="estscan"
-KEYWORDS="~amd64 ~x86"
-IUSE="icc ifc"
-
-DEPEND="
- dev-perl/BTLib
- icc? ( dev-lang/icc )
- ifc? ( dev-lang/ifc )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
- default
- sed \
- -e 's/\\rm -f/rm -rf/' \
- -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \
- -i "${P}"/Makefile || die "failed to edit Makefile"
-
- # fix hard-coded paths
- sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i
"${P}"/${PN}.c || die
- sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i
"${P}"/${PN}.spec || die
-
- if ! use icc; then
- sed \
- -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i
"${P}"/Makefile || die
- fi
-
- if ! use ifc; then
- sed \
- -e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \
- -e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i
"${P}"/Makefile \
- || die
- fi
-
- if use icc; then
- # FIXME: I would use $(tc-getCC) instead of hard-coded icc but
it gives
- # me gcc instead, same for $(tc-getF77)
- # Moreover, the if/else logic here should separate users having
only icc
- # while not ifort (and vice-versa) from those having only
- # gcc/gfortran/g77
- #
- # FIXME: below as a dirty hack I force gfortran instead of
ifort for
- # my testing purposes. Didn't ebuild contain "PROVIDES" line?
- # Same for FFLAGS.
- sed \
- -e "s:^# CC = icc:CC = icc:" \
- -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo
-axP:" \
- -e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \
- -e "s/^ CC = gcc/# CC = gcc/" \
- -i "${P}"/Makefile || die "sed failed to fix CFLAGS and
CC"
-
- fi
-
- if use ifc; then
- sed \
- -e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo
-axP:" \
- -e "s/^# F77 = ifort/F77 = gfortran/" \
- -e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \
- -e "s/^ F77 = g77/# F77 = g77/" \
- -i "${P}"/Makefile || die "sed failed to fix FFLAGS and
F77"
- fi
-}
-
-src_compile() {
- emake -C ${P}
-}
-
-src_install() {
- # FIXME: Some kind of documentation is in {P}/${PN}.spec
- cd ${P} || die "Failed to chdir to ${P}"
- dobin \
- build_model ${PN} evaluate_model extract_EST extract_UG_EST \
- extract_mRNA makesmat maskred prepare_data winsegshuffle
- # the file build_model_utils.pl should go into some PERL site-packages
dir
- #
[gentoo-commits] proj/sci:master commit in: profiles/updates/
commit: c7e3da7347207bebbff82d9b74e8be738c85 Author: Bernd Waibel posteo net> AuthorDate: Thu Nov 3 12:57:03 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Nov 15 12:01:33 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7e3da73 profiles/updates: move sci-mathematics/netgen -> media-gfx/netgen Signed-off-by: Bernd Waibel posteo.net> Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/updates/4Q-2022 | 1 + 1 file changed, 1 insertion(+) diff --git a/profiles/updates/4Q-2022 b/profiles/updates/4Q-2022 new file mode 100644 index 0..b80d5a910 --- /dev/null +++ b/profiles/updates/4Q-2022 @@ -0,0 +1 @@ +move sci-mathematics/netgen media-gfx/netgen
[gentoo-commits] proj/sci:master commit in: profiles/, sci-libs/mlpack/
commit: b4d398416ab722252f8522ad30388c2c52a90657
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Aug 23 12:19:47 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Aug 23 12:19:53 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4d39841
sci-libs/mlpack: treeclean, more recent version in ::guru
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.use.mask | 6 --
sci-libs/mlpack/metadata.xml| 27 -
sci-libs/mlpack/mlpack-3.4.1.ebuild | 112 --
sci-libs/mlpack/mlpack-3.4.2.ebuild | 118
4 files changed, 263 deletions(-)
diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 508ab17db..8aff1df94 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -30,9 +30,3 @@ sci-biology/estscan icc ifc
# Christoph Junghans (05 Nov 2013)
# gui sandbox error
dev-lang/conceptual gui
-
-# Andrew Ammerlaan (15 Jan 2022)
-# dependencies not available
-# https://github.com/gentoo/sci/issues/1085
-# https://github.com/gentoo/sci/issues/1084
-sci-libs/mlpack go R
diff --git a/sci-libs/mlpack/metadata.xml b/sci-libs/mlpack/metadata.xml
deleted file mode 100644
index f587c48a7..0
--- a/sci-libs/mlpack/metadata.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- gen...@aisha.cc
- Aisha Tammy
-
-
- s...@gentoo.org
- Gentoo Science Project
-
-
- mlpack is a C++ machine learning library with emphasis on
- scalability, speed, and ease-of-use. Its aim is to make machine
- learning possible for novice users by means of a simple,
consistent
- API, while simultaneously exploiting C++ language features to
- provide maximum performance and maximum flexibility for expert
- users.
-
-
- build with armadillo dbug symbols
- build go bindings
- build julia bindings
- build matlab bindings
- build R bindings
-
-
diff --git a/sci-libs/mlpack/mlpack-3.4.1.ebuild
b/sci-libs/mlpack/mlpack-3.4.1.ebuild
deleted file mode 100644
index d03dd9ab1..0
--- a/sci-libs/mlpack/mlpack-3.4.1.ebuild
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit cmake python-single-r1
-
-DESCRIPTION="scalable C++ machine learning library"
-HOMEPAGE="https://www.mlpack.org/;
-SRC_URI="https://www.mlpack.org/files/${P}.tar.gz;
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE+="arma-debug debug doc go julia matlab openmp profile R test"
-REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
- ${PYTHON_DEPS}
- julia? ( || (
- dev-lang/julia
- dev-lang/julia-bin:*
- )
- )
- go? ( dev-lang/go )
- R? ( dev-lang/R )
-"
-
-RDEPEND="
- ${CDEPEND}
- $(python_gen_cond_dep '
- dev-libs/boost[${PYTHON_USEDEP}]
- dev-libs/libxml2[${PYTHON_USEDEP}]
- ')
- dev-python/pandas
- dev-python/cython
- dev-python/numpy
- dev-libs/stb
- >=sci-libs/armadillo-8.4.0[arpack,blas,lapack]
- sci-libs/ensmallen
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- ${CDEPEND}
- app-text/txt2man
- virtual/pkgconfig
- doc? (
- app-doc/doxygen
- dev-libs/mathjax
- )
- test? ( $( python_gen_cond_dep '
- dev-python/pytest[${PYTHON_USEDEP}]
- ')
- )
-"
-
-pkg_setup() {
- elog "If you want to build matlab bindings then you"
- elog "need to make sure that matlab has been installed"
- elog "prior to building this package and it is available"
- elog "in the standard locations to be found by"
- elog "CMake, library finders, header includes and other"
- elog "trinkets that are used while compiling."
- elog "Matlab will not be entertained as a first class"
- elog "citizen until we have enough personnel"
-
- python-single-r1_pkg_setup
-}
-
-src_prepare() {
- sed -i \
- -e "s:share/doc/mlpack:share/doc/${PF}:" \
- -e 's/-O3//g' \
- CMakeLists.txt || die
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DDISABLE_DOWNLOADS=ON
- -DDOWNLOAD_ENSMALLEN=OFF
- -DDOWNLOAD_STB_IMAGE=OFF
- -DBUILD_WITH_COVERAGE=OFF
- -DBUILD_PYTHON_BINDINGS=ON
- -DBUILD_SHARED_LIBS=ON
- -DBUILD_CLI_EXECUTABLES=ON
- -DTEST_VERBOSE=$(usex test)
-
[gentoo-commits] proj/sci:master commit in: profiles/
commit: c148e18f7f7b17200ec761f7d2afbe758c5ab72c Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Aug 23 08:06:31 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Aug 23 10:58:13 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c148e18f profiles: mask gdcm[python] depends on non-existent vtk version Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.use.mask | 4 1 file changed, 4 insertions(+) diff --git a/profiles/package.use.mask b/profiles/package.use.mask index 92d1d843a..508ab17db 100644 --- a/profiles/package.use.mask +++ b/profiles/package.use.mask @@ -15,6 +15,10 @@ ## =media-video/mplayer-0.90_pre5-r1 foo # +# Andrew Ammerlaan (23 Aug 2022) +# vtk<9 no longer available in ::gentoo +sci-libs/gdcm python + # Andrew Savchenko (02 Jun 2016) # doesn't link with plotutils-2.6 sci-physics/qcl plotutils
[gentoo-commits] proj/sci:master commit in: profiles/
commit: df2784cdca02e3bf9ad4ace128474dd7495676c5 Author: Andrew Ammerlaan gentoo org> AuthorDate: Mon Aug 22 15:14:48 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Mon Aug 22 15:14:48 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=df2784cd profiles: mask more revdeps Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 1 + 1 file changed, 1 insertion(+) diff --git a/profiles/package.mask b/profiles/package.mask index a635ec62c..a21bb9773 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -36,3 +36,4 @@ sci-biology/caftools sci-biology/salmon sci-biology/staden sci-biology/staden_doc +sci-biology/roche454ace2caf
[gentoo-commits] proj/sci:master commit in: profiles/
commit: bb8f8e9511ac3c146629af13822d6d18e8d295ea Author: Andrew Ammerlaan gentoo org> AuthorDate: Mon Aug 22 15:12:21 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Mon Aug 22 15:12:21 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bb8f8e95 profiles: mask revdeps of sci-libs/io_lib Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 7 +++ 1 file changed, 7 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..a635ec62c 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,10 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (2022-08-22) +# Depends on removed sci-libs/io_lib. removal in 30 days +sci-biology/caftools +sci-biology/salmon +sci-biology/staden +sci-biology/staden_doc
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 0207d357e76c949c828c97a8013a2eb7384705c9
Author: Yiyang Wu gmail com>
AuthorDate: Thu Aug 4 09:30:01 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Aug 7 08:40:44 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0207d357
profiles: unmask dev-python/{numba,llvmlite}
The newset version can depend on llvm:13 which is still in ::gentoo
And there is ongoing efforts of migrating to llvm:14
See https://github.com/numba/llvmlite/pull/830
Signed-off-by: Yiyang Wu gmail.com>
Closes: https://github.com/gentoo/sci/pull/1164
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 10 --
1 file changed, 10 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index e7a18b54f..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,13 +29,3 @@
## app-misc/some-package
#--- END OF EXAMPLES ---
-
-# Andrew Ammerlaan (20 Jul 2022)
-# Depends on removed llvm:12
-# removal in 30 days
-dev-python/llvmlite
-# reverse dependencies of llvmlite
-dev-python/numba
-dev-python/pynndescent
-# reverse dependencies of numba
-dev-python/umap-learn
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 2c4dd4f6d3ce90943deb1e7c35caeb5fd70b0674 Author: Andrew Ammerlaan gentoo org> AuthorDate: Wed Jul 20 09:55:03 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Wed Jul 20 09:55:03 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2c4dd4f6 profiles: mask dev-python/umap-learn Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 2 ++ 1 file changed, 2 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 97229a503..e7a18b54f 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -37,3 +37,5 @@ dev-python/llvmlite # reverse dependencies of llvmlite dev-python/numba dev-python/pynndescent +# reverse dependencies of numba +dev-python/umap-learn
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 52eabadff644fd21f6a66671a493efcef3bac059 Author: Andrew Ammerlaan gentoo org> AuthorDate: Wed Jul 20 09:49:36 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Wed Jul 20 09:49:57 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=52eabadf profiles: mask revdeps of llvmlite Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 3 +++ 1 file changed, 3 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 18b8386b7..97229a503 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -34,3 +34,6 @@ # Depends on removed llvm:12 # removal in 30 days dev-python/llvmlite +# reverse dependencies of llvmlite +dev-python/numba +dev-python/pynndescent
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 67bbcb562b65f49f3d32f5aaa2ed9b54c6c25071 Author: Andrew Ammerlaan gentoo org> AuthorDate: Wed Jul 20 09:44:35 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Wed Jul 20 09:44:35 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=67bbcb56 profiles: mask dev-python/llvmlite for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 5 + 1 file changed, 5 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..18b8386b7 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,8 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (20 Jul 2022) +# Depends on removed llvm:12 +# removal in 30 days +dev-python/llvmlite
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 9136a0e12311f8f0220a6fb09195398cb1b0f93f Author: Andrew Ammerlaan gentoo org> AuthorDate: Sun May 15 12:28:23 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Sun May 15 12:30:55 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9136a0e1 profiles/package.mask: mask jeuclid-core for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 6 ++ 1 file changed, 6 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..b338c8d20 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,9 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (15 May 2022) +# Requires old and removed batik:1.9::gentoo +# No updates since 2019 +# Mask for removal in 30 days +dev-java/jeuclid-core
[gentoo-commits] proj/sci:master commit in: profiles/, sci-libs/superlu_dist/
commit: 689c58f6e7b62c8569ab1bca5705e4fc0d0c7800
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Mon May 2 12:18:29 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Mon May 2 12:18:29 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=689c58f6
sci-libs/superlu_dist: drop masked package
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 5 ---
sci-libs/superlu_dist/metadata.xml | 26 ---
sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild | 42 -
3 files changed, 73 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index effdccc93..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,8 +29,3 @@
## app-misc/some-package
#--- END OF EXAMPLES ---
-
-# Andrew Ammerlaan (15 Mar 2022)
-# Missing dependencies, bumping is non-trivial, requires patches to get it to
-# compile without errors or sandbox violations. Mask for removal, no revdeps
-sci-libs/superlu_dist
diff --git a/sci-libs/superlu_dist/metadata.xml
b/sci-libs/superlu_dist/metadata.xml
deleted file mode 100644
index 0bd32bba5..0
--- a/sci-libs/superlu_dist/metadata.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- s...@gentoo.org
- Gentoo Science Project
-
-
-SuperLU is a general purpose library for the direct solution of
-large, sparse, nonsymmetric systems of linear equations on high
-performance machines. The library is written in C and is callable
-from either C or Fortran. The library routines will perform an LU
-decomposition with partial pivoting and triangular system solves
-through forward and back substitution. The LU factorization routines
-can handle non-square matrices but the triangular solves are
-performed only for square matrices. The matrix columns may be
-preordered (before factorization) either through library or user
-supplied routines. This preordering for sparsity is completely
-separate from the factorization. Working precision iterative
-refinement subroutines are provided for improved backward
-stability. Routines are also provided to equilibrate the system,
-estimate the condition number, calculate the relative backward
-error, and estimate error bounds for the refined solutions.
-This is the distributed version (MPI based).
-
-
diff --git a/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild
b/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild
deleted file mode 100644
index 8c7be2874..0
--- a/sci-libs/superlu_dist/superlu_dist-6.4.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DOCS_BUILDER="doxygen"
-DOCS_CONFIG_NAME="DoxyConfig"
-
-inherit cmake docs
-
-MYPN=SuperLU_DIST
-
-DESCRIPTION="MPI distributed sparse LU factorization library"
-HOMEPAGE="https://portal.nersc.gov/project/sparse/superlu/
https://github.com/xiaoyeli/superlu_dist;
-SRC_URI="https://github.com/xiaoyeli/superlu_dist/archive/v${PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- sci-libs/parmetis[mpi(-)]
- virtual/mpi"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_configure() {
- local mycmakeargs=(
- -DTPL_PARMETIS_LIBRARIES="/usr/$(get_libdir)/libmetis.so"
- -DTPL_PARMETIS_INCLUDE_DIRS="/usr/include/"
- -Denable_examples=$(usex examples ON OFF)
- -Denable_tests=$(usex test ON OFF)
- )
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- default
-}
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 1ddc16c78ccae513b383e39f2556c3afadf25613 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Mar 15 19:12:15 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Mar 15 19:12:15 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ddc16c7 package.mask: mask superlu_dist for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 5 + 1 file changed, 5 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..effdccc93 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,8 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (15 Mar 2022) +# Missing dependencies, bumping is non-trivial, requires patches to get it to +# compile without errors or sandbox violations. Mask for removal, no revdeps +sci-libs/superlu_dist
[gentoo-commits] proj/sci:master commit in: profiles/, sci-libs/jhdf5/
commit: 6c2920e26f3e67da709383112ed5782a3c1f3706
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Sun Jan 23 12:58:05 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Jan 23 12:58:05 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c2920e2
sci-libs/jhdf5: remove old java package
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 2 --
sci-libs/jhdf5/jhdf5-19.04.0.ebuild | 37 -
sci-libs/jhdf5/metadata.xml | 12
3 files changed, 51 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index a5e397fa4..d86099342 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -50,7 +50,5 @@ dev-java/jcommon
dev-java/skinlf
dev-java/jrosetta
dev-java/freehep-graphicsio-emf
-# depends on dev-java/args4j which is being last-rited from ::gentoo
-sci-libs/jhdf5
# ancient java, can't update due to gradle/maven limitation
dev-java/htsjdk
diff --git a/sci-libs/jhdf5/jhdf5-19.04.0.ebuild
b/sci-libs/jhdf5/jhdf5-19.04.0.ebuild
deleted file mode 100644
index 588503cfe..0
--- a/sci-libs/jhdf5/jhdf5-19.04.0.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java binding for HDF5 compatible with HDF5 1.6/1.8"
-HOMEPAGE="https://wiki-bsse.ethz.ch/display/JHDF5;
-SRC_URI="https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-${PV}.zip;
-# first SIS release:
https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.0-r33145.zip
-# last CISD release:
https://wiki-bsse.ethz.ch/download/attachments/26609237/cisd-jhdf5-13.06.2-r29633.zip
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- >=virtual/jdk-1.7:*
- app-arch/unzip
- dev-java/args4j:*
- dev-java/commons-io:*
- dev-java/commons-lang:*
-"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-S="${WORKDIR}/sis-jhdf5"
-
-src_install() {
- dobin bin/h5ar
- java-pkg_newjar lib/sis-${P}.jar sis-${PN}.jar
- java-pkg_dolauncher sis-${PN} --jar sis-${PN}.jar
- java-pkg_newjar lib/sis-${PN}-h5ar-cli-${PV}.jar sis-${PN}-h5ar-cli.jar
- java-pkg_dolauncher sis-${PN}-h5ar-cli --jar sis-${PN}-h5ar-cli.jar
- dodoc doc/JHDF5-${PV}.*
-}
diff --git a/sci-libs/jhdf5/metadata.xml b/sci-libs/jhdf5/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-libs/jhdf5/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/conrad/
commit: bbe535dab6b27aead446cd142b5385fb47f10496
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Sun Jan 23 12:57:22 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Jan 23 12:57:22 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bbe535da
sci-biology/conrad: remove ancient java package
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 2 --
sci-biology/conrad/conrad-1.ebuild | 52 --
sci-biology/conrad/metadata.xml| 15 ---
3 files changed, 69 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 3c8ff3880..a5e397fa4 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -50,8 +50,6 @@ dev-java/jcommon
dev-java/skinlf
dev-java/jrosetta
dev-java/freehep-graphicsio-emf
-# and also mask this which hasn't seen an upstream release since 2007!
-sci-biology/conrad
# depends on dev-java/args4j which is being last-rited from ::gentoo
sci-libs/jhdf5
# ancient java, can't update due to gradle/maven limitation
diff --git a/sci-biology/conrad/conrad-1.ebuild
b/sci-biology/conrad/conrad-1.ebuild
deleted file mode 100644
index bca495174..0
--- a/sci-biology/conrad/conrad-1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF
predictor"
-HOMEPAGE="https://sourceforge.net/projects/conradcrf;
-SRC_URI="https://downloads.sourceforge.net/project/conradcrf/conradcrf/Version%201/conradSrc.zip
-> ${P}.zip"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- >=virtual/jre-1.5:*
- =dev-java/commons-lang-2.1:*
- dev-java/colt
- dev-java/dom4j
- "
- # spring # see bug #97004
- # dev-java/LBFGS # LBFGS is a numericla library we use internally for
the solver
-DEPEND="${RDEPEND}
- >=virtual/jdk-1.5:*
- =dev-java/jfreechart-1.0.3
- >=dev-java/jcommon-1.0.6
- >=dev-java/commons-math-1.1
- "
-BDEPEND="app-arch/unzip"
-S="${WORKDIR}"
-
-src_prepare(){
- default
- sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i
bin/conrad.sh || die
-}
-
-src_compile(){
- cd dev || die
- ant compile || die
-}
-
-src_install() {
- dobin bin/conrad.sh
- java-pkg_dojar lib/conrad.jar
- java-pkg_dolauncher conrad --jar conrad.jar
- dodoc -r docs models samples trainingFiles
-}
diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml
deleted file mode 100644
index 814dcabcc..0
--- a/sci-biology/conrad/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- conradcrf
-
-
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/pilon-bin/
commit: d0fcff8a955005d6edf20a3e019ab83d0f0a7864
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Sun Jan 23 12:55:20 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Jan 23 12:55:20 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d0fcff8a
sci-biology/cramtools: remove old java package
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 1 -
sci-biology/pilon-bin/metadata.xml | 12
sci-biology/pilon-bin/pilon-bin-1.24.ebuild | 29 -
3 files changed, 42 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 275d7f3fc..1440925e0 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -56,7 +56,6 @@ sci-biology/conrad
sci-libs/jhdf5
# ancient java, can't update due to gradle/maven limitation
dev-java/htsjdk
-sci-biology/pilon-bin
sci-misc/opennlp-maxent
# Andrew Ammerlaan
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
diff --git a/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
b/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
deleted file mode 100644
index 49d15366f..0
--- a/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2
-
-DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs"
-HOMEPAGE="
- https://github.com/broadinstitute/pilon
- https://github.com/broadinstitute/pilon/wiki;
-SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar;
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-# contains bundled sbt-assembly module
-DEPEND=">=virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*
- >=dev-java/htsjdk-1.130"
-
-S="${WORKDIR}"
-
-src_install(){
- cp -p "${DISTDIR}"/pilon-${PV}.jar . || die
- java-pkg_dojar pilon-${PV}.jar
-}
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/quorum/, sci-biology/quorum/files/
commit: bbd189a0826dc274c1378aa8a791b63c9d101c5a
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Sun Jan 23 12:54:13 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Jan 23 12:54:13 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bbd189a0
sci-biology/quorum: remove old java package
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 7 --
.../quorum/files/quorum-0.2.1-use-jellyfish1.patch | 74 --
sci-biology/quorum/metadata.xml| 12
sci-biology/quorum/quorum-1.1.1.ebuild | 28
4 files changed, 121 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 020a30666..cfebeb744 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -64,10 +64,3 @@ sci-misc/opennlp-maxent
# Broken, no consumers
# Removal in 30 days
dev-lang/terra
-
-# Andrew Ammerlaan https://github.com/gmarcais/Quorum/issues/2
-# https://github.com/gmarcais/Quorum/issues/1
-# Removal in 30 days
-sci-biology/quorum
diff --git a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
b/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
deleted file mode 100644
index b5b68a8fb..0
--- a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
+++ /dev/null
@@ -1,74 +0,0 @@
src/error_correct_reads.cc 2018-04-21 14:25:41.310473159 +0200
-+++ src/error_correct_reads.cc 2018-04-21 14:26:58.262493179 +0200
-@@ -25,9 +25,9 @@
- #endif
-
- //#define DEBUG 1
--#include
--#include
--#include
-+#include
-+#include
-+#include
-
- #include
- #include
src/combine_jf_dbs.cc 2018-04-21 14:25:50.220707057 +0200
-+++ src/combine_jf_dbs.cc 2018-04-21 14:27:04.652660923 +0200
-@@ -1,9 +1,9 @@
--#include
--#include
--#include
--#include
--#include
--#include
-+#include
-+#include
-+#include
-+#include
-+#include
-+#include
- #include
-
- int main(int argc, char *argv[])
src/error_correct_reads.hpp2018-04-21 14:26:10.091228666 +0200
-+++ src/error_correct_reads.hpp2018-04-21 14:27:09.792795853 +0200
-@@ -2,12 +2,12 @@
- #define __ERROR_CORRECT_READS_HPP__
-
- #include
--#include
--#include
--#include
--#include
--#include
--#include
-+#include
-+#include
-+#include
-+#include
-+#include
-+#include
- #include
- #include
- #include
configure.ac.ori 2018-04-21 15:00:35.225439196 +0200
-+++ configure.ac 2018-04-21 15:01:37.977086449 +0200
-@@ -28,7 +28,7 @@
- JELLYFISH_VERSION=$(pkg-config --modversion jellyfish-1.1)
- AC_SUBST([JELLYFISH_VERSION])
- AC_ARG_VAR([JELLYFISH], [Jellyfish executable absolute path (default to
looking in PATH)])
--AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish],
[false])])
-+AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish1],
[false])])
-
- AC_ARG_VAR([JF_LIB_PATH], [Append this path to LD_LIBRARY_PATH in quorum])
-
-@@ -47,7 +47,7 @@
- # --with-relative-jf-path
- AC_ARG_WITH([relative-jf-path],
- [AC_HELP_STRING([--with-relative-jf-path], [relative path from
quorum to jellyfish (use an absolute path if not given. default to "." if given
with no argument)])],
--[case "$withval" in (yes) with_relative_jf_path="jellyfish" ;;
(no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish ;;
esac],
-+[case "$withval" in (yes) with_relative_jf_path="jellyfish1" ;;
(no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish1 ;;
esac],
- [with_relative_jf_path= ])
- AC_SUBST([RELATIVE_JF_PATH], $with_relative_jf_path)
- AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x])
diff --git a/sci-biology/quorum/metadata.xml b/sci-biology/quorum/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/quorum/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
diff --git a/sci-biology/quorum/quorum-1.1.1.ebuild
b/sci-biology/quorum/quorum-1.1.1.ebuild
deleted file mode 100644
index 4af286fcb..0
--- a/sci-biology/quorum/quorum-1.1.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Correct substitution errors in Illumina reads"
-HOMEPAGE="http://www.genome.umd.edu/quorum.html
- https://github.com/gmarcais/Quorum;
-SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v${PV}/${P}.tar.gz;
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=">=sci-biology/jellyfish-2.1.4:2"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- default
- # fix jellyfish include path
- find
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/jtreeview/
commit: adf7383fa934d9a68a5ebb9d394fd963b1dd8c57
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Sun Jan 23 12:53:13 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Jan 23 12:53:13 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=adf7383f
sci-biology/jtreeview: remove old java package
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask| 4 ---
sci-biology/jtreeview/jtreeview-1.2.0.ebuild | 39
sci-biology/jtreeview/jtreeview-.ebuild | 30 -
sci-biology/jtreeview/metadata.xml | 16
4 files changed, 89 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 0781ef1e3..9a0a75e44 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -76,7 +76,3 @@ sci-biology/quorum
# No updates since 2009(!), no longer compiles
# Removal in 30 days
sci-biology/jigsaw
-
-# Andrew Ammerlaan http://jtreeview.sourceforge.net/; # no https
-SRC_URI="
-
https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-src.tar.gz
-
https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz
-"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=">virtual/jdk-1.7:*
- dev-java/nanoxml"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-S="${WORKDIR}/TreeView-${PV}-src"
-JAVA_PKG_BSFIX_NAME="${S}"
-
-# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
-
-src_install(){
- java-pkg_dojar TreeView.jar
- java-pkg_dolauncher ${PN} TreeView.jar
- cd ../helper-scripts-0.0.2 || die
- perl_set_version
- perl_domodule *.pm
- perl_domodule *.pl
- insinto /usr/share/"${PN}"/examples
- doins blues.color
- newdoc README README.helper-scripts
-}
diff --git a/sci-biology/jtreeview/jtreeview-.ebuild
b/sci-biology/jtreeview/jtreeview-.ebuild
deleted file mode 100644
index 316368b4e..0
--- a/sci-biology/jtreeview/jtreeview-.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module java-pkg-2 java-ant-2 git-r3
-
-DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net/; # no https
-EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND=">virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-src_install(){
- java-pkg_dojar TreeView.jar
- java-pkg_dolauncher ${PN} TreeView.jar
- cd ../helper-scripts-0.0.2 || die
- perl_set_version
- perl_domodule *.pm
- perl_domodule *.pl
- insinto /usr/share/"${PN}"/examples
- doins blues.color
- newdoc README README.helper-scripts
-}
diff --git a/sci-biology/jtreeview/metadata.xml
b/sci-biology/jtreeview/metadata.xml
deleted file mode 100644
index 5139daeeb..0
--- a/sci-biology/jtreeview/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- TreeView3Dev/treeview3
- jtreeview
-
-
[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/jigsaw/
commit: 63e2ae8446c888f254baf9d9b4d6128488dbd110
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Sun Jan 23 12:53:46 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Jan 23 12:53:46 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=63e2ae84
sci-biology/jigsaw: remove old java package
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask| 5 -
sci-biology/jigsaw/jigsaw-3.2.10m.ebuild | 28
sci-biology/jigsaw/metadata.xml | 12
3 files changed, 45 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 9a0a75e44..020a30666 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -71,8 +71,3 @@ dev-lang/terra
# https://github.com/gmarcais/Quorum/issues/1
# Removal in 30 days
sci-biology/quorum
-
-# Andrew Ammerlaan https://www.cbcb.umd.edu/software/jigsaw;
-SRC_URI="https://www.cbcb.umd.edu/software/jigsaw/${P}.tar.gz;
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-
-S="${WORKDIR}/${PN}-${PV//m}"
-
-src_compile() {
- cd src/main || die
- emake
- cd ../../lib/oc1
- emake
-}
-
-src_install() {
- cd src/main || die
- emake DESTDIR="${ED}" install
- cd ../../lib/oc1
- emake DESTDIR="${ED}" install
-}
diff --git a/sci-biology/jigsaw/metadata.xml b/sci-biology/jigsaw/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/jigsaw/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
[gentoo-commits] proj/sci:master commit in: profiles/, sci-chemistry/MotionCor2/
commit: cff1f0a939454d8008a82d979c5fec491dd3f376 Author: Andrew Ammerlaan gentoo org> AuthorDate: Sun Jan 23 12:02:18 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Sun Jan 23 12:02:18 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cff1f0a9 sci-chemistry/MotionCor2: remove cuda flag note says it has cuda 11 support but I can't test due to fetch restriction Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask| 1 - sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild | 5 - 2 files changed, 6 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index a1c408aaf..97bf66dcd 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -34,7 +34,6 @@ # cuda-10 is being removed from ::gentoo, mask revdeps in ::sci # for removal too. Removal in 90 days sci-physics/opticks -sci-chemistry/MotionCor2 # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/, sci-misc/europa-bin/
commit: a07eea4472011a3432752345ec02b29269820149
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Sun Jan 23 12:52:13 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sun Jan 23 12:52:13 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a07eea44
sci-misc/europa-bin: remove package
Signed-off-by: Andrew Ammerlaan gentoo.org>
profiles/package.mask | 4 --
sci-misc/europa-bin/europa-bin-1.1.0.ebuild | 57 -
sci-misc/europa-bin/metadata.xml| 12 --
3 files changed, 73 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 0063312a2..0781ef1e3 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -65,10 +65,6 @@ sci-misc/opennlp-maxent
# Removal in 30 days
dev-lang/terra
-# Andrew Ammerlaan https://github.com/gmarcais/Quorum/issues/2
diff --git a/sci-misc/europa-bin/europa-bin-1.1.0.ebuild
b/sci-misc/europa-bin/europa-bin-1.1.0.ebuild
deleted file mode 100644
index ad502cfac..0
--- a/sci-misc/europa-bin/europa-bin-1.1.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit xdg
-
-DESCRIPTION="JupyterLab's Desktop client in electron"
-HOMEPAGE="https://github.com/suyashmahar/europa;
-SRC_URI="https://drive.google.com/uc?export=download=1c6NYXJgioU4_2v-CQ6oxtb1jzMMhDeMo
-> ${P}.tar.xz"
-
-KEYWORDS="-* ~amd64"
-LICENSE="GPL-3"
-SLOT="0"
-
-RDEPEND="
- app-accessibility/at-spi2-atk:2
- dev-libs/atk
- dev-libs/expat
- dev-libs/libappindicator
- dev-libs/nspr
- dev-libs/nss
- dev-python/jupyterlab
- media-libs/alsa-lib
- net-print/cups
- x11-libs/cairo
- x11-libs/gdk-pixbuf:2
- x11-libs/gtk+:3
- x11-libs/libnotify
- x11-libs/libxcb
- x11-libs/libX11
- x11-libs/libXcomposite
- x11-libs/libXcursor
- x11-libs/libXdamage
- x11-libs/libXext
- x11-libs/libXfixes
- x11-libs/libXi
- x11-libs/libxkbcommon
- x11-libs/libXrandr
- x11-libs/libXrender
- x11-libs/libXtst
- x11-libs/libXScrnSaver
- x11-libs/pango
-"
-
-QA_PREBUILT="/opt/${PN//-bin}*"
-
-S="${WORKDIR}"
-
-src_install() {
- # Move icon to correct dir
- mv usr/share/icons/hicolor/0x0 usr/share/icons/hicolor/256x256 || die
- # Write name in desktop file with capital letter
- sed -i -e 's/Name=europa/Name=Europa/g'
usr/share/applications/europa.desktop || die
-
- mv "${S}"/* "${ED}" || die
-}
diff --git a/sci-misc/europa-bin/metadata.xml b/sci-misc/europa-bin/metadata.xml
deleted file mode 100644
index 0c2747670..0
--- a/sci-misc/europa-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- suyashmahar/europa
- https://github.com/suyashmahar/europa/issues
-
-
- s...@gentoo.org
- Gentoo Science Project
-
-
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 10134bf04fc57433391c27830f2da6c91460f0f2 Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Jan 21 14:09:42 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Jan 21 14:09:42 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=10134bf0 package.mask: mask jtreeview for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 4 1 file changed, 4 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 672cc7b74..a1c408aaf 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -86,3 +86,7 @@ sci-biology/quorum # No updates since 2009(!), no longer compiles # Removal in 30 days sci-biology/jigsaw + +# Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 3a82e2bee5be713c92ad86e6f4bec8d297fa472b Author: Andrew Ammerlaan gentoo org> AuthorDate: Sun Jan 16 09:51:57 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Sun Jan 16 09:51:57 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a82e2be package.mask: mask opennlp-maxent for removal depends on dev-java/trove which is being removed from ::gentoo Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 1 + 1 file changed, 1 insertion(+) diff --git a/profiles/package.mask b/profiles/package.mask index 4583876b4..672cc7b74 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -64,6 +64,7 @@ sci-libs/jhdf5 dev-java/htsjdk sci-biology/cramtools sci-biology/pilon-bin +sci-misc/opennlp-maxent # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 9dfb78c05aaa8ff9edc2c795c2aac8692d3ed944 Author: Andrew Ammerlaan gentoo org> AuthorDate: Sat Jan 15 14:09:41 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Sat Jan 15 14:09:41 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9dfb78c0 package.use.mask: mask R and go flags on mlpack Closes: https://github.com/gentoo/sci/issues/1084 Closes: https://github.com/gentoo/sci/issues/1085 Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.use.mask | 6 ++ 1 file changed, 6 insertions(+) diff --git a/profiles/package.use.mask b/profiles/package.use.mask index 13ff264bb..92d1d843a 100644 --- a/profiles/package.use.mask +++ b/profiles/package.use.mask @@ -26,3 +26,9 @@ sci-biology/estscan icc ifc # Christoph Junghans (05 Nov 2013) # gui sandbox error dev-lang/conceptual gui + +# Andrew Ammerlaan (15 Jan 2022) +# dependencies not available +# https://github.com/gentoo/sci/issues/1085 +# https://github.com/gentoo/sci/issues/1084 +sci-libs/mlpack go R
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 03f1c71db6066efd9c47237b96aedfa11cdecff2 Author: Andrew Ammerlaan gentoo org> AuthorDate: Sat Jan 15 11:58:16 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Sat Jan 15 11:58:16 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=03f1c71d package.mask: mask jigsaw for removal Closes: https://github.com/gentoo/sci/issues/1071 Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 5 + 1 file changed, 5 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 3107e5030..4583876b4 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -80,3 +80,8 @@ sci-misc/europa-bin # https://github.com/gmarcais/Quorum/issues/1 # Removal in 30 days sci-biology/quorum + +# Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/updates/
commit: ed0fc83ddc6f9d5a7a7b432227f433a73debd0d3 Author: Andrew Ammerlaan gentoo org> AuthorDate: Sat Jan 15 11:13:52 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Sat Jan 15 11:13:52 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ed0fc83d profiles/updates: fix pkg move Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/updates/1Q-2022 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/profiles/updates/1Q-2022 b/profiles/updates/1Q-2022 index e905430ca..8b44d82fa 100644 --- a/profiles/updates/1Q-2022 +++ b/profiles/updates/1Q-2022 @@ -1 +1 @@ -sci-biology/sra_sdk sci-biology/sra-tools +move sci-biology/sra_sdk sci-biology/sra-tools
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 88587a13f6f13736d25c31bf6cf260f51b9bf16d Author: Andrew Ammerlaan gentoo org> AuthorDate: Fri Jan 14 10:13:56 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Jan 14 10:13:56 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=88587a13 package.mask: mask quorum for removal Closes: https://github.com/gentoo/sci/issues/833 Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 7 +++ 1 file changed, 7 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index dd0cb7d5c..3107e5030 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -73,3 +73,10 @@ dev-lang/terra # Andrew Ammerlaan https://github.com/gmarcais/Quorum/issues/2 +# https://github.com/gmarcais/Quorum/issues/1 +# Removal in 30 days +sci-biology/quorum
[gentoo-commits] proj/sci:master commit in: profiles/
commit: cf53c7003709db2c588a46db1195b3a55c3872a7 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 13 15:50:28 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 13 15:50:28 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf53c700 package.mask: mask terra for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 5 + 1 file changed, 5 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d67bd8056..dd0cb7d5c 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -65,6 +65,11 @@ dev-java/htsjdk sci-biology/cramtools sci-biology/pilon-bin +# Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 1a7f60be1e3372c066797beac859021a2282d013 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 13 15:46:52 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 13 15:46:52 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a7f60be package.mask: mask htsjdk for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 4 1 file changed, 4 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 63ccdbfb5..d67bd8056 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -60,6 +60,10 @@ dev-java/freehep-graphicsio-emf sci-biology/conrad # depends on dev-java/args4j which is being last-rited from ::gentoo sci-libs/jhdf5 +# ancient java, can't update due to gradle/maven limitation +dev-java/htsjdk +sci-biology/cramtools +sci-biology/pilon-bin # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: aaec9e65494575293b7e816c08540ca06d062115 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 13 15:24:13 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 13 15:24:13 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=aaec9e65 package.use.mask: drop obsolete use mask Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.use.mask | 5 - 1 file changed, 5 deletions(-) diff --git a/profiles/package.use.mask b/profiles/package.use.mask index 3668ef20d..13ff264bb 100644 --- a/profiles/package.use.mask +++ b/profiles/package.use.mask @@ -15,11 +15,6 @@ ## =media-video/mplayer-0.90_pre5-r1 foo # -# Benda Xu (24 Jan 2021) -# It doesn't work, mask 30 days for removal, unless someone come up -# with a fix. cf. https://github.com/gentoo/sci/issues/1011 -sci-libs/pytorch mkl - # Andrew Savchenko (02 Jun 2016) # doesn't link with plotutils-2.6 sci-physics/qcl plotutils
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 3897eb42a444bea12ba5c954b974f474c4e89846 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 13 15:15:50 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 13 15:15:50 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3897eb42 package.mask: mask jhdf5 for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 2 ++ 1 file changed, 2 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 4ac2f8a95..63ccdbfb5 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -58,6 +58,8 @@ dev-java/jrosetta dev-java/freehep-graphicsio-emf # and also mask this which hasn't seen an upstream release since 2007! sci-biology/conrad +# depends on dev-java/args4j which is being last-rited from ::gentoo +sci-libs/jhdf5 # Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: ccd3711ad09044f68b18e0f72fe3c193ed472831 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Jan 11 19:36:18 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Jan 11 19:36:18 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccd3711a package.mask: mask sci-misc/europa-bin for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 4 1 file changed, 4 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index 1721e4aca..4ac2f8a95 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -58,3 +58,7 @@ dev-java/jrosetta dev-java/freehep-graphicsio-emf # and also mask this which hasn't seen an upstream release since 2007! sci-biology/conrad + +# Andrew Ammerlaan
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 4726904c820b3c4b0977197aafaba5a1361182b9 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Jan 11 19:23:52 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Jan 11 19:23:52 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4726904c profiles/package.mask: mask sci-biology/conrad for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 2 ++ 1 file changed, 2 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d3d18176e..1721e4aca 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -56,3 +56,5 @@ dev-java/jcommon dev-java/skinlf dev-java/jrosetta dev-java/freehep-graphicsio-emf +# and also mask this which hasn't seen an upstream release since 2007! +sci-biology/conrad
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 663249d5cd32e04a40cfa97104cd122d78703211 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Jan 11 19:20:11 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Jan 11 19:20:11 2022 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=663249d5 profiles/package.mask: mask scilab and friends for removal Use scilab-bin instead Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 20 1 file changed, 20 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index b1561a9ac..d3d18176e 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -36,3 +36,23 @@ sci-physics/opticks sci-chemistry/MotionCor2 +# Andrew Ammerlaan dev-java/lucene-4 +dev-java/flexdock +dev-java/gluegen +dev-java/jogl +dev-java/jlatexmath +dev-java/jlatexmath-fop +dev-java/jfreechart +dev-java/jfreesvg +dev-java/jgraphx +dev-java/jcommon +dev-java/skinlf +dev-java/jrosetta +dev-java/freehep-graphicsio-emf
[gentoo-commits] proj/sci:master commit in: profiles/
commit: 6439a0a6bf53f99d37ffd4e71e00cfda062d2654 Author: Andrew Ammerlaan gentoo org> AuthorDate: Sun Dec 26 10:37:14 2021 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Sun Dec 26 10:38:25 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6439a0a6 package.mask: mask revdeps of cuda-10 for removal Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 7 +++ 1 file changed, 7 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..b1561a9ac 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,10 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (26 Dec 2021) +# cuda-10 is being removed from ::gentoo, mask revdeps in ::sci +# for removal too. Removal in 90 days +sci-physics/opticks +sci-chemistry/MotionCor2 +
[gentoo-commits] proj/sci:master commit in: profiles/
commit: a30c84d5f32898dafdd9d72ac4acd7dc3029ab8c Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Nov 4 09:01:31 2021 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Nov 4 09:08:17 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a30c84d5 profiles/package.mask: mask sci-libs/geom for removal Bug: https://github.com/gentoo/sci/issues/1119 Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 10 ++ 1 file changed, 10 insertions(+) diff --git a/profiles/package.mask b/profiles/package.mask index d39812beb..a01fccbca 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,3 +29,13 @@ ## app-misc/some-package #--- END OF EXAMPLES --- + +# Andrew Ammerlaan (04 Nov 2021) +# No upstream activity since 2011, does not build with sci-libs/opencascade:7.5. +# Note that this package is NOT the salome geometry module but a standalone +# version of that module that now appears to be abandoned. Packaging the +# original salome geometry module requires packaging the salome kernel and the +# salome gui module. +# Masked for removal in 30 days or whenever sci-libs/opencascade:7.4.0:::gentoo +# is removed. +sci-libs/geom
