commit: b20587d17391fd67cf942830328eb1befffed609 Author: Jérôme Carretero <cJ <AT> zougloub <DOT> eu> AuthorDate: Sat Nov 12 10:12:23 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue Nov 15 11:53:43 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b20587d1
add github remote-id when possible Semi-automatically done with: https://gitlab.com/cJ/gentoo-bug-881037-github-reproducible-downloads Closes: https://github.com/gentoo/sci/pull/1182 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> app-arch/libdeflate/metadata.xml | 5 ++++- dev-cpp/Fastor/metadata.xml | 3 +++ dev-cpp/highwayhash/metadata.xml | 3 +++ dev-cpp/xor_singleheader/metadata.xml | 3 +++ dev-lang/yaggo/metadata.xml | 3 +++ dev-libs/simclist/metadata.xml | 3 +++ dev-libs/tut/metadata.xml | 5 ++++- dev-ml/lacaml/metadata.xml | 1 + dev-python/asciitree/metadata.xml | 5 ++++- dev-python/fiat/metadata.xml | 1 + dev-python/hopcroftkarp/metadata.xml | 19 +++++++++++-------- dev-python/json_tricks/metadata.xml | 2 +- dev-python/kmapper/metadata.xml | 3 +++ dev-python/meshpy/metadata.xml | 1 + dev-python/numba/metadata.xml | 3 +++ dev-python/python-gantt/metadata.xml | 5 ++++- dev-python/pyvote/metadata.xml | 5 ++++- dev-python/pyzo/metadata.xml | 3 +++ dev-python/repsep_utils/metadata.xml | 13 ++++++++----- dev-python/snakemake/metadata.xml | 1 + dev-python/sphinx-argparse/metadata.xml | 3 +++ dev-python/ufl/metadata.xml | 1 + dev-util/makefile2graph/metadata.xml | 3 +++ dev-util/plog/metadata.xml | 3 +++ media-libs/libgfx/metadata.xml | 3 +++ media-libs/mmg/metadata.xml | 3 +++ sci-biology/BRAKER/metadata.xml | 3 +++ sci-biology/GAL/metadata.xml | 3 +++ sci-biology/RAILS/metadata.xml | 3 +++ sci-biology/VelvetOptimiser/metadata.xml | 3 +++ sci-biology/afni/metadata.xml | 3 +++ sci-biology/angsd/metadata.xml | 3 +++ sci-biology/ants/metadata.xml | 3 +++ sci-biology/bamql/metadata.xml | 3 +++ sci-biology/barrnap/metadata.xml | 3 +++ sci-biology/bismark/metadata.xml | 3 +++ sci-biology/btl_bloomfilter/metadata.xml | 3 +++ sci-biology/bx-python/metadata.xml | 1 + sci-biology/dcm2niix/metadata.xml | 3 +++ sci-biology/dcmstack/metadata.xml | 3 +++ sci-biology/diamond/metadata.xml | 3 +++ sci-biology/fastqc/metadata.xml | 3 +++ sci-biology/ffindex/metadata.xml | 3 +++ sci-biology/longstitch/metadata.xml | 3 +++ sci-biology/mreps/metadata.xml | 3 +++ sci-biology/nextclip/metadata.xml | 3 +++ sci-biology/ngs/metadata.xml | 3 +++ sci-biology/ntCard/metadata.xml | 3 +++ sci-biology/prokka/metadata.xml | 3 +++ sci-biology/pyfaidx/metadata.xml | 1 + sci-biology/quicktree/metadata.xml | 3 +++ sci-biology/rtg-tools/metadata.xml | 3 +++ sci-biology/seqtk/metadata.xml | 3 +++ sci-biology/spm/metadata.xml | 3 +++ sci-biology/trans-abyss/metadata.xml | 3 +++ sci-biology/trim_galore/metadata.xml | 3 +++ sci-biology/ugene/metadata.xml | 3 +++ sci-chemistry/erkale/metadata.xml | 3 +++ sci-chemistry/relion/metadata.xml | 3 +++ sci-libs/HDF5Plugin-Zstandard/metadata.xml | 3 +++ sci-libs/fast5/metadata.xml | 3 +++ sci-libs/nipy/metadata.xml | 1 + sci-libs/scikits_video/metadata.xml | 1 + sci-libs/spyking-circus/metadata.xml | 3 +++ sci-libs/torchvision/metadata.xml | 17 ++++++++++------- sci-libs/vxl/metadata.xml | 1 + sci-libs/wannier90/metadata.xml | 1 + sci-mathematics/freefem++/metadata.xml | 3 +++ sci-mathematics/pulp/metadata.xml | 1 + sci-mathematics/ripser/metadata.xml | 27 +++++++++++++++------------ sci-misc/elmer-fem/metadata.xml | 1 + sci-physics/feyncalc/metadata.xml | 3 +++ sci-physics/qcdloop/metadata.xml | 3 +++ sci-visualization/clip/metadata.xml | 3 +++ sci-visualization/fsleyes/metadata.xml | 5 ++++- 75 files changed, 235 insertions(+), 39 deletions(-) diff --git a/app-arch/libdeflate/metadata.xml b/app-arch/libdeflate/metadata.xml index 6e347494a..fe240766f 100644 --- a/app-arch/libdeflate/metadata.xml +++ b/app-arch/libdeflate/metadata.xml @@ -8,9 +8,12 @@ <maintainer type="person"> <email>[email protected]</email> <name>Aisha Tammy</name> - </maintainer> + </maintainer> <maintainer type="project"> <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ebiggers/libdeflate</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-cpp/Fastor/metadata.xml b/dev-cpp/Fastor/metadata.xml index e97c4322a..9937ac435 100644 --- a/dev-cpp/Fastor/metadata.xml +++ b/dev-cpp/Fastor/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">romeric/Fastor</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-cpp/highwayhash/metadata.xml b/dev-cpp/highwayhash/metadata.xml index ef6b5dcd5..ce99f4b00 100644 --- a/dev-cpp/highwayhash/metadata.xml +++ b/dev-cpp/highwayhash/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Christoph Junghans</name> </maintainer> + <upstream> + <remote-id type="github">google/highwayhash</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-cpp/xor_singleheader/metadata.xml b/dev-cpp/xor_singleheader/metadata.xml index e97c4322a..cebb00f2c 100644 --- a/dev-cpp/xor_singleheader/metadata.xml +++ b/dev-cpp/xor_singleheader/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">FastFilter/xor_singleheader</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-lang/yaggo/metadata.xml b/dev-lang/yaggo/metadata.xml index 138cb7705..61d3a34e2 100644 --- a/dev-lang/yaggo/metadata.xml +++ b/dev-lang/yaggo/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gmarcais/yaggo</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/simclist/metadata.xml b/dev-libs/simclist/metadata.xml index 8426fdb21..62c13e1e4 100644 --- a/dev-libs/simclist/metadata.xml +++ b/dev-libs/simclist/metadata.xml @@ -15,4 +15,7 @@ <flag name="dump">Disable building of dump and restore functionalities</flag> <flag name="hash">Allow list_hash() to work exclusively on memory locations</flag> </use> + <upstream> + <remote-id type="github">mij/simclist</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/tut/metadata.xml b/dev-libs/tut/metadata.xml index 026cdb22b..7a070008d 100644 --- a/dev-libs/tut/metadata.xml +++ b/dev-libs/tut/metadata.xml @@ -1,8 +1,11 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> <maintainer type="project"> <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">mrzechonek/tut-framework</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-ml/lacaml/metadata.xml b/dev-ml/lacaml/metadata.xml index 1094bf3da..24157e1f0 100644 --- a/dev-ml/lacaml/metadata.xml +++ b/dev-ml/lacaml/metadata.xml @@ -15,5 +15,6 @@ </longdescription> <upstream> <remote-id type="bitbucket">mmottl/lacaml</remote-id> + <remote-id type="github">mmottl/lacaml</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/asciitree/metadata.xml b/dev-python/asciitree/metadata.xml index f6f63a810..8b000b491 100644 --- a/dev-python/asciitree/metadata.xml +++ b/dev-python/asciitree/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">mbr/asciitree</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/fiat/metadata.xml b/dev-python/fiat/metadata.xml index d08e0d509..23d9fd64c 100644 --- a/dev-python/fiat/metadata.xml +++ b/dev-python/fiat/metadata.xml @@ -17,5 +17,6 @@ support Hermite and nonconforming elements. </longdescription> <upstream> <remote-id type="bitbucket">fenics-project/fiat</remote-id> + <remote-id type="github">FEniCS/fiat</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/hopcroftkarp/metadata.xml b/dev-python/hopcroftkarp/metadata.xml index 2f2c0b51c..6959005e7 100644 --- a/dev-python/hopcroftkarp/metadata.xml +++ b/dev-python/hopcroftkarp/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Science Project</name> - </maintainer> + <maintainer type="person"> + <email>[email protected]</email> + <name>Aisha Tammy</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">sofiatolaosebikan/hopcroftkarp</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/json_tricks/metadata.xml b/dev-python/json_tricks/metadata.xml index f5804b4b0..2967a86bd 100644 --- a/dev-python/json_tricks/metadata.xml +++ b/dev-python/json_tricks/metadata.xml @@ -21,6 +21,6 @@ </longdescription> <upstream> <remote-id type="pypi">json-tricks</remote-id> + <remote-id type="github">mverleg/pyjson_tricks</remote-id> </upstream> </pkgmetadata> - diff --git a/dev-python/kmapper/metadata.xml b/dev-python/kmapper/metadata.xml index e97c4322a..006b418f5 100644 --- a/dev-python/kmapper/metadata.xml +++ b/dev-python/kmapper/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">scikit-tda/kepler-mapper</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/meshpy/metadata.xml b/dev-python/meshpy/metadata.xml index fff86775c..77991f7a8 100644 --- a/dev-python/meshpy/metadata.xml +++ b/dev-python/meshpy/metadata.xml @@ -15,5 +15,6 @@ Hang Si. Both are included in the package in slightly modified versions. </longdescription> <upstream> <remote-id type="pypi">MeshPy</remote-id> + <remote-id type="github">inducer/meshpy</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/numba/metadata.xml b/dev-python/numba/metadata.xml index e97c4322a..43b02aeec 100644 --- a/dev-python/numba/metadata.xml +++ b/dev-python/numba/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">numba/numba</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/python-gantt/metadata.xml b/dev-python/python-gantt/metadata.xml index 3febd988f..18071f943 100644 --- a/dev-python/python-gantt/metadata.xml +++ b/dev-python/python-gantt/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> <maintainer type="person"> @@ -13,4 +13,7 @@ Python-Gantt makes it possible to easily draw gantt charts from Python and export outputs as scalable vector graphics (SVG). </longdescription> + <upstream> + <remote-id type="github">stefanSchinkel/gantt</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyvote/metadata.xml b/dev-python/pyvote/metadata.xml index d208f0f55..5fbf687f3 100644 --- a/dev-python/pyvote/metadata.xml +++ b/dev-python/pyvote/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> <maintainer type="person"> @@ -16,4 +16,7 @@ (or normal) probability density function for outcomes, or a fixed outcome probability. </longdescription> + <upstream> + <remote-id type="github">TheChymera/pyvote</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyzo/metadata.xml b/dev-python/pyzo/metadata.xml index ae9640ffb..8019eb9d1 100644 --- a/dev-python/pyzo/metadata.xml +++ b/dev-python/pyzo/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">pyzo/pyzo</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/repsep_utils/metadata.xml b/dev-python/repsep_utils/metadata.xml index aa31ba351..9656580bb 100644 --- a/dev-python/repsep_utils/metadata.xml +++ b/dev-python/repsep_utils/metadata.xml @@ -1,15 +1,18 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Horea Christian</name> - </maintainer> - <longdescription lang="en"> + <maintainer type="person"> + <email>[email protected]</email> + <name>Horea Christian</name> + </maintainer> + <longdescription lang="en"> Utilities for compiling and developing RepSeP-style articles, such as the reference implementation. The package contains generic boilerplate code for PythonTeX-interaction, as used by all RepSeP-style articles, as well as an executable file allowing single-script execution for development and debugging purposes. </longdescription> + <upstream> + <remote-id type="github">TheChymera/repsep_utils</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml index 440b5758f..d9550c50f 100644 --- a/dev-python/snakemake/metadata.xml +++ b/dev-python/snakemake/metadata.xml @@ -8,5 +8,6 @@ <upstream> <remote-id type="bitbucket">johanneskoester/snakemake</remote-id> <remote-id type="pypi">snakemake</remote-id> + <remote-id type="github">snakemake/snakemake</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/sphinx-argparse/metadata.xml b/dev-python/sphinx-argparse/metadata.xml index ae9640ffb..3b119bca0 100644 --- a/dev-python/sphinx-argparse/metadata.xml +++ b/dev-python/sphinx-argparse/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">ashb/sphinx-argparse</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ufl/metadata.xml b/dev-python/ufl/metadata.xml index 142da2a70..3dff10f36 100644 --- a/dev-python/ufl/metadata.xml +++ b/dev-python/ufl/metadata.xml @@ -14,5 +14,6 @@ mathematical notation. </longdescription> <upstream> <remote-id type="bitbucket">fenics-project/ufl</remote-id> + <remote-id type="github">FEniCS/ufl</remote-id> </upstream> </pkgmetadata> diff --git a/dev-util/makefile2graph/metadata.xml b/dev-util/makefile2graph/metadata.xml index 138cb7705..41bb35aa0 100644 --- a/dev-util/makefile2graph/metadata.xml +++ b/dev-util/makefile2graph/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">lindenb/makefile2graph</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-util/plog/metadata.xml b/dev-util/plog/metadata.xml index 7203fb853..40a8e36c6 100644 --- a/dev-util/plog/metadata.xml +++ b/dev-util/plog/metadata.xml @@ -4,4 +4,7 @@ <maintainer type="person"> <email>[email protected]</email> </maintainer> + <upstream> + <remote-id type="github">SergiusTheBest/plog</remote-id> + </upstream> </pkgmetadata> diff --git a/media-libs/libgfx/metadata.xml b/media-libs/libgfx/metadata.xml index ae9640ffb..2103548da 100644 --- a/media-libs/libgfx/metadata.xml +++ b/media-libs/libgfx/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">mjgarland/libgfx</remote-id> + </upstream> </pkgmetadata> diff --git a/media-libs/mmg/metadata.xml b/media-libs/mmg/metadata.xml index 2b9123050..bd7221f19 100644 --- a/media-libs/mmg/metadata.xml +++ b/media-libs/mmg/metadata.xml @@ -13,4 +13,7 @@ <flag name="scotch">Use SCOTCH TOOL for renumbering</flag> <flag name="vtk">Use VTK I/O</flag> </use> + <upstream> + <remote-id type="github">MmgTools/mmg</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/BRAKER/metadata.xml b/sci-biology/BRAKER/metadata.xml index 138cb7705..aa4766e73 100644 --- a/sci-biology/BRAKER/metadata.xml +++ b/sci-biology/BRAKER/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">Gaius-Augustus/BRAKER</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/GAL/metadata.xml b/sci-biology/GAL/metadata.xml index 138cb7705..480ba370b 100644 --- a/sci-biology/GAL/metadata.xml +++ b/sci-biology/GAL/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">The-Sequence-Ontology/GAL</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/RAILS/metadata.xml b/sci-biology/RAILS/metadata.xml index 138cb7705..a3f152e56 100644 --- a/sci-biology/RAILS/metadata.xml +++ b/sci-biology/RAILS/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/RAILS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/VelvetOptimiser/metadata.xml b/sci-biology/VelvetOptimiser/metadata.xml index 138cb7705..cc34f33b5 100644 --- a/sci-biology/VelvetOptimiser/metadata.xml +++ b/sci-biology/VelvetOptimiser/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">tseemann/VelvetOptimiser</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml index acf637dca..cbb8a4299 100644 --- a/sci-biology/afni/metadata.xml +++ b/sci-biology/afni/metadata.xml @@ -13,4 +13,7 @@ Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity. </longdescription> + <upstream> + <remote-id type="github">afni/afni</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml index 138cb7705..ed9e5b12d 100644 --- a/sci-biology/angsd/metadata.xml +++ b/sci-biology/angsd/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ANGSD/angsd</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ants/metadata.xml b/sci-biology/ants/metadata.xml index 9f969ddf9..e8372d21b 100644 --- a/sci-biology/ants/metadata.xml +++ b/sci-biology/ants/metadata.xml @@ -21,4 +21,7 @@ <use> <flag name="vtk">Optional support for a number of surface enabled tools (via sci-libs/vtk).</flag> </use> + <upstream> + <remote-id type="github">ANTsX/ANTs</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bamql/metadata.xml b/sci-biology/bamql/metadata.xml index 138cb7705..927a160ba 100644 --- a/sci-biology/bamql/metadata.xml +++ b/sci-biology/bamql/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">BoutrosLaboratory/bamql</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/barrnap/metadata.xml b/sci-biology/barrnap/metadata.xml index 138cb7705..9183ef1ec 100644 --- a/sci-biology/barrnap/metadata.xml +++ b/sci-biology/barrnap/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">tseemann/barrnap</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bismark/metadata.xml b/sci-biology/bismark/metadata.xml index 4c433a8ca..4ee13c559 100644 --- a/sci-biology/bismark/metadata.xml +++ b/sci-biology/bismark/metadata.xml @@ -20,4 +20,7 @@ and gapped alignments; (4) Alignment seed length, number of mismatches etc. are adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context. </longdescription> + <upstream> + <remote-id type="github">FelixKrueger/Bismark</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/btl_bloomfilter/metadata.xml b/sci-biology/btl_bloomfilter/metadata.xml index 138cb7705..1e02bb596 100644 --- a/sci-biology/btl_bloomfilter/metadata.xml +++ b/sci-biology/btl_bloomfilter/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/btl_bloomfilter</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index 3e13342e3..80a22b44a 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -12,5 +12,6 @@ <upstream> <remote-id type="bitbucket">james_taylor/bx-python</remote-id> <remote-id type="pypi">bx-python</remote-id> + <remote-id type="github">bxlab/bx-python</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml index 9c9e19081..773e706a6 100644 --- a/sci-biology/dcm2niix/metadata.xml +++ b/sci-biology/dcm2niix/metadata.xml @@ -19,4 +19,7 @@ format to the NIfTI format. ICOM provides many ways to store/compress image data, known as transfer syntaxes. </longdescription> + <upstream> + <remote-id type="github">rordenlab/dcm2niix</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/dcmstack/metadata.xml b/sci-biology/dcmstack/metadata.xml index ae9640ffb..0272cf14e 100644 --- a/sci-biology/dcmstack/metadata.xml +++ b/sci-biology/dcmstack/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">moloney/dcmstack</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/diamond/metadata.xml b/sci-biology/diamond/metadata.xml index 138cb7705..ac7dfc24a 100644 --- a/sci-biology/diamond/metadata.xml +++ b/sci-biology/diamond/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bbuchfink/diamond</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml index 7c86089a2..f13c6ccba 100644 --- a/sci-biology/fastqc/metadata.xml +++ b/sci-biology/fastqc/metadata.xml @@ -13,4 +13,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">s-andrews/FastQC</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml index 138cb7705..a9577a9c3 100644 --- a/sci-biology/ffindex/metadata.xml +++ b/sci-biology/ffindex/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ahcm/ffindex</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/longstitch/metadata.xml b/sci-biology/longstitch/metadata.xml index 138cb7705..b25087121 100644 --- a/sci-biology/longstitch/metadata.xml +++ b/sci-biology/longstitch/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/LongStitch</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mreps/metadata.xml b/sci-biology/mreps/metadata.xml index 8417d1580..a60e8c1b5 100644 --- a/sci-biology/mreps/metadata.xml +++ b/sci-biology/mreps/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gregorykucherov/mreps</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/nextclip/metadata.xml b/sci-biology/nextclip/metadata.xml index 138cb7705..b0874714e 100644 --- a/sci-biology/nextclip/metadata.xml +++ b/sci-biology/nextclip/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">richardmleggett/nextclip</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml index 138cb7705..f165e6cbc 100644 --- a/sci-biology/ngs/metadata.xml +++ b/sci-biology/ngs/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ncbi/ngs</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ntCard/metadata.xml b/sci-biology/ntCard/metadata.xml index 138cb7705..fb03df79c 100644 --- a/sci-biology/ntCard/metadata.xml +++ b/sci-biology/ntCard/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/ntCard</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml index 138cb7705..9272f0d9c 100644 --- a/sci-biology/prokka/metadata.xml +++ b/sci-biology/prokka/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">tseemann/prokka</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml index fd0f24633..47cc39d79 100644 --- a/sci-biology/pyfaidx/metadata.xml +++ b/sci-biology/pyfaidx/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="pypi">pyfaidx</remote-id> + <remote-id type="github">mdshw5/pyfaidx</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml index 8417d1580..e3ce321ed 100644 --- a/sci-biology/quicktree/metadata.xml +++ b/sci-biology/quicktree/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">khowe/quicktree</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml index 138cb7705..026053b60 100644 --- a/sci-biology/rtg-tools/metadata.xml +++ b/sci-biology/rtg-tools/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">RealTimeGenomics/rtg-tools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/seqtk/metadata.xml b/sci-biology/seqtk/metadata.xml index 138cb7705..a2d91d1c4 100644 --- a/sci-biology/seqtk/metadata.xml +++ b/sci-biology/seqtk/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">lh3/seqtk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/spm/metadata.xml b/sci-biology/spm/metadata.xml index ae9640ffb..d888971d1 100644 --- a/sci-biology/spm/metadata.xml +++ b/sci-biology/spm/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">spm/spm12</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/trans-abyss/metadata.xml b/sci-biology/trans-abyss/metadata.xml index 138cb7705..079fb5aae 100644 --- a/sci-biology/trans-abyss/metadata.xml +++ b/sci-biology/trans-abyss/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/transabyss</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/trim_galore/metadata.xml b/sci-biology/trim_galore/metadata.xml index 138cb7705..ac0e44aa7 100644 --- a/sci-biology/trim_galore/metadata.xml +++ b/sci-biology/trim_galore/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">FelixKrueger/TrimGalore</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ugene/metadata.xml b/sci-biology/ugene/metadata.xml index a3daeebd2..36e8936e5 100644 --- a/sci-biology/ugene/metadata.xml +++ b/sci-biology/ugene/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">ugeneunipro/ugene</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/erkale/metadata.xml b/sci-chemistry/erkale/metadata.xml index eea62e858..996e48735 100644 --- a/sci-chemistry/erkale/metadata.xml +++ b/sci-chemistry/erkale/metadata.xml @@ -18,4 +18,7 @@ ground-state electron momentum densities and Compton profiles, and core (x-ray absorption and x-ray Raman scattering) and valence electron excitation spectra of atoms and molecules. </longdescription> + <upstream> + <remote-id type="github">susilehtola/erkale</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml index cdabe7f2c..33e6e7e5d 100644 --- a/sci-chemistry/relion/metadata.xml +++ b/sci-chemistry/relion/metadata.xml @@ -12,4 +12,7 @@ <use> <flag name="gui">Enable relion gui</flag> </use> + <upstream> + <remote-id type="github">3dem/relion</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/HDF5Plugin-Zstandard/metadata.xml b/sci-libs/HDF5Plugin-Zstandard/metadata.xml index 753464ee5..a171606a6 100644 --- a/sci-libs/HDF5Plugin-Zstandard/metadata.xml +++ b/sci-libs/HDF5Plugin-Zstandard/metadata.xml @@ -5,4 +5,7 @@ <email>[email protected]</email> <name>Yiyang Wu</name> </maintainer> + <upstream> + <remote-id type="github">aparamon/HDF5Plugin-Zstandard</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/fast5/metadata.xml b/sci-libs/fast5/metadata.xml index 138cb7705..6f7127e91 100644 --- a/sci-libs/fast5/metadata.xml +++ b/sci-libs/fast5/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">mateidavid/fast5</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml index 327dd23d3..30440d9a2 100644 --- a/sci-libs/nipy/metadata.xml +++ b/sci-libs/nipy/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="pypi">nipy</remote-id> + <remote-id type="github">nipy/nipy</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/scikits_video/metadata.xml b/sci-libs/scikits_video/metadata.xml index 186bb5c9c..bdfe14284 100644 --- a/sci-libs/scikits_video/metadata.xml +++ b/sci-libs/scikits_video/metadata.xml @@ -14,5 +14,6 @@ </longdescription> <upstream> <remote-id type="pypi">scikit-video</remote-id> + <remote-id type="github">scikit-video/scikit-video</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/spyking-circus/metadata.xml b/sci-libs/spyking-circus/metadata.xml index 844f386de..89a208f6f 100644 --- a/sci-libs/spyking-circus/metadata.xml +++ b/sci-libs/spyking-circus/metadata.xml @@ -16,4 +16,7 @@ on datasets coming from in vitro retina with 252 electrodes MEA, from in vivo hippocampus with tetrodes, and in vivo and in vitro cortex data. </longdescription> + <upstream> + <remote-id type="github">spyking-circus/spyking-circus</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/torchvision/metadata.xml b/sci-libs/torchvision/metadata.xml index ad3ef354b..28985da70 100644 --- a/sci-libs/torchvision/metadata.xml +++ b/sci-libs/torchvision/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Jorge Pizarro Callejas</name> - </maintainer> - <use> - <flag name="cuda">Enable CUDA support if enabled in PyTorch</flag> - </use> + <maintainer type="person"> + <email>[email protected]</email> + <name>Jorge Pizarro Callejas</name> + </maintainer> + <use> + <flag name="cuda">Enable CUDA support if enabled in PyTorch</flag> + </use> + <upstream> + <remote-id type="github">pytorch/vision</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/vxl/metadata.xml b/sci-libs/vxl/metadata.xml index 22feba67c..f7d43af09 100644 --- a/sci-libs/vxl/metadata.xml +++ b/sci-libs/vxl/metadata.xml @@ -13,5 +13,6 @@ written in ANSI/ISO C++ and is designed to be portable over many platforms. </longdescription> <upstream> <remote-id type="sourceforge">vxl</remote-id> + <remote-id type="github">vxl/vxl</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/wannier90/metadata.xml b/sci-libs/wannier90/metadata.xml index a7ac8e977..273952673 100644 --- a/sci-libs/wannier90/metadata.xml +++ b/sci-libs/wannier90/metadata.xml @@ -18,5 +18,6 @@ <upstream> <doc>http://www.wannier.org/</doc> <remote-id type="launchpad">wannier90</remote-id> + <remote-id type="github">wannier-developers/wannier90</remote-id> </upstream> </pkgmetadata> diff --git a/sci-mathematics/freefem++/metadata.xml b/sci-mathematics/freefem++/metadata.xml index a605d78d7..5cee338ce 100644 --- a/sci-mathematics/freefem++/metadata.xml +++ b/sci-mathematics/freefem++/metadata.xml @@ -10,4 +10,7 @@ FreeFem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily. </longdescription> + <upstream> + <remote-id type="github">FreeFem/FreeFem-sources</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/pulp/metadata.xml b/sci-mathematics/pulp/metadata.xml index ce584d233..c86c3b501 100644 --- a/sci-mathematics/pulp/metadata.xml +++ b/sci-mathematics/pulp/metadata.xml @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="pypi">PuLP</remote-id> + <remote-id type="github">coin-or/pulp</remote-id> </upstream> </pkgmetadata> diff --git a/sci-mathematics/ripser/metadata.xml b/sci-mathematics/ripser/metadata.xml index fbef5ab11..05f38b851 100644 --- a/sci-mathematics/ripser/metadata.xml +++ b/sci-mathematics/ripser/metadata.xml @@ -1,16 +1,19 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Science Project</name> - </maintainer> - <use> - <flag name="progress">print progress of calculations in console</flag> - <flag name="sparsehash">use google sparsehash for storage</flag> - </use> + <maintainer type="person"> + <email>[email protected]</email> + <name>Aisha Tammy</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="progress">print progress of calculations in console</flag> + <flag name="sparsehash">use google sparsehash for storage</flag> + </use> + <upstream> + <remote-id type="github">Ripser/ripser</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/elmer-fem/metadata.xml b/sci-misc/elmer-fem/metadata.xml index feab34b47..37464c70a 100644 --- a/sci-misc/elmer-fem/metadata.xml +++ b/sci-misc/elmer-fem/metadata.xml @@ -7,6 +7,7 @@ </maintainer> <upstream> <remote-id type="sourceforge">svn</remote-id> + <remote-id type="github">ElmerCSC/elmerfem</remote-id> </upstream> <use> <flag name="gui">Build the ElmerGUI</flag> diff --git a/sci-physics/feyncalc/metadata.xml b/sci-physics/feyncalc/metadata.xml index 9e87f772e..826061ef4 100644 --- a/sci-physics/feyncalc/metadata.xml +++ b/sci-physics/feyncalc/metadata.xml @@ -19,4 +19,7 @@ <use> <flag name="FCtraditionalFormOutput">Use TraditionalForm typesetting.</flag> </use> + <upstream> + <remote-id type="github">FeynCalc/feyncalc</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/qcdloop/metadata.xml b/sci-physics/qcdloop/metadata.xml index 5b1b9cd40..84c79dc3b 100644 --- a/sci-physics/qcdloop/metadata.xml +++ b/sci-physics/qcdloop/metadata.xml @@ -12,4 +12,7 @@ <longdescription lang="en"> QCDLoop is a library of one-loop scalar Feynman integrals, evaluated close to four dimensions. First documented in arXiv:0712.1851 and recently in arXiv:1605.03181. </longdescription> + <upstream> + <remote-id type="github">scarrazza/qcdloop</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-visualization/clip/metadata.xml b/sci-visualization/clip/metadata.xml index e97c4322a..8f000a818 100644 --- a/sci-visualization/clip/metadata.xml +++ b/sci-visualization/clip/metadata.xml @@ -9,4 +9,7 @@ <email>[email protected]</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">asmuth/clip</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-visualization/fsleyes/metadata.xml b/sci-visualization/fsleyes/metadata.xml index 805623e43..d38edeff2 100644 --- a/sci-visualization/fsleyes/metadata.xml +++ b/sci-visualization/fsleyes/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> <maintainer type="person"> @@ -15,4 +15,7 @@ to FSLView, and aims to improve and expand upon this functionality in many ways. </longdescription> + <upstream> + <remote-id type="github">pauldmccarthy/fsleyes</remote-id> + </upstream> </pkgmetadata>
