Copied .gentoo standard file layout

.gentoo/install.sh

@@ -13,4 +13,4 @@ EBUILD="$(find "${ROOT}" -name "*.ebuild" | head -n1)"
 echo "Installing ebuild $EBUILD"
 
 localexec ebuild "$EBUILD" manifest
-localexec emerge "$@" "$EBUILD" 
+localexec emerge "$@" "$EBUILD"

.gentoo/metadata/layout.conf

@@ -1 +1,49 @@
-masters = science
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+# For details on this file, see the layout.conf section of the
+# portage(5) man page.
+
+repo-name = science
+
+# manifest-hashes specify hashes used for new/updated entries
+# the current set went live on 2017-11-21, per 2017-11-12 Council meeting
+# https://archives.gentoo.org/gentoo-dev/message/ba2e5d9666ebd7e1bff1143485a37856
+manifest-hashes = BLAKE2B SHA512
+
+# The following hashes are required on all Manifest entries. If any
+# of them are missing, repoman will refetch and rehash old distfiles.
+# Otherwise, old distfiles will keep using their current hash set.
+manifest-required-hashes = BLAKE2B
+
+# 2013-04-09 gentoo's council says to deprecate EAPIs 1 and 2 (bug #470670).
+# 2014-02-25 council meeting deprecated EAPIs 0 and 3.
+# 2014-03-11 council meeting banned EAPI 1.
+# 2015-10-11 council meeting deprecated EAPI 4.
+# 2016-01-10 council meeting banned EAPI 3.
+# 2018-05-13 council meeting deprecated EAPI 5 for ebuilds.
+eapis-banned = 0 1 2 3 4 5 6
+
+# Bug #337853 - gentoo's council says to enable
+# --echangelog by default for the "gentoo" repo
+# INFRA NOTE 2015/08/08: No more old ChangeLogs in Git
+update-changelog = false
+
+# Make egencache generate newer (more reliable)
+# md5-dict cache format (see bug #409445).
+# NOTE: list md5-dict first so clients prefer it
+# INFRA NOTE: Format 'pms' was removed on Aug 6 2012. (Announced prior as Aug 1
+# 2012 was the removal date)
+cache-formats = md5-dict
+
+# Support for implicit masters is deprecated, so we need to explicitly
+# specify that this repo does not depend on any masters, in order
+# to distinguish it from repos that rely on the deprecated behavior.
+masters = gentoo
+
+# Use thin Manifests for Git
+thin-manifests = true
+
+# Sign Git commits, and NOT Manifests
+sign-commits = true
+sign-manifests = false

.gentoo/overlay/metadata/layout.conf

@@ -0,0 +1,2 @@
+masters = gentoo science
+auto-sync = false

.gentoo/overlay/profiles/repo_name

@@ -0,0 +1 @@
+local_opfvta

.gentoo/overlay/sci-misc/opfvta/metadata.xml

@@ -0,0 +1,34 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>horea.christ@gmail.com</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<longdescription lang="en">
+		Given the need for inter-subject and inter-study comparability, spatial
+		map registration to a standardized space is an indispensable part of
+		Magnetic Resonance Imaging (MRI). Mouse MRI workflows commonly utilize
+		high-level interfaces optimized for human data --- and adapt the data
+		to the interface rather than vice-versa. Quality control (QC) is
+		commonly performed by interactive operator inspection, making it
+		infrequent, open to bias, slow, and unreproducible. In this paper we
+		present a novel registration workflow accessible via both Bash and
+		Python, which uses the full flexibility of low-level interfaces from
+		one of the most popular normalization toolkits (ANTs). We provide an
+		optimized set of parameters for mouse brain registration, and propose
+		a standard space suited to harmonize mouse brain data across
+		modalities. Additionally, we present QC workflows, which can
+		automatically assess the registration quality of current as well as
+		past processed datasets. With regard to both structural and functional
+		considerations, we showcase the capabilities of this novel workflow
+		compared to a legacy workflow (representative of common practices
+		--- which we detail and comment).
+	</longdescription>
+	<use>
+		<flag name="scanner-data">Use primary data in proprietary scanner format.</flag>
+	</use>
+	<upstream>
+		<remote-id type="bitbucket">TheChymera/irsabi</remote-id>
+	</upstream>
+</pkgmetadata>

.gentoo/overlay/sci-misc/opfvta/opfvta-99999.ebuild

@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Whole-Brain Map and Assay Analysis of Mouse VTA Dopaminergic Activation"
+HOMEPAGE="https://bitbucket.org/TheChymera/opfvta"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="scanner-data"
+KEYWORDS=""
+
+DEPEND=""
+RDEPEND="
+	>=dev-python/repsep_utils-0.3.1
+	>=dev-python/seaborn-0.9.0
+	>=dev-python/statsmodels-0.9.0
+	>=dev-tex/pythontex-0.16
+	app-text/texlive[publishers,science,xetex]
+	dev-python/matplotlib
+	dev-python/numpy
+	dev-python/pandas
+	dev-tex/biblatex
+	dev-tex/rubber
+	media-gfx/graphviz
+	sci-biology/ABI-connectivity-data
+	sci-biology/samri
+	scanner-data? ( sci-biology/opfvta_data )
+	!scanner-data? ( sci-biology/opfvta_bidsdata )
+"

.gentoo/overlays/science

@@ -1,5 +1,5 @@
 [science]
-location = /var/repos/science
+location = /var/db/repos/science
 sync-type = git
 sync-uri = https://anongit.gentoo.org/git/proj/sci.git
 priority = 7777

.gentoo/portage/make.conf

@@ -0,0 +1,14 @@
+COMMON_FLAGS="-O2 -pipe"
+CFLAGS="${COMMON_FLAGS}"
+CXXFLAGS="${COMMON_FLAGS}"
+FCFLAGS="${COMMON_FLAGS}"
+FFLAGS="${COMMON_FLAGS}"
+
+# NOTE: This stage was built with the bindist Use flag enabled
+
+# This sets the language of build output to English.
+# Please keep this setting intact when reporting bugs.
+LC_MESSAGES=C
+
+USE="${USE} latex science"
+ACCEPT_LICENSE="*"

.gentoo/portage/package.accept_keywords/gen

@@ -0,0 +1,2 @@
+*/* ~amd64
+=sci-misc/opfvta-99999 **

.gentoo/portage/package.mask/bugs

@@ -0,0 +1,2 @@
+# Not migrated to >=pandas-2.0.0 yet
+>=dev-python/pandas-2.0.0

.gentoo/portage/repos.conf/gentoo

@@ -0,0 +1,13 @@
+[gentoo]
+location = /var/db/repos/gentoo
+sync-type = git
+# Official "sync-friendly git mirror of repo/gentoo with caches and metadata"
+# Currently not suggested for production use.
+# sync-uri = https://anongit.gentoo.org/git/repo/sync/gentoo.git
+# GitHub mirror which saves the Gentoo project bandwidth. *This* sync-friendly git mirror is preferred)
+sync-uri = https://github.com/gentoo-mirror/gentoo.git
+sync-git-verify-commit-signature = yes
+
+# Default clone-depth setting does a shallow clone of the git repository.
+# For a full clone and ability to view git log/changes, set clone-depth = 0.
+# NOTE: A full clone o

.gentoo/portage/repos.conf/local_opfvta

@@ -0,0 +1,2 @@
+[local_opfvta]
+location = /var/db/repos/local_opfvta

.gentoo/portage/repos.conf/science

@@ -0,0 +1,5 @@
+[science]
+location = /var/db/repos/science
+sync-type = git
+sync-uri = https://anongit.gentoo.org/git/proj/sci.git
+priority = 7777

.gentoo/profiles/categories

@@ -0,0 +1 @@
+sci-publications

.gentoo/profiles/repo_name

@@ -1 +1 @@
-mouse-brain-atlases_generator_gentoo
+opfvta_gentoo

.gentoo/sci-publications/opfvta/metadata.xml

@@ -0,0 +1,34 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>horea.christ@gmail.com</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<longdescription lang="en">
+		Given the need for inter-subject and inter-study comparability, spatial
+		map registration to a standardized space is an indispensable part of
+		Magnetic Resonance Imaging (MRI). Mouse MRI workflows commonly utilize
+		high-level interfaces optimized for human data --- and adapt the data
+		to the interface rather than vice-versa. Quality control (QC) is
+		commonly performed by interactive operator inspection, making it
+		infrequent, open to bias, slow, and unreproducible. In this paper we
+		present a novel registration workflow accessible via both Bash and
+		Python, which uses the full flexibility of low-level interfaces from
+		one of the most popular normalization toolkits (ANTs). We provide an
+		optimized set of parameters for mouse brain registration, and propose
+		a standard space suited to harmonize mouse brain data across
+		modalities. Additionally, we present QC workflows, which can
+		automatically assess the registration quality of current as well as
+		past processed datasets. With regard to both structural and functional
+		considerations, we showcase the capabilities of this novel workflow
+		compared to a legacy workflow (representative of common practices
+		--- which we detail and comment).
+	</longdescription>
+	<use>
+		<flag name="scanner-data">Use primary data in proprietary scanner format.</flag>
+	</use>
+	<upstream>
+		<remote-id type="bitbucket">TheChymera/irsabi</remote-id>
+	</upstream>
+</pkgmetadata>

.gentoo/sci-publications/opfvta/opfvta-99999.ebuild

@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit distutils-r1
+
+DESCRIPTION="Whole-Brain Map and Assay Analysis of Mouse VTA Dopaminergic Activation"
+HOMEPAGE="https://bitbucket.org/TheChymera/opfvta"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="scanner-data"
+KEYWORDS=""
+
+DEPEND=""
+RDEPEND="
+	app-text/texlive[publishers,science,xetex]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	>=dev-python/seaborn-0.9.0[${PYTHON_USEDEP}]
+	>=dev-python/statsmodels-0.9.0[${PYTHON_USEDEP}]
+	>=dev-tex/pythontex-0.16[${PYTHON_USEDEP}]
+	media-gfx/graphviz
+	>=sci-biology/samri-0.4[${PYTHON_USEDEP}]
+	scanner-data? ( sci-biology/opfvta_data )
+	!scanner-data? ( sci-biology/opfvta_bidsdata )
+"

Containerfile

@@ -108,4 +108,6 @@ RUN printf '{ \
     } \
   ] \
 }' > /.reproenv.json
+RUN apt-get update -qq 
+RUN apt-get install make -qq 
 # End saving to specification to JSON.