py-antspyx: new package (#30964)

* py-antspyx: new package

Also adds required dependencies.

Requires options to ITK to enable the right support libraries, and
patches to remove tune the setup and provide resources rather than
downloading libraries/"submodules" on the fly.

* Fix patch URL

* Style fixes.

* bump version and re-include `git clone ...` as resource

5 files changed, 144 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/itk/package.py b/var/spack/repos/builtin/packages/itk/package.py
index 0c26de59d3..b38659642f 100644
--- a/var/spack/repos/builtin/packages/itk/package.py
+++ b/var/spack/repos/builtin/packages/itk/package.py
@@ -38,6 +38,7 @@ class Itk(CMakePackage):
     variant("review", default=False, description="enable modules under review")
     variant("rtk", default=False, description="build the RTK (Reconstruction Toolkit module")
     variant("minc", default=False, description="enable support for MINC files")
+    variant("antspy", default=False, description="enable support features for antspy")
 
     # TODO: This will not work if the resource is pulled from a spack mirror.
     # The build process will checkout the appropriate commit but it needs to be
@@ -76,6 +77,9 @@ class Itk(CMakePackage):
             self.define_from_variant("Module_RTK", "rtk"),
             self.define_from_variant("Module_ITKIOMINC", "minc"),
             self.define_from_variant("Module_ITKIOTransformMINC", "minc"),
+            self.define_from_variant("Module_MGHIO", "antspy"),
+            self.define_from_variant("Module_GenericLabelInterpolator", "antspy"),
+            self.define_from_variant("Module_AdaptiveDenoising", "antspy"),
         ]
 
         if not use_mkl:
diff --git a/var/spack/repos/builtin/packages/py-antspyx/fix-itk-gtest.diff b/var/spack/repos/builtin/packages/py-antspyx/fix-itk-gtest.diff
new file mode 100644
index 0000000000..f1794db931
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-antspyx/fix-itk-gtest.diff
@@ -0,0 +1,12 @@
+--- spack-src/ants/lib/CMakeLists.txt.orig	2021-11-17 20:09:44.586523746 +0100
++++ spack-src/ants/lib/CMakeLists.txt	2021-11-17 20:10:14.057924013 +0100
+@@ -10,6 +10,9 @@
+ find_package(ITK REQUIRED)
+ include(${ITK_USE_FILE})
+ 
++# Somehow not passed through from ITK
++find_package(GTest REQUIRED)
++
+ 
+ ## SETUP PYBIND11 ##
+ add_subdirectory(pybind11)
diff --git a/var/spack/repos/builtin/packages/py-antspyx/package.py b/var/spack/repos/builtin/packages/py-antspyx/package.py
new file mode 100644
index 0000000000..54315c5163
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-antspyx/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyAntspyx(PythonPackage):
+    """Advanced Normalization Tools in Python."""
+
+    homepage = "https://pypi.org/project/antspyx/"
+    pypi = "antspyx/antspyx-0.3.7.tar.gz"
+
+    version("0.3.7", sha256="cd831eb966d4ce82cc0afb65edddd8e2db6b439d418316e6356199f966104c1b")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("cmake@3.10:", type="build")
+    depends_on("itk+review+antspy")
+
+    depends_on("pil", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-scikit-image", type=("build", "run"))
+    depends_on("py-scikit-learn", type=("build", "run"))
+    depends_on("py-statsmodels", type=("build", "run"))
+    depends_on("py-webcolors", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-chart-studio", type=("build", "run"))
+    depends_on("py-nibabel", type=("build", "run"))
+
+    # from ITK, somehow does not get passed through. Required for building, together with
+    # the following patch
+    depends_on("googletest")
+    patch("fix-itk-gtest.diff")
+
+    patch("submodule-imposter.diff")
+
+    resource(
+        name="submodule-imposter-pybind11",
+        git="https://github.com/stnava/pybind11/",
+        destination="ants/lib",
+    )
+
+    resource(
+        name="submodule-imposter-antscore",
+        git="https://github.com/ANTsX/ANTs.git",
+        commit="871cad073908952b095e4b520335fc441e059264",
+        destination="ants/lib",
+        when="@0.3.7",  # ANTs dependency needs updating for every version
+    )
+
+    def setup_build_environment(self, env):
+        env.set("ITK_DIR", self.spec["itk"].prefix)
diff --git a/var/spack/repos/builtin/packages/py-antspyx/submodule-imposter.diff b/var/spack/repos/builtin/packages/py-antspyx/submodule-imposter.diff
new file mode 100644
index 0000000000..994548b757
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-antspyx/submodule-imposter.diff
@@ -0,0 +1,52 @@
+--- spack-src/scripts/configure_ANTsPy.sh.orig	2021-11-19 13:27:28.551737371 +0100
++++ spack-src/scripts/configure_ANTsPy.sh	2021-11-19 13:28:07.422251249 +0100
+@@ -1,26 +1,7 @@
+ #!/bin/bash
+ 
+ # ---------------------------------------------
+-# clone pybind11 into library directory
+-
+-cd ants/lib # go to lib dir
+-if [[ ! -d ~/pybind11 ]]; then
+-  git clone https://github.com/stnava/pybind11.git
+-#  git clone https://github.com/ncullen93/pybind11.git
+-fi
+-cd ../../ # go back to main dir
+-
+-# ---------------------------------------------
+-# create local ~/.antspy dir and move package data to it
+-
+-if [[ ! -d ~/.antspy ]]; then
+-    mkdir ~/.antspy
+-fi
+-
+-cp data/* ~/.antspy/
+-
+-# ---------------------------------------------
+-# clone ANTs and move all files into library directory
++# move all files from ANTs into library directory
+ 
+ antsgit=https://github.com/ANTsX/ANTs.git
+ antstag=4528978446c73ed09927ea5ae1721b280d534dc0 # 2020 n4 type
+@@ -30,20 +11,11 @@
+ 
+ # if antscore doesnt exist, create it
+ if [[ ! -d antscore ]] ; then
+-    git clone $antsbranch $antsgit antsrepo
+-
+     if [[ ! -d antscore ]] ; then
+         mkdir antscore
+     fi
+ 
+-    cd antsrepo # go to antscore
+-    # check out right branch
+-    if [[ -d .git ]]; then
+-        git checkout master
+-        git pull
+-        git checkout $antstag
+-    fi
+-    cd ..
++    ln -sf ANTs antsrepo
+     # copy antscore files into library
+     cp -r antsrepo/Examples/*  antscore/
+     cp -r antsrepo/Examples/include/*  antscore
diff --git a/var/spack/repos/builtin/packages/py-webcolors/package.py b/var/spack/repos/builtin/packages/py-webcolors/package.py
new file mode 100644
index 0000000000..4cd4740675
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-webcolors/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyWebcolors(PythonPackage):
+    """Working with color names and values formats defined by HTML and CSS."""
+
+    homepage = "https://pypi.org/project/webcolors/"
+    pypi = "webcolors/webcolors-1.11.1.tar.gz"
+
+    version("1.11.1", sha256="76f360636957d1c976db7466bc71dcb713bb95ac8911944dffc55c01cb516de6")
+
+    depends_on("python@3.5:", type=("build", "run"))
+    depends_on("py-setuptools", type=("build"))