py-pycortex: add new package (#27432)

1 files changed, 53 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-pycortex/package.py b/var/spack/repos/builtin/packages/py-pycortex/package.py
new file mode 100644
index 0000000000..158c600114
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pycortex/package.py
@@ -0,0 +1,53 @@
+# Copyright 2013-2021 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 import *
+
+
+class PyPycortex(PythonPackage):
+    """Python Cortical mapping software for fMRI data."""
+
+    # When pycortex is started it creates a user config file (on linux located
+    # in ~/.config/pycortex) which can be problematic when reinstalling a newer
+    # version with spack due to hardscoded absolute paths of the pycortex module
+
+    homepage = "https://github.com/gallantlab/pycortex"
+    pypi = "pycortex/pycortex-1.2.2.tar.gz"
+
+    version('1.2.2', sha256='ac46ed6a1dc727c3126c2b5d7916fc0ac21a6510c32a5edcd3b8cfb7b2128414')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython', type='build')
+    depends_on('py-future', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-tornado@4.3:', type=('build', 'run'))
+    depends_on('py-shapely', type=('build', 'run'))
+    depends_on('py-lxml', type=('build', 'run'))
+    depends_on('py-html5lib', type=('build', 'run'))
+    depends_on('py-h5py', type=('build', 'run'))
+    depends_on('py-numexpr', type=('build', 'run'))
+    depends_on('py-cython', type=('build', 'run'))  # is in install_requires
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('pil', type=('build', 'run'))
+    depends_on('py-nibabel', type=('build', 'run'))
+    depends_on('py-networkx@2.1:', type=('build', 'run'))
+    depends_on('py-imageio', type=('build', 'run'))
+    depends_on('py-wget', type=('build', 'run'))
+
+    # inkscape is not in spack
+    # TODO remove this patch and add inkscape dependency once it is in
+    def patch(self):
+        # remove inkscape dependency
+        filter_file('from .testing_utils import INKSCAPE_VERSION', '',
+                    'cortex/utils.py',
+                    string=True)
+        filter_file('open_inkscape=True', 'open_inkscape=False',
+                    'cortex/utils.py',
+                    string=True)
+        filter_file('from .testing_utils import INKSCAPE_VERSION',
+                    'INKSCAPE_VERSION = None',
+                    'cortex/svgoverlay.py',
+                    string=True)