New package: py-imagecodecs (#34098)

* [libjpeg-turbo] Added version 2.1.3

* [imagecodecs] Added jpeg deependency commented outconglicting libraries

* [WIP]

* [py-imagecodecs] modifying setup.py to work with spack install locations

* [py-imagecodecs] Removed comments and unneeded dependencies

* [py-imagecodecs] removed some comments and fixed up some flake8 complaints

* [py-imagecodecs] flake8

* [py-imagecodecs] fixed import

* [@spackbot] updating style on behalf of qwertos

Co-authored-by: James A Zilberman <jazrc@rit.edu>
Co-authored-by: qwertos <qwertos@users.noreply.github.com>

1 files changed, 110 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-imagecodecs/package.py b/var/spack/repos/builtin/packages/py-imagecodecs/package.py
new file mode 100644
index 0000000000..cd669aedc3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-imagecodecs/package.py
@@ -0,0 +1,110 @@
+# 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 PyImagecodecs(PythonPackage):
+    """Imagecodecs is a Python library that provides block-oriented,
+    in-memory buffer transformation, compression, and decompression
+    functions for use in the tifffile, czifile, zarr, and other
+    scientific image input/output modules.."""
+
+    homepage = "https://www.lfd.uci.edu/~gohlke/"
+    pypi = "imagecodecs/imagecodecs-2022.2.22.tar.gz"
+
+    version("2022.2.22", sha256="062bef6b003290a8163abed2744b406854238208dfdd41cf7165253c6e01c0bd")
+
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-numpy@1.19.2:", type=("build", "run"))
+    depends_on("py-setuptools@18.0:", type="build")
+    depends_on("py-cython@0.29.27:", type="build")
+    depends_on("py-bitshuffle@0.3.5:", type=("build", "run"))
+
+    depends_on("brotli@1.0.9:")
+    depends_on("bzip2@1.0.8:")
+    depends_on("c-blosc@1.21.1:")
+    depends_on("cfitsio@3.49:")
+    depends_on("giflib@5.2.1:")
+    depends_on("jxrlib-debian@1.1: +shared")
+    depends_on("lcms@2.13.1:")
+    depends_on("libaec@1.0.6:")
+    depends_on("libdeflate@1.10:")
+    depends_on("jpeg")
+    depends_on("liblzf@3.6:")
+    depends_on("xz@5.2.5:")
+    depends_on("libpng@1.6.37:")
+    depends_on("libspng@0.7.2:")
+    depends_on("libtiff@4.3.0:")
+    depends_on("libwebp@1.2.2:")
+    depends_on("openjpeg@2.4.0:")
+    depends_on("snappy@1.1.9:")
+    depends_on("zlib@1.2.11:")
+    depends_on("zopfli@1.0.3: +shared")
+    depends_on("zstd@1.5.2:")
+
+    def patch(self):
+        spec = self.spec
+
+        filter_file(
+            "'/usr/include/openjpeg-2.3', '/usr/include/openjpeg-2.4'",
+            "'{0}',".format(
+                join_path(
+                    spec["openjpeg"].prefix.include,
+                    "openjpeg-{0}".format(spec["openjpeg"].version.up_to(2)),
+                )
+            ),
+            "setup.py",
+        )
+        # 238
+        filter_file(
+            "'/usr/include/zopfli'", "'{0}'".format(spec["zopfli"].prefix.include), "setup.py"
+        )
+        # 239
+        filter_file(
+            "append\('/usr/include/jxrlib'\)",  # noqa: W605
+            "extend(('{0}/libjxr/image', '{0}/libjxr/common', '{0}/libjxr/glue'))".format(  # noqa: E501
+                spec["jxrlib-debian"].prefix.include
+            ),
+            "setup.py",
+        )
+
+        # 367
+        filter_file(
+            "'os.path.join(include_base_path, 'zopfli')'",
+            "'{0}'".format(spec["zopfli"].prefix.include),
+            "setup.py",
+        )
+        # 377
+        filter_file(
+            "'os.path.join(include_base_path, 'libjxr')'",
+            "'{0}/libjxr'".format(spec["jxrlib-debian"].prefix.include),
+            "setup.py",
+        )
+        # 397
+        filter_file(
+            "'os.path.join(libjpeg12_base_path, 'include')'",
+            "'{0}'".format(spec["jpeg"].prefix.include),
+            "setup.py",
+        )
+        # 454
+        filter_file(
+            "'os.path.join(os.environ['LIBRARY_INC'], 'openjpeg-' + os.environ['openjpeg'])'",  # noqa: E501
+            "'{0}'".format(spec["openjpeg"].prefix.include),
+            "setup.py",
+        )
+        # 473
+        filter_file(
+            "'os.path.join(os.environ['PREFIX'], 'include', 'zopfli')'",
+            "'{0}'".format(spec["zopfli"].prefix.include),
+            "setup.py",
+        )
+        # 476
+        filter_file(
+            "'os.path.join(os.environ['PREFIX'], 'include', 'jxrlib')'",
+            "'{0}/libjxr'".format(spec["jxrlib-debian"].prefix.include),
+            "setup.py",
+        )