Fix: py-adios Cython run (#28223)

* Fix: py-adios Cython run

Always run Cython before `py-adios` installs.
This makes sure the `.cpp` files from `.pyx` files are freshly
created and work with newer CPython versions than the one checked
in.

* Cleanup: `rm` -> `os.remove`

1 files changed, 23 insertions, 21 deletions

diff --git a/var/spack/repos/builtin/packages/py-adios/package.py b/var/spack/repos/builtin/packages/py-adios/package.py
index e7c6d87df3..ef60055d09 100644
--- a/var/spack/repos/builtin/packages/py-adios/package.py
+++ b/var/spack/repos/builtin/packages/py-adios/package.py
@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack import *
 
 
@@ -10,19 +12,25 @@ class PyAdios(PythonPackage):
     """NumPy bindings of ADIOS1"""
 
     homepage = "https://csmd.ornl.gov/adios"
-    url      = "https://github.com/ornladios/ADIOS/archive/v1.12.0.tar.gz"
+    url      = "https://github.com/ornladios/ADIOS/archive/v1.13.1.tar.gz"
     git      = "https://github.com/ornladios/ADIOS.git"
 
-    maintainers = ['ax3l']
+    maintainers = ['ax3l', 'jychoi-hpc']
 
     version('develop', branch='master')
     version('1.13.1', sha256='b1c6949918f5e69f701cabfe5987c0b286793f1057d4690f04747852544e157b')
-    version('1.13.0', sha256='7b5ee8ff7a5f7215f157c484b20adb277ec0250f87510513edcc25d2c4739f50')
-    version('1.12.0', sha256='22bc22c157322abec2d1a0817a259efd9057f88c2113e67d918a9a5ebcb3d88d')
-    version('1.11.1', sha256='9f5c10b9471a721ba57d1cf6e5a55a7ad139a6c12da87b4dc128539e9eef370e')
-    version('1.11.0', sha256='e89d14ccbe7181777225e0ba6c272c0941539b8ccd440e72ed5a9457441dae83')
-    version('1.10.0', sha256='6713069259ee7bfd4d03f47640bf841874e9114bab24e7b0c58e310c42a0ec48')
-    version('1.9.0', sha256='23b2bb70540d51ab0855af0b205ca484fd1bd963c39580c29e3133f9e6fffd46')
+    version('1.13.0', sha256='7b5ee8ff7a5f7215f157c484b20adb277ec0250f87510513edcc25d2c4739f50',
+            deprecated=True)
+    version('1.12.0', sha256='22bc22c157322abec2d1a0817a259efd9057f88c2113e67d918a9a5ebcb3d88d',
+            deprecated=True)
+    version('1.11.1', sha256='9f5c10b9471a721ba57d1cf6e5a55a7ad139a6c12da87b4dc128539e9eef370e',
+            deprecated=True)
+    version('1.11.0', sha256='e89d14ccbe7181777225e0ba6c272c0941539b8ccd440e72ed5a9457441dae83',
+            deprecated=True)
+    version('1.10.0', sha256='6713069259ee7bfd4d03f47640bf841874e9114bab24e7b0c58e310c42a0ec48',
+            deprecated=True)
+    version('1.9.0', sha256='23b2bb70540d51ab0855af0b205ca484fd1bd963c39580c29e3133f9e6fffd46',
+            deprecated=True)
 
     variant('mpi', default=True,
             description='Enable MPI support')
@@ -36,14 +44,6 @@ class PyAdios(PythonPackage):
                    when='@{0} +mpi'.format(v),
                    type=['build', 'link', 'run'])
 
-    # NOTE: this dependency is a work-around for a bug in Adios itself.
-    # Specifically, Adios uses code that was generated by Cython 0.28.2.
-    # This code won't compile against the Python 3.7 C API.
-    # See https://github.com/ornladios/ADIOS/issues/202 and
-    # the first entry under "Bug Fixes" at
-    # https://github.com/cython/cython/blob/0.29.x/CHANGES.rst
-    depends_on('python@:3.6')
-
     depends_on('py-numpy', type=['build', 'run'])
     depends_on('mpi', when='+mpi')
     depends_on('py-mpi4py', type=['run'], when='+mpi')
@@ -60,10 +60,12 @@ class PyAdios(PythonPackage):
             return 'setup.py'
 
     def build_clib(self, spec, prefix):
-        # calls: make [MPI=y] python
-        args = ''
+        # calls: make CYTHON=y [MPI=y] python
+        args = ['CYTHON=y']
         if '+mpi' in self.spec:
-            args = 'MPI=y '
-        args += 'python'
+            args += ['MPI=y']
+        args += ['python']
         with working_dir(self.build_directory):
-            make(args)
+            os.remove('adios.cpp')
+            os.remove('adios_mpi.cpp')
+            make(*args, parallel=False)