py-gpy: re-cythonize & drop python upperbound (#40089)

* py-gpy: drop cython induced python upperbound

* py-gpy: bump scipy

* py-fn-py: python bounds for old version, new version w/o

* py-statsmodels: force recythonization

* py-gpy: clarifying comment about cython build type

3 files changed, 24 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/py-fn-py/package.py b/var/spack/repos/builtin/packages/py-fn-py/package.py
index 543bbe5a36..253ebf7ead 100644
--- a/var/spack/repos/builtin/packages/py-fn-py/package.py
+++ b/var/spack/repos/builtin/packages/py-fn-py/package.py
@@ -13,6 +13,10 @@ class PyFnPy(PythonPackage):
     homepage = "https://github.com/fnpy/fn.py"
     url = "https://github.com/fnpy/fn.py/archive/v0.5.2.tar.gz"
 
+    version("0.6.0", sha256="85d4d4ae6ce3c13e9dbe45df2895188f742ebddbf100a95d360d73a8965ee0c8")
     version("0.5.2", sha256="fda2253d792867a79514496932630622df9340f214a2f4b2d597b60a8cc3d96b")
 
     depends_on("py-setuptools", type="build")
+
+    # Uses inspect.getargspec
+    depends_on("python@:3.10", when="@:0.5", type=("run", "build"))
diff --git a/var/spack/repos/builtin/packages/py-gpy/package.py b/var/spack/repos/builtin/packages/py-gpy/package.py
index ad21efa1eb..82a85e94ec 100644
--- a/var/spack/repos/builtin/packages/py-gpy/package.py
+++ b/var/spack/repos/builtin/packages/py-gpy/package.py
@@ -13,13 +13,23 @@ class PyGpy(PythonPackage):
     pypi = "gpy/GPy-1.9.9.tar.gz"
     maintainers("liuyangzhuan")
 
+    version("1.10.0", sha256="a2b793ef8d0ac71739e7ba1c203bc8a5afa191058b42caa617e0e29aa52aa6fb")
     version("1.9.9", sha256="04faf0c24eacc4dea60727c50a48a07ddf9b5751a3b73c382105e2a31657c7ed")
     version("0.8.8", sha256="e135d928cf170e2ec7fb058a035b5a7e334dc6b84d0bfb981556782528341988")
 
     depends_on("py-setuptools", type="build")
     depends_on("py-numpy@1.7:", type=("build", "run"))
     depends_on("py-scipy@0.16:", type=("build", "run"))
+    depends_on("py-scipy@1.3:", when="@1.10.0:", type=("build", "run"))
     depends_on("py-six", type=("build", "run"))
     depends_on("py-paramz@0.9.0:", type=("build", "run"))
+    # cython is install_requires, but not used at runtime, so stick to build type
     depends_on("py-cython@0.29:", type="build")
-    depends_on("python@:3.8", type=("build", "run"))
+
+    @run_before("install")
+    def touch_sources(self):
+        # This packages uses deprecated build_ext, for which we cannot
+        # automatically force recythonization.
+        # See also https://github.com/SheffieldML/GPy/pull/1020
+        for src in find(".", "*.pyx"):
+            touch(src)
diff --git a/var/spack/repos/builtin/packages/py-statsmodels/package.py b/var/spack/repos/builtin/packages/py-statsmodels/package.py
index 10cc6c39cc..c99901d9ae 100644
--- a/var/spack/repos/builtin/packages/py-statsmodels/package.py
+++ b/var/spack/repos/builtin/packages/py-statsmodels/package.py
@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack.package import *
 
 
@@ -50,6 +52,13 @@ class PyStatsmodels(PythonPackage):
 
     depends_on("py-pytest", type="test")
 
+    @run_before("install")
+    def remove_generated_sources(self):
+        # Automatic recythonization doesn't work here, because cythonize is called
+        # with force=False by default, so remove generated C files manually.
+        for f in find(".", "*.c"):
+            os.unlink(f)
+
     @run_after("install")
     @on_package_attributes(run_tests=True)
     def build_test(self):