Update biopython, gsd, and griddataformats (#35827)

* update mda dependencies

* apply black

* Update var/spack/repos/builtin/packages/py-gsd/package.py

* Update var/spack/repos/builtin/packages/py-griddataformats/package.py

* Update var/spack/repos/builtin/packages/py-griddataformats/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* remove numpy upper bound

* Update var/spack/repos/builtin/packages/py-griddataformats/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-gsd/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

3 files changed, 44 insertions, 8 deletions

diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py
index 06cf81f4b8..20cd97de50 100644
--- a/var/spack/repos/builtin/packages/py-biopython/package.py
+++ b/var/spack/repos/builtin/packages/py-biopython/package.py
@@ -15,6 +15,10 @@ class PyBiopython(PythonPackage):
     homepage = "https://biopython.org/wiki/Main_Page"
     pypi = "biopython/biopython-1.79.tar.gz"
 
+    maintainers("RMeli")
+
+    version("1.81", sha256="2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0")
+    version("1.80", sha256="52805e9af88767e450e2df8113b5bc59e964e2e8a7bb803a83570bdbb51c0e43")
     version("1.79", sha256="edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b")
     version("1.78", sha256="1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564")
     version("1.73", sha256="70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0")
diff --git a/var/spack/repos/builtin/packages/py-griddataformats/package.py b/var/spack/repos/builtin/packages/py-griddataformats/package.py
index a5195336ad..f4dc0ddca6 100644
--- a/var/spack/repos/builtin/packages/py-griddataformats/package.py
+++ b/var/spack/repos/builtin/packages/py-griddataformats/package.py
@@ -15,12 +15,39 @@ class PyGriddataformats(PythonPackage):
     homepage = "http://www.mdanalysis.org/GridDataFormats"
     pypi = "GridDataFormats/GridDataFormats-0.5.0.tar.gz"
 
-    version("0.5.0", sha256="f317ed60708de22d1b2a76ce89a00f722d903291b1055ff1018d441870c39d69")
-    version("0.4.1", sha256="b362662c2dc475e2a3895fe044eaaa9a707bd660fd109a63dac84a47236690a3")
-    version("0.4.0", sha256="f81d6b75aa7ebd9e8b64e14558c2d2583a0589829382beb4ef69860110261512")
-    version("0.3.3", sha256="938f0efcb3bc2f58ec85048b933942da8a52c134170acc97cb095f09d3698fbd")
+    maintainers("RMeli")
+
+    version("1.0.1", sha256="ad2c9ab7d672a6d8c426de7d083eee4f3e2b0bd59391675d30683c768ab83cc4")
+    version(
+        "0.5.0",
+        sha256="f317ed60708de22d1b2a76ce89a00f722d903291b1055ff1018d441870c39d69",
+        deprecated=True,
+    )
+    version(
+        "0.4.1",
+        sha256="b362662c2dc475e2a3895fe044eaaa9a707bd660fd109a63dac84a47236690a3",
+        deprecated=True,
+    )
+    version(
+        "0.4.0",
+        sha256="f81d6b75aa7ebd9e8b64e14558c2d2583a0589829382beb4ef69860110261512",
+        deprecated=True,
+    )
+    version(
+        "0.3.3",
+        sha256="938f0efcb3bc2f58ec85048b933942da8a52c134170acc97cb095f09d3698fbd",
+        deprecated=True,
+    )
 
-    depends_on("python@2.7:")
     depends_on("py-setuptools", type="build")
-    depends_on("py-numpy@1.0.3:", type=("build", "run"))
-    depends_on("py-six", type=("build", "run"))
+
+    depends_on("python@3.8:", when="@1:", type=("build", "run"))
+
+    depends_on("py-numpy@1.19:", when="@1:", type=("build", "run"))
+    depends_on("py-scipy", when="@1:", type=("build", "run"))
+    depends_on("py-mrcfile", when="@1:", type=("build", "run"))
+
+    # Deprecated
+    depends_on("python@2.7:", when="@0", type=("build", "run"))
+    depends_on("py-numpy@1.0.3:", when="@0", type=("build", "run"))
+    depends_on("py-six", when="@0", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-gsd/package.py b/var/spack/repos/builtin/packages/py-gsd/package.py
index 222016b91a..0b6d6ffb52 100644
--- a/var/spack/repos/builtin/packages/py-gsd/package.py
+++ b/var/spack/repos/builtin/packages/py-gsd/package.py
@@ -18,8 +18,13 @@ class PyGsd(PythonPackage):
     homepage = "https://gsd.readthedocs.io/en/stable/#"
     pypi = "gsd/gsd-1.9.3.tar.gz"
 
+    maintainers("RMeli")
+
+    version("2.8.0", sha256="f2b031a26a7a5bee5f3940dc2f36c5a5b6670307b297c526adf2e26c1f5b46ae")
     version("1.9.3", sha256="c6b37344e69020f69fda2b8d97f894cb41fd720840abeda682edd680d1cff838")
 
     depends_on("py-setuptools", type="build")
+    depends_on("py-setuptools@42:", type="build", when="@2.8.0:")
     depends_on("py-cython", type="build")
-    depends_on("py-numpy@1.9.3:19", type=("build", "run"))
+    depends_on("py-numpy@1.9.3:", type=("build", "run"))
+    depends_on("py-numpy@1.9.3:1", when="@:1", type=("build", "run"))