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Update biopython, gsd, and griddataformats (#35827)

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* 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>
This commit is contained in:
Rocco Meli 2023-03-07 17:47:04 +01:00 committed by GitHub
parent c4e5ee8831
commit 335ae31a59
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 44 additions and 8 deletions
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4
var/spack/repos/builtin/packages/py-biopython/package.py
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@ -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")

41
var/spack/repos/builtin/packages/py-griddataformats/package.py
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@ -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"))

7
var/spack/repos/builtin/packages/py-gsd/package.py
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@ -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"))