meson, py-meson-python, py-pandas, py-pyproject-metadata, py-tzdata: bump

bluebrain/deployment/environments/applications_nse.yaml

@@ -20,7 +20,6 @@ spack:
           - py-bluepysnap
           - py-connectome-manipulator
           - py-entity-management
-          - py-minis-validation
           - py-morphio
           - py-morph-tool
           - py-neuror
@@ -46,15 +45,14 @@ spack:
     - emsim
     - placement-algorithm
     - psp-validation
-    - py-archngv
+    # - py-archngv
     - py-atlas-building-tools
     - py-bbp-analysis-framework
     - py-bbp-workflow
     - py-bbp-workflow-cli
     - py-bluepy
     - py-bluepysnap
     - py-entity-management
-    - py-minis-validation
     - py-morphio
     - py-neuror
     - py-morph-tool+neuron

bluebrain/repo-bluebrain/packages/py-bluepy/package.py

@@ -13,12 +13,12 @@ class PyBluepy(PythonPackage):
     git = "ssh://git@bbpgitlab.epfl.ch/nse/bluepy.git"
 
     version("develop", branch="main")
-    version("2.5.1", tag="bluepy-v2.5.1")
+    version("2.5.2", tag="bluepy-v2.5.2")
 
     depends_on("py-setuptools", type=("build", "run"))
 
     depends_on("py-libsonata@0.1.7:0", type=("build", "run"))
-    depends_on("py-pandas@1", type=("build", "run"))
+    depends_on("py-pandas@1,2.0.1:2", type=("build", "run"))
     depends_on("py-bluepy-configfile@0.1.20:", type=("build", "run"))
     depends_on("py-numpy@1.8:", type=("build", "run"))
     depends_on("py-h5py@3.0.1:3", type=("build", "run"))

bluebrain/repo-bluebrain/packages/py-fz-td-recipe/package.py

@@ -21,3 +21,4 @@ class PyFzTdRecipe(PythonPackage):
 
     depends_on("py-lxml", type=("build", "run"))
     depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))

bluebrain/sysconfig/bluebrain5/packages.yaml

@@ -138,6 +138,8 @@ packages:
     version: [1.22.4]  # bluepye{model,fe}: <1.24, neurondamus: <1.23
   py-numpy-quaternion:
     require: ~numba~scipy  # pulls in LLVM, spatial-index does not need that
+  py-pandas:
+    version: [2.1.0]
   py-setuptools:
     version: [63.0.0]  # required by py-numpy
   qt:

var/spack/repos/builtin/packages/meson/package.py

@@ -18,6 +18,11 @@ class Meson(PythonPackage):
 
     maintainers("eli-schwartz", "michaelkuhn")
 
+    version("1.2.0", sha256="603489f0aaa6305f806c6cc4a4455a965f22290fc74f65871f589b002110c790")
+    version("1.1.1", sha256="1c3b9e1a3a36b51adb5de498d582fd5cbf6763fadbcf151de9f2a762e02bd2e6")
+    version("1.1.0", sha256="f29a3e14062043d75e82d16f1e41856e6b1ed7a7c016e10c7b13afa7ee6364cc")
+    version("1.0.2", sha256="1f1239c3091668643f7d2086663d6afd8cc87fbab84fe7462bc18b9ba6d65de8")
+    version("1.0.1", sha256="4ab3a5c0060dc22bdefb04507efc6c38acb910e91bcd467a38e1fa211e5a6cfe")
     version("1.0.0", sha256="a2ada84d43c7e57400daee80a880a1f5003d062b2cb6c9be1747b0db38f2eb8d")
     version("0.64.1", sha256="1d12a4bc1cf3ab18946d12cf0b6452e5254ada1ad50aacc97f87e2cccd7da315")
     version("0.64.0", sha256="6477993d781b6efea93091616a6d6a0766c0e026076dbeb11249bf1c9b49a347")
@@ -60,7 +65,9 @@ class Meson(PythonPackage):
     depends_on("python@3.7:", when="@0.62.0:", type=("build", "run"))
     depends_on("python@3.6:", when="@0.57.0:", type=("build", "run"))
     depends_on("python@3.5:", type=("build", "run"))
+    depends_on("py-setuptools@42:", when="@0.62.0:", type=("build", "run"))
     depends_on("py-setuptools", type=("build", "run"))
+    depends_on("ninja@1.8.2:", when="@0.62.0:", type="run")
     depends_on("ninja", type="run")
 
     # By default, Meson strips the rpath on installation. This patch disables

var/spack/repos/builtin/packages/py-meson-python/package.py

@@ -14,6 +14,13 @@ class PyMesonPython(PythonPackage):
 
     maintainers("eli-schwartz", "adamjstewart", "rgommers")
 
+    # Needed for py-scikit-image, deprecate and remove once 0.13.0 is officially released
+    version("0.13.1", sha256="63b3170001425c42fa4cfedadb9051cbd28925ff8eed7c40d36ba0099e3c7618")
+    version(
+        "0.13.0.pre0",
+        sha256="8d537a0304709c31c11ffa34872a62a4c06a6a6c24fc862b7fb4306f3e881b95",
+        deprecated=True,
+    )
     version("0.12.0", sha256="8cb159a8093a2e73cfa897f8092ec93b74e3842f94dff7fde381c6fe0e0b064d")
     version("0.11.0", sha256="110258837c2ffe762f5f855c7ea5385f1edd44074e93a0f317ffefc7aab42b09")
     version("0.10.0", sha256="08dd122c1074dbd5c55b53993a719cca73dd8216372c91217f7a550260f9e7e1")
@@ -22,19 +29,22 @@ class PyMesonPython(PythonPackage):
     version("0.8.0", sha256="b5c8a2727e6f6feaffc1db513244c9bdb5d0f689b45e24f4529b649b7710daf7")
     version("0.7.0", sha256="9fcfa350f44ca80dd4f5f9c3d251725434acf9a07d9618f382e6cc4629dcbe84")
 
-    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-colorama", when="platform=windows", type=("build", "run"))
     depends_on("meson@0.63.3:", when="@0.11:", type=("build", "run"))
     depends_on("meson@0.63:", when="@0.9:0.10", type=("build", "run"))
     depends_on("meson@0.62:", type=("build", "run"))
+    depends_on("py-pyproject-metadata@0.7.1:", when="@0.13:", type=("build", "run"))
     depends_on("py-pyproject-metadata@0.6.1:", when="@0.12:", type=("build", "run"))
     depends_on("py-pyproject-metadata@0.5:", type=("build", "run"))
     depends_on("py-tomli@1:", when="@0.11: ^python@:3.10", type=("build", "run"))
     depends_on("py-tomli@1:", when="@:0.10", type=("build", "run"))
-    depends_on("py-typing-extensions@3.7.4:", when="@0.12: ^python@:3.9", type=("build", "run"))
-    depends_on("py-typing-extensions@3.7.4:", when="@:0.11 ^python@:3.7", type=("build", "run"))
-    depends_on("py-colorama", when="platform=windows", type=("build", "run"))
+    depends_on("py-setuptools@60:", when="@0.13: ^python@3.12:", type=("build", "run"))
 
     # https://github.com/mesonbuild/meson-python/pull/111
     conflicts("platform=darwin os=ventura", when="@:0.7")
     conflicts("platform=darwin os=monterey", when="@:0.7")
     conflicts("platform=darwin os=bigsur", when="@:0.7")
+
+    # Historical dependencies
+    depends_on("py-typing-extensions@3.7.4:", when="@0.12 ^python@:3.9", type=("build", "run"))
+    depends_on("py-typing-extensions@3.7.4:", when="@:0.11 ^python@:3.7", type=("build", "run"))

var/spack/repos/builtin/packages/py-pandas/package.py

@@ -1,4 +1,4 @@
-# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2023 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)
@@ -15,8 +15,15 @@ class PyPandas(PythonPackage):
     homepage = "https://pandas.pydata.org/"
     pypi = "pandas/pandas-1.2.0.tar.gz"
 
-    maintainers = ["adamjstewart"]
+    maintainers("adamjstewart")
 
+    version("2.1.0", sha256="62c24c7fc59e42b775ce0679cfa7b14a5f9bfb7643cfbe708c960699e05fb918")
+    version("2.0.3", sha256="c02f372a88e0d17f36d3093a644c73cfc1788e876a7c4bcb4020a77512e2043c")
+    version("2.0.2", sha256="dd5476b6c3fe410ee95926873f377b856dbc4e81a9c605a0dc05aaccc6a7c6c6")
+    version("2.0.1", sha256="19b8e5270da32b41ebf12f0e7165efa7024492e9513fb46fb631c5022ae5709d")
+    version("2.0.0", sha256="cda9789e61b44463c1c4fe17ef755de77bcd13b09ba31c940d20f193d63a5dc8")
+    version("1.5.3", sha256="74a3fd7e5a7ec052f183273dc7b0acd3a863edf7520f5d3a1765c04ffdb3b0b1")
+    version("1.5.2", sha256="220b98d15cee0b2cd839a6358bd1f273d0356bf964c1a1aeb32d47db0215488b")
     version("1.5.1", sha256="249cec5f2a5b22096440bd85c33106b6102e0672204abd2d5c014106459804ee")
     version("1.5.0", sha256="3ee61b881d2f64dd90c356eb4a4a4de75376586cd3c9341c6c0fcaae18d52977")
     version("1.4.4", sha256="ab6c0d738617b675183e5f28db32b5148b694ad9bba0a40c3ea26d96b431db67")
@@ -55,70 +62,74 @@ class PyPandas(PythonPackage):
     version("0.24.2", sha256="4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2")
     version("0.24.1", sha256="435821cb2501eabbcee7e83614bd710940dc0cf28b5afbc4bdb816c31cec71af")
     version("0.23.4", sha256="5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4")
-    version("0.21.1", sha256="c5f5cba88bf0659554c41c909e1f78139f6fce8fa9315a29a23692b38ff9788a")
-    version("0.20.0", sha256="54f7a2bb2a7832c0446ad51d779806f07ec4ea2bb7c9aea4b83669fa97e778c4")
-    version("0.19.2", sha256="6f0f4f598c2b16746803c8bafef7c721c57e4844da752d36240c0acf97658014")
-    version("0.19.0", sha256="4697606cdf023c6b7fcb74e48aaf25cf282a1a00e339d2d274cf1b663748805b")
-    version("0.18.0", sha256="c975710ce8154b50f39a46aa3ea88d95b680191d1d9d4b5dd91eae7215e01814")
-    version("0.16.1", sha256="570d243f8cb068bf780461b9225d2e7bef7c90aa10d43cf908fe541fc92df8b6")
-    version("0.16.0", sha256="4013de6f8796ca9d2871218861823bd9878a8dfacd26e08ccf9afdd01bbad9f1")
 
     # Required dependencies
+    # https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#python-version-support
+    depends_on("python@3.9:3.11", when="@2.1:", type=("build", "run"))
+    depends_on("python@3.8:3.11", when="@1.5:2.0", type=("build", "run"))
+    depends_on("python@3.8:3.10", when="@1.4", type=("build", "run"))
+    depends_on("python@:3.10", when="@1.3.3:1.3", type=("build", "run"))
+    depends_on("python@:3.9", when="@1.1.3:1.3.2", type=("build", "run"))
+    depends_on("python@:3.8", when="@0.25.2:1.1.2", type=("build", "run"))
+    depends_on("python@:3.7", when="@:0.25.1", type=("build", "run"))
+
+    # pyproject.toml
+    depends_on("py-meson-python@0.13.1", when="@2.1:", type="build")
+    depends_on("meson@1.0.1", when="@2.1:", type="build")
+    depends_on("py-cython@0.29.33:2", when="@2:", type="build")
+    depends_on("py-cython@0.29.32:2", when="@1.4.4:", type="build")
+    depends_on("py-cython@0.29.30:2", when="@1.4.3:", type="build")
+    depends_on("py-cython@0.29.24:2", when="@1.3.4:", type="build")
+    depends_on("py-cython@0.29.21:2", when="@1.1.3:", type="build")
+    depends_on("py-cython@0.29.16:2", when="@1.1:", type="build")
+    depends_on("py-cython@0.29.13:2", when="@1:", type="build")
+    depends_on("py-versioneer+toml", when="@2:", type="build")
+
     # https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#dependencies
-    depends_on("python@3.8:", type=("build", "run"), when="@1.4:")
-    depends_on("python@3.7.1:", type=("build", "run"), when="@1.2:")
-    depends_on("python@3.6.1:", type=("build", "run"), when="@1:")
-    depends_on("python@3.5.3:", type=("build", "run"), when="@0.25:")
-    depends_on("py-cython@0.29.13:2", type="build", when="@1:")
-    depends_on("py-cython@0.29.16:2", type="build", when="@1.1:")
-    depends_on("py-cython@0.29.21:2", type="build", when="@1.1.3:")
-    depends_on("py-cython@0.29.24:2", type="build", when="@1.3.4:")
-    depends_on("py-cython@0.29.30:2", type="build", when="@1.4.3:")
-    depends_on("py-cython@0.29.32:2", type="build", when="@1.4.4:")
-    depends_on("py-setuptools@24.2.0:", type="build")
-    depends_on("py-setuptools@38.6.0:", type="build", when="@1.3:")
-    depends_on("py-setuptools@51.0.0:", type="build", when="@1.3.2:")
+    depends_on("py-numpy@1.22.4:", when="@2.1:", type=("build", "run"))
+    depends_on("py-numpy@1.20.3:", when="@1.5:", type=("build", "run"))
+    depends_on("py-numpy@1.18.5:", when="@1.4:", type=("build", "run"))
+    depends_on("py-numpy@1.17.3:", when="@1.3:", type=("build", "run"))
+    depends_on("py-numpy@1.16.5:", when="@1.2:", type=("build", "run"))
+    depends_on("py-numpy@1.15.4:", when="@1.1:", type=("build", "run"))
+    depends_on("py-numpy@1.13.3:", when="@0.25:", type=("build", "run"))
     depends_on("py-numpy", type=("build", "run"))
     # 'NUMPY_IMPORT_ARRAY_RETVAL' was removed in numpy@1.19
-    depends_on("py-numpy@:1.18", type=("build", "run"), when="@:0.25")
-    depends_on("py-numpy@1.13.3:", type=("build", "run"), when="@0.25:")
-    depends_on("py-numpy@1.15.4:", type=("build", "run"), when="@1.1:")
-    depends_on("py-numpy@1.16.5:", type=("build", "run"), when="@1.2:")
-    depends_on("py-numpy@1.17.3:", type=("build", "run"), when="@1.3:")
-    depends_on("py-numpy@1.18.5:", type=("build", "run"), when="@1.4:")
-    depends_on("py-numpy@1.20.3:", type=("build", "run"), when="@1.5:")
+    depends_on("py-numpy@:1.18", when="@:0.25", type=("build", "run"))
+    depends_on("py-python-dateutil@2.8.2:", when="@2:", type=("build", "run"))
+    depends_on("py-python-dateutil@2.8.1:", when="@1.4:", type=("build", "run"))
+    depends_on("py-python-dateutil@2.7.3:", when="@1.1:", type=("build", "run"))
+    depends_on("py-python-dateutil@2.6.1:", when="@0.25:", type=("build", "run"))
     depends_on("py-python-dateutil", type=("build", "run"))
-    depends_on("py-python-dateutil@2.6.1:", type=("build", "run"), when="@0.25:")
-    depends_on("py-python-dateutil@2.7.3:", type=("build", "run"), when="@1.1:")
-    depends_on("py-python-dateutil@2.8.1:", type=("build", "run"), when="@1.4:")
+    depends_on("py-pytz@2020.1:", when="@1.4:", type=("build", "run"))
+    depends_on("py-pytz@2017.3:", when="@1.2:", type=("build", "run"))
     depends_on("py-pytz@2017.2:", type=("build", "run"))
-    depends_on("py-pytz@2017.3:", type=("build", "run"), when="@1.2:")
-    depends_on("py-pytz@2020.1:", type=("build", "run"), when="@1.4:")
+    depends_on("py-tzdata@2022.1:", when="@2:", type=("build", "run"))
 
     # Recommended dependencies
-    # https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#recommended-dependencies
+    # https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#performance-dependencies-recommended
+    depends_on("py-numexpr@2.8.0:", when="@2.1:", type=("build", "run"))
+    depends_on("py-numexpr@2.7.3:", when="@1.5:", type=("build", "run"))
+    depends_on("py-numexpr@2.7.1:", when="@1.4:", type=("build", "run"))
+    depends_on("py-numexpr@2.7.0:", when="@1.3:", type=("build", "run"))
+    depends_on("py-numexpr@2.6.8:", when="@1.2:", type=("build", "run"))
+    depends_on("py-numexpr@2.6.2:", when="@0.25:", type=("build", "run"))
     depends_on("py-numexpr", type=("build", "run"))
-    depends_on("py-numexpr@2.6.2:", type=("build", "run"), when="@0.25:")
-    depends_on("py-numexpr@2.6.8:", type=("build", "run"), when="@1.2:")
-    depends_on("py-numexpr@2.7.0:", type=("build", "run"), when="@1.3:")
-    depends_on("py-numexpr@2.7.1:", type=("build", "run"), when="@1.4:")
-    depends_on("py-numexpr@2.7.3:", type=("build", "run"), when="@1.5:")
+    depends_on("py-bottleneck@1.3.4:", when="@2.1:", type=("build", "run"))
+    depends_on("py-bottleneck@1.3.2:", when="@1.5:", type=("build", "run"))
+    depends_on("py-bottleneck@1.3.1:", when="@1.4:", type=("build", "run"))
+    depends_on("py-bottleneck@1.2.1:", when="@0.25:", type=("build", "run"))
     depends_on("py-bottleneck", type=("build", "run"))
-    depends_on("py-bottleneck@1.2.1:", type=("build", "run"), when="@0.25:")
-    depends_on("py-bottleneck@1.3.1:", type=("build", "run"), when="@1.4:")
-    depends_on("py-bottleneck@1.3.2:", type=("build", "run"), when="@1.5:")
+    depends_on("py-numba@0.55.2:", when="@2.1:", type=("build", "run"))
+    depends_on("py-numba@0.53.1:", when="@2.0:", type=("build", "run"))
 
     # Optional dependencies
     # https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html#optional-dependencies
 
-    @property
-    def import_modules(self):
-        modules = super(__class__, self).import_modules
-
-        ignored_imports = [
-            "pandas.tests",
-            "pandas.plotting._matplotlib",
-            "pandas.core._numba.kernels",
-        ]
+    # Historical dependencies
+    depends_on("py-setuptools@61:", when="@2.0", type="build")
+    depends_on("py-setuptools@51:", when="@1.3.2:1", type="build")
+    depends_on("py-setuptools@38.6:", when="@1.3.0:1.3.1", type="build")
+    depends_on("py-setuptools@24.2:", when="@:1.2", type="build")
 
-        return [i for i in modules if not any(map(i.startswith, ignored_imports))]
+    skip_modules = ["pandas.tests", "pandas.plotting._matplotlib", "pandas.core._numba.kernels"]

var/spack/repos/builtin/packages/py-pyproject-metadata/package.py

@@ -1,4 +1,4 @@
-# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2023 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)
@@ -12,8 +12,8 @@ class PyPyprojectMetadata(PythonPackage):
     homepage = "https://github.com/FFY00/python-pyproject-metadata"
     pypi = "pyproject-metadata/pyproject-metadata-0.6.1.tar.gz"
 
+    version("0.7.1", sha256="0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67")
     version("0.6.1", sha256="b5fb09543a64a91165dfe85796759f9e415edc296beb4db33d1ecf7866a862bd")
 
-    depends_on("python@3.7:", type=("build", "run"))
     depends_on("py-setuptools@42:", type="build")
     depends_on("py-packaging@19:", type=("build", "run"))

var/spack/repos/builtin/packages/py-tzdata/package.py

@@ -0,0 +1,17 @@
+# Copyright 2013-2023 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 PyTzdata(PythonPackage):
+    """Provider of IANA time zone data."""
+
+    homepage = "https://github.com/python/tzdata"
+    pypi = "tzdata/tzdata-2023.3.tar.gz"
+
+    version("2023.3", sha256="11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a")
+
+    depends_on("py-setuptools@40.8:", type="build")