diff --git a/packages/bazel/package.py b/packages/bazel/package.py
index 64df14b13074675a697b11db7f52d5d302b08c58..72e562ca62928c2a718db9355fc709fc89b8b1b3 100644
--- a/packages/bazel/package.py
+++ b/packages/bazel/package.py
@@ -482,13 +482,14 @@ class Bazel(Package):
# https://blog.bazel.build/2021/05/21/bazel-4-1.html
conflicts("platform=darwin target=aarch64:", when="@:4.0")
- # patches for compiling bazel-4.1:4 with gcc-11
+ # patches for compiling various older bazels which had ICWYU
+ # violations revealed by (but not unique to) GCC 11 header changes.
# these are derived from
# https://gitlab.alpinelinux.org/alpine/aports/-/merge_requests/29084/
- patch("gcc11_1.patch", when="@0.3.2:4%gcc@11:")
- patch("gcc11_2.patch", when="@0.3.2:4%gcc@11:")
- patch("gcc11_3.patch", when="@0.3:4%gcc@11:")
- patch("gcc11_4.patch", when="@4.1:4%gcc@11:")
+ patch("gcc11_1.patch", when="@0.3.2:4")
+ patch("gcc11_2.patch", when="@0.3.2:4")
+ patch("gcc11_3.patch", when="@0.3:4")
+ patch("gcc11_4.patch", when="@4.1:4")
# bazel-4.0.0 does not compile with gcc-11
# newer versions of grpc and abseil dependencies are needed but are not in
@@ -526,13 +527,6 @@ class Bazel(Package):
"--color=no --host_javabase=@local_jdk//:jdk"
# Enable verbose output for failures
" --verbose_failures"
- # Ask bazel to explain what it's up to
- # Needs a filename as argument
- " --explain=explainlogfile.txt"
- # Increase verbosity of explanation,
- " --verbose_explanations"
- # Show (formatted) subcommands being executed
- " --subcommands=pretty_print"
# expose LD_LIBRARY_PATH (to fix protoc runtime error during build)
" --action_env=LD_LIBRARY_PATH"
" --jobs={0}".format(make_jobs),
diff --git a/packages/gcc/detection_test.yaml b/packages/gcc/detection_test.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..5e53101a699d77c314c0c07e939c9195a09f6d04
--- /dev/null
+++ b/packages/gcc/detection_test.yaml
@@ -0,0 +1,38 @@
+paths:
+ # Ubuntu 18.04, system compilers without Fortran
+ - layout:
+ - executables:
+ - "bin/gcc"
+ - "bin/g++"
+ script: "echo 7.5.0"
+ results:
+ - spec: "gcc@7.5.0 languages=c,c++"
+ # Mock a version < 7 of GCC that requires -dumpversion and
+ # errors with -dumpfullversion
+ - layout:
+ - executables:
+ - "bin/gcc-5"
+ - "bin/g++-5"
+ - "bin/gfortran-5"
+ script: |
+ if [[ "$1" == "-dumpversion" ]] ; then
+ echo "5.5.0"
+ else
+ echo "gcc-5: fatal error: no input files"
+ echo "compilation terminated."
+ exit 1
+ fi
+ results:
+ - spec: "gcc@5.5.0 languages=c,c++,fortran"
+ # Multiple compilers present at the same time
+ - layout:
+ - executables:
+ - "bin/x86_64-linux-gnu-gcc-6"
+ script: 'echo 6.5.0'
+ - executables:
+ - "bin/x86_64-linux-gnu-gcc-10"
+ - "bin/x86_64-linux-gnu-g++-10"
+ script: "echo 10.1.0"
+ results:
+ - spec: "gcc@6.5.0 languages=c"
+ - spec: "gcc@10.1.0 languages=c,c++"
\ No newline at end of file
diff --git a/packages/gcc/package.py b/packages/gcc/package.py
index f572a133bd47a412aebcc627bb3e422385c95f5f..a8d36dc14145be0c21304b5b192e920a6219d713 100644
--- a/packages/gcc/package.py
+++ b/packages/gcc/package.py
@@ -35,16 +35,19 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
version("master", branch="master")
+ version("13.2.0", sha256="e275e76442a6067341a27f04c5c6b83d8613144004c0413528863dc6b5c743da")
version("13.1.0", sha256="61d684f0aa5e76ac6585ad8898a2427aade8979ed5e7f85492286c4dfc13ee86")
version("12.3.0", sha256="949a5d4f99e786421a93b532b22ffab5578de7321369975b91aec97adfda8c3b")
version("12.2.0", sha256="e549cf9cf3594a00e27b6589d4322d70e0720cdd213f39beb4181e06926230ff")
version("12.1.0", sha256="62fd634889f31c02b64af2c468f064b47ad1ca78411c45abe6ac4b5f8dd19c7b")
+ version("11.4.0", sha256="3f2db222b007e8a4a23cd5ba56726ef08e8b1f1eb2055ee72c1402cea73a8dd9")
version("11.3.0", sha256="b47cf2818691f5b1e21df2bb38c795fac2cfbd640ede2d0a5e1c89e338a3ac39")
version("11.2.0", sha256="d08edc536b54c372a1010ff6619dd274c0f1603aa49212ba20f7aa2cda36fa8b")
version("11.1.0", sha256="4c4a6fb8a8396059241c2e674b85b351c26a5d678274007f076957afa1cc9ddf")
+ version("10.5.0", sha256="25109543fdf46f397c347b5d8b7a2c7e5694a5a51cce4b9c6e1ea8a71ca307c1")
version("10.4.0", sha256="c9297d5bcd7cb43f3dfc2fed5389e948c9312fd962ef6a4ce455cff963ebe4f1")
version("10.3.0", sha256="64f404c1a650f27fc33da242e1f2df54952e3963a49e06e73f6940f3223ac344")
version("10.2.0", sha256="b8dd4368bb9c7f0b98188317ee0254dd8cc99d1e3a18d0ff146c855fe16c1d8c")
@@ -179,7 +182,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
depends_on("isl@0.15:0.20", when="@9:9.9")
depends_on("isl@0.15:", when="@10:")
- depends_on("zlib", when="@6:")
+ depends_on("zlib-api", when="@6:")
depends_on("zstd", when="@10:")
depends_on("diffutils", type="build")
depends_on("iconv", when="platform=darwin")
@@ -334,11 +337,11 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
# on XCode 12.5
conflicts("+bootstrap", when="@:11.1 %apple-clang@12.0.5")
- # aarch64/M1 is supported in GCC 11.3-12.2
- conflicts(
- "@:11.2,12.3:",
+ # aarch64/M1 is supported in GCC 11.3-12.2 and 13
+ requires(
+ "@11.3,12.2,13.1:",
when="target=aarch64: platform=darwin",
- msg="Only GCC 11.3-12.2 support macOS M1 (aarch64)",
+ msg="Only GCC 11.3-12.2, 13.1+ support macOS M1 (aarch64)",
)
# Newer binutils than RHEL's is required to run `as` on some instructions
@@ -410,7 +413,17 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
sha256="a7843b5c6bf1401e40c20c72af69c8f6fc9754ae980bb4a5f0540220b3dcb62d",
when="@12.2.0 target=aarch64:",
)
- conflicts("+bootstrap", when="@11.3.0 target=aarch64:")
+ patch(
+ "https://raw.githubusercontent.com/Homebrew/formula-patches/5c206c47/gcc/gcc-13.1.0.diff",
+ sha256="cb4e8a89387f748a744da0273025d0dc2e3c76780cc390b18ada704676afea11",
+ when="@13.1.0 target=aarch64:",
+ )
+ patch(
+ "https://raw.githubusercontent.com/Homebrew/formula-patches/3c5cbc8e9cf444a1967786af48e430588e1eb481/gcc/gcc-13.2.0.diff",
+ sha256="2df7ef067871a30b2531a2013b3db661ec9e61037341977bfc451e30bf2c1035",
+ when="@13.2.0 target=aarch64:",
+ )
+ conflicts("+bootstrap", when="@11.3.0,13.1: target=aarch64:")
# Use -headerpad_max_install_names in the build,
# otherwise updated load commands won't fit in the Mach-O header.
@@ -627,7 +640,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
"7.1.0"
):
self.gnu_mirror_path = self.gnu_mirror_path.replace("xz", "bz2")
- return super(Gcc, self).url_for_version(version)
+ return super().url_for_version(version)
def patch(self):
spec = self.spec
@@ -649,9 +662,11 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
# Use installed libz
if self.version >= Version("6"):
- filter_file("@zlibdir@", "-L{0}".format(spec["zlib"].prefix.lib), "gcc/Makefile.in")
filter_file(
- "@zlibinc@", "-I{0}".format(spec["zlib"].prefix.include), "gcc/Makefile.in"
+ "@zlibdir@", "-L{0}".format(spec["zlib-api"].prefix.lib), "gcc/Makefile.in"
+ )
+ filter_file(
+ "@zlibinc@", "-I{0}".format(spec["zlib-api"].prefix.include), "gcc/Makefile.in"
)
if spec.satisfies("+nvptx"):
@@ -768,6 +783,11 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
"--with-as=" + binutils.join("as"),
]
)
+ elif spec.satisfies("%apple-clang@15:"):
+ # https://github.com/iains/gcc-darwin-arm64/issues/117
+ # https://github.com/iains/gcc-12-branch/issues/22
+ # https://github.com/iains/gcc-13-branch/issues/8
+ options.append("--with-ld=/Library/Developer/CommandLineTools/usr/bin/ld-classic")
# enable_bootstrap
if spec.satisfies("+bootstrap"):
@@ -1015,11 +1035,11 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage):
"""
# Detect GCC package in the directory of the GCC compiler
# or in the $PATH if self.compiler.cc is not an absolute path:
- from spack.detection import by_executable
+ from spack.detection import by_path
compiler_dir = os.path.dirname(self.compiler.cc)
- detected_packages = by_executable(
- [self.__class__], path_hints=([compiler_dir] if os.path.isdir(compiler_dir) else None)
+ detected_packages = by_path(
+ [self.name], path_hints=([compiler_dir] if os.path.isdir(compiler_dir) else None)
)
# We consider only packages that satisfy the following constraint:
diff --git a/packages/openbabel/package.py b/packages/openbabel/package.py
index ea99f8d4fc7f1d0b85f171a8a51a7a4515c4f131..2bf09af891251d33bcc0c3e5ff2408ea04a82c35 100644
--- a/packages/openbabel/package.py
+++ b/packages/openbabel/package.py
@@ -19,11 +19,11 @@ class Openbabel(CMakePackage):
maintainers("RMeli")
version("master", branch="master")
- version("3.1.1", tag="openbabel-3-1-1")
- version("3.1.0", tag="openbabel-3-1-0")
- version("3.0.0", tag="openbabel-3-0-0")
- version("2.4.1", tag="openbabel-2-4-1")
- version("2.4.0", tag="openbabel-2-4-0")
+ version("3.1.1", tag="openbabel-3-1-1", commit="cbd4db43f8908b874864280fdc03bf92569eebc1")
+ version("3.1.0", tag="openbabel-3-1-0", commit="1e593abc1edf47352d5e8a0887654edf69a2f5f3")
+ version("3.0.0", tag="openbabel-3-0-0", commit="49f9cfb32bd0bc6ea440639d338123eb27accbe2")
+ version("2.4.1", tag="openbabel-2-4-1", commit="701f6049c483b1349118c2ff736a7f609a84dedd")
+ version("2.4.0", tag="openbabel-2-4-0", commit="087f33320e6796f39e6a1da04f4de7ec46bec4af")
variant("python", default=True, description="Build Python bindings")
variant("gui", default=True, description="Build with GUI")
@@ -44,7 +44,7 @@ class Openbabel(CMakePackage):
depends_on("pango", when="+cairo") # custom cairo requires custom pango
depends_on("eigen@3.0:") # required if using the language bindings
depends_on("libxml2") # required to read/write CML files, XML formats
- depends_on("zlib") # required to support reading gzipped files
+ depends_on("zlib-api") # required to support reading gzipped files
depends_on("rapidjson") # required to support JSON
depends_on("libsm")
depends_on("uuid")
diff --git a/packages/py-astropy/package.py b/packages/py-astropy/package.py
index 47bd618496931d77ed46838265318fe113be113b..d0707cc8eeac91f1e577eea646dca47125fb1ffc 100644
--- a/packages/py-astropy/package.py
+++ b/packages/py-astropy/package.py
@@ -15,6 +15,7 @@ class PyAstropy(PythonPackage):
homepage = "https://astropy.org/"
pypi = "astropy/astropy-4.0.1.post1.tar.gz"
+ git = "https://github.com/astropy/astropy.git"
version("5.2.2", sha256="e6a9e34716bda5945788353c63f0644721ee7e5447d16b1cdcb58c48a96b0d9c")
version("5.1", sha256="1db1b2c7eddfc773ca66fa33bd07b25d5b9c3b5eee2b934e0ca277fa5b1b7b7e")
@@ -26,17 +27,15 @@ class PyAstropy(PythonPackage):
version("1.1.2", sha256="6f0d84cd7dfb304bb437dda666406a1d42208c16204043bc920308ff8ffdfad1")
version("1.1.post1", sha256="64427ec132620aeb038e4d8df94d6c30df4cc8b1c42a6d8c5b09907a31566a21")
- variant("extras", default=False, description="Enable extra functionality")
+ variant("all", default=False, when="@3.2:", description="Enable all functionality")
# Required dependencies
depends_on("python@3.8:", when="@5.1:", type=("build", "run"))
- depends_on("python@3.6:", when="@4.0:", type=("build", "run"))
- depends_on("python@3.5:", when="@3.0:", type=("build", "run"))
- depends_on("python@2.7:2.8,3.4:", when="@2.0:", type=("build", "run"))
- depends_on("python@2.7:2.8,3.3:", when="@1.2:", type=("build", "run"))
- depends_on("python@2.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-cython@0.29.13:", type="build")
+ # in newer pip versions --install-option does not exist
+ depends_on("py-pip@:23.0", type="build")
+
depends_on("py-numpy@1.18:", when="@5.1:", type=("build", "run"))
depends_on("py-numpy@1.16:", when="@4.0:", type=("build", "run"))
depends_on("py-numpy@1.13:", when="@3.1:", type=("build", "run"))
@@ -52,24 +51,47 @@ class PyAstropy(PythonPackage):
depends_on("py-extension-helpers", when="@5.1:", type="build")
depends_on("pkgconfig", type="build")
+ depends_on("py-pytest@7:", type="test")
+ depends_on("py-pytest-doctestplus@0.12:", type="test")
+ depends_on("py-pytest-astropy-header@0.2.1:", type="test")
+ depends_on("py-pytest-astropy@0.10:", type="test")
+ depends_on("py-pytest-xdist", type="test")
+
# Optional dependencies
- depends_on("py-scipy@0.18:", when="+extras", type=("build", "run"))
- depends_on("py-h5py", when="+extras", type=("build", "run"))
- depends_on("py-beautifulsoup4", when="+extras", type=("build", "run"))
- depends_on("py-html5lib", when="+extras", type=("build", "run"))
- depends_on("py-bleach", when="+extras", type=("build", "run"))
- depends_on("py-pyyaml", when="+extras", type=("build", "run"))
- depends_on("py-pandas", when="+extras", type=("build", "run"))
- depends_on("py-bintrees", when="+extras", type=("build", "run"))
- depends_on("py-sortedcontainers", when="+extras", type=("build", "run"))
- depends_on("py-pytz", when="+extras", type=("build", "run"))
- depends_on("py-jplephem", when="+extras", type=("build", "run"))
- depends_on("py-matplotlib@2.0:", when="+extras", type=("build", "run"))
- depends_on("py-scikit-image", when="+extras", type=("build", "run"))
- depends_on("py-mpmath", when="+extras", type=("build", "run"))
- depends_on("py-asdf@2.3:", when="+extras", type=("build", "run"))
- depends_on("py-bottleneck", when="+extras", type=("build", "run"))
- depends_on("py-pytest", when="+extras", type=("build", "run"))
+ with when("+all"):
+ depends_on("py-scipy@1.3:", when="@5:", type=("build", "run"))
+ depends_on("py-scipy@0.18:", type=("build", "run"))
+ depends_on("py-matplotlib@3.1:", when="@5:", type=("build", "run"))
+ depends_on("py-matplotlib@2.1:", when="@4:", type=("build", "run"))
+ depends_on("py-matplotlib@2.0:", type=("build", "run"))
+ depends_on("py-certifi", when="@4.3:", type=("build", "run"))
+ depends_on("py-dask+array", when="@4.1:", type=("build", "run"))
+ depends_on("py-h5py", type=("build", "run"))
+ depends_on("py-pyarrow@5:", when="@5:", type=("build", "run"))
+ depends_on("py-beautifulsoup4", type=("build", "run"))
+ depends_on("py-html5lib", type=("build", "run"))
+ depends_on("py-bleach", type=("build", "run"))
+ depends_on("py-pandas", type=("build", "run"))
+ depends_on("py-sortedcontainers", type=("build", "run"))
+ depends_on("py-pytz", type=("build", "run"))
+ depends_on("py-jplephem", type=("build", "run"))
+ depends_on("py-mpmath", type=("build", "run"))
+ depends_on("py-asdf@2.10:", when="@5.1:", type=("build", "run"))
+ depends_on("py-asdf@2.5:", when="@4.0.1post1:", type=("build", "run"))
+ depends_on("py-asdf@2.3:", type=("build", "run"))
+ depends_on("py-bottleneck", type=("build", "run"))
+ depends_on("py-ipython@4.2:", when="@4.3:", type=("build", "run"))
+ depends_on("py-ipython", type=("build", "run"))
+ depends_on("py-pytest@7:", when="@5.0.2:", type=("build", "run"))
+ depends_on("py-pytest", type=("build", "run"))
+ depends_on("py-typing-extensions@3.10.0.1:", when="@5.0.2:", type=("build", "run"))
+
+ # Historical optional dependencies
+ depends_on("py-pyyaml", when="@:5", type=("build", "run"))
+ depends_on("py-scikit-image", when="@:4.0", type=("build", "run"))
+ depends_on("py-bintrees", when="@:3.2.1", type=("build", "run"))
+
+ conflicts("^py-matplotlib@3.4.0,3.5.2")
# System dependencies
depends_on("erfa")
@@ -101,3 +123,12 @@ class PyAstropy(PythonPackage):
def install_test(self):
with working_dir("spack-test", create=True):
python("-c", "import astropy; astropy.test()")
+
+ @property
+ def skip_modules(self):
+ modules = []
+
+ if self.spec.satisfies("~extras"):
+ modules.append("astropy.visualization.wcsaxes")
+
+ return modules
diff --git a/packages/py-ipycanvas/package.py b/packages/py-ipycanvas/package.py
index 4456c1fdfac3679290a84f517169a9c88f331500..0b70aa45e00cf3f140ffddef478acc44d364fa6d 100644
--- a/packages/py-ipycanvas/package.py
+++ b/packages/py-ipycanvas/package.py
@@ -22,9 +22,7 @@ class PyIpycanvas(PythonPackage):
depends_on("python@3.6:", when="@10:", type=("build", "run"))
depends_on("python@3.7:", when="@11:", type=("build", "run"))
depends_on("py-setuptools@40.8:", type="build")
- # TODO: replace this after concretizer learns how to concretize separate build deps
- depends_on("py-jupyter-packaging7", type="build")
- # depends_on('py-jupyter-packaging@0.7.0:0.7', type='build')
+ depends_on("py-jupyter-packaging@0.7", type="build")
depends_on("py-jupyterlab@3.0:3", type="build")
depends_on("py-ipywidgets@7.6:", type=("build", "run"))
depends_on("pil@6:", type=("build", "run"))
diff --git a/packages/py-matplotlib-scalebar/package.py b/packages/py-matplotlib-scalebar/package.py
deleted file mode 100644
index 31907e85922ecf0ccd2f057f4329f31d380afd29..0000000000000000000000000000000000000000
--- a/packages/py-matplotlib-scalebar/package.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 2013-2022 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 PyMatplotlibScalebar(PythonPackage):
- """Matplotlib-Scalebar provides a new artist for matplotlib to display a scale bar, aka micron bar."""
-
- homepage = "https://kolibril13.github.io/plywood-gallery-matplotlib-scalebar/"
- pypi = "matplotlib-scalebar/matplotlib-scalebar-0.8.1.tar.gz"
- git = "https://github.com/ppinard/matplotlib-scalebar.git"
-
- # list of GitHub accounts to notify when the package is updated.
- maintainers = ["ppinard"]
-
- version("0.8.1", sha256="14887af1093579c5e6afae51a0a1ecc3f715cdbc5c4d7ef59cdeec76ee6bb15d")
-
- depends_on("py-matplotlib", type=("build", "run"))
diff --git a/packages/py-pynrrd/package.py b/packages/py-pynrrd/package.py
deleted file mode 100644
index 99093c34d46e6e8a116842e9db56449cfe0238fe..0000000000000000000000000000000000000000
--- a/packages/py-pynrrd/package.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# 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 PyPynrrd(PythonPackage):
- """Python library for reading and writing NRRD files into and from numpy arrays"""
-
- homepage = "https://github.com/mhe/pynrrd"
- pypi = "pynrrd/pynrrd-0.4.0.tar.gz"
-
- version("1.0.0", sha256="4eb4caba03fbca1b832114515e748336cb67bce70c7f3ae36bfa2e135fc990d2")
-
- depends_on("py-setuptools", type="build")
- depends_on("py-numpy@1.11.1:", type=("build", "run"))
- depends_on("py-nptyping", type=("build", "run"))
- depends_on("py-typing-extensions", type=("build", "run"))
-
diff --git a/packages/sbml/package.py b/packages/sbml/package.py
index 25504b607647581f8b1efdf4a48185bb7239a62d..52abe1383d4136f6a3217290f27c6e14371b6d4f 100644
--- a/packages/sbml/package.py
+++ b/packages/sbml/package.py
@@ -60,7 +60,7 @@ class Sbml(CMakePackage):
depends_on("swig@2:", type="build")
depends_on("cmake", type="build")
- depends_on("zlib")
+ depends_on("zlib-api")
depends_on("bzip2")
depends_on("libxml2")