temuller / piscola Goto Github PK
View Code? Open in Web Editor NEWSupernova light-curve fitting code
Home Page: https://piscola.readthedocs.io
License: MIT License
Supernova light-curve fitting code
Home Page: https://piscola.readthedocs.io
License: MIT License
The following error is encountered while trying to install the package under M1 arch, PyCharm (Python 3.10 virtual env):
× Building wheel for extinction (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [228 lines of output]
running bdist_wheel
running build
running build_ext
/private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/Cython/Compiler/Main.py:384: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-install-p0_kspjg/extinction_ea97bb6848ae466d9da50beeec276146/extinction.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
warning: extinction.pyx:289:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:290:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:291:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:292:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:293:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:294:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:295:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:492:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:493:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:494:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:495:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:496:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:497:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:498:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:499:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:500:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
warning: extinction.pyx:501:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
Compiling extinction.pyx because it changed.
[1/1] Cythonizing extinction.pyx
building 'extinction' extension
creating build
creating build/temp.macosx-10.9-universal2-cpython-310
creating build/temp.macosx-10.9-universal2-cpython-310/extern
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include -Iextern -I/Users/cstarzero/PycharmProjects/LightCurveFitting/venv/include -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c extern/bs.c -o build/temp.macosx-10.9-universal2-cpython-310/extern/bs.o -std=c99
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include -Iextern -I/Users/cstarzero/PycharmProjects/LightCurveFitting/venv/include -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c extinction.c -o build/temp.macosx-10.9-universal2-cpython-310/extinction.o -std=c99
In file included from extinction.c:1183:
In file included from /private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:
/private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
extinction.c:4817:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:6312:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:6434:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:6888:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:7044:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:7346:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:7506:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11250:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11364:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11478:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11610:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11741:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11863:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:14689:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:14811:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:18070:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:20697:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:21391:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:22136:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:22437:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:22927:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:23050:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:23232:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:23711:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:24485:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:24952:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:25197:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:29410:76: warning: code will never be executed [-Wunreachable-code]
if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad;
^~~~~~~~
extinction.c:29410:73: note: silence by adding parentheses to mark code as explicitly dead
if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad;
^
/* DISABLES CODE */ ( )
29 warnings generated.
In file included from extinction.c:1183:
In file included from /private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:
/private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-n96y9ol1/overlay/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
extinction.c:4817:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:6312:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:6434:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:6888:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:7044:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:7346:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:7506:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11250:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11364:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11478:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11610:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11741:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:11863:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:14689:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:14811:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:18070:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:20697:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:21391:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:22136:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:22437:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:22927:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:23050:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:23232:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:23711:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:24485:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:24952:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:25197:3: warning: code will never be executed [-Wunreachable-code]
goto __pyx_L3_error;
^~~~~~~~~~~~~~~~~~~
extinction.c:29410:76: warning: code will never be executed [-Wunreachable-code]
if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad;
^~~~~~~~
extinction.c:29410:73: note: silence by adding parentheses to mark code as explicitly dead
if (__Pyx_PyTuple_SET_ITEM(argstuple, (Py_ssize_t)i, args[i]) < 0) goto bad;
^
/* DISABLES CODE */ ( )
29 warnings generated.
creating build/lib.macosx-10.9-universal2-cpython-310
clang -bundle -undefined dynamic_lookup -arch arm64 -arch x86_64 -g build/temp.macosx-10.9-universal2-cpython-310/extern/bs.o build/temp.macosx-10.9-universal2-cpython-310/extinction.o -o build/lib.macosx-10.9-universal2-cpython-310/extinction.cpython-310-darwin.so
ld: warning: ignoring file /usr/local/Cellar/llvm@9/9.0.1_4/lib/clang/9.0.1/lib/darwin/libclang_rt.osx.a, missing required architecture arm64 in file /usr/local/Cellar/llvm@9/9.0.1_4/lib/clang/9.0.1/lib/darwin/libclang_rt.osx.a (2 slices)
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/lib/libSystem.tbd' for architecture arm64
clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
error: command '/usr/local/opt/llvm@9/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for extinction
Building wheel for george (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for george (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [98 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-universal2-cpython-310
creating build/lib.macosx-10.9-universal2-cpython-310/george
copying src/george/george_version.py -> build/lib.macosx-10.9-universal2-cpython-310/george
copying src/george/metrics.py -> build/lib.macosx-10.9-universal2-cpython-310/george
copying src/george/gp.py -> build/lib.macosx-10.9-universal2-cpython-310/george
copying src/george/__init__.py -> build/lib.macosx-10.9-universal2-cpython-310/george
copying src/george/utils.py -> build/lib.macosx-10.9-universal2-cpython-310/george
copying src/george/kernels.py -> build/lib.macosx-10.9-universal2-cpython-310/george
copying src/george/modeling.py -> build/lib.macosx-10.9-universal2-cpython-310/george
creating build/lib.macosx-10.9-universal2-cpython-310/george/solvers
copying src/george/solvers/trivial.py -> build/lib.macosx-10.9-universal2-cpython-310/george/solvers
copying src/george/solvers/__init__.py -> build/lib.macosx-10.9-universal2-cpython-310/george/solvers
copying src/george/solvers/hodlr.py -> build/lib.macosx-10.9-universal2-cpython-310/george/solvers
copying src/george/solvers/basic.py -> build/lib.macosx-10.9-universal2-cpython-310/george/solvers
running egg_info
writing src/george.egg-info/PKG-INFO
writing dependency_links to src/george.egg-info/dependency_links.txt
writing requirements to src/george.egg-info/requires.txt
writing top-level names to src/george.egg-info/top_level.txt
listing git files failed - pretending there aren't any
reading manifest file 'src/george.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching '.*'
no previously-included directories found matching '.github'
no previously-included directories found matching 'docs'
no previously-included directories found matching 'paper'
no previously-included directories found matching 'kernels'
no previously-included directories found matching 'templates'
adding license file 'LICENSE'
adding license file 'AUTHORS.rst'
writing manifest file 'src/george.egg-info/SOURCES.txt'
/private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-1ai70ht7/overlay/lib/python3.10/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'george.include.george' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'george.include.george' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'george.include.george' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'george.include.george' to be distributed and are
already explicitly excluding 'george.include.george' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
copying src/george/kernel_interface.cpp -> build/lib.macosx-10.9-universal2-cpython-310/george
creating build/lib.macosx-10.9-universal2-cpython-310/george/include
creating build/lib.macosx-10.9-universal2-cpython-310/george/include/george
copying src/george/include/george/exceptions.h -> build/lib.macosx-10.9-universal2-cpython-310/george/include/george
copying src/george/include/george/george.h -> build/lib.macosx-10.9-universal2-cpython-310/george/include/george
copying src/george/include/george/hodlr.h -> build/lib.macosx-10.9-universal2-cpython-310/george/include/george
copying src/george/include/george/kernels.h -> build/lib.macosx-10.9-universal2-cpython-310/george/include/george
copying src/george/include/george/metrics.h -> build/lib.macosx-10.9-universal2-cpython-310/george/include/george
copying src/george/include/george/parser.h -> build/lib.macosx-10.9-universal2-cpython-310/george/include/george
copying src/george/include/george/subspace.h -> build/lib.macosx-10.9-universal2-cpython-310/george/include/george
copying src/george/solvers/_hodlr.cpp -> build/lib.macosx-10.9-universal2-cpython-310/george/solvers
running build_ext
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/Users/cstarzero/PycharmProjects/LightCurveFitting/venv/include -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c flagcheck.cpp -o flagcheck.o -std=c++17
building 'george.kernel_interface' extension
creating build/temp.macosx-10.9-universal2-cpython-310
creating build/temp.macosx-10.9-universal2-cpython-310/src
creating build/temp.macosx-10.9-universal2-cpython-310/src/george
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -Isrc/george/include -Ivendor/eigen -I/private/var/folders/jz/ygpfpq953fj96p5kvm9_q3x00000gn/T/pip-build-env-1ai70ht7/overlay/lib/python3.10/site-packages/pybind11/include -I/Users/cstarzero/PycharmProjects/LightCurveFitting/venv/include -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c src/george/kernel_interface.cpp -o build/temp.macosx-10.9-universal2-cpython-310/src/george/kernel_interface.o -std=c++17 -mmacosx-version-min=10.14 -fvisibility=hidden -g0
clang++ -bundle -undefined dynamic_lookup -arch arm64 -arch x86_64 -g build/temp.macosx-10.9-universal2-cpython-310/src/george/kernel_interface.o -o build/lib.macosx-10.9-universal2-cpython-310/george/kernel_interface.cpython-310-darwin.so -mmacosx-version-min=10.14
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/lib/libc++.tbd' for architecture arm64
clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
error: command '/usr/local/opt/llvm@9/bin/clang++' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for george
Failed to build extinction george
ERROR: Could not build wheels for extinction, george, which is required to install pyproject.toml-based projects
---------------------------------------------------------------------------
LinAlgError Traceback (most recent call last)
Input In [29], in <cell line: 1>()
----> 1 sn.fit()
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/piscola/sn_class.py:281, in Supernova.fit(self, kernel1, kernel2, gp_mean)
264 def fit(self, kernel1="matern52", kernel2="squaredexp", gp_mean="mean"):
265 """Fits and corrects the multi-colour light curves.
266
267 The corrections include Milky-Way dust extinction and mangling of the SED.
(...)
279 Gaussian process mean function. Either ``mean``, ``max`` or ``min``.
280 """
--> 281 self._fit_lcs(kernel1, kernel2, gp_mean) # to get initial tmax
283 sed_lcs = self.sed.obs_lcs_fit # interpolated light curves
284 sed_times = sed_lcs.phase.values + self.init_tmax
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/piscola/sn_class.py:228, in Supernova._fit_lcs(self, kernel1, kernel2, gp_mean)
212 """Fits the multi-colour light-curve data with gaussian process.
213
214 The time of rest-frame B-band peak luminosity is estimated by finding where the derivative is equal to zero.
(...)
225 Gaussian process mean function. Either ``mean``, ``max`` or ``min``.
226 """
227 self._stack_lcs()
--> 228 timeXwave, lc_mean, lc_std, gp_pred, gp = gp_2d_fit(
229 self._stacked_time,
230 self._stacked_wave,
231 self._stacked_flux,
232 self._stacked_flux_err,
233 kernel1,
234 kernel2,
235 gp_mean,
236 )
238 self.init_fits["timeXwave"], self.init_fits["lc_mean"] = timeXwave, lc_mean
239 self.init_fits["lc_std"], self.init_fits["gp_pred"] = lc_std, gp_pred
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/piscola/gaussian_process.py:190, in gp_2d_fit(x1_data, x2_data, y_data, yerr_data, kernel1, kernel2, gp_mean)
188 # optimization routine for hyperparameters
189 p0 = gp.get_parameter_vector()
--> 190 results = scipy.optimize.minimize(
191 neg_ln_like, p0, jac=grad_neg_ln_like, method="BFGS"
192 )
193 gp.set_parameter_vector(results.x)
195 # extrapolation edges
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_minimize.py:694, in minimize(fun, x0, args, method, jac, hess, hessp, bounds, constraints, tol, callback, options)
692 res = _minimize_cg(fun, x0, args, jac, callback, **options)
693 elif meth == 'bfgs':
--> 694 res = _minimize_bfgs(fun, x0, args, jac, callback, **options)
695 elif meth == 'newton-cg':
696 res = _minimize_newtoncg(fun, x0, args, jac, hess, hessp, callback,
697 **options)
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_optimize.py:1309, in _minimize_bfgs(fun, x0, args, jac, callback, gtol, norm, eps, maxiter, disp, return_all, finite_diff_rel_step, **unknown_options)
1306 pk = -np.dot(Hk, gfk)
1307 try:
1308 alpha_k, fc, gc, old_fval, old_old_fval, gfkp1 = \
-> 1309 _line_search_wolfe12(f, myfprime, xk, pk, gfk,
1310 old_fval, old_old_fval, amin=1e-100, amax=1e100)
1311 except _LineSearchError:
1312 # Line search failed to find a better solution.
1313 warnflag = 2
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_optimize.py:1087, in _line_search_wolfe12(f, fprime, xk, pk, gfk, old_fval, old_old_fval, **kwargs)
1073 """
1074 Same as line_search_wolfe1, but fall back to line_search_wolfe2 if
1075 suitable step length is not found, and raise an exception if a
(...)
1082
1083 """
1085 extra_condition = kwargs.pop('extra_condition', None)
-> 1087 ret = line_search_wolfe1(f, fprime, xk, pk, gfk,
1088 old_fval, old_old_fval,
1089 **kwargs)
1091 if ret[0] is not None and extra_condition is not None:
1092 xp1 = xk + ret[0] * pk
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_linesearch.py:84, in line_search_wolfe1(f, fprime, xk, pk, gfk, old_fval, old_old_fval, args, c1, c2, amax, amin, xtol)
80 return np.dot(gval[0], pk)
82 derphi0 = np.dot(gfk, pk)
---> 84 stp, fval, old_fval = scalar_search_wolfe1(
85 phi, derphi, old_fval, old_old_fval, derphi0,
86 c1=c1, c2=c2, amax=amax, amin=amin, xtol=xtol)
88 return stp, fc[0], gc[0], fval, old_fval, gval[0]
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_linesearch.py:160, in scalar_search_wolfe1(phi, derphi, phi0, old_phi0, derphi0, c1, c2, amax, amin, xtol)
158 if task[:2] == b'FG':
159 alpha1 = stp
--> 160 phi1 = phi(stp)
161 derphi1 = derphi(stp)
162 else:
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_linesearch.py:75, in line_search_wolfe1.<locals>.phi(s)
73 def phi(s):
74 fc[0] += 1
---> 75 return f(xk + s*pk, *args)
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_differentiable_functions.py:267, in ScalarFunction.fun(self, x)
265 if not np.array_equal(x, self.x):
266 self._update_x_impl(x)
--> 267 self._update_fun()
268 return self.f
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_differentiable_functions.py:251, in ScalarFunction._update_fun(self)
249 def _update_fun(self):
250 if not self.f_updated:
--> 251 self._update_fun_impl()
252 self.f_updated = True
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_differentiable_functions.py:155, in ScalarFunction.__init__.<locals>.update_fun()
154 def update_fun():
--> 155 self.f = fun_wrapped(self.x)
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/optimize/_differentiable_functions.py:137, in ScalarFunction.__init__.<locals>.fun_wrapped(x)
133 self.nfev += 1
134 # Send a copy because the user may overwrite it.
135 # Overwriting results in undefined behaviour because
136 # fun(self.x) will change self.x, with the two no longer linked.
--> 137 fx = fun(np.copy(x), *args)
138 # Make sure the function returns a true scalar
139 if not np.isscalar(fx):
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/piscola/gaussian_process.py:142, in gp_2d_fit.<locals>.neg_ln_like(p)
140 def neg_ln_like(p):
141 gp.set_parameter_vector(p)
--> 142 return -gp.log_likelihood(y)
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/george/gp.py:385, in GP.log_likelihood(self, y, quiet)
369 def log_likelihood(self, y, quiet=False):
370 """
371 Compute the logarithm of the marginalized likelihood of a set of
372 observations under the Gaussian process model. You must call
(...)
383
384 """
--> 385 if not self.recompute(quiet=quiet):
386 return -np.inf
387 try:
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/george/gp.py:355, in GP.recompute(self, quiet, **kwargs)
351 raise RuntimeError("You need to compute the model first")
352 try:
353 # Update the model making sure that we store the original
354 # ordering of the points.
--> 355 self.compute(self._x, np.sqrt(self._yerr2), **kwargs)
356 except (ValueError, LinAlgError):
357 if quiet:
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/george/gp.py:331, in GP.compute(self, x, yerr, **kwargs)
329 # Include the white noise term.
330 yerr = np.sqrt(self._yerr2 + np.exp(self._call_white_noise(self._x)))
--> 331 self.solver.compute(self._x, yerr, **kwargs)
333 self._const = -0.5 * (
334 len(self._x) * np.log(2 * np.pi) + self.solver.log_determinant
335 )
336 self.computed = True
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/george/solvers/basic.py:68, in BasicSolver.compute(self, x, yerr)
65 K[np.diag_indices_from(K)] += yerr ** 2
67 # Factor the matrix and compute the log-determinant.
---> 68 self._factor = (cholesky(K, overwrite_a=True, lower=False), False)
69 self.log_determinant = 2 * np.sum(np.log(np.diag(self._factor[0])))
70 self.computed = True
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/linalg/_decomp_cholesky.py:88, in cholesky(a, lower, overwrite_a, check_finite)
45 def cholesky(a, lower=False, overwrite_a=False, check_finite=True):
46 """
47 Compute the Cholesky decomposition of a matrix.
48
(...)
86
87 """
---> 88 c, lower = _cholesky(a, lower=lower, overwrite_a=overwrite_a, clean=True,
89 check_finite=check_finite)
90 return c
File /opt/conda/anaconda3/envs/pisco/lib/python3.10/site-packages/scipy/linalg/_decomp_cholesky.py:37, in _cholesky(a, lower, overwrite_a, clean, check_finite)
35 c, info = potrf(a1, lower=lower, overwrite_a=overwrite_a, clean=clean)
36 if info > 0:
---> 37 raise LinAlgError("%d-th leading minor of the array is not positive "
38 "definite" % info)
39 if info < 0:
40 raise ValueError('LAPACK reported an illegal value in {}-th argument'
41 'on entry to "POTRF".'.format(-info))
LinAlgError: 104-th leading minor of the array is not positive definite
piscola/src/piscola/sn_class.py
Line 252 in f4f6116
if peak is first point or before, fails, should warn but maybe use max as peak?
Or extrapolate longer when it fails? If slope is steep no peak.
SN2011jt failed:index 0 is out of bounds for axis 0 with size 0
Just a usability suggestions: Allow users to give SVO filter name (or instrument name) to auto create the right filter.
Using SVO python script automatically download the filter profile and use it, instead of having to manually add a filter.
(I can make a PR for this later if you want).
https://piscola.readthedocs.io/en/latest/examples/sn_file.html
Here, filter directory should be "https://github.com/temuller/piscola/tree/master/src/piscola/filters" instead of main
Hi,
I want to use piscola, I have light curves in magnitudes in AB system, but I do not know how to convert them to flux and then make a input file for piscola. What should I do?
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