PyQUDA 0.9.1__tar.gz

pyquda-0.9.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022-2024 PyQUDA Developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyquda-0.9.1/MANIFEST.in

@@ -0,0 +1,13 @@
+# .gitignore
+exclude pyquda/src/quda_constants.pxd
+exclude pyquda/src/enum_quda.pxd
+exclude pyquda/src/quda.pxd
+exclude pyquda/src/pyquda.pyx
+exclude pyquda/enum_quda.py
+exclude pyquda/src/*.c
+exclude pyquda/src/*.cpp
+
+include pyquda_pyx.py
+include pycparser/LICENSE
+recursive-include pycparser/pycparser *.py *.cfg LICENSE
+recursive-include pycparser/utils/fake_libc_include *.h

pyquda-0.9.1/PKG-INFO

@@ -0,0 +1,116 @@
+Metadata-Version: 2.1
+Name: PyQUDA
+Version: 0.9.1
+Summary: Python wrapper for QUDA written in Cython
+Author-email: SaltyChiang <SaltyChiang@users.noreply.github.com>
+Maintainer-email: SaltyChiang <SaltyChiang@users.noreply.github.com>
+License: MIT License
+        
+        Copyright (c) 2022-2024 PyQUDA Developers
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/CLQCD/PyQUDA
+Project-URL: Documentation, https://github.com/CLQCD/PyQUDA/wiki/Documentation
+Project-URL: Repository, https://github.com/CLQCD/PyQUDA.git
+Project-URL: Issues, https://github.com/CLQCD/PyQUDA/issues
+Keywords: lattice-gauge-theory,lattice-field-theory,lattice-qcd,hep-lat
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Cython
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Environment :: GPU
+Classifier: Environment :: GPU :: NVIDIA CUDA
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mpi4py
+Requires-Dist: numpy
+
+# PyQUDA
+
+Python wrapper for [QUDA](https://github.com/lattice/quda) written in Cython.
+
+This project aims to benefit from the optimized linear algebra library [CuPy](https://cupy.dev/) in Python based on CUDA. CuPy and QUDA will allow us to perform most lattice QCD research operations with high performance. [PyTorch](https://pytorch.org/) is an alternative option.
+
+This project is based on the latest QUDA `develop` branch. PyQUDA should be compatible with any commit of QUDA after https://github.com/lattice/quda/pull/1489, but leave some features disabled.
+
+## Feature
+
+- Multi-GPU supported
+  - with [MPI for Python](https://mpi4py.readthedocs.io/en/stable/) package
+- File I/O
+  - Read gauge and propagator in Chroma format
+  - Read gauge and propagator in MILC format
+  - Read/write gauge and propagator in KYU format
+  - Read/write gauge and propagator in XQCD format
+  - Read/write gauge and propagator in NPY format (numpy)
+- Quark propagator
+  - Isotropic/anisotropic Wilson fermion action with multigrid support
+  - Isotropic/anisotropic Clover fermion action with multigrid support
+  - Isotropic HISQ fermion action
+- HMC
+  - Isotropic Wilson gauge action
+  - Isotropic Symanzik gauge action
+  - 1-flavor isotropic clover fermion action
+  - 2-flavor isotropic clover fermion action
+- Gauge fixing
+  - Rotation field with over-relaxation method (waiting for QUDA merge)
+- Gauge smearing
+  - 3D/4D APE smearing
+  - 3D/4D stout smearing
+  - 3D/4D HYP smearing
+- Fermion smearing
+  - Gaussian smearing
+- Gradient flow
+  - Wilson flow
+  - Symanzik flow
+
+## Installation
+
+Refer to https://github.com/CLQCD/PyQUDA/wiki/Installation for detailed instructions to install PyQUDA from the source.
+
+## Benchmark
+
+Refer to https://github.com/CLQCD/PyQUDA/wiki/Benchmark for detailed instructions to run the PyQUDA benchmark.
+
+## Documentation (draft)
+
+https://github.com/CLQCD/PyQUDA/wiki/Documentation
+
+## Development
+
+We recommend building PyQUDA using in-place mode instead of installing PyQUDA for development.
+
+```bash
+git clone https://github.com/CLQCD/PyQUDA.git
+cd PyQUDA
+ln -s pyquda_core/pyquda pyquda
+cd pyquda_core
+export QUDA_PATH=/path/to/quda/build/usqcd
+python3 setup.py build_ext --inplace
+```
+
+Now you can modify Python files in the project and immediately get the new result by running scripts. Adding the root directory to `sys.path` is needed if you are running scripts from other directories.
+
+## Maintenance
+
+Function definitions (mainly in `quda.in.pxd` and `pyquda.in.pyx`) and most docstrings (mainly in `pyquda.pyi` and `enum_quda.in.py`) should be manually updated as they cannot be autogenerated now. This also means PyQUDA should work well with future versions if the API remains unchanged.

pyquda-0.9.1/PyQUDA.egg-info/PKG-INFO

@@ -0,0 +1,116 @@
+Metadata-Version: 2.1
+Name: PyQUDA
+Version: 0.9.1
+Summary: Python wrapper for QUDA written in Cython
+Author-email: SaltyChiang <SaltyChiang@users.noreply.github.com>
+Maintainer-email: SaltyChiang <SaltyChiang@users.noreply.github.com>
+License: MIT License
+        
+        Copyright (c) 2022-2024 PyQUDA Developers
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/CLQCD/PyQUDA
+Project-URL: Documentation, https://github.com/CLQCD/PyQUDA/wiki/Documentation
+Project-URL: Repository, https://github.com/CLQCD/PyQUDA.git
+Project-URL: Issues, https://github.com/CLQCD/PyQUDA/issues
+Keywords: lattice-gauge-theory,lattice-field-theory,lattice-qcd,hep-lat
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Cython
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Environment :: GPU
+Classifier: Environment :: GPU :: NVIDIA CUDA
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mpi4py
+Requires-Dist: numpy
+
+# PyQUDA
+
+Python wrapper for [QUDA](https://github.com/lattice/quda) written in Cython.
+
+This project aims to benefit from the optimized linear algebra library [CuPy](https://cupy.dev/) in Python based on CUDA. CuPy and QUDA will allow us to perform most lattice QCD research operations with high performance. [PyTorch](https://pytorch.org/) is an alternative option.
+
+This project is based on the latest QUDA `develop` branch. PyQUDA should be compatible with any commit of QUDA after https://github.com/lattice/quda/pull/1489, but leave some features disabled.
+
+## Feature
+
+- Multi-GPU supported
+  - with [MPI for Python](https://mpi4py.readthedocs.io/en/stable/) package
+- File I/O
+  - Read gauge and propagator in Chroma format
+  - Read gauge and propagator in MILC format
+  - Read/write gauge and propagator in KYU format
+  - Read/write gauge and propagator in XQCD format
+  - Read/write gauge and propagator in NPY format (numpy)
+- Quark propagator
+  - Isotropic/anisotropic Wilson fermion action with multigrid support
+  - Isotropic/anisotropic Clover fermion action with multigrid support
+  - Isotropic HISQ fermion action
+- HMC
+  - Isotropic Wilson gauge action
+  - Isotropic Symanzik gauge action
+  - 1-flavor isotropic clover fermion action
+  - 2-flavor isotropic clover fermion action
+- Gauge fixing
+  - Rotation field with over-relaxation method (waiting for QUDA merge)
+- Gauge smearing
+  - 3D/4D APE smearing
+  - 3D/4D stout smearing
+  - 3D/4D HYP smearing
+- Fermion smearing
+  - Gaussian smearing
+- Gradient flow
+  - Wilson flow
+  - Symanzik flow
+
+## Installation
+
+Refer to https://github.com/CLQCD/PyQUDA/wiki/Installation for detailed instructions to install PyQUDA from the source.
+
+## Benchmark
+
+Refer to https://github.com/CLQCD/PyQUDA/wiki/Benchmark for detailed instructions to run the PyQUDA benchmark.
+
+## Documentation (draft)
+
+https://github.com/CLQCD/PyQUDA/wiki/Documentation
+
+## Development
+
+We recommend building PyQUDA using in-place mode instead of installing PyQUDA for development.
+
+```bash
+git clone https://github.com/CLQCD/PyQUDA.git
+cd PyQUDA
+ln -s pyquda_core/pyquda pyquda
+cd pyquda_core
+export QUDA_PATH=/path/to/quda/build/usqcd
+python3 setup.py build_ext --inplace
+```
+
+Now you can modify Python files in the project and immediately get the new result by running scripts. Adding the root directory to `sys.path` is needed if you are running scripts from other directories.
+
+## Maintenance
+
+Function definitions (mainly in `quda.in.pxd` and `pyquda.in.pyx`) and most docstrings (mainly in `pyquda.pyi` and `enum_quda.in.py`) should be manually updated as they cannot be autogenerated now. This also means PyQUDA should work well with future versions if the API remains unchanged.

pyquda-0.9.1/PyQUDA.egg-info/SOURCES.txt

@@ -0,0 +1,186 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+pyquda_pyx.py
+setup.py
+PyQUDA.egg-info/PKG-INFO
+PyQUDA.egg-info/SOURCES.txt
+PyQUDA.egg-info/dependency_links.txt
+PyQUDA.egg-info/entry_points.txt
+PyQUDA.egg-info/requires.txt
+PyQUDA.egg-info/top_level.txt
+pycparser/LICENSE
+pycparser/pycparser/__init__.py
+pycparser/pycparser/_ast_gen.py
+pycparser/pycparser/_build_tables.py
+pycparser/pycparser/_c_ast.cfg
+pycparser/pycparser/ast_transforms.py
+pycparser/pycparser/c_ast.py
+pycparser/pycparser/c_generator.py
+pycparser/pycparser/c_lexer.py
+pycparser/pycparser/c_parser.py
+pycparser/pycparser/plyparser.py
+pycparser/pycparser/ply/LICENSE
+pycparser/pycparser/ply/__init__.py
+pycparser/pycparser/ply/cpp.py
+pycparser/pycparser/ply/ctokens.py
+pycparser/pycparser/ply/lex.py
+pycparser/pycparser/ply/yacc.py
+pycparser/pycparser/ply/ygen.py
+pycparser/utils/fake_libc_include/_ansi.h
+pycparser/utils/fake_libc_include/_fake_defines.h
+pycparser/utils/fake_libc_include/_fake_typedefs.h
+pycparser/utils/fake_libc_include/_syslist.h
+pycparser/utils/fake_libc_include/aio.h
+pycparser/utils/fake_libc_include/alloca.h
+pycparser/utils/fake_libc_include/ar.h
+pycparser/utils/fake_libc_include/argz.h
+pycparser/utils/fake_libc_include/assert.h
+pycparser/utils/fake_libc_include/complex.h
+pycparser/utils/fake_libc_include/cpio.h
+pycparser/utils/fake_libc_include/ctype.h
+pycparser/utils/fake_libc_include/dirent.h
+pycparser/utils/fake_libc_include/dlfcn.h
+pycparser/utils/fake_libc_include/emmintrin.h
+pycparser/utils/fake_libc_include/endian.h
+pycparser/utils/fake_libc_include/envz.h
+pycparser/utils/fake_libc_include/errno.h
+pycparser/utils/fake_libc_include/fastmath.h
+pycparser/utils/fake_libc_include/fcntl.h
+pycparser/utils/fake_libc_include/features.h
+pycparser/utils/fake_libc_include/fenv.h
+pycparser/utils/fake_libc_include/float.h
+pycparser/utils/fake_libc_include/fmtmsg.h
+pycparser/utils/fake_libc_include/fnmatch.h
+pycparser/utils/fake_libc_include/ftw.h
+pycparser/utils/fake_libc_include/getopt.h
+pycparser/utils/fake_libc_include/glob.h
+pycparser/utils/fake_libc_include/grp.h
+pycparser/utils/fake_libc_include/iconv.h
+pycparser/utils/fake_libc_include/ieeefp.h
+pycparser/utils/fake_libc_include/immintrin.h
+pycparser/utils/fake_libc_include/inttypes.h
+pycparser/utils/fake_libc_include/iso646.h
+pycparser/utils/fake_libc_include/langinfo.h
+pycparser/utils/fake_libc_include/libgen.h
+pycparser/utils/fake_libc_include/libintl.h
+pycparser/utils/fake_libc_include/limits.h
+pycparser/utils/fake_libc_include/locale.h
+pycparser/utils/fake_libc_include/malloc.h
+pycparser/utils/fake_libc_include/math.h
+pycparser/utils/fake_libc_include/monetary.h
+pycparser/utils/fake_libc_include/mqueue.h
+pycparser/utils/fake_libc_include/ndbm.h
+pycparser/utils/fake_libc_include/netdb.h
+pycparser/utils/fake_libc_include/newlib.h
+pycparser/utils/fake_libc_include/nl_types.h
+pycparser/utils/fake_libc_include/paths.h
+pycparser/utils/fake_libc_include/poll.h
+pycparser/utils/fake_libc_include/process.h
+pycparser/utils/fake_libc_include/pthread.h
+pycparser/utils/fake_libc_include/pwd.h
+pycparser/utils/fake_libc_include/reent.h
+pycparser/utils/fake_libc_include/regdef.h
+pycparser/utils/fake_libc_include/regex.h
+pycparser/utils/fake_libc_include/sched.h
+pycparser/utils/fake_libc_include/search.h
+pycparser/utils/fake_libc_include/semaphore.h
+pycparser/utils/fake_libc_include/setjmp.h
+pycparser/utils/fake_libc_include/signal.h
+pycparser/utils/fake_libc_include/smmintrin.h
+pycparser/utils/fake_libc_include/spawn.h
+pycparser/utils/fake_libc_include/stdalign.h
+pycparser/utils/fake_libc_include/stdarg.h
+pycparser/utils/fake_libc_include/stdatomic.h
+pycparser/utils/fake_libc_include/stdbool.h
+pycparser/utils/fake_libc_include/stddef.h
+pycparser/utils/fake_libc_include/stdint.h
+pycparser/utils/fake_libc_include/stdio.h
+pycparser/utils/fake_libc_include/stdlib.h
+pycparser/utils/fake_libc_include/stdnoreturn.h
+pycparser/utils/fake_libc_include/string.h
+pycparser/utils/fake_libc_include/strings.h
+pycparser/utils/fake_libc_include/stropts.h
+pycparser/utils/fake_libc_include/syslog.h
+pycparser/utils/fake_libc_include/tar.h
+pycparser/utils/fake_libc_include/termios.h
+pycparser/utils/fake_libc_include/tgmath.h
+pycparser/utils/fake_libc_include/threads.h
+pycparser/utils/fake_libc_include/time.h
+pycparser/utils/fake_libc_include/trace.h
+pycparser/utils/fake_libc_include/ulimit.h
+pycparser/utils/fake_libc_include/unctrl.h
+pycparser/utils/fake_libc_include/unistd.h
+pycparser/utils/fake_libc_include/utime.h
+pycparser/utils/fake_libc_include/utmp.h
+pycparser/utils/fake_libc_include/utmpx.h
+pycparser/utils/fake_libc_include/wchar.h
+pycparser/utils/fake_libc_include/wctype.h
+pycparser/utils/fake_libc_include/wordexp.h
+pycparser/utils/fake_libc_include/zlib.h
+pycparser/utils/fake_libc_include/X11/Intrinsic.h
+pycparser/utils/fake_libc_include/X11/Xlib.h
+pycparser/utils/fake_libc_include/X11/_X11_fake_defines.h
+pycparser/utils/fake_libc_include/X11/_X11_fake_typedefs.h
+pycparser/utils/fake_libc_include/arpa/inet.h
+pycparser/utils/fake_libc_include/asm-generic/int-ll64.h
+pycparser/utils/fake_libc_include/linux/socket.h
+pycparser/utils/fake_libc_include/linux/version.h
+pycparser/utils/fake_libc_include/mir_toolkit/client_types.h
+pycparser/utils/fake_libc_include/net/if.h
+pycparser/utils/fake_libc_include/netinet/in.h
+pycparser/utils/fake_libc_include/netinet/tcp.h
+pycparser/utils/fake_libc_include/openssl/err.h
+pycparser/utils/fake_libc_include/openssl/evp.h
+pycparser/utils/fake_libc_include/openssl/hmac.h
+pycparser/utils/fake_libc_include/openssl/ssl.h
+pycparser/utils/fake_libc_include/openssl/x509v3.h
+pycparser/utils/fake_libc_include/sys/ioctl.h
+pycparser/utils/fake_libc_include/sys/ipc.h
+pycparser/utils/fake_libc_include/sys/mman.h
+pycparser/utils/fake_libc_include/sys/msg.h
+pycparser/utils/fake_libc_include/sys/poll.h
+pycparser/utils/fake_libc_include/sys/resource.h
+pycparser/utils/fake_libc_include/sys/select.h
+pycparser/utils/fake_libc_include/sys/sem.h
+pycparser/utils/fake_libc_include/sys/shm.h
+pycparser/utils/fake_libc_include/sys/socket.h
+pycparser/utils/fake_libc_include/sys/stat.h
+pycparser/utils/fake_libc_include/sys/statvfs.h
+pycparser/utils/fake_libc_include/sys/sysctl.h
+pycparser/utils/fake_libc_include/sys/time.h
+pycparser/utils/fake_libc_include/sys/times.h
+pycparser/utils/fake_libc_include/sys/types.h
+pycparser/utils/fake_libc_include/sys/uio.h
+pycparser/utils/fake_libc_include/sys/un.h
+pycparser/utils/fake_libc_include/sys/utsname.h
+pycparser/utils/fake_libc_include/sys/wait.h
+pycparser/utils/fake_libc_include/xcb/xcb.h
+pyquda/__init__.py
+pyquda/__main__.py
+pyquda/_version.py
+pyquda/enum_quda.in.py
+pyquda/field.py
+pyquda/hmc.py
+pyquda/pointer.pxd
+pyquda/pointer.pyi
+pyquda/pyquda.pyi
+pyquda/action/__init__.py
+pyquda/action/abstract.py
+pyquda/action/clover_wilson.py
+pyquda/action/gauge.py
+pyquda/action/hisq.py
+pyquda/dirac/__init__.py
+pyquda/dirac/abstract.py
+pyquda/dirac/clover_wilson.py
+pyquda/dirac/gauge.py
+pyquda/dirac/general.py
+pyquda/dirac/hisq.py
+pyquda/dirac/staggered.py
+pyquda/dirac/wilson.py
+pyquda/src/malloc_pyquda.pyx
+pyquda/src/malloc_quda.pxd
+pyquda/src/pointer.pyx
+pyquda/src/pyquda.in.pyx
+pyquda/src/quda.in.pxd

pyquda-0.9.1/PyQUDA.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

pyquda-0.9.1/PyQUDA.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+pyquda = pyquda.__main__:main

pyquda-0.9.1/PyQUDA.egg-info/requires.txt

@@ -0,0 +1,2 @@
+mpi4py
+numpy

pyquda-0.9.1/PyQUDA.egg-info/top_level.txt

@@ -0,0 +1 @@
+pyquda

pyquda-0.9.1/README.md

@@ -0,0 +1,69 @@
+# PyQUDA
+
+Python wrapper for [QUDA](https://github.com/lattice/quda) written in Cython.
+
+This project aims to benefit from the optimized linear algebra library [CuPy](https://cupy.dev/) in Python based on CUDA. CuPy and QUDA will allow us to perform most lattice QCD research operations with high performance. [PyTorch](https://pytorch.org/) is an alternative option.
+
+This project is based on the latest QUDA `develop` branch. PyQUDA should be compatible with any commit of QUDA after https://github.com/lattice/quda/pull/1489, but leave some features disabled.
+
+## Feature
+
+- Multi-GPU supported
+  - with [MPI for Python](https://mpi4py.readthedocs.io/en/stable/) package
+- File I/O
+  - Read gauge and propagator in Chroma format
+  - Read gauge and propagator in MILC format
+  - Read/write gauge and propagator in KYU format
+  - Read/write gauge and propagator in XQCD format
+  - Read/write gauge and propagator in NPY format (numpy)
+- Quark propagator
+  - Isotropic/anisotropic Wilson fermion action with multigrid support
+  - Isotropic/anisotropic Clover fermion action with multigrid support
+  - Isotropic HISQ fermion action
+- HMC
+  - Isotropic Wilson gauge action
+  - Isotropic Symanzik gauge action
+  - 1-flavor isotropic clover fermion action
+  - 2-flavor isotropic clover fermion action
+- Gauge fixing
+  - Rotation field with over-relaxation method (waiting for QUDA merge)
+- Gauge smearing
+  - 3D/4D APE smearing
+  - 3D/4D stout smearing
+  - 3D/4D HYP smearing
+- Fermion smearing
+  - Gaussian smearing
+- Gradient flow
+  - Wilson flow
+  - Symanzik flow
+
+## Installation
+
+Refer to https://github.com/CLQCD/PyQUDA/wiki/Installation for detailed instructions to install PyQUDA from the source.
+
+## Benchmark
+
+Refer to https://github.com/CLQCD/PyQUDA/wiki/Benchmark for detailed instructions to run the PyQUDA benchmark.
+
+## Documentation (draft)
+
+https://github.com/CLQCD/PyQUDA/wiki/Documentation
+
+## Development
+
+We recommend building PyQUDA using in-place mode instead of installing PyQUDA for development.
+
+```bash
+git clone https://github.com/CLQCD/PyQUDA.git
+cd PyQUDA
+ln -s pyquda_core/pyquda pyquda
+cd pyquda_core
+export QUDA_PATH=/path/to/quda/build/usqcd
+python3 setup.py build_ext --inplace
+```
+
+Now you can modify Python files in the project and immediately get the new result by running scripts. Adding the root directory to `sys.path` is needed if you are running scripts from other directories.
+
+## Maintenance
+
+Function definitions (mainly in `quda.in.pxd` and `pyquda.in.pyx`) and most docstrings (mainly in `pyquda.pyi` and `enum_quda.in.py`) should be manually updated as they cannot be autogenerated now. This also means PyQUDA should work well with future versions if the API remains unchanged.

pyquda-0.9.1/pycparser/LICENSE

@@ -0,0 +1,27 @@
+pycparser -- A C parser in Python
+
+Copyright (c) 2008-2022, Eli Bendersky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this 
+  list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice, 
+  this list of conditions and the following disclaimer in the documentation 
+  and/or other materials provided with the distribution.
+* Neither the name of the copyright holder nor the names of its contributors may 
+  be used to endorse or promote products derived from this software without 
+  specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE 
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) 
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT 
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pyquda-0.9.1/pycparser/pycparser/__init__.py

@@ -0,0 +1,93 @@
+#-----------------------------------------------------------------
+# pycparser: __init__.py
+#
+# This package file exports some convenience functions for
+# interacting with pycparser
+#
+# Eli Bendersky [https://eli.thegreenplace.net/]
+# License: BSD
+#-----------------------------------------------------------------
+__all__ = ['c_lexer', 'c_parser', 'c_ast']
+__version__ = '2.22'
+
+import io
+from subprocess import check_output
+from .c_parser import CParser
+
+
+def preprocess_file(filename, cpp_path='cpp', cpp_args=''):
+    """ Preprocess a file using cpp.
+
+        filename:
+            Name of the file you want to preprocess.
+
+        cpp_path:
+        cpp_args:
+            Refer to the documentation of parse_file for the meaning of these
+            arguments.
+
+        When successful, returns the preprocessed file's contents.
+        Errors from cpp will be printed out.
+    """
+    path_list = [cpp_path]
+    if isinstance(cpp_args, list):
+        path_list += cpp_args
+    elif cpp_args != '':
+        path_list += [cpp_args]
+    path_list += [filename]
+
+    try:
+        # Note the use of universal_newlines to treat all newlines
+        # as \n for Python's purpose
+        text = check_output(path_list, universal_newlines=True)
+    except OSError as e:
+        raise RuntimeError("Unable to invoke 'cpp'.  " +
+            'Make sure its path was passed correctly\n' +
+            ('Original error: %s' % e))
+
+    return text
+
+
+def parse_file(filename, use_cpp=False, cpp_path='cpp', cpp_args='',
+               parser=None, encoding=None):
+    """ Parse a C file using pycparser.
+
+        filename:
+            Name of the file you want to parse.
+
+        use_cpp:
+            Set to True if you want to execute the C pre-processor
+            on the file prior to parsing it.
+
+        cpp_path:
+            If use_cpp is True, this is the path to 'cpp' on your
+            system. If no path is provided, it attempts to just
+            execute 'cpp', so it must be in your PATH.
+
+        cpp_args:
+            If use_cpp is True, set this to the command line arguments strings
+            to cpp. Be careful with quotes - it's best to pass a raw string
+            (r'') here. For example:
+            r'-I../utils/fake_libc_include'
+            If several arguments are required, pass a list of strings.
+
+        encoding:
+            Encoding to use for the file to parse
+
+        parser:
+            Optional parser object to be used instead of the default CParser
+
+        When successful, an AST is returned. ParseError can be
+        thrown if the file doesn't parse successfully.
+
+        Errors from cpp will be printed out.
+    """
+    if use_cpp:
+        text = preprocess_file(filename, cpp_path, cpp_args)
+    else:
+        with io.open(filename, encoding=encoding) as f:
+            text = f.read()
+
+    if parser is None:
+        parser = CParser()
+    return parser.parse(text, filename)