initial commit

Author: Felix Igelbrink

LICENSE

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-BSD 3-Clause License
+MIT License
 
-Copyright (c) 2021, Felix Igelbrink
-All rights reserved.
+Copyright (c) 2021 Felix Igelbrink
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+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:
 
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
-2. 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.
-
-3. 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.
+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.

MANIFEST.in

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+include LICENSE

README.md

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-# numba_progress
-Using progress bars in numba
+# Numba-progress
+ 
+A progress bar implementation for numba functions using tqdm.
+The module provides the class `ProgressBar` that works as a wrapper around the 
+`tqdm.tqdm` progress bar. 
+
+It works by spawning a separate thread that updates the `tqdm` progress bar 
+based on an atomic counter which can be accessed within a numba nopython function.
+
+The progress bar works with parallel as well as sequential numba functions.
+
+## Installation
+
+### Using pip
+```
+pip install numba-progress
+```
+
+### From source
+```
+git clone https://github.com/mortacious/numba-progress.git
+cd numba-progress
+python setup.py install
+```
+
+## Usage
+
+```python
+from numba import njit
+from numba_progress import ProgressBar
+
+num_iterations = 100
+
+@njit(nogil=True)
+def numba_function(num_iterations, progress_proxy):
+    for i in range(num_iterations):
+        #<DO CUSTOM WORK HERE>
+        progress_proxy.update(1)
+
+with ProgressBar(total=num_iterations) as progress:
+    numba_function(num_iterations, progress)
+```
+
+The `ProgressBar` also works within parallel functions out of the box.
+
+```python
+from numba import njit, prange
+from numba_progress import ProgressBar
+
+num_iterations = 100
+
+@njit(nogil=True, parallel=True)
+def numba_function(num_iterations, progress_proxy):
+    for i in prange(num_iterations):
+        #<DO CUSTOM WORK HERE>
+        progress_proxy.update(1)
+
+with ProgressBar(total=num_iterations) as progress:
+    numba_function(num_iterations, progress)
+```
+
+See also the `examples` folder for more usage examples.

examples/__init__.py

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+from sleep import usleep
+import numba as nb
+from numba_progress import ProgressBar
+
+
+@nb.njit(nogil=True, parallel=True)
+def numba_parallel_sleeper(num_iterations, sleep_us, progress_hook):
+    for i in nb.prange(num_iterations):
+        usleep(sleep_us)
+        progress_hook.update(1)
+
+
+if __name__ == "__main__":
+    num_iterations = 30*8
+    sleep_time_us = 250_000
+    with ProgressBar(total=num_iterations, ncols=80) as numba_progress:
+        numba_parallel_sleeper(num_iterations, sleep_time_us, numba_progress)
+

examples/example_parallel.py

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+from sleep import usleep
+import numba as nb
+from numba_progress import ProgressBar
+
+
+@nb.njit(nogil=True)
+def numba_sleeper(num_iterations, sleep_us, progress_hook):
+    for i in range(num_iterations):
+        usleep(sleep_us)
+        progress_hook.update(1)
+
+
+if __name__ == "__main__":
+    num_iterations = 30
+    sleep_time_us = 250_000
+    with ProgressBar(total=num_iterations, ncols=80) as numba_progress:
+        numba_sleeper(num_iterations, sleep_time_us, numba_progress)

examples/example_sequential.py

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+import numba as nb
+
+
+@nb.generated_jit(nogil=True, nopython=True)
+def usleep(usec):
+    # c usleep function in numba
+    import ctypes
+    libc = ctypes.CDLL('libc.so.6')
+    libc.usleep.argtypes = (ctypes.c_uint,)
+    func_usleep = libc.usleep
+
+    def usleep_impl(usec):
+        func_usleep(usec)
+
+    return usleep_impl

examples/sleep.py

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+from .progress import ProgressBar
+from ._version import __version__

numba_progress/__init__.py

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+__version__ = "0.0.1"

numba_progress/_version.py

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+# source from https://github.com/KatanaGraph/katana/blob/master/python/katana/numba_support/numpy_atomic.py
+
+# The 3-Clause BSD License
+#
+# Copyright 2018 The University of Texas at Austin
+#
+# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+#
+# 2. 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.
+#
+# 3. 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.
+
+
+from numba import types
+from numba.core import cgutils
+from numba.core.typing.arraydecl import get_array_index_type
+from numba.extending import lower_builtin, type_callable
+from numba.np.arrayobj import basic_indexing, make_array, normalize_indices
+
+__all__ = ["atomic_add", "atomic_sub", "atomic_max", "atomic_min"]
+
+
+def atomic_rmw(context, builder, op, arrayty, val, ptr):
+    assert arrayty.aligned  # We probably have to have aligned arrays.
+    dataval = context.get_value_as_data(builder, arrayty.dtype, val)
+    return builder.atomic_rmw(op, ptr, dataval, "monotonic")
+
+
+def declare_atomic_array_op(iop, uop, fop):
+    def decorator(func):
+        @type_callable(func)
+        def func_type(context):
+            def typer(ary, idx, val):
+                out = get_array_index_type(ary, idx)
+                if out is not None:
+                    res = out.result
+                    if context.can_convert(val, res):
+                        return res
+                return None
+
+            return typer
+
+        _ = func_type
+
+        @lower_builtin(func, types.Buffer, types.Any, types.Any)
+        def func_impl(context, builder, sig, args):
+            """
+            array[a] = scalar_or_array
+            array[a,..,b] = scalar_or_array
+            """
+            aryty, idxty, valty = sig.args
+            ary, idx, val = args
+
+            if isinstance(idxty, types.BaseTuple):
+                index_types = idxty.types
+                indices = cgutils.unpack_tuple(builder, idx, count=len(idxty))
+            else:
+                index_types = (idxty,)
+                indices = (idx,)
+
+            ary = make_array(aryty)(context, builder, ary)
+
+            # First try basic indexing to see if a single array location is denoted.
+            index_types, indices = normalize_indices(context, builder, index_types, indices)
+            dataptr, shapes, _strides = basic_indexing(
+                context, builder, aryty, ary, index_types, indices, boundscheck=context.enable_boundscheck,
+            )
+            if shapes:
+                raise NotImplementedError("Complex shapes are not supported")
+
+            # Store source value the given location
+            val = context.cast(builder, val, valty, aryty.dtype)
+            op = None
+            if isinstance(aryty.dtype, types.Integer) and aryty.dtype.signed:
+                op = iop
+            elif isinstance(aryty.dtype, types.Integer) and not aryty.dtype.signed:
+                op = uop
+            elif isinstance(aryty.dtype, types.Float):
+                op = fop
+            if op is None:
+                raise TypeError("Atomic operation not supported on " + str(aryty))
+            return atomic_rmw(context, builder, op, aryty, val, dataptr)
+
+        _ = func_impl
+
+        return func
+
+    return decorator
+
+
+@declare_atomic_array_op("add", "add", "fadd")
+def atomic_add(ary, i, v):
+    """
+    Atomically, perform `ary[i] += v` and return the previous value of `ary[i]`.
+
+    i must be a simple index for a single element of ary. Broadcasting and vector operations are not supported.
+
+    This should be used from numba compiled code.
+    """
+    orig = ary[i]
+    ary[i] += v
+    return orig
+
+
+@declare_atomic_array_op("sub", "sub", "fsub")
+def atomic_sub(ary, i, v):
+    """
+    Atomically, perform `ary[i] -= v` and return the previous value of `ary[i]`.
+
+    i must be a simple index for a single element of ary. Broadcasting and vector operations are not supported.
+
+    This should be used from numba compiled code.
+    """
+    orig = ary[i]
+    ary[i] -= v
+    return orig
+
+
+@declare_atomic_array_op("max", "umax", None)
+def atomic_max(ary, i, v):
+    """
+    Atomically, perform `ary[i] = max(ary[i], v)` and return the previous value of `ary[i]`.
+    This operation does not support floating-point values.
+
+    i must be a simple index for a single element of ary. Broadcasting and vector operations are not supported.
+
+    This should be used from numba compiled code.
+    """
+    orig = ary[i]
+    ary[i] = max(ary[i], v)
+    return orig
+
+
+@declare_atomic_array_op("min", "umin", None)
+def atomic_min(ary, i, v):
+    """
+    Atomically, perform `ary[i] = min(ary[i], v)` and return the previous value of `ary[i]`.
+    This operation does not support floating-point values.
+
+    i must be a simple index for a single element of ary. Broadcasting and vector operations are not supported.
+
+    This should be used from numba compiled code.
+    """
+    orig = ary[i]
+    ary[i] = min(ary[i], v)
+    return orig