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migrate to newer numpy
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bennahugo committed Mar 26, 2024
1 parent 5c2be7c commit 8e609b9
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Showing 8 changed files with 25 additions and 21 deletions.
4 changes: 3 additions & 1 deletion docker/python36.docker
Original file line number Diff line number Diff line change
Expand Up @@ -16,4 +16,6 @@ ADD . /code
WORKDIR /code

# Install base + testing packages
RUN pip3 install .[testing]
RUN pip3 install .[testing]

RUN python3 -m pytest --flake8 -s -vvv .
2 changes: 2 additions & 0 deletions docker/python38.docker
Original file line number Diff line number Diff line change
Expand Up @@ -17,3 +17,5 @@ WORKDIR /code

# Install base + testing packages
RUN pip3 install .[testing]

RUN python3 -m pytest --flake8 -s -vvv .
16 changes: 8 additions & 8 deletions setup.py
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Expand Up @@ -9,14 +9,14 @@
readme = readme_file.read()

requirements = [
'dask[array] == 2021.2.0',
'donfig >= 0.4.0',
'numpy >= 1.14.0, <= 1.19.5', # breakage in newer numpy + numerical errors
'numba >= 0.43.0',
'scipy >= 1.2.0',
'threadpoolctl >= 1.0.0',
'dask-ms == 0.2.6',
'zarr >= 2.3.1'
'dask[array] >= 2021.2.0, <=2024.3.1',
'donfig >= 0.4.0, <0.8.2',
'numpy >= 1.14.0, <= 1.22.0', # breakage in newer numpy + numerical errors
'numba >= 0.43.0, <= 0.59.1',
'scipy >= 1.2.0, <=1.12.0',
'threadpoolctl >= 1.0.0, <=3.4.0',
'dask-ms >= 0.2.6, <=0.2.20',
'zarr >= 2.3.1, <=2.17.1'
]

extras_require = {'testing': ['pytest',
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2 changes: 1 addition & 1 deletion tricolour/apps/tricolour/app.py
Original file line number Diff line number Diff line change
Expand Up @@ -386,7 +386,7 @@ def _main(args):
# Generate unflagged defaults if we should ignore existing flags
# otherwise take flags from the dataset
if args.ignore_flags is True:
flags = da.full_like(vis, False, dtype=np.bool)
flags = da.full_like(vis, False, dtype=bool)
log.critical("Completely ignoring measurement set "
"flags as per '-if' request. "
"Strategy WILL NOT or with original flags, even if "
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2 changes: 1 addition & 1 deletion tricolour/mask.py
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ def load_mask(filename, dilate):
# Load mask
mask = np.load(filename)

if mask.dtype[0] != np.bool or mask.dtype[1] != np.float64:
if mask.dtype[0] != bool or mask.dtype[1] != np.float64:
raise ValueError("Mask %s is not a valid static mask "
"with labelled channel axis "
"[dtype == (bool, float64)]" % filename)
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4 changes: 2 additions & 2 deletions tricolour/packing.py
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ def _create_window_dask(name, ntime, nchan, nbl, ncorr, token,

graph = HighLevelGraph.from_collections(collection_name, layers, ())
chunks = ((0,),) # One chunk containing single zarr array object
return da.Array(graph, collection_name, chunks, dtype=np.object)
return da.Array(graph, collection_name, chunks, dtype=object)


def create_vis_windows(ntime, nchan, nbl, ncorr, token,
Expand Down Expand Up @@ -343,7 +343,7 @@ def pack_data(time_inv, ubl,
flags, ("row", "chan", "corr"),
vis_win_obj, ("windim",),
flag_win_obj, ("windim",),
dtype=np.bool)
dtype=bool)

# Expose visibility data at it's full resolution
vis_windows = da.blockwise(_packed_windows, _WINDOW_SCHEMA,
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8 changes: 4 additions & 4 deletions tricolour/tests/test_flagging_additional.py
Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ def test_apply_static_mask(wsrt_ants, unique_baselines,
accumulation_mode="or")

# Check that first mask's flags are applied
chan_sel = np.zeros(chan_freqs.shape[0], dtype=np.bool)
chan_sel = np.zeros(chan_freqs.shape[0], dtype=bool)
chan_sel[[2, 10]] = True

assert np.all(new_flags[:, :, :, chan_sel] == 1)
Expand All @@ -144,7 +144,7 @@ def test_apply_static_mask(wsrt_ants, unique_baselines,
accumulation_mode="or")

# Check that both mask's flags have been applied
chan_sel = np.zeros(chan_freqs.shape[0], dtype=np.bool)
chan_sel = np.zeros(chan_freqs.shape[0], dtype=bool)
chan_sel[[2, 10, 4, 11, 5]] = True

assert np.all(new_flags[:, :, :, chan_sel] == 1)
Expand All @@ -157,7 +157,7 @@ def test_apply_static_mask(wsrt_ants, unique_baselines,
accumulation_mode="override")

# Check that only last mask's flags applied
chan_sel = np.zeros(chan_freqs.shape[0], dtype=np.bool)
chan_sel = np.zeros(chan_freqs.shape[0], dtype=bool)
chan_sel[[4, 11, 5]] = True

assert np.all(new_flags[:, :, :, chan_sel] == 1)
Expand All @@ -176,7 +176,7 @@ def test_apply_static_mask(wsrt_ants, unique_baselines,
uvrange=uvrange)

# Check that both mask's flags have been applied
chan_sel = np.zeros(chan_freqs.shape[0], dtype=np.bool)
chan_sel = np.zeros(chan_freqs.shape[0], dtype=bool)
chan_sel[[2, 10, 4, 11, 5]] = True

# Select baselines based on the uvrange
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8 changes: 4 additions & 4 deletions tricolour/window_statistics.py
Original file line number Diff line number Diff line change
Expand Up @@ -123,21 +123,21 @@ def window_stats(flag_window, ubls, chan_freqs,
field_name, None,
ddid, None,
nchanbins, None,
meta=np.empty((0,), dtype=np.object))
meta=np.empty((0,), dtype=object))

# Create an empty stats object if the user hasn't supplied one
if prev_stats is None:
def _window_stat_creator():
return WindowStatistics(nchanbins)

prev_stats = da.blockwise(_window_stat_creator, (),
meta=np.empty((), dtype=np.object))
meta=np.empty((), dtype=object))

# Combine per-baseline stats into a single stats object
return da.blockwise(_combine_baseline_window_stats, (),
stats, ("bl",),
prev_stats, (),
meta=np.empty((), dtype=np.object))
meta=np.empty((), dtype=object))


def _combine_window_stats(*args):
Expand Down Expand Up @@ -167,7 +167,7 @@ def combine_window_stats(window_stats):
args = (v for ws in window_stats for v in (ws, ()))

return da.blockwise(_combine_window_stats, (),
*args, dtype=np.object)
*args, dtype=object)


class WindowStatistics(object):
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