migrate to newer numpy

docker/python36.docker

@@ -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 .

docker/python38.docker

@@ -17,3 +17,5 @@ WORKDIR /code
 
 # Install base + testing packages
 RUN pip3 install .[testing]
+
+RUN python3 -m pytest --flake8 -s -vvv .

setup.py

@@ -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',

tricolour/apps/tricolour/app.py

@@ -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 "

tricolour/mask.py

@@ -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)

tricolour/packing.py

@@ -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,
@@ -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,

tricolour/tests/test_flagging_additional.py

@@ -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)
@@ -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)
@@ -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)
@@ -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

tricolour/window_statistics.py

@@ -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):
@@ -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):