Upate for numpy deprications (#101)

.github/workflows/linters.yml

@@ -19,19 +19,20 @@ jobs:
       - name: Install isort
         run: |
           python -m pip install -r requirements/extras.txt
+          python -m pip install colorama
       - name: Retrieve isort version
         run: |
           ISORTVERSION=$(python -c "import isort; print(isort.__version__)")
           echo "ISORT_VERSION=${ISORTVERSION}" >> $GITHUB_ENV
       - name: Which isort version
-        uses: isort/isort-action@master
+        uses: isort/isort-action@v1.1.0
         with:
-          isortVersion: "${{ env.ISORT_VERSION }}"
+          isort-version: "${{ env.ISORT_VERSION }}"
           configuration: "--version"
       - name: Run isort checks
-        uses: isort/isort-action@master
+        uses: isort/isort-action@v1.1.0
         with:
-          isortVersion: "${{ env.ISORT_VERSION }}"
+          isort-version: "${{ env.ISORT_VERSION }}"
           configuration: "--check-only --diff --color"
 
   black:

.github/workflows/tests.yml

@@ -107,8 +107,8 @@ jobs:
             min-install: h5py==3.0
             python: '3.7'
 
-          - spec-name: h5py v3.0 numpy v1.17
-            min-install: h5py==3.0 numpy==1.17
+          - spec-name: h5py v3.0 numpy v1.20
+            min-install: h5py==3.0 numpy==1.20
             python: '3.7'
 
     steps:

bapsflib/_hdf/maps/controls/tests/fauxsixk.py

@@ -341,8 +341,8 @@ def _add_datasets(self):
                 ("z", np.float64),
                 ("theta", np.float64),
                 ("phi", np.float64),
-                ("Motion list", np.bytes0, 120),
-                ("Probe name", np.bytes0, 120),
+                ("Motion list", np.bytes_, 120),
+                ("Probe name", np.bytes_, 120),
             ]
         )
 

bapsflib/_hdf/maps/digitizers/tests/fauxsis3301.py

@@ -47,7 +47,7 @@ def active_brdch(self, val):
             if isinstance(val, np.ndarray):
                 if (
                     val.shape == (13, 8)
-                    and np.issubdtype(val.dtype, np.bool)
+                    and np.issubdtype(val.dtype, bool)
                     and np.any(val)
                 ):
                     self._faux._active_brdch = val

bapsflib/_hdf/maps/digitizers/tests/fauxsiscrate.py

@@ -67,11 +67,11 @@ def active_brdch(self, val):
             # - prevent enabling channels that can't be enabled for
             #   the SIS 3305 mode
             if self.sis3305_mode == 2:
-                mask = np.array(2 * [True, False, False, False], dtype=np.bool)
+                mask = np.array(2 * [True, False, False, False], dtype=bool)
             elif self.sis3305_mode == 1:
-                mask = np.array(2 * [True, False, True, False], dtype=np.bool)
+                mask = np.array(2 * [True, False, True, False], dtype=bool)
             else:
-                mask = np.ones(8, dtype=np.bool)
+                mask = np.ones(8, dtype=bool)
             mask = np.logical_not(mask)
             mask = mask.reshape(1, 8)
             mask = np.append(mask, mask, axis=0)
@@ -495,7 +495,7 @@ def _default_setup(self):
         self._sn_size = 100
         self._nt = 10000
         self._active_brdch = np.zeros(
-            (), dtype=[("SIS 3302", np.bool, (4, 8)), ("SIS 3305", np.bool, (2, 8))]
+            (), dtype=[("SIS 3302", bool, (4, 8)), ("SIS 3305", bool, (2, 8))]
         )
         self._active_brdch["SIS 3302"][0][0] = True
         self._active_brdch["SIS 3305"][0][0] = True

bapsflib/_hdf/maps/digitizers/tests/test_map_digis.py

@@ -46,7 +46,7 @@ def tearDownClass(cls):
 
     @property
     def group(self) -> h5py.Group:
-        """Data group holding digitizer gorups."""
+        """Data group holding digitizer groups."""
         return self.f[self.DIGI_ROOT]
 
     @property

bapsflib/_hdf/utils/hdfreaddata.py

@@ -57,7 +57,7 @@ class HDFReadData(np.ndarray):
 
     .. note::
 
-        * Evey returned numpy array will have the :code:`'xyz'` field,
+        * Every returned numpy array will have the :code:`'xyz'` field,
           which is reserved for probe position data.  If a control
           device specifies this field, then field will be filled with
           the control device data;otherwise, the field will be filled
@@ -362,7 +362,7 @@ def __new__(
             shotnum = dheader[index.tolist(), shotnumkey]
 
             # define sni
-            sni = np.ones(shotnum.shape[0], dtype=np.bool)
+            sni = np.ones(shotnum.shape[0], dtype=bool)
 
             # print execution timing
             if timeit:  # pragma: no cover

bapsflib/_hdf/utils/tests/test_hdfreadcontrol.py

@@ -305,7 +305,7 @@ def test_nan_fill(self, _bf: File, mock_controls):
                 ("bits", np.uint32),
                 ("signal", np.float32),
                 ("command", np.bytes_, 10),
-                ("valid", np.bool),
+                ("valid", bool),
             ],
         )
         data["Shot number"] = np.arange(1, 11, 1, dtype=np.uint32)
@@ -372,7 +372,7 @@ def _build_configs(self):
                             "dset paths": dset_paths,
                             "dset field": ("valid",),
                             "shape": (),
-                            "dtype": np.bool,
+                            "dtype": bool,
                         },
                     },
                 }

changelog/101.pkg_management.1.rst

@@ -0,0 +1 @@
+Updated `numpy` dependency to ``>=1.20``.

changelog/101.pkg_management.2.rst

@@ -0,0 +1 @@
+Fixed `towncrier` dependency to `towncrier==22.8.0`.

changelog/101.trivial.1.rst

@@ -0,0 +1,2 @@
+Replaced several instances of `numpy` deprecated functionality: `numpy.bool` to
+`bool` and `numpy.bytes0` to `numpy.bytes_`.

docs/using_lapd/read_from_digi.inc.rst

@@ -326,7 +326,7 @@ fields.
     configuration. The configuration has be unique to a block of
     recorded data.  For the :code:`'6K Compumotor'` the receptacle
     number is used as the configuration name, whereas, for the
-    :code:`'Waveform'` control the confiugration name is the name of the
+    :code:`'Waveform'` control the configuration name is the name of the
     configuration group inside the :code:`'Waveform` group.  Since the
     configurations are contain in the
     :code:`f.file_map.contorols[con_name].configs` dictionary, the

requirements/docs.txt

@@ -7,4 +7,4 @@ sphinx-automodapi >= 0.13
 sphinx-changelog
 sphinx-gallery
 sphinx_rtd_theme
-towncrier >= 19.2.0
+towncrier == 22.8.0

requirements/install.txt

@@ -3,5 +3,5 @@
 -r build.txt
 astropy >= 4.3.1
 h5py >= 3.0
-numpy >= 1.17
+numpy >= 1.20
 scipy >= 0.19

setup.cfg

@@ -47,7 +47,7 @@ install_requires =
     # ought to mirror requirements/install.txt
     astropy >= 4.3.1
     h5py >= 3.0
-    numpy >= 1.17
+    numpy >= 1.20
     scipy >= 0.19
 
 [options.extras_require]
@@ -70,7 +70,7 @@ docs =
     sphinx-changelog
     sphinx-gallery
     sphinx_rtd_theme
-    towncrier >= 19.2.0
+    towncrier == 22.8.0
 developer =
     # install everything for developers
     %(docs)s
@@ -81,3 +81,4 @@ developer =
 skip = *.png,*cache*,*egg*,.git,.hypothesis,.idea,.tox,_build,venv
 ignore-words-list =
     crate,
+    oce,