Merge pull request #3461 from obspy/np2

numpy 2.0 compatibility

.github/test_conda_env.yml

@@ -7,7 +7,7 @@ dependencies:
   - decorator
   - lxml
   - matplotlib
-  - numpy
+  - numpy < 2
   - scipy
   - requests
   - setuptools

.github/test_mindep_conda_env.yml

@@ -7,7 +7,7 @@ dependencies:
   - decorator
   - lxml
   - matplotlib
-  - numpy
+  - numpy < 2
   - scipy
   - requests
   - setuptools

.github/test_np2_conda_env.yml

@@ -0,0 +1,27 @@
+name: test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  # obspy
+  - decorator
+  - lxml
+  - matplotlib
+  - numpy >= 2.0.0rc2
+  # dummy package needed to install the np2 rc via conda
+  - conda-forge/label/numpy_rc::_numpy_rc
+  - scipy
+  - requests
+  - setuptools
+  # see #3258
+  - sqlalchemy < 2.0
+  # soft dependencies
+  - cartopy
+  - geographiclib
+  - pyshp
+  # tests
+  - packaging
+  - pyproj
+  - pytest
+  - pytest-cov
+  - pytest-json-report >= 1.4

.github/workflows/tests.yml

@@ -122,6 +122,16 @@ jobs:
           - os: ubuntu-latest
             python-version: '3.12'
             options: default warnings
+          # numpy 2 specific builds
+          - os: ubuntu-latest
+            python-version: '3.12'
+            options: default warnings np2
+          - os: macos-latest
+            python-version: '3.12'
+            options: default warnings np2
+          - os: windows-latest
+            python-version: '3.12'
+            options: default warnings np2
           - os: ubuntu-latest
             python-version: '3.12'
             options: ${{ (github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'test_network')) && 'network warnings' || 'default' }}
@@ -136,7 +146,7 @@ jobs:
       # set individual cache key
       cache_key: ${{ matrix.os }}-py${{ matrix.python-version }}-${{ contains(matrix.options, 'mindep') }}-${{ contains(matrix.options, 'mindepversion') }}
       # set conda environment file with dependencies
-      env_file: .github/test${{ contains(matrix.options, 'mindepversion') && '_mindepversion' || contains(matrix.options, 'mindep') && '_mindep' || '' }}_conda_env.yml
+      env_file: .github/test${{ contains(matrix.options, 'np2') && '_np2' || contains(matrix.options, 'mindepversion') && '_mindepversion' || contains(matrix.options, 'mindep') && '_mindep' || '' }}_conda_env.yml
       # set additional runtest options (--keep-images, --network, -W error)
       runtest_options: ${{ github.event_name == 'pull_request' && '--keep-images' || '' }} ${{ contains(matrix.options, 'network') && '--network' || '' }} ${{ contains(matrix.options, 'warnings') && '-W error' || '' }}
     steps:

obspy/__init__.py

@@ -28,9 +28,20 @@
     (https://www.gnu.org/copyleft/lesser.html)
 """
 import sys
+import warnings
 
 # don't change order
-from obspy.core.utcdatetime import UTCDateTime  # NOQA
+# ignore pkg resources deprecation warning for now
+# we really only need this here for one single reason: this file here gets
+# imported during the pytest startup phase before ignore rules in pytest.ini
+# take effect. otherwise we could just add this warning to the ignore list in
+# pytest.ini (see #3333)
+# The warning capture can be removed after #3333 gets finalized and merged
+with warnings.catch_warnings(record=True) as w:
+    msg = ('pkg_resources is deprecated as an API')
+    warnings.filterwarnings(
+        'ignore', message=msg, category=DeprecationWarning, module='obspy')
+    from obspy.core.utcdatetime import UTCDateTime  # NOQA
 from obspy.core.util import _get_version_string
 __version__ = _get_version_string(abbrev=10)
 from obspy.core.trace import Trace  # NOQA

obspy/core/preview.py

@@ -15,6 +15,7 @@
 from obspy.core.stream import Stream
 from obspy.core.trace import Trace
 from obspy.core.utcdatetime import UTCDateTime
+from obspy.core.util.misc import ptp
 
 
 def create_preview(trace, delta=60):
@@ -66,7 +67,7 @@ def create_preview(trace, delta=60):
     # reshape matrix
     data = trace.data[start:end].reshape([number_of_slices, samples_per_slice])
     # get minimum and maximum for each row
-    diff = data.ptp(axis=1)
+    diff = ptp(data, axis=1)
     # fill masked values with -1 -> means missing data
     if isinstance(diff, np.ma.masked_array):
         diff = np.ma.filled(diff, -1)

obspy/core/stream.py

@@ -28,7 +28,8 @@
                                   _read_from_plugin, _generic_reader)
 from obspy.core.util.decorator import (map_example_filename,
                                        raise_if_masked, uncompress_file)
-from obspy.core.util.misc import get_window_times, buffered_load_entry_point
+from obspy.core.util.misc import (
+    get_window_times, buffered_load_entry_point, ptp)
 from obspy.core.util.obspy_types import ObsPyException
 
 
@@ -3353,13 +3354,13 @@ def stack(self, group_by='all', stack_type='linear', npts_tol=0,
                 raise ValueError(msg)
             if 'starttime' not in header and time_tol > 0:
                 times = [tr.stats.starttime for tr in traces]
-                if np.ptp(times) <= time_tol:
+                if ptp(times) <= time_tol:
                     # use high median as starttime
                     header['starttime'] = sorted(times)[len(times) // 2]
             header['stack'] = AttribDict(group=groupid, count=len(traces),
                                          type=stack_type)
             npts_all = [len(tr) for tr in traces]
-            npts_dif = np.ptp(npts_all)
+            npts_dif = ptp(npts_all)
             npts = min(npts_all)
             if npts_dif > npts_tol:
                 msg = ('Difference of number of points of the traces is higher'
@@ -3407,7 +3408,7 @@ def _dummy_stream_from_string(s):
             sampling_rate = float(items[6])
             npts = int(items[8])
             tr = Trace()
-            tr.data = np.ones(npts, dtype=np.float_)
+            tr.data = np.ones(npts, dtype=np.float64)
             tr.stats.station = sta
             tr.stats.network = net
             tr.stats.location = loc

obspy/core/tests/test_trace.py

@@ -1427,7 +1427,7 @@ def test_times(self):
         tr.data = np.ma.ones(100)
         tr.data[30:40] = np.ma.masked
         tm = tr.times()
-        assert np.alltrue(tr.data.mask == tm.mask)
+        assert np.all(tr.data.mask == tm.mask)
         # test relative with reftime
         tr.data = np.ones(100)
         shift = 9.5

obspy/core/tests/test_utcdatetime.py

@@ -44,19 +44,19 @@ def test_from_numpy_string(self):
         Tests importing from NumPy strings.
         """
         # some strange patterns
-        dt = UTC(np.string_("1970-01-01 12:23:34"))
+        dt = UTC(np.bytes_("1970-01-01 12:23:34"))
         assert dt == UTC(1970, 1, 1, 12, 23, 34)
-        dt = UTC(np.string_("1970,01,01,12:23:34"))
+        dt = UTC(np.bytes_("1970,01,01,12:23:34"))
         assert dt == UTC(1970, 1, 1, 12, 23, 34)
-        dt = UTC(np.string_("1970,001,12:23:34"))
+        dt = UTC(np.bytes_("1970,001,12:23:34"))
         assert dt == UTC(1970, 1, 1, 12, 23, 34)
-        dt = UTC(np.string_("20090701121212"))
+        dt = UTC(np.bytes_("20090701121212"))
         assert dt == UTC(2009, 7, 1, 12, 12, 12)
-        dt = UTC(np.string_("19700101"))
+        dt = UTC(np.bytes_("19700101"))
         assert dt == UTC(1970, 1, 1, 0, 0)
         # non ISO8601 strings should raise an exception
         with pytest.raises(Exception):
-            UTC(np.string_("1970,001,12:23:34"), iso8601=True)
+            UTC(np.bytes_("1970,001,12:23:34"), iso8601=True)
 
     def test_from_python_date_time(self):
         """

obspy/core/tests/test_util_testing.py

@@ -69,7 +69,7 @@ def test_nan(self):
         Ensure NaNs eval equal if equal_nan is used, else they do not.
         """
         tr1, tr2 = read()[0], read()[0]
-        tr1.data[0], tr2.data[0] = np.NaN, np.NaN
+        tr1.data[0], tr2.data[0] = np.nan, np.nan
         assert traces_almost_equal(tr1, tr2, equal_nan=True)
         assert not traces_almost_equal(tr1, tr2, equal_nan=False)
 

obspy/core/trace.py

@@ -1735,7 +1735,7 @@ def resample(self, sampling_rate, window='hann', no_filter=True,
             self.filter('lowpass_cheby_2', freq=freq, maxorder=12)
 
         # resample in the frequency domain. Make sure the byteorder is native.
-        x = rfft(self.data.newbyteorder("="))
+        x = rfft(self.data.view(self.data.dtype.newbyteorder("=")))
         # Cast the value to be inserted to the same dtype as the array to avoid
         # issues with numpy rule 'safe'.
         x = np.insert(x, 1, x.dtype.type(0))

obspy/core/utcdatetime.py

@@ -995,6 +995,12 @@ def __add__(self, value):
             msg = ("unsupported operand type(s) for +: 'UTCDateTime' and "
                    "'UTCDateTime'")
             raise TypeError(msg)
+        # need to make sure we don't get e.g. np.float32 singl precision input
+        # or worse, because then numpy is in charge of the calculations and
+        # numpy 2.0 is not automatically upcasting to avoid precision loss
+        # which means we can't keep full precision when converting input
+        # seconds to nanoseconds
+        value = float(value)
         return UTCDateTime(ns=self._ns + int(round(value * 1e9)))
 
     def __sub__(self, value):

obspy/core/util/misc.py

@@ -708,6 +708,20 @@ def func(obj, parent=None, attr=None):
     return func(obj)
 
 
+def ptp(a, *args, **kwargs):
+    """
+    Replacement for :meth:`numpy.ndarray.ptp()` and the corresponding method on
+    `MaskedArray` objects which are being removed in numpy 2.0
+    Basically just makes sure we call the correct replacement function numpy
+    put in place for regular and masked arrays.
+
+    :type a: :class:`numpy.ndarray` or :class:`numpy.ma.MaskedArray`
+    """
+    if isinstance(a, np.ma.MaskedArray):
+        return np.ma.ptp(a, *args, **kwargs)
+    return np.ptp(a, *args, **kwargs)
+
+
 if __name__ == '__main__':
     import doctest
     doctest.testmod(exclude_empty=True)

obspy/io/alsep/core.py

@@ -24,11 +24,14 @@ def _read_header(file):
         # np.fromfile accepts file path on-disk file-like
         # objects. In all other cases, use np.frombuffer:
         try:
-            return np.fromfile(file, dtype='u1', count=16)
+            header = np.fromfile(file, dtype='u1', count=16)
         except UnsupportedOperation:
             # stream does not support fileno
             buffer = io_stream.read(16)
-            return np.frombuffer(buffer, dtype='u1')
+            header = np.frombuffer(buffer, dtype='u1')
+    # manual upcast for later bitshifting etc
+    header = np.require(header, dtype=np.int64)
+    return header
 
 
 def _is_pse(file):

obspy/io/alsep/pse/frame.py

@@ -6,7 +6,7 @@
 
 class PseFrame(object):
     def __init__(self, frame, _is_old_format):
-        self.data = frame
+        self.data = np.require(frame, dtype=np.int64)
         self._is_old_format = _is_old_format
         # Frame header parameters
         self.software_time_flag = None

obspy/io/alsep/wt/frame.py

@@ -8,7 +8,7 @@
 class _WtFrame(object):
 
     def __init__(self, frame):
-        self.data = frame
+        self.data = np.require(frame, dtype=np.int64)
         # Frame header parameters
         self.flag_bit = None
         self.msec_of_year = None

obspy/io/ascii/core.py

@@ -349,8 +349,7 @@ def _write_slist(stream, filename, custom_fmt=None,
             else:
                 data = trace.data
             data = data.reshape((-1, 6))
-            np.savetxt(fh, data, delimiter=b'\t',
-                       fmt=fmt.encode('ascii', 'strict'))
+            np.savetxt(fh, data, delimiter='\t', fmt=fmt)
             if rest:
                 fh.write(('\t'.join([fmt % d for d in trace.data[-rest:]]) +
                          '\n').encode('ascii', 'strict'))

obspy/io/mseed/util.py

@@ -1609,7 +1609,7 @@ def shift_time_of_file(input_file, output_file, timeshift):
         # This should rarely be the case.
         if current_time_shift == 0 and is_time_correction_applied:
             # This sets bit 2 of the activity flags to 0.
-            current_record[36] = current_record[36] & (~2)
+            current_record[36] = np.int64(current_record[36]) & (~2)
             is_time_correction_applied = False
         # This is the case if the time correction has been applied. This
         # requires some more work by changing both, the actual time and the

obspy/io/nordic/ellipse.py

@@ -374,7 +374,9 @@ def subtended_angle(self, pt=(0, 0)):
         temp.y -= pt[1]
         t0, t1 = temp._get_tangents((0, 0))
         cosang = np.dot(t0, t1)
-        sinang = np.linalg.norm(np.cross(t0, t1))
+        # avoid np.cross() complaining about 2-d vectors
+        # see https://github.com/obspy/obspy/pull/3461#issuecomment-2149488336
+        sinang = abs(t0[0] * t1[1] - t0[1] * t1[0])
         return np.degrees(np.arctan2(sinang, cosang))
 
     def plot(self, linewidth=2, color='k',

obspy/io/reftek/core.py

@@ -186,7 +186,7 @@ def drop_not_implemented_packet_types(self):
         Checks if there are packets of a type that is currently not implemented
         and drop them showing a warning message.
         """
-        is_implemented = np.in1d(
+        is_implemented = np.isin(
             self._data['packet_type'],
             [x.encode() for x in PACKET_TYPES_IMPLEMENTED])
         # if all packets are of a type that is implemented, the nothing to do..