fix ci builds (PPSD and others)

.travis.yml

@@ -79,6 +79,8 @@ install:
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
+  - conda config --set restore_free_channel true
+  - conda config --add channels conda-forge
   # Useful for debugging any issues with conda
   - conda info -a
   - |
@@ -89,6 +91,7 @@ install:
         # no basemap version works with this old numpy, so leave out
         BASEMAP=""
         PYPROJ="pyproj"
+        GFORTRAN="libgfortran=1"
         PROJ4="proj4"
         # ancient matplotlib needs to be turned to AGG before anything else,
         # otherwise it tries to import incompatible version of Qt as a backend
@@ -104,6 +107,7 @@ install:
         BASEMAP="basemap"
         PYPROJ="pyproj"
         PROJ4="proj4"
+        GFORTRAN=""
       # elif [[ "$ARCHITECTURE_32BIT" == "True" ]]; then
       #   # Special packages for 32bit. Also let conda resolve to the latest
       #   # versions.
@@ -122,13 +126,15 @@ install:
         BASEMAP="basemap"
         PYPROJ="pyproj"
         PROJ4="proj4=4.9.3"
+        GFORTRAN=""
       else
         NUMPY="numpy"
         SCIPY="scipy"
         MATPLOTLIB="matplotlib>=2.0.0"
         BASEMAP="basemap"
         PYPROJ="pyproj"
         PROJ4="proj4"
+        GFORTRAN=""
       fi
   - |
     if [[ "${PYTHON_VERSION}" == '3.7' ]]; then
@@ -145,6 +151,7 @@ install:
         $BASEMAP
         $PYPROJ
         $PROJ4
+        $GFORTRAN
         coverage
         decorator
         docopt

CHANGELOG.txt

@@ -125,6 +125,7 @@ master:
  - obspy.signal.polarization:
    * Fix an issue in selecting Z/N/E traces from given stream (see #2365)
  - obspy.signal.PPSD:
+   * Changed numpy-based serialization as to not require pickling (see #2424).
    * Fixed exact trace cutting for PSD segments (see #2040).
    * Timestamp representations internally and in npz I/O were changed to use
      integer nanosecond POSIX timestamps to avoid any potential floating point

obspy/imaging/source.py

@@ -62,11 +62,13 @@ def _setup_figure_and_axes(kind, fig=None, subplot_size=4.0):
         ncols_ = len(row)
         for j, kind__ in enumerate(row):
             kind_.append(kind__)
-            kwargs = {"aspect": "equal", "adjustable": "datalim"}
+            kwargs = {"adjustable": "datalim"}
             if kind__ in ("p_quiver", "p_sphere", "s_quiver", "s_sphere"):
                 kwargs["projection"] = "3d"
-            axes.append(fig.add_subplot(
-                nrows, ncols_, i * ncols_ + j + 1, **kwargs))
+            else:  # equal aspect never worked on 3d plot, see mpl #13474
+                kwargs["aspect"] = "equal"
+            ax = fig.add_subplot(nrows, ncols_, i * ncols_ + j + 1, **kwargs)
+            axes.append(ax)
     return fig, axes, kind_
 
 

obspy/signal/spectral_estimation.py

@@ -222,6 +222,10 @@ class PPSD(object):
         NPZ_STORE_KEYS_LIST_TYPES +
         NPZ_STORE_KEYS_SIMPLE_TYPES +
         NPZ_STORE_KEYS_VERSION_NUMBERS)
+    # A mapping of values for storing info in the NPZ file. This is needed
+    # because some types are not loadable without allowing pickle (#2409).
+    NPZ_SIMPLE_TYPE_MAP = {None: ''}
+    NPZ_SIMPLE_TYPE_MAP_R = {v: i for i, v in NPZ_SIMPLE_TYPE_MAP.items()}
 
     def __init__(self, stats, metadata, skip_on_gaps=False,
                  db_bins=(-200, -50, 1.), ppsd_length=3600.0, overlap=0.5,
@@ -1274,7 +1278,14 @@ def save_npz(self, filename):
         :type filename: str
         :param filename: Name of numpy .npz output file
         """
-        out = dict([(key, getattr(self, key)) for key in self.NPZ_STORE_KEYS])
+        out = {}
+        for key in self.NPZ_STORE_KEYS:
+            value = getattr(self, key)
+            # Some values need to be replaced to allow non-pickle
+            # serialization (#2409).
+            if key in self.NPZ_STORE_KEYS_SIMPLE_TYPES:
+                value = self.NPZ_SIMPLE_TYPE_MAP.get(value, value)
+            out[key] = value
         np.savez_compressed(filename, **out)
 
     @staticmethod
@@ -1315,6 +1326,7 @@ def _load(data):
                 elif key in (ppsd.NPZ_STORE_KEYS_SIMPLE_TYPES +
                              ppsd.NPZ_STORE_KEYS_VERSION_NUMBERS):
                     data_ = data_.item()
+                    data_ = ppsd.NPZ_SIMPLE_TYPE_MAP_R.get(data_, data_)
                 # convert floating point POSIX second timestamps from older npz
                 # files
                 if (key in ppsd.NPZ_STORE_KEYS_LIST_TYPES and
@@ -1331,7 +1343,7 @@ def _load(data):
 
         # XXX get rid of if/else again when bumping minimal numpy to 1.7
         if NUMPY_VERSION >= [1, 7]:
-            with np.load(filename) as data:
+            with np.load(filename, allow_pickle=True) as data:
                 return _load(data)
         else:
             data = np.load(filename)
@@ -1369,7 +1381,9 @@ def _add(data):
             _check_npz_ppsd_version(self, data)
             # check if all metadata agree
             for key in self.NPZ_STORE_KEYS_SIMPLE_TYPES:
-                if getattr(self, key) != data[key].item():
+                value_ = data[key].item()
+                value = self.NPZ_SIMPLE_TYPE_MAP_R.get(value_, value_)
+                if getattr(self, key) != value:
                     msg = ("Mismatch in '%s' attribute.\n\tCurrent:\n\t%s\n\t"
                            "Loaded:\n\t%s")
                     msg = msg % (key, getattr(self, key), data[key].item())

obspy/signal/tests/test_spectral_estimation.py

@@ -9,6 +9,7 @@
 from future.utils import native_str
 
 import gzip
+import io
 import os
 import unittest
 import warnings
@@ -136,7 +137,7 @@ def test_obspy_psd_vs_pitsa(self):
         fn_psd_pitsa = "pitsa_noise_psd_samprate_100_nfft_512_noverlap_0.npy"
         file_psd_pitsa = os.path.join(self.path, fn_psd_pitsa)
 
-        noise = np.load(file_noise)
+        noise = np.load(file_noise, allow_pickle=True)
         # in principle to mimic PITSA's results detrend should be specified as
         # some linear detrending (e.g. from matplotlib.mlab.detrend_linear)
         psd_obspy, _ = psd(noise, NFFT=nfft, Fs=sampling_rate,
@@ -802,7 +803,7 @@ def test_exception_reading_newer_npz(self):
                "consider updating your ObsPy installation.".format(
                    PPSD(stats=Stats(), metadata=None).ppsd_version))
         # 1 - loading a npz
-        data = np.load(self.example_ppsd_npz)
+        data = np.load(self.example_ppsd_npz, allow_pickle=True)
         # we have to load, modify 'ppsd_version' and save the npz file for the
         # test..
         items = {key: data[key] for key in data.files}
@@ -836,6 +837,21 @@ def test_nice_ringlaser_metadata_error_msg(self):
                     "stating the overall sensitivity`.")
         self.assertEqual(str(e.exception), expected)
 
+    def test_can_read_npz_without_pickle(self):
+        """
+        Ensures that a default PPSD can be written and read without having to
+        allow np.load the use of pickle. See #2409.
+        """
+        # Init a test PPSD and empty byte stream.
+        ppsd = PPSD.load_npz(self.example_ppsd_npz)
+        byte_me = io.BytesIO()
+        # Save PPSD to byte stream and rewind to 0.
+        ppsd.save_npz(byte_me)
+        byte_me.seek(0)
+        # Load dict, will raise an exception if pickle is needed.
+        loaded_dict = dict(np.load(byte_me, allow_pickle=False))
+        self.assertIsInstance(loaded_dict, dict)
+
 
 def suite():
     return unittest.makeSuite(PsdTestCase, 'test')