Ref/tdem testing

.travis.yml

@@ -50,10 +50,6 @@ before_install:
   - ./miniconda.sh -b -p $HOME/miniconda
   - export PATH=/home/travis/anaconda/bin:/home/travis/miniconda/bin:$PATH
   - conda update --yes conda
-  - echo $PWD
-  - ls $PWD
-  - echo $TRAVIS_BUILD_DIR
-  - ls $TRAVIS_BUILD_DIR
 
 install:
   - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then
@@ -68,20 +64,25 @@ install:
       openssl aes-256-cbc -K $encrypted_7e0a8632ac3f_key -iv $encrypted_7e0a8632ac3f_iv -in credentials.tar.gz.enc -out credentials.tar.gz -d ;
       tar -xzf credentials.tar.gz ;
       gcloud auth activate-service-account --key-file credentials/client-secret-docs.json ;
-      gsutil cp gs://simpeg/_build.tar.gz $PWD/docs/ ;
-      mkdir $PWD/docs/_build ;
-      tar -xzf $PWD/docs/_build.tar.gz -C $PWD/docs/_build ;
-      ls $PWD/docs/_build/ ;
+      gsutil cp gs://simpeg/_build.tar.gz $PWD/docs ;
+      gsutil cp gs://simpeg/examples.tar.gz $PWD/docs/content ;
+      cd docs ;
+      tar -xzf _build.tar.gz _build;
+      cd content ;
+      tar -xzf examples.tar.gz examples;
+      cd ../../ ;
     fi
 
 # Run test
 script:
   # - nosetests $TEST_DIR --with-cov --cov SimPEG --cov-config .coveragerc -v -s
   - if [ "$TEST_DIR" = "$DEPLOY_DIR" -a ${TRAVIS_PYTHON_VERSION:0:1} == "3" ]; then
-      cd docs; make html-noplot ; cd ../;
+      cd docs; make html-noplot ; cd ../ ;
     else
       nosetests $TEST_DIR --with-cov --cov SimPEG --cov-config .coveragerc -v -s;
     fi
+
+
 # Calculate coverage
 after_success:
   - bash <(curl -s https://codecov.io/bash)
@@ -106,7 +107,10 @@ after_success:
         gcloud auth activate-service-account --key-file credentials/client-secret.json ;
         export GAE_PROJECT=simpegdocs ;
       elif [ "$TRAVIS_BRANCH" = "$DEV_BRANCH" ]; then
+        cd docs; tar -cvzf _build.tar.gz _build ;
+        cd content; tar -cvzf examples.tar.gz examples ; cd ..;
         gsutil cp docs/_build.tar.gz gs://simpeg ;
+        gsutil cp docs/content/examples.tar.gz gs://simpeg ;
         gcloud auth activate-service-account --key-file credentials/client-secret-dev.json ;
         export GAE_PROJECT=simpeg-dev-docs ;
       fi ;

SimPEG/Problem.py

@@ -123,7 +123,15 @@ def unpair(self):
     deleteTheseOnModelUpdate = []
 
     @properties.observer('model')
-    def _on_model_update(self, value):
+    def _on_model_update(self, change):
+        if change['previous'] is change['value']:
+            return
+        if (
+            isinstance(change['previous'], np.ndarray) and
+            isinstance(change['value'], np.ndarray) and
+            np.allclose(change['previous'], change['value'])
+        ):
+            return
         for prop in self.deleteTheseOnModelUpdate:
             if hasattr(self, prop):
                 delattr(self, prop)

SimPEG/Utils/modelutils.py

@@ -2,9 +2,27 @@
 import numpy as np
 from scipy.interpolate import griddata, interp1d
 
-def surface2ind_topo(mesh, topo, gridLoc='CC', method='cubic', fill_value=np.nan):
+def surface2ind_topo(mesh, topo, gridLoc='CC', method='nearest', fill_value=np.nan):
     """
     Get active indices from topography
+
+    Parameters
+    ----------
+
+    :param TensorMesh mesh: TensorMesh object on which to discretize the topography
+    :param numpy.ndarray topo: [X,Y,Z] topographic data
+    :param str gridLoc: 'CC' or 'N'. Default is 'CC'.
+                        Discretize the topography
+                        on cells-center 'CC' or nodes 'N'
+    :param str method: 'nearest' or 'linear' or 'cubic'. Default is 'nearest'.
+                       Interpolation method for the topographic data
+    :param float fill_value: default is np.nan. Filling value for extrapolation
+
+    Returns
+    -------
+
+    :param numpy.array actind: index vector for the active cells on the mesh
+                               below the topography
     """
 
     if mesh.dim == 3:

examples/00_published/plot_booky_1D_time_freq_inv.py

@@ -392,7 +392,7 @@ def run(plotIt=True, saveFig=False, cleanup=True):
 
     ax0.semilogx(sigma_re, z, 'k', lw=2, label="RESOLVE")
     ax0.semilogx(sigma_sky, z, 'b', lw=2, label="SkyTEM")
-    ax0.set_ylim(-100, 0)
+    ax0.set_ylim(-50, 0)
     # ax0.set_xlim(5e-4, 1e2)
     ax0.grid(True)
     ax0.set_ylabel("Depth (m)")
@@ -459,6 +459,12 @@ def run(plotIt=True, saveFig=False, cleanup=True):
         plt.show()
 
     if cleanup:
+        print( os.path.split(directory)[:-1])
+        os.remove(
+            os.path.sep.join(
+                directory.split()[:-1] + ["._bookpurnong_inversion"]
+            )
+        )
         os.remove(downloads)
         shutil.rmtree(directory)
 

examples/04-grav/plot_laguna_del_maule_inversion.py

@@ -13,6 +13,7 @@
 """
 import os
 import shutil
+import tarfile
 import SimPEG.PF as PF
 from SimPEG import Maps, Regularization, Optimization, DataMisfit,\
                    InvProblem, Directives, Inversion
@@ -24,15 +25,16 @@
 def run(plotIt=True, cleanAfterRun=True):
 
     # Start by downloading files from the remote repository
-    url = "https://storage.googleapis.com/simpeg/Chile_GRAV_4_Miller/"
-    cloudfiles = [
-        'LdM_grav_obs.grv', 'LdM_mesh.mesh',
-        'LdM_topo.topo', 'LdM_input_file.inp'
-    ]
+    # directory where the downloaded files are
 
-    # Download to Downloads/SimPEGtemp
-    basePath = os.path.expanduser('~/Downloads/simpegtemp')
-    download([url+f for f in cloudfiles], folder=basePath, overwrite=True)
+    url = "https://storage.googleapis.com/simpeg/Chile_GRAV_4_Miller/Chile_GRAV_4_Miller.tar.gz"
+    downloads = download(url, overwrite=True)
+    basePath = downloads.split(".")[0]
+
+    # unzip the tarfile
+    tar = tarfile.open(downloads, "r")
+    tar.extractall()
+    tar.close()
 
     input_file = basePath + os.path.sep + 'LdM_input_file.inp'
     # %% User input
@@ -133,6 +135,7 @@ def run(plotIt=True, cleanAfterRun=True):
     mrec = inv.run(mstart)
 
     if cleanAfterRun:
+        os.remove(downloads)
         shutil.rmtree(basePath)
 
     # %%

tests/em/static/test_DC_jvecjtvecadj.py

@@ -130,7 +130,8 @@ def test_misfit(self):
                 self.survey.dpred(m), lambda mx: self.p.Jvec(self.m0, mx)
             ],
             self.m0,
-            plotIt=False
+            plotIt=False,
+            num=3
         )
         self.assertTrue(passed)
 
@@ -149,7 +150,8 @@ def test_dataObj(self):
         passed = Tests.checkDerivative(
             lambda m: [self.dmis(m), self.dmis.deriv(m)],
             self.m0,
-            plotIt=False
+            plotIt=False,
+            num=3
         )
         self.assertTrue(passed)