Merging master branch to solve pynbody pip building problems

pynbody · Feb 21, 2019 · 56a55d1 · 56a55d1
2 parents a8c08b2 + 357e0bc
commit 56a55d1
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Showing 4 changed files with 11 additions and 8 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -3,7 +3,7 @@
 language: c
 # use language: c to be able to use a matrix of python and numpy versions -- see https://github.com/rmcgibbo/mdtraj/blob/master/.travis.yml
 
-sudo: false 
+sudo: false
 
 # specify different versions of python and numpy
 env:
@@ -22,12 +22,15 @@ before_install:
   - conda update --yes conda
 
 install:
-  - conda create --yes -n ${PYTHON}_${NUMPY_VERSION}_{$CYTHON_VERSION} python=$PYTHON numpy=$NUMPY_VERSION scipy matplotlib nose h5py pip webtest pyquery sphinx pygments pandas sqlalchemy cython=$CYTHON_VERSION pyramid pyramid_mako ipython
-  - source activate ${PYTHON}_${NUMPY_VERSION}_{$CYTHON_VERSION}
+  - conda create --yes -n ${PYTHON}_${NUMPY_VERSION} python=$PYTHON numpy=$NUMPY_VERSION scipy matplotlib nose h5py pip webtest pyquery sphinx pygments pandas sqlalchemy cython pyramid ipython
+  - pip install pyramid_mako  # anaconda does not yet have pyramid_mako for py3.7
+  - source activate ${PYTHON}_${NUMPY_VERSION}
   - python setup.py install
   - python -c "import tangos" # ensure tangos can be imported without pynbody present
-  - pip install numpy==1.16.1
-  - pip install git+git://github.com/pynbody/pynbody.git
+  - git clone https://github.com/pynbody/pynbody.git
+  - cd pynbody
+  - python setup.py install
+  - cd ..
   - pip install yt>=3.4.0
 
 

diff --git a/docs/custom_input_handlers.md b/docs/custom_input_handlers.md
@@ -66,7 +66,7 @@ class MyHandler(tangos.input_handlers.HandlerBase):
     def enumerate_objects(self, timestep_extension, object_typetag, min_halo_particles):
         if object_typetag!="halo":
             # we only know about objects called 'halo'
-            raise StopIteration
+            return
 
         if timestep_extension=="my_timestep_1":
             # suppose timestep 1 has 100 halos

diff --git a/tangos/input_handlers/pynbody.py b/tangos/input_handlers/pynbody.py
@@ -220,7 +220,7 @@ def enumerate_objects(self, ts_extension, object_typetag="halo", min_halo_partic
                 h = self._construct_halo_cat(ts_extension, object_typetag)
             except:
                 logger.warn("Unable to read %ss using pynbody; assuming step has none", object_typetag)
-                raise StopIteration
+                return
 
             logger.warn(" => enumerating %ss directly using pynbody", object_typetag)
 

diff --git a/tangos/input_handlers/yt.py b/tangos/input_handlers/yt.py
@@ -48,7 +48,7 @@ def match_objects(self, ts1, ts2, halo_min, halo_max, dm_only=False, threshold=0
 
     def enumerate_objects(self, ts_extension, object_typetag="halo", min_halo_particles=config.min_halo_particles):
         if object_typetag!="halo":
-            raise StopIteration
+            return
         if self._can_enumerate_objects_from_statfile(ts_extension, object_typetag):
             for X in self._enumerate_objects_from_statfile(ts_extension, object_typetag):
                 yield X