Merge pull request #95 from trident-project/sph-viz

Mergin sph-viz into master
trident-project · Sep 22, 2019 · ff34a76 · ff34a76
2 parents 494e1d2 + 3d9e4e0
commit ff34a76
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Showing 22 changed files with 236 additions and 549 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -20,9 +20,9 @@ env:
     TRIDENT_ION_DATA=$HOME/.trident
     TRIDENT_ANSWER_DATA=$HOME/answer_test_data
     TRIDENT_CONFIG=$TRIDENT_ION_DATA/config.tri
-    YT_GOLD=953248239966
-    YT_HEAD=master
-    TRIDENT_GOLD=test-standard-v4
+    YT_GOLD=4f56c4c9b534106fd45e8dfe644280755236fb5d
+    YT_HEAD=yt-4.0
+    TRIDENT_GOLD=test-standard-sph-viz-v3
 
 before_install:
   - |
@@ -44,13 +44,13 @@ install:
     pip install --upgrade setuptools
     pip install cython scipy
     # Install dependencies
-    # install yt
+    # install yt-4.0 branch
     if [ ! -f $YT_DIR/README.md ]; then
-        git clone --branch=master https://github.com/yt-project/yt $YT_DIR
+        git clone --branch=yt-4.0 https://github.com/yt-project/yt $YT_DIR
     fi
     pushd $YT_DIR
-    git checkout master
-    git pull origin master
+    git checkout $YT_HEAD
+    git pull origin $YT_HEAD
     git checkout $YT_GOLD
     pip install -e .
     popd
@@ -103,11 +103,6 @@ script:
 
 jobs:
   include:
-    - stage: tests
-      name: "tests with Python 2.7 and yt-dev"
-      python: 2.7
-      env: YT_VER=$YT_HEAD
-
     - stage: tests
       name: "tests with Python 3.5 and yt-dev"
       python: 3.5
@@ -119,11 +114,6 @@ jobs:
       env: YT_VER=$YT_HEAD
       after_success: coveralls
 
-    - stage: tests
-      name: "tests with Python 2.7 and yt stable"
-      python: 2.7
-      env: YT_VER=$YT_GOLD
-
     - stage: tests
       name: "tests with Python 3.5 and yt stable"
       python: 3.5

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -12,7 +12,6 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-from __future__ import absolute_import
 import sys
 import os
 import shlex

diff --git a/examples/gizmo_script.py b/examples/gizmo_script.py
@@ -10,7 +10,7 @@
 
 # Set the dataset filename, load it into yt and define the trajectory
 # of the LightRay.  This uses the maximum density location as the one end of
-# the ray.  Define desired spectral features to include # all H, C, N, O, and
+# the ray.  Define desired spectral features to include all H, C, N, O, and
 # Mg lines.
 fn = 'FIRE_M12i_ref11/snapshot_600.hdf5'
 ds = yt.load(fn)
@@ -22,15 +22,14 @@
 # Make a LightRay object including all necessary fields so you can add
 # all H, C, N, O, and Mg fields to the resulting spectrum from your dataset.
 # Save LightRay to ray.h5 and use it locally as ray object.
-# Note: We use PartType0, the gas particle field type as our ftype!
 ray = trident.make_simple_ray(ds, start_position=ray_start,
                               end_position=ray_end, data_filename='ray.h5',
-                              lines=line_list, ftype='PartType0')
+                              lines=line_list)
 
 # Create a projection of the dataset in density along the x axis,
 # overplot the trajectory of the ray, and save it.
-# Note that this is using the 'gas' field type, which is the field deposited
-# to the grid.
+# Note that this is using the 'gas' field type, the field aliased to the
+# particle field.
 p = yt.ProjectionPlot(ds, 'x', ('gas', 'density'))
 p.annotate_ray(ray, arrow=True)
 p.save('projection.png')

diff --git a/examples/working_script.py b/examples/working_script.py
@@ -18,7 +18,7 @@
 # Save LightRay to ray.h5 and use it locally as ray object.
 ray = trident.make_simple_ray(ds, start_position=ray_start,
                               end_position=ray_end, data_filename='ray.h5',
-                              lines=line_list, ftype='gas')
+                              lines=line_list)
 
 # Create a projection of the dataset in density along the x axis,
 # overplot the trajectory of the ray, and save it.

diff --git a/setup.py b/setup.py
@@ -59,7 +59,6 @@ def get_version(filename):
       },
     install_requires=[
         'astropy',
-        'future',
         'h5py',
         'matplotlib',
         'numpy!=1.14.0',

diff --git a/tests/gold_standard_versions.py b/tests/gold_standard_versions.py
@@ -11,7 +11,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 #-----------------------------------------------------------------------------
 
-from __future__ import print_function
 from trident import path as trident_path
 import os
 

diff --git a/tests/test_instrument.py b/tests/test_instrument.py
@@ -11,8 +11,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 #-----------------------------------------------------------------------------
 
-from __future__ import absolute_import
-from __future__ import print_function
 from trident.instrument import Instrument
 
 def test_instrument():

diff --git a/tests/test_ion_balance.py b/tests/test_ion_balance.py
@@ -11,7 +11,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 #-----------------------------------------------------------------------------
 
-from __future__ import absolute_import
 from trident.ion_balance import \
     add_ion_fraction_field, \
     add_ion_number_density_field, \
@@ -46,10 +45,9 @@ def test_add_ion_fraction_field_to_grid_ds():
                                    "velocity_z", "temperature", "metallicity"),
                            units= ('g/cm**3', 'cm/s', 'cm/s',
                                    'cm/s', 'K', ''))
-    ftype = 'stream'
     ad = ds.all_data()
-    add_ion_fraction_field('O', 6, ds, ftype=ftype)
-    field = ('stream', 'O_p5_ion_fraction')
+    add_ion_fraction_field('O', 6, ds)
+    field = ('gas', 'O_p5_ion_fraction')
     assert field in ds.derived_field_list
     assert isinstance(ad[field], np.ndarray)
 
@@ -65,10 +63,9 @@ def test_add_ion_number_density_field_to_grid_ds():
                                    "velocity_z", "temperature", "metallicity"),
                            units= ('g/cm**3', 'cm/s', 'cm/s',
                                    'cm/s', 'K', ''))
-    ftype = 'stream'
     ad = ds.all_data()
-    add_ion_mass_field('O', 6, ds, ftype=ftype)
-    field = ('stream', 'O_p5_number_density')
+    add_ion_mass_field('O', 6, ds)
+    field = ('gas', 'O_p5_number_density')
     assert field in ds.derived_field_list
     assert isinstance(ad[field], np.ndarray)
 
@@ -84,10 +81,9 @@ def test_add_ion_density_field_to_grid_ds():
                                    "velocity_z", "temperature", "metallicity"),
                            units= ('g/cm**3', 'cm/s', 'cm/s',
                                    'cm/s', 'K', ''))
-    ftype = 'stream'
     ad = ds.all_data()
-    add_ion_mass_field('O', 6, ds, ftype=ftype)
-    field = ('stream', 'O_p5_density')
+    add_ion_mass_field('O', 6, ds)
+    field = ('gas', 'O_p5_density')
     assert field in ds.derived_field_list
     assert isinstance(ad[field], np.ndarray)
 
@@ -103,10 +99,9 @@ def test_add_ion_mass_field_to_grid_ds():
                                    "velocity_z", "temperature", "metallicity"),
                            units= ('g/cm**3', 'cm/s', 'cm/s',
                                    'cm/s', 'K', ''))
-    ftype = 'stream'
     ad = ds.all_data()
-    add_ion_mass_field('O', 6, ds, ftype=ftype)
-    field = ('stream', 'O_p5_mass')
+    add_ion_mass_field('O', 6, ds, ftype='gas')
+    field = ('gas', 'O_p5_mass')
     assert field in ds.derived_field_list
     assert isinstance(ad[field], np.ndarray)
 
@@ -120,10 +115,9 @@ def test_add_ion_fraction_fields_to_amr_ds():
     """
     ds = fake_amr_ds(fields=("density", "velocity_x", "velocity_y",
                              "velocity_z", "temperature", "metallicity"))
-    ftype = 'stream'
     ad = ds.all_data()
-    add_ion_fraction_field('O', 6, ds, ftype=ftype)
-    field = ('stream', 'O_p5_ion_fraction')
+    add_ion_fraction_field('O', 6, ds)
+    field = ('gas', 'O_p5_ion_fraction')
     assert field in ds.derived_field_list
     assert isinstance(ad[field], np.ndarray)
 
@@ -137,10 +131,9 @@ def test_add_ion_number_density_fields_to_amr_ds():
     """
     ds = fake_amr_ds(fields=("density", "velocity_x", "velocity_y",
                              "velocity_z", "temperature", "metallicity"))
-    ftype = 'stream'
     ad = ds.all_data()
-    add_ion_number_density_field('O', 6, ds, ftype=ftype)
-    field = ('stream', 'O_p5_number_density')
+    add_ion_number_density_field('O', 6, ds)
+    field = ('gas', 'O_p5_number_density')
     assert field in ds.derived_field_list
     assert isinstance(ad[field], np.ndarray)
 
@@ -154,10 +147,9 @@ def test_add_ion_density_fields_to_amr_ds():
     """
     ds = fake_amr_ds(fields=("density", "velocity_x", "velocity_y",
                              "velocity_z", "temperature", "metallicity"))
-    ftype = 'stream'
     ad = ds.all_data()
-    add_ion_density_field('O', 6, ds, ftype=ftype)
-    field = ('stream', 'O_p5_density')
+    add_ion_density_field('O', 6, ds)
+    field = ('gas', 'O_p5_density')
     assert field in ds.derived_field_list
     assert isinstance(ad[field], np.ndarray)
 
@@ -171,10 +163,9 @@ def test_add_ion_mass_fields_to_amr_ds():
     """
     ds = fake_amr_ds(fields=("density", "velocity_x", "velocity_y",
                              "velocity_z", "temperature", "metallicity"))
-    ftype = 'stream'
     ad = ds.all_data()
-    add_ion_mass_field('O', 6, ds, ftype=ftype)
-    field = ('stream', 'O_p5_mass')
+    add_ion_mass_field('O', 6, ds)
+    field = ('gas', 'O_p5_mass')
     assert field in ds.derived_field_list
     assert isinstance(ad[field], np.ndarray)
 
@@ -190,10 +181,10 @@ def test_add_ion_fields_to_grid_ds():
                                    "velocity_z", "temperature", "metallicity"),
                            units= ('g/cm**3', 'cm/s', 'cm/s',
                                    'cm/s', 'K', ''))
-    ftype = 'stream'
+    ftype = 'gas'
     ad = ds.all_data()
     ions = ['H', 'O', 'N V']
-    add_ion_fields(ds, ions, ftype=ftype)
+    add_ion_fields(ds, ions)
     fields = ['H_ion_fraction', 'H_p0_number_density', 'O_p5_mass', 'N_p4_density']
     # Assure that a sampling of fields are added and can be sliced
     dirpath = tempfile.mkdtemp()
@@ -212,9 +203,9 @@ def test_add_all_ion_fields_to_grid_ds():
                                    "velocity_z", "temperature", "metallicity"),
                            units= ('g/cm**3', 'cm/s', 'cm/s',
                                    'cm/s', 'K', ''))
-    ftype = 'stream'
+    ftype = 'gas'
     ad = ds.all_data()
-    add_ion_fields(ds, 'all', ftype=ftype)
+    add_ion_fields(ds, 'all')
     fields = ['H_ion_fraction', 'H_p0_number_density', 'O_p5_mass', 'N_p4_density']
     # Assure that a sampling of fields are added and can be sliced
     dirpath = tempfile.mkdtemp()
@@ -233,7 +224,7 @@ def test_add_all_ion_fields_to_grid_ds_from_file():
                                    "velocity_z", "temperature", "metallicity"),
                            units= ('g/cm**3', 'cm/s', 'cm/s',
                                    'cm/s', 'K', ''))
-    ftype = 'stream'
+    ftype = 'gas'
     ad = ds.all_data()
     add_ion_fields(ds, 'all', ftype=ftype, line_database='lines.txt')
     fields = ['H_ion_fraction', 'H_p0_number_density', 'O_p5_mass', 'N_p4_density']
@@ -252,7 +243,7 @@ def test_add_all_ion_fields_to_amr_ds():
     """
     ds = fake_amr_ds(fields=("density", "velocity_x", "velocity_y",
                              "velocity_z", "temperature", "metallicity"))
-    ftype = 'stream'
+    ftype = 'gas'
     ad = ds.all_data()
     ions = ['H', 'O', 'N V']
     add_ion_fields(ds, ions, ftype=ftype)
@@ -317,7 +308,9 @@ def test_to_not_overwrite_fields_for_grid():
     Test to not overwrite an existing ion field
     """
     ds = load(ISO_GALAXY)
-    val_before = ds.r['H_p0_number_density'][0]
+    # temporary fix until p0 fields are fixed in yt
+    # val_before = ds.r['H_p0_number_density'][0]
+    val_before = ds.r['H_number_density'][0]
     add_ion_fields(ds, ['H'], ftype='gas')
     val_after = ds.r['H_p0_number_density'][0]
     assert val_before == val_after

diff --git a/tests/test_light_ray.py b/tests/test_light_ray.py
@@ -30,6 +30,8 @@
                           "enzo_cosmology_plus/AMRCosmology.enzo")
 COSMO_PLUS_SINGLE = os.path.join(answer_test_data_dir,
                                  "enzo_cosmology_plus/RD0009/RD0009")
+GIZMO_COSMO_SINGLE = os.path.join(answer_test_data_dir,
+                                 "gizmo_cosmology_plus/snap_N128L16_150.hdf5")
 
 def compare_light_ray_solutions(lr1, lr2):
     assert len(lr1.light_ray_solution) == len(lr2.light_ray_solution)
@@ -129,3 +131,13 @@ def test_light_ray_non_cosmo_from_dataset(self):
 
         ds = load('lightray.h5')
         compare_light_ray_solutions(lr, ds)
+
+    def test_light_ray_redshift_coverage(self):
+        """
+        Tests to assure a light ray covers the full redshift range appropriate
+        for that comoving line of sight distance.  Was not always so!
+        """
+        ds = load(GIZMO_COSMO_SINGLE)
+        ray = make_simple_ray(ds, start_position=ds.domain_left_edge, end_position=ds.domain_right_edge, lines=['H'])
+        assert_almost_equal(ray.r['redshift'][0], 0.00489571, decimal=8)
+        assert_almost_equal(ray.r['redshift'][-1], -0.00416831, decimal=8)
diff --git a/tests/test_line_database.py b/tests/test_line_database.py
@@ -11,8 +11,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 #-----------------------------------------------------------------------------
 
-from __future__ import absolute_import
-from __future__ import print_function
 from trident.line_database import \
     uniquify, \
     Line, \
@@ -22,7 +20,6 @@
 import numpy as np
 from shutil import copyfile
 import os.path
-from six.moves import range
 
 def test_uniquify():
     """

diff --git a/tests/test_lsf.py b/tests/test_lsf.py
@@ -11,8 +11,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 #-----------------------------------------------------------------------------
 
-from __future__ import absolute_import
-from __future__ import print_function
 import pytest
 from trident.lsf import LSF
 import numpy as np