Merge pull request #190 from jwise77/fix-test-suite

Updating test suite to yt-4.x and concurrent testing

.circleci/config.yml

@@ -11,8 +11,12 @@ commands:
             echo 'export ENZOTEST_DIR=$HOME/enzo_test' >> $BASH_ENV
             echo 'export ANSWER_NAME="push_suite"' >> $BASH_ENV
             echo 'export HYPRE=2.20.0' >> $BASH_ENV
-            # get tags from the main repository (for the current gold standard)
+            source $BASH_ENV
+            # get tags from the main and PR repository (for the current gold standard)
             git fetch --tags https://github.com/enzo-project/enzo-dev
+            if [ -n "$CIRCLE_PR_REPONAME" ]; then
+              git fetch --tags https://github.com/$CIRCLE_PR_USERNAME/$CIRCLE_PR_REPONAME
+            fi
             # tag the tip so we can go back to it
             git tag tip
 
@@ -24,14 +28,21 @@ commands:
           command: |
             source $BASH_ENV
             sudo apt-get update
-            sudo apt-get install -y csh libhdf5-serial-dev libopenmpi-dev openmpi-bin gfortran libtool-bin
+            sudo apt-get install -y csh libhdf5-serial-dev libopenmpi-dev openmpi-bin gfortran libtool-bin xutils-dev
             python3 -m venv $HOME/venv
             source $HOME/venv/bin/activate
             pip install --upgrade pip
             pip install --upgrade wheel
             pip install --upgrade setuptools
-            pip install 'matplotlib<3.3.0'
-            pip install Cython numpy h5py fastcache flake8 nose yt==3.6.1 girder-client
+            pip install Cython numpy h5py fastcache flake8 nose girder-client matplotlib pytest gitpython # yt
+            # Temporary workaround to use updated answer testing from the yt dev repository
+            # instead of pip until next yt point release
+            git clone https://github.com/yt-project/yt
+            cd yt
+            git checkout main
+            pip install -e .
+            cd ..
+            pip install yt_astro_analysis
             # Install hypre
             mkdir -p $HOME/local
             if [ ! -f $HOME/local/lib/libHYPRE.a ]; then
@@ -108,9 +119,9 @@ commands:
               make machine-ubuntu
               make load-config-test-suite
               make clean
-              make -j 4
+              make -j 6
               cd ../../run
-              python ./test_runner.py --suite=push -o $ENZOTEST_DIR --answer-name=$ANSWER_NAME --local --strict=high --verbose << parameters.flags >>
+              python ./test_runner.py --suite=push -o $ENZOTEST_DIR --answer-name=$ANSWER_NAME --local --machine=local_nompi --strict=high --verbose --jrun=4 << parameters.flags >>
             fi
 
   compile-test:
@@ -135,7 +146,7 @@ commands:
             make precision-$prec
             make particles-$part
             make clean
-            make -j 4 || (make show-config ; exit 1)
+            make -j 6 || (make show-config ; exit 1)
             done ; done
             # return this to default
             make precision-64
@@ -151,19 +162,19 @@ commands:
             make integers-$inte
             make particle-id-$pids
             make clean
-            make -j 4 || (make show-config ; exit 1)
+            make -j 6 || (make show-config ; exit 1)
             done ; done
             make integers-64
             make particle-id-64
             # test without mpi
             make use-mpi-no
             make clean
-            make -j 4 || (make show-config ; exit 1)
+            make -j 6 || (make show-config ; exit 1)
             make use-mpi-yes
             # test ray-tracing
             make photon-no
             make clean
-            make -j 4 || (make show-config ; exit 1)
+            make -j 6 || (make show-config ; exit 1)
 
   build-docs:
     description: "Test the docs build."
@@ -180,6 +191,7 @@ jobs:
     docker:
       - image: cimg/python:3.8.5
 
+    resource_class: large
     working_directory: ~/enzo-dev
 
     steps:
@@ -188,13 +200,13 @@ jobs:
 
       - restore_cache:
           name: "Restore dependencies cache."
-          key: dependencies-v2
+          key: dependencies-v3
 
       - install-dependencies
 
       - save_cache:
           name: "Save dependencies cache"
-          key: dependencies-v2
+          key: dependencies-v3
           paths:
             - ~/.cache/pip
             - ~/venv
@@ -205,16 +217,16 @@ jobs:
 
       - restore_cache:
           name: "Restore test answers."
-          key: test-answers-v14
+          key: test-answers-v15a
 
       - build-and-test:
-          tag: gold-standard-v14
+          tag: gold-standard-v15
           skipfile: ~/enzo_test/push_suite
           flags: --answer-store
 
       - save_cache:
           name: "Save test answers cache."
-          key: test-answers-v14
+          key: test-answers-v15a
           paths:
             - ~/enzo_test/push_suite
 
@@ -227,6 +239,7 @@ jobs:
     docker:
       - image: cimg/python:3.8.5
 
+    resource_class: large
     working_directory: ~/enzo-dev
 
     steps:
@@ -235,13 +248,13 @@ jobs:
 
       - restore_cache:
           name: "Restore dependencies cache."
-          key: dependencies-v1
+          key: dependencies-v3
 
       - install-dependencies
 
       - save_cache:
           name: "Save dependencies cache"
-          key: dependencies-v1
+          key: dependencies-v3
           paths:
             - ~/.cache/pip
             - ~/venv

run/Cooling/CoolingTest_Cloudy/CoolingTest_Cloudy__test_cooling.py

@@ -1,4 +1,4 @@
-from yt.mods import *
+import os
 from yt.testing import *
 from yt.utilities.answer_testing.framework import \
      FieldValuesTest, \
@@ -15,7 +15,7 @@ def test_cooling_time():
     sim = sim_dir_load(_pf_name, path=_dir_name,
                        find_outputs=True)
     sim.get_time_series()
-    tolerance = ytcfg.getint("yt", "answer_testing_tolerance")
+    tolerance = ytcfg.get("yt", "answer_testing_tolerance")
     pf = sim[-1]
     for field in _fields:
         yield FieldValuesTest(pf, field, decimals=tolerance)

run/Cooling/CoolingTest_Grackle/CoolingTest_Grackle__test_cooling.py

@@ -1,4 +1,4 @@
-from yt.mods import *
+import os
 from yt.testing import *
 from yt.utilities.answer_testing.framework import \
      FieldValuesTest, \
@@ -15,7 +15,7 @@ def test_cooling_time():
     sim = sim_dir_load(_pf_name, path=_dir_name,
                        find_outputs=True)
     sim.get_time_series()
-    tolerance = ytcfg.getint("yt", "answer_testing_tolerance")
+    tolerance = ytcfg.get("yt", "answer_testing_tolerance")
     pf = sim[-1]
     for field in _fields:
         yield FieldValuesTest(pf, field, decimals=tolerance)

run/Cooling/CoolingTest_JHW/CoolingTest_JHW__test_cooling.py

@@ -1,4 +1,4 @@
-from yt.mods import *
+import os
 from yt.testing import *
 from yt.utilities.answer_testing.framework import \
      FieldValuesTest, \
@@ -15,7 +15,7 @@ def test_cooling_time():
     sim = sim_dir_load(_pf_name, path=_dir_name,
                        find_outputs=True)
     sim.get_time_series()
-    tolerance = ytcfg.getint("yt", "answer_testing_tolerance")
+    tolerance = ytcfg.get("yt", "answer_testing_tolerance")
     pf = sim[-1]
     for field in _fields:
         yield FieldValuesTest(pf, field, decimals=tolerance)

run/Cooling/OneZoneFreefallTest/OneZoneFreefallTest__test_freefall.py

@@ -1,4 +1,4 @@
-from yt.mods import *
+import os
 from yt.testing import *
 from yt.utilities.answer_testing.framework import \
      FieldValuesTest, \
@@ -16,7 +16,7 @@ def test_freefall():
     sim = sim_dir_load(_pf_name, path=_dir_name,
                        find_outputs=True)
     sim.get_time_series()
-    tolerance = ytcfg.getint("yt", "answer_testing_tolerance")
+    tolerance = ytcfg.get("yt", "answer_testing_tolerance")
     pf = sim[-1]
     for field in _fields:
         yield FieldValuesTest(pf, field, decimals=tolerance)

run/Cosmology/AMRZeldovichPancake/AMRZeldovichPancake__test_almost_standard.py

@@ -3,7 +3,6 @@
 ###
 
 import os
-from yt.mods import *
 from yt.testing import *
 from yt.utilities.answer_testing.framework import \
     VerifySimulationSameTest, \
@@ -29,7 +28,7 @@ def test_standard():
     sim.get_time_series()
     yield VerifySimulationSameTest(sim)
     base_pf = sim[0]
-    fields = [f for f in _base_fields if f in base_pf.h.field_list]
+    fields = [f for f in _base_fields if f in base_pf.field_list]
     # Only test the last output.
     pf = sim[-1]
     for test in standard_small_simulation(pf, fields): yield test

run/Cosmology/MHDZeldovichPancake/MHDZeldovichPancake.enzo

@@ -6,7 +6,7 @@
 #
 ProblemType                = 20      // Zeldovich pancake
 TopGridRank                = 1
-TopGridDimensions          = 500 64 2
+TopGridDimensions          = 500
 SelfGravity                = 1       // gravity on
 TopGridGravityBoundary     = 0       // Periodic BC for gravity
 LeftFaceBoundaryCondition  = 3       // same for fluid

run/Cosmology/ZeldovichPancake/ZeldovichPancake__test_almost_standard.py

@@ -3,7 +3,6 @@
 ###
 
 import os
-from yt.mods import *
 from yt.testing import *
 from yt.utilities.answer_testing.framework import \
     VerifySimulationSameTest, \
@@ -29,7 +28,7 @@ def test_almost_standard():
     sim.get_time_series()
     yield VerifySimulationSameTest(sim)
     base_pf = sim[0]
-    fields = [f for f in _base_fields if f in base_pf.h.field_list]
+    fields = [f for f in _base_fields if f in base_pf.field_list]
     # Only test the last output.
     pf = sim[-1]
     for test in standard_small_simulation(pf, fields): yield test

run/CosmologySimulation/amr_cosmology/test_amr_cosmology.py

@@ -3,8 +3,7 @@
 import matplotlib.pyplot as plt 
 import numpy as np
 import os
-from yt.analysis_modules.halo_mass_function.api import *
-from yt.analysis_modules.halo_analysis.api import HaloCatalog
+from yt_astro_analysis.halo_analysis import HaloCatalog
 from yt.testing import assert_rel_equal
 from numpy.testing import assert_equal
 
@@ -30,7 +29,7 @@ def test_hmf():
         data_ds=ds, finder_method='fof',
         output_dir=os.path.join(_dir_name, "halo_catalogs/catalog"))
     hc.create()
-    masses = hc.data_source['particle_mass'].in_units('Msun')  
+    masses = hc.data_ds.r[('all', 'particle_mass')].in_units('Msun')  
     h = ds.hubble_constant
     mtot = np.log10(masses*1.2) - np.log10(h)
     masses_sim = np.sort(mtot)
@@ -69,12 +68,12 @@ def test_max_density_halo_quantities():
 
     # Find the point of maximum density, center a sphere of radius
     # 1 Mpc around it, and sum the masses inside
-    val,pos = ds.find_max('Density')
+    val,pos = ds.find_max(('enzo', 'Density'))
     sp = ds.sphere(pos,(1000.,'kpc'))
-    ct = sp['creation_time']
+    ct = sp[('nbody', 'creation_time')]
     dm = (ct < 0)
-    dm_mass = np.sum(sp['particle_mass'][dm]).in_units('Msun')
-    gas_mass = np.sum(sp['cell_mass'].in_units('Msun'))
+    dm_mass = np.sum(sp[('all', 'particle_mass')][dm]).in_units('Msun')
+    gas_mass = np.sum(sp[('gas', 'cell_mass')].in_units('Msun'))
 
     # Also look at the radial profiles of density and temperature
     # within these spheres. The bin size is chosen to make the profiles
@@ -115,9 +114,9 @@ def test_dark_matter_mass():
     data  = ds.all_data()
 
     # sum masses
-    MDM   = np.sum(data['particle_mass'][ data['particle_type'] == 1 ].to('Msun'))
+    MDM   = np.sum(data[('all', 'particle_mass')][ data[('all', 'particle_type')] == 1 ].to('Msun'))
 
-    output_data    = {'mass' : MDM}
+    output_data    = {(('data', 'mass') : MDM}
 
     # save
     filename = "DM_mass_results.h5"
@@ -130,7 +129,7 @@ def test_dark_matter_mass():
         return
 
     ds_comp          = yt.load(compare_filename)
-    assert_rel_equal(output_data['mass'], ds_comp.data['mass'], tolerance)
+    assert_rel_equal(output_data[('data', 'mass')], ds_comp.data[('data', 'mass')], tolerance)
 
 def test_individual_baryon_mass():
     # gather most recent data set
@@ -145,8 +144,8 @@ def test_individual_baryon_mass():
     data  = ds.all_data()
 
     # sum masses
-    Mstar = np.sum(data['particle_mass'][ data['particle_type'] == 2 ].to('Msun'))
-    Mgas  = np.sum(data['cell_mass'].to('Msun'))
+    Mstar = np.sum(data[('all', 'particle_mass')][ data[('all', 'particle_type')] == 2 ].to('Msun'))
+    Mgas  = np.sum(data[('gas', 'cell_mass')].to('Msun'))
 
     output_data    = {'masses' : np.array([Mstar, Mgas])}
 
@@ -176,8 +175,8 @@ def test_total_baryon_mass():
     data  = ds.all_data()
 
     # sum masses
-    Mstar = np.sum(data['particle_mass'][ data['particle_type'] == 2 ].to('Msun'))
-    Mgas  = np.sum(data['cell_mass'].to('Msun'))
+    Mstar = np.sum(data[('all', 'particle_mass')][ data[('all', 'particle_type')] == 2 ].to('Msun'))
+    Mgas  = np.sum(data[('gas', 'cell_mass')].to('Msun'))
 
     output_data    = {'masses' : Mstar + Mgas}
 
@@ -228,21 +227,21 @@ def test_phase():
                            ("gas", "cooling_time")],
                           weight_field=('gas', 'cell_mass'))
     density = profile.x
-    temperature = profile['gas', 'temperature']
-    cooling_time = profile1['gas', 'cooling_time']
-    cell_mass = profile['gas', 'cell_mass']
+    temperature = profile[('gas', 'temperature')]
+    cooling_time = profile1[('gas', 'cooling_time')]
+    cell_mass = profile[('gas', 'cell_mass')]
 
     filename = 'phase_data.h5'
     save_filename = os.path.join(_dir_name, filename)
-    data = {'density': density, 'temperature': temperature,
-            'cooling_time': cooling_time, 'cell_mass': cell_mass}
+    data = {('data', 'density'): density, ('data', 'temperature'): temperature,
+            ('data', 'cooling_time'): cooling_time, ('data', 'cell_mass'): cell_mass}
     yt.save_as_dataset(ds, save_filename, data)
 
-    pp = yt.PhasePlot(ad, 'density', 'temperature', 'cell_mass')
-    pp.set_unit('cell_mass', 'Msun')
+    pp = yt.PhasePlot(ad, ('gas', 'density'), ('gas', 'temperature'), ('gas', 'cell_mass'))
+    pp.set_unit(('gas', 'cell_mass'), 'Msun')
     pp.save(_dir_name)
-    pp1 = yt.PhasePlot(ad, 'density', 'temperature', 'cooling_time',
-                       weight_field='cell_mass')
+    pp1 = yt.PhasePlot(ad, ('gas', 'density'), ('gas', 'temperature'), ('gas', 'cooling_time'),
+                       weight_field=('gas', 'cell_mass'))
     pp1.save(_dir_name)
 
     compare_filename = os.path.join(test_data_dir, filename)
@@ -254,7 +253,7 @@ def test_phase():
     ds_comp = yt.load(compare_filename)
 
     # assert quality to 8 decimals
-    assert_rel_equal(data['density'], ds_comp.data['density'], 8)
-    assert_rel_equal(data['temperature'], ds_comp.data['temperature'], 8)
-    assert_rel_equal(data['cooling_time'], ds_comp.data['cooling_time'], 8)
-    assert_rel_equal(data['cell_mass'], ds_comp.data['cell_mass'], 8)
+    assert_rel_equal(data[('data', 'density')], ds_comp.data[('data', 'density')], 8)
+    assert_rel_equal(data[('data', 'temperature')], ds_comp.data[('data', 'temperature')], 8)
+    assert_rel_equal(data[('data', 'cooling_time')], ds_comp.data[('data', 'cooling_time')], 8)
+    assert_rel_equal(data[('data', 'cell_mass')], ds_comp.data[('data', 'cell_mass')], 8)