Merge pull request tardis-sn#1173 from epassaro/fix-plasma-tests

Fix GUI and plasma tests
atharva-2001 · May 28, 2020 · bcd4c5f · bcd4c5f
2 parents 5b05b90 + a364c4d
commit bcd4c5f
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diff --git a/azure-pipelines/simple_test_framework.yml b/azure-pipelines/simple_test_framework.yml
@@ -3,66 +3,61 @@
 # Add steps that analyze code, save the dist with the build record, publish to a PyPI-compatible index, and more:
 # https://docs.microsoft.com/azure/devops/pipelines/languages/python
 
-
 trigger:
-- master
+  - master
 
 variables:
-  system.debug: 'true'
-  ref.data.home: '$(Agent.BuildDirectory)/tardis-refdata'
+  system.debug: "true"
+  ref.data.home: "$(Agent.BuildDirectory)/tardis-refdata"
 
-  ref.data.github.url: 'https://github.com/tardis-sn/tardis-refdata.git'
+  ref.data.github.url: "https://github.com/tardis-sn/tardis-refdata.git"
   tardis.build.dir: $(Build.Repository.LocalPath)
 
-
-
 jobs:
-
-- job: 'Test'
-  pool:
-    vmImage: $[variables.vm_Image]
-
-  strategy:
-    matrix:
-      linux:
-        vm_Image: 'Ubuntu-16.04'
-        conda: '/usr/share/miniconda'
-      mac:
-        vm_Image: 'macOS-10.14'
-        miniconda.url: 'http://repo.continuum.io/miniconda/Miniconda2-latest-mac-x86_64.sh'
-    maxParallel: 4
-
-  steps:
-  - bash: |
+  - job: "Test"
+    pool:
+      vmImage: $[variables.vm_Image]
+
+    strategy:
+      matrix:
+        linux:
+          vm_Image: "Ubuntu-16.04"
+          conda: "/usr/share/miniconda"
+        mac:
+          vm_Image: "macOS-10.14"
+          miniconda.url: "http://repo.continuum.io/miniconda/Miniconda2-latest-mac-x86_64.sh"
+      maxParallel: 4
+
+    steps:
+      - bash: |
           echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
-
-  - bash: |
-      sudo chown -R $USER $CONDA
-      # conda update -y conda
-    displayName: updating conda and activating
-
-  - bash: |
-        sh ci-helpers/install_tardis_env.sh
-    displayName: 'Install TARDIS env'
-
-  - bash: |
-        sh ci-helpers/fetch_reference_data.sh
-    displayName: 'Fetch Reference Data'
-
-  - bash: |
-        source activate tardis
-        python setup.py build_ext --inplace
-    displayName: 'TARDIS build'
-
-  - bash: |
-        source activate tardis
-        conda install -y pytest-cov
-        pip install git+https://github.com/tonybaloney/pytest-azurepipelines.git
-        export QT_API=pyqt
-        pytest tardis --tardis-refdata=$(ref.data.home) --cov=tardis --cov-report=xml --cov-report=html
-
-    displayName: 'TARDIS test'
-  - script: |
-      bash <(curl -s https://codecov.io/bash)
-    displayName: 'Upload to codecov.io'
+        displayName: Add conda to PATH
+
+      - bash: |
+          sudo chown -R $USER $CONDA
+          # conda update -y conda
+        displayName: updating conda and activating
+
+      - bash: |
+          sh ci-helpers/install_tardis_env.sh
+        displayName: "Install TARDIS env"
+
+      - bash: |
+          sh ci-helpers/fetch_reference_data.sh
+        displayName: "Fetch Reference Data"
+
+      - bash: |
+          source activate tardis
+          python setup.py build_ext --inplace
+        displayName: "TARDIS build"
+
+      - bash: |
+          source activate tardis
+          conda install -y pytest-cov
+          pip install git+https://github.com/tonybaloney/pytest-azurepipelines.git
+          pytest tardis --tardis-refdata=$(ref.data.home) --cov=tardis --cov-report=xml --cov-report=html
+
+        displayName: "TARDIS test"
+      - script: |
+          bash <(curl -s https://codecov.io/bash)
+        displayName: "Upload to codecov.io"
diff --git a/tardis/gui/tests/test_gui.py b/tardis/gui/tests/test_gui.py
@@ -1,28 +1,27 @@
+from PyQt5 import QtWidgets
 import os
 import pytest
 from tardis.io.config_reader import Configuration
 from tardis.simulation import Simulation
 import astropy.units as u
-from tardis.gui.widgets import Tardis 
-from tardis.gui.datahandler import SimpleTableModel
-from PyQt5 import QtWidgets
-
-
 
+if 'QT_API' in os.environ:
+    from tardis.gui.widgets import Tardis
+    from tardis.gui.datahandler import SimpleTableModel
 
 
 @pytest.fixture(scope='module')
 def refdata(tardis_ref_data):
     def get_ref_data(key):
         return tardis_ref_data[os.path.join(
-                'test_simulation', key)]
+            'test_simulation', key)]
     return get_ref_data
 
 
 @pytest.fixture(scope='module')
 def config():
     return Configuration.from_yaml(
-            'tardis/io/tests/data/tardis_configv1_verysimple.yml')
+        'tardis/io/tests/data/tardis_configv1_verysimple.yml')
 
 
 @pytest.fixture(scope='module')
@@ -38,7 +37,8 @@ def simulation_one_loop(
     simulation.run()
 
     return simulation
-
+
+
 @pytest.mark.skipif('QT_API' not in os.environ, reason="enviroment variable QT_API is not set")
 def test_gui(simulation_one_loop):
     simulation = simulation_one_loop

diff --git a/tardis/io/atom_data/base.py b/tardis/io/atom_data/base.py
@@ -216,9 +216,6 @@ def __init__(self, atom_data, ionization_data, levels=None, lines=None,
         # Convert energy to CGS
         levels.loc[:, "energy"] = Quantity(levels["energy"].values, 'eV').cgs
 
-        # Sort the dataframe before indexing to improve performance
-        lines.sort_index(inplace=True)
-
         # Create a new columns with wavelengths in the CGS units
         lines.loc[:, 'wavelength_cm'] = Quantity(
                 lines['wavelength'], 'angstrom').cgs