Porting #2450 (test job updates) to yt-4.0

.travis.yml

@@ -1,7 +1,5 @@
 language: python
 dist: xenial
-sudo: required
-dist: xenial
 cache:
   pip: true
   directories:
@@ -51,11 +49,17 @@ install:
     $PIP install --upgrade pip
     $PIP install --upgrade wheel
     $PIP install --upgrade setuptools
+    echo "Travis build stage: $TRAVIS_BUILD_STAGE_NAME"
     # install dependencies yt
-    if [[ $TRAVIS_BUILD_STAGE_NAME != "Lint" ]]; then
+    if [[ ${TRAVIS_BUILD_STAGE_NAME} == "lint" ]]; then
+      export TRAVIS_BUILD_STAGE_NAME="Lint"
+    fi
+    if [[ ${TRAVIS_BUILD_STAGE_NAME} != "Lint" ]]; then
       if [[ $MINIMAL == 1 ]]; then
         # Ensure numpy and cython are installed so dependencies that need to be built
         # don't error out
+        # The first numpy to support py3.6 is 1.12, but numpy 1.13 matches 
+        # unyt so we'll match it here. 
         $PIP install numpy==1.13.3 cython==0.26.1
         $PIP install -r tests/test_minimal_requirements.txt
       else
@@ -64,8 +68,8 @@ install:
         # pyproject.toml in cartopy.
         # These versions are pinned, so we will need to update/remove them when
         # the hack is no longer necessary.
-        $PIP install numpy==1.16.2 cython==0.29
-        $PIP install -r tests/test_requirements.txt
+        $PIP install numpy==1.18.1 cython==0.29.6
+        CFLAGS="$CFLAGS -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H" $PIP install -r tests/test_requirements.txt
       fi
       $PIP install -e .
     else
@@ -74,37 +78,29 @@ install:
 
 jobs:
   include:
-    - stage: lint
-      python: 3.7
+    - stage: Lint
+      python: 3.6
       script: flake8 yt/
 
     - stage: tests
-      name: "Minimal Dependency Version Unit Tests"
-      python: 3.5
+      name: "Python: 3.6 Minimal Dependency Unit Tests"
+      python: 3.6
       env: MINIMAL=1
       script: coverage run $(which nosetests) -c nose_unit.cfg
 
-    - stage: tests
-      name: "Python: 3.5 Unit Tests"
-      python: 3.5
-      script: coverage run $(which nosetests) -c nose_unit.cfg
-
     - stage: tests
       name: "Python: 3.6 Unit Tests"
       python: 3.6
       script: coverage run $(which nosetests) -c nose_unit.cfg
 
     - stage: tests
-      name: "Python: 3.7 Unit Tests"
-      python: 3.7
+      name: "Python: 3.8 Unit Tests"
+      python: 3.8
       script: coverage run $(which nosetests) -c nose_unit.cfg
-
-    - name: "Minimal Dependency Version Answer Tests"
-      python: 3.5
-      env: MINIMAL=1
-      script: coverage run $(which nosetests) -c nose_answer.cfg
-      after_failure: python tests/report_failed_answers.py -f -m --xunit-file "answer_nosetests.xml"
 
+      # This is not necessarily going to be forever -- once we merge yt-4.0
+      # with master we will likely change this around to reduce the number of
+      # versions we test on.
     - stage: tests
       name: "Python: 3.7 Answer Tests"
       python: 3.7
@@ -127,6 +123,9 @@ jobs:
 
 after_success:
   - |
-    if [[ $TRAVIS_BUILD_STAGE_NAME != "Lint" ]]; then
+    if [[ ${TRAVIS_BUILD_STAGE_NAME} == "lint" ]]; then
+      export TRAVIS_BUILD_STAGE_NAME="Lint"
+    fi
+    if [[ ${TRAVIS_BUILD_STAGE_NAME} != "Lint" ]]; then
       codecov
     fi

appveyor.yml

@@ -8,7 +8,7 @@ environment:
 
   matrix:
       - PYTHON_VERSION: "3.6"
-        NUMPY_VERSION: "1.16"
+      - PYTHON_VERSION: "3.8"
 
 platform:
     -x64
@@ -30,16 +30,16 @@ install:
     - "python --version"
 
     # Install specified version of numpy and dependencies
-    - "conda install --yes -c conda-forge numpy==%NUMPY_VERSION% scipy nose setuptools ipython
-    Cython sympy fastcache h5py matplotlib mock pandas cartopy conda-build unyt pooch"
+    - "conda install --yes -c conda-forge numpy scipy nose pytest setuptools ipython
+    Cython sympy fastcache h5py matplotlib=3.1.3 mock pandas cartopy conda-build unyt pooch pyyaml"
     # install yt
-    - "conda develop -b ."
+    - "pip install -e ."
 
 # Not a .NET project
 build: false
 
 test_script:
-  - "nosetests --nologcapture -sv yt"
+    - "nosetests --nologcapture -sv --traverse-namespace yt"
 
 # Enable this to be able to login to the build worker. You can use the
 # `remmina` program in Ubuntu, use the login information that the line below

tests/test_minimal_requirements.txt

@@ -5,4 +5,4 @@ nose==1.3.7
 nose-timer==0.7.3
 coverage==4.5.1
 codecov==2.0.15
-unyt==2.2.2
+unyt==2.7.1

tests/test_requirements.txt

@@ -5,21 +5,25 @@ fastcache==1.0.2
 glueviz==0.13.3
 h5py==2.8.0
 ipython==7.1.1
-matplotlib==3.0.1
+matplotlib==3.1.3
 nose-timer==0.7.3
 nose==1.3.7
 pandas==0.23.4
+pytest~=5.2
 requests==2.20.0
-scipy==1.1.0
-sympy==1.3
+scipy==1.3.3
+sympy==1.5
 pyqt5==5.11.3
 pint==0.8.1
-netCDF4==1.4.2
+netCDF4==1.5.3
 libconf==1.0.1
 cartopy==0.17.0
 pyaml==17.10.0
-mpi4py==3.0.0
-unyt==2.2.2
+mpi4py==3.0.3
+unyt==2.7.1
 pyyaml>=4.2b1
+xarray==0.12.3
+firefly_api>=0.0.2
+f90nml>=1.1.2
 MiniballCpp>=0.2.1
 pooch>=0.7.0

yt/utilities/lib/pixelization_routines.pyx

@@ -749,6 +749,7 @@ def pixelize_element_mesh(np.ndarray[np.float64_t, ndim=2] coords,
                           int index_offset = 0):
     cdef np.ndarray[np.float64_t, ndim=3] img
     img = np.zeros(buff_size, dtype="float64")
+    img[:] = np.nan
     # Two steps:
     #  1. Is image point within the mesh bounding box?
     #  2. Is image point within the mesh element?

yt/visualization/color_maps.py

@@ -391,10 +391,10 @@ def make_colormap(ctuple_list, name=None, interpolate=True):
 
         # Interpolate the R, G, and B channels from one color to the next
         # Use np.round to make sure you're on a discrete index
-        interval = np.round(next_index)-np.round(rolling_index)
+        interval = int(np.round(next_index)-np.round(rolling_index))
         for j in np.arange(3):
             cmap[int(np.rint(rolling_index)):int(np.rint(next_index)), j] = \
-                np.linspace(color[j], next_color[j], interval)
+                np.linspace(color[j], next_color[j], num=interval)
 
         rolling_index = next_index
 

yt/visualization/plot_container.py

@@ -95,8 +95,8 @@ def get_log_minorticks(vmin, vmax):
     """
     expA = np.floor(np.log10(vmin))
     expB = np.floor(np.log10(vmax))
-    cofA = np.ceil(vmin/10**expA)
-    cofB = np.floor(vmax/10**expB)
+    cofA = np.ceil(vmin/10**expA).astype("int64")
+    cofB = np.floor(vmax/10**expB).astype("int64")
     lmticks = []
     while cofA*10**expA <= cofB*10**expB:
         if expA < expB:

yt/visualization/tests/test_geo_projections.py

@@ -56,7 +56,6 @@ def setUp(self):
 
     def tearDown(self):
         del self.ds
-        del self.slc
 
     def test_geo_projection_setup(self):