Update test dependencies

.travis.yml

@@ -30,7 +30,7 @@ before_install:
     else
       sudo mkdir -p /usr/local/man
       sudo chown -R "${USER}:admin" /usr/local/man
-      brew update
+      # brew update  # do not update to save build time
       brew install python ccache hdf5 proj geos openmpi netcdf
       brew uninstall gdal postgis numpy
       export PATH=/usr/local/opt/ccache/libexec:$PATH
@@ -68,7 +68,7 @@ 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==1.18.1 cython==0.29.6
+        $PIP install numpy==1.18.1 cython==0.29.14
         CFLAGS="$CFLAGS -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H" $PIP install -r tests/test_requirements.txt
       fi
       $PIP install -e .
@@ -116,14 +116,11 @@ jobs:
       name: "MacOS: Unit Tests"
       os: osx
       osx_image: xcode10.1
-      language: generic  # https://github.com/travis-ci/travis-ci/issues/2312
+      language: shell
       env: PIP=pip3
       cache:
-        pip: false
-        directories:
+        - directories:
           - $HOME/Library/Caches/pip
-          # `cache` does not support `env`-like `global` so copy-paste from top
-          - $HOME/.ccache  # https://github.com/travis-ci/travis-ci/issues/5853
       script: nosetests -c nose_unit.cfg
 
 after_success:

doc/Makefile

@@ -49,7 +49,7 @@ html:
 ifneq ($(READTHEDOCS),True)
 	SPHINX_APIDOC_OPTIONS=members,undoc-members,inherited-members,show-inheritance sphinx-apidoc \
         -o source/reference/api/ \
-        -e ../yt ../yt/extern* $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp*
+        -e ../yt ../yt/extern* $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp* ../yt/analysis_modules/*
 endif
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo

tests/test_requirements.txt

@@ -1,15 +1,15 @@
-astropy==3.0.5
+astropy==3.2.3
 codecov==2.0.15
-coverage==4.5.1
+coverage==4.5.4
 fastcache==1.0.2
 glueviz==0.13.3
 h5py==2.10.0
 ipython==7.1.1
-matplotlib==3.1.3
+matplotlib==3.3.0
 mock==2.0.0; python_version < '3.0'
-nose-timer==0.7.3
+nose-timer==1.0.0
 nose==1.3.7
-pandas==0.23.4
+pandas==0.25.3
 pytest~=5.2
 requests==2.20.0
 scipy==1.3.3

tests/tests.yaml

@@ -44,7 +44,7 @@ answer_tests:
     - yt/frontends/enzo/tests/test_outputs.py:test_ecp
     - yt/frontends/enzo/tests/test_outputs.py:test_nuclei_density_fields
 
-  local_enzo_p_007:
+  local_enzo_p_008:  # PR 2735
     - yt/frontends/enzo_p/tests/test_outputs.py:test_hello_world
     - yt/frontends/enzo_p/tests/test_outputs.py:test_particle_fields
 
@@ -86,7 +86,7 @@ answer_tests:
     - yt/frontends/owls/tests/test_outputs.py:test_snapshot_033
     - yt/frontends/owls/tests/test_outputs.py:test_OWLS_particlefilter
 
-  local_pw_029:
+  local_pw_030:  # PR 2735
     - yt/visualization/tests/test_plotwindow.py:test_attributes
     - yt/visualization/tests/test_plotwindow.py:test_attributes_wt
     - yt/visualization/tests/test_particle_plot.py:test_particle_projection_answers
@@ -162,5 +162,6 @@ other_tests:
   unittests:
      - '--exclude=test_mesh_slices'  # disable randomly failing test
      - '--exclude=test_load_from_path'  # py2
+     - '--exclude=test_Snipshot'  # until PR 2645 is merged
   cookbook:
      - 'doc/source/cookbook/tests/test_cookbook.py'

yt/funcs.py

@@ -18,6 +18,7 @@
 import urllib.parse
 import urllib.request
 import warnings
+from distutils.version import LooseVersion
 from functools import lru_cache, wraps
 from math import ceil, floor
 from numbers import Number as numeric_type
@@ -1265,10 +1266,13 @@ def matplotlib_style_context(style_name=None, after_reset=False):
     available, returns a dummy context manager.
     """
     if style_name is None:
-        style_name = {
-            "mathtext.fontset": "cm",
-            "mathtext.fallback_to_cm": True,
-        }
+        import matplotlib
+
+        style_name = {"mathtext.fontset": "cm"}
+        if LooseVersion(matplotlib.__version__) >= LooseVersion("3.3.0"):
+            style_name["mathtext.fallback"] = "cm"
+        else:
+            style_name["mathtext.fallback_to_cm"] = True
     try:
         import matplotlib.style
 

yt/geometry/oct_container.pyx

@@ -727,12 +727,13 @@ cdef class OctreeContainer:
                    np.int64_t offset = 0):
         cdef np.ndarray[np.float64_t, ndim=2] source
         cdef np.ndarray[np.float64_t, ndim=1] dest
-        cdef int i
+        cdef int i, lvl
 
         for key in dest_fields:
             dest = dest_fields[key]
             source = source_fields[key]
-            for i, lvl in enumerate(levels):
+            for i in range(levels.shape[0]):
+                lvl = levels[i]
                 if lvl != level: continue
                 if file_inds[i] < 0:
                     dest[i + offset] = np.nan
@@ -819,13 +820,16 @@ cdef class OctreeContainer:
         """
         cdef np.ndarray[np.float64_t, ndim=2] source
         cdef np.ndarray[np.float64_t, ndim=1] dest
-        cdef int i, count
+        cdef int i, count, lev
+        cdef np.int32_t dom
 
         for key in dest_fields:
             dest = dest_fields[key]
             source = source_fields[key]
             count = 0
-            for i, (lev, dom) in enumerate(zip(levels, domains)):
+            for i in range(levels.shape[0]):
+                lev = levels[i]
+                dom = domains[i]
                 if lev != level or dom != domain: continue
                 count += 1
                 if file_inds[i] < 0:

yt/utilities/command_line.py

@@ -1,3 +1,4 @@
+# isort: skip-file
 import argparse
 import base64
 import getpass
@@ -28,7 +29,7 @@
     mylog,
     update_hg_or_git,
 )
-from yt.startup_tasks import parser, subparsers
+
 from yt.utilities.configure import set_config
 from yt.utilities.exceptions import (
     YTCommandRequiresModule,
@@ -38,7 +39,12 @@
 from yt.utilities.metadata import get_metadata
 from yt.visualization.plot_window import ProjectionPlot, SlicePlot
 
-ytcfg["yt", "__command_line"] = "True"
+# isort: off
+# This needs to be set before importing startup_tasks
+ytcfg["yt", "__command_line"] = "True"  # isort: skip
+from yt.startup_tasks import parser, subparsers  # isort: skip # noqa: E402
+
+# isort: on
 
 # loading field plugins for backward compatibility, since this module
 # used to do "from yt.mods import *"

yt/utilities/lib/pixelization_routines.pyx

@@ -245,7 +245,7 @@ def pixelize_cartesian(np.float64_t[:,:] buff,
                                 # conservative about the iteration indices.
                                 # This will reduce artifacts if we ever move to
                                 # compositing instead of replacing bitmaps.
-                                if overlap1 * overlap2 == 0.0: continue
+                                if overlap1 * overlap2 < 1.e-6: continue
                                 buff[i,j] += (dsp * overlap1) * overlap2
                             else:
                                 buff[i,j] = dsp

yt/utilities/png_writer.py

@@ -13,7 +13,7 @@ def call_png_write_png(buffer, fileobj, dpi):
     try:
         _png.write_png(buffer, fileobj, dpi)
     except NameError:
-        Image.fromarray(buffer).save(fileobj, dpi=(dpi, dpi))
+        Image.fromarray(buffer).save(fileobj, dpi=(dpi, dpi), format="png")
 
 
 def write_png(buffer, filename, dpi=100):

yt/utilities/tests/test_config.py

@@ -82,12 +82,18 @@ def testConfigCommands(self):
         if mock is None:
             return
 
+        def remove_spaces_and_breaks(s):
+            return "".join(s.split())
+
         self.assertFalse(os.path.exists(CURRENT_CONFIG_FILE))
 
         info = self._runYTConfig(["--help"])
         self.assertEqual(info["rc"], 0)
         self.assertEqual(info["stderr"], "")
-        self.assertIn("Get and set configuration values for yt", info["stdout"])
+        self.assertIn(
+            remove_spaces_and_breaks("Get and set configuration values for yt"),
+            remove_spaces_and_breaks(info["stdout"]),
+        )
 
         info = self._runYTConfig(["list"])
         self.assertEqual(info["rc"], 0)

yt/visualization/base_plot_types.py

@@ -134,7 +134,9 @@ def save(self, name, mpl_kwargs=None, canvas=None):
 
         if mpl_kwargs is None:
             mpl_kwargs = {}
-        if "papertype" not in mpl_kwargs:
+        if "papertype" not in mpl_kwargs and LooseVersion(
+            matplotlib.__version__
+        ) < LooseVersion("3.3.0"):
             mpl_kwargs["papertype"] = "auto"
 
         suffix = get_image_suffix(name)