Merge branch 'main' into open-compressed-files

yt-project · Sep 7, 2021 · 2542744 · 2542744
2 parents 723bdb5 + 0f57663
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diff --git a/.github/workflows/bleeding-edge.yaml b/.github/workflows/bleeding-edge.yaml
@@ -13,6 +13,7 @@ on:
   schedule:
     # run this every day at 3 am UTC
     - cron: '0 3 * * *'
+  workflow_dispatch:
 
 jobs:
   build:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -28,17 +28,17 @@ repos:
     - id: no-commit-to-branch
       args: [--branch, main]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.23.0
+    rev: v2.25.0
     hooks:
     - id: pyupgrade
       args: [--py36-plus]
 -   repo: https://github.com/psf/black
-    rev: 21.7b0
+    rev: 21.8b0
     hooks:
     - id: black
       language_version: python3
 -   repo: https://github.com/PyCQA/isort
-    rev: '5.9.2'
+    rev: '5.9.3'
     hooks:
     - id: isort
       name: isort (python)
@@ -55,10 +55,10 @@ repos:
         flake8-2020==1.6.0,
       ]
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.10.0
+    rev: v1.11.0
     hooks:
     -   id: blacken-docs
-        additional_dependencies: [black==20.8b1]
+        additional_dependencies: [black==21.8b0]
 -   repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.9.0
     hooks:

diff --git a/README.md b/README.md
@@ -63,12 +63,12 @@ can be found on [the project's website](https://yt-project.org/docs/dev/installi
 yt is designed to provide meaningful analysis of data.  We have some Quickstart
 example notebooks in the repository:
 
- * [Introduction](doc/source/quickstart/1\)_Introduction.ipynb)
- * [Data Inspection](doc/source/quickstart/2\)_Data_Inspection.ipynb)
- * [Simple Visualization](doc/source/quickstart/3\)_Simple_Visualization.ipynb)
- * [Data Objects and Time Series](doc/source/quickstart/4\)_Data_Objects_and_Time_Series.ipynb)
- * [Derived Fields and Profiles](doc/source/quickstart/5\)_Derived_Fields_and_Profiles.ipynb)
- * [Volume Rendering](doc/source/quickstart/6\)_Volume_Rendering.ipynb)
+ * [Introduction](https://github.com/yt-project/yt/tree/main/doc/source/quickstart/1\)_Introduction.ipynb)
+ * [Data Inspection](https://github.com/yt-project/yt/tree/main/doc/source/quickstart/2\)_Data_Inspection.ipynb)
+ * [Simple Visualization](https://github.com/yt-project/yt/tree/main/doc/source/quickstart/3\)_Simple_Visualization.ipynb)
+ * [Data Objects and Time Series](https://github.com/yt-project/yt/tree/main/doc/source/quickstart/4\)_Data_Objects_and_Time_Series.ipynb)
+ * [Derived Fields and Profiles](https://github.com/yt-project/yt/tree/main/doc/source/quickstart/5\)_Derived_Fields_and_Profiles.ipynb)
+ * [Volume Rendering](https://github.com/yt-project/yt/tree/main/doc/source/quickstart/6\)_Volume_Rendering.ipynb)
 
 If you'd like to try these online, you can visit our [yt Hub](https://hub.yt/)
 and run a notebook next to some of our example data.

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -261,6 +261,7 @@
     "trident": ("https://trident.readthedocs.io/en/latest/", None),
     "yt_astro_analysis": ("https://yt-astro-analysis.readthedocs.io/en/latest/", None),
     "yt_attic": ("https://yt-attic.readthedocs.io/en/latest/", None),
+    "pytest": ("https://docs.pytest.org/en/stable", None),
 }
 
 if not on_rtd:

diff --git a/doc/source/developing/testing.rst b/doc/source/developing/testing.rst
diff --git a/doc/source/examining/Loading_Generic_Array_Data.ipynb b/doc/source/examining/Loading_Generic_Array_Data.ipynb
@@ -266,7 +266,7 @@
    },
    "outputs": [],
    "source": [
-    "data = {k:(v.value,u) for (k,v), u in zip(f.items(),units)}\n",
+    "data = {k:(v[()],u) for (k,v), u in zip(f.items(),units)}\n",
     "bbox = np.array([[-0.5, 0.5], [-0.5, 0.5], [-0.5, 0.5]])"
    ]
   },

diff --git a/doc/source/installing.rst b/doc/source/installing.rst
@@ -29,7 +29,7 @@ or pip, and we will *assume* that you do so in an isolated environment.
 Also note that each yt release supports a limited range of Python versions.
 Here's a summary for most recent releases
 
-+------------+------------+----------------------------------+
++------------+------------+----------------+-----------------+
 | yt release | Python 2.7 | Python3 min    | Python3 max     |
 +============+============+================+=================+
 | 4.1.x      | no         | 3.7 (expected) | 3.10 (expected) |
@@ -120,7 +120,7 @@ yt as by appending ``[full]`` to the target name when calling pip, i.e.,
 Testing Your Installation
 +++++++++++++++++++++++++
 
-To test to make sure everything is installed properly, try running yt at
+To make sure everything is installed properly, try running yt at
 the command line:
 
 .. code-block:: bash

diff --git a/nose_unit.cfg b/nose_unit.cfg
@@ -6,5 +6,5 @@ nologcapture=1
 verbosity=2
 where=yt
 with-timer=1
-ignore-files=(test_load_errors.py|test_load_sample.py|test_commons.py|test_ambiguous_fields.py|test_field_access_pytest.py|test_save.py|test_load_archive.py)
+ignore-files=(test_load_errors.py|test_load_sample.py|test_commons.py|test_ambiguous_fields.py|test_field_access_pytest.py|test_save.py|test_load_archive.py|test_line_annotation_unit.py|test_eps_writer.py)
 exclude-test=yt.frontends.gdf.tests.test_outputs.TestGDF
diff --git a/setup.cfg b/setup.cfg
@@ -74,7 +74,7 @@ full =
     astropy>=4.0.1,<5.0.0
     f90nml>=1.1.2
     fastcache~=1.0.2
-    firefly-vis>=2.0.0
+    firefly-vis>=2.0.0,<2.0.3 #https://github.com/ageller/Firefly/issues/62
     glueviz~=0.13.3
     h5py>=3.1.0,<4.0.0
     libconf~=1.0.1

diff --git a/tests/tests.yaml b/tests/tests.yaml
@@ -182,10 +182,12 @@ other_tests:
      - '--ignore=test_outputs_pytest'
      - '--ignore-files=test_load_errors.py'
      - '--ignore-files=test_commons.py'
+     - '--ignore-files=test_line_annotation_unit.py'
      - '--ignore-files=test_load_sample.py'
      - '--ignore-files=test_load_archive.py'
      - '--ignore-files=test_field_access_pytest.py'
      - '--ignore-files=test_ambiguous_fields.py'
+     - '--ignore-files=test_eps_writer.py'
      - "--ignore-files=test_save.py"
      - '--exclude-test=yt.frontends.gdf.tests.test_outputs.TestGDF'
   cookbook:

diff --git a/yt/data_objects/construction_data_containers.py b/yt/data_objects/construction_data_containers.py
@@ -648,12 +648,19 @@ def __init__(
         self.right_edge = self.left_edge + self.ActiveDimensions * self.dds
         self._num_ghost_zones = num_ghost_zones
         self._use_pbar = use_pbar
-        self.global_startindex = np.rint(
-            (self.left_edge - self.ds.domain_left_edge) / self.dds
-        ).astype("int64")
+        self.global_startindex = (
+            np.rint((self.left_edge - self.ds.domain_left_edge) / self.dds).astype(
+                "int64"
+            )
+            + self.ds.domain_offset
+        )
         self._setup_data_source()
         self.get_data(fields)
 
+    def get_global_startindex(self):
+        r"""Get the global start index of the covering grid."""
+        return self.global_startindex
+
     def to_xarray(self, fields=None):
         r"""Export this fixed-resolution object to an xarray Dataset
 
@@ -1405,8 +1412,7 @@ def _fill_fields(self, fields):
             warnings.warn(
                 "Something went wrong during field computation. "
                 "This is likely due to missing ghost-zones support "
-                "in class %s",
-                self.ds.__class__,
+                f"in class {type(self.ds)}",
                 category=RuntimeWarning,
             )
             mylog.debug("Caught %d runtime errors.", runtime_errors_count)

diff --git a/yt/data_objects/static_output.py b/yt/data_objects/static_output.py
@@ -136,6 +136,9 @@ class Dataset(abc.ABC):
     domain_left_edge = MutableAttribute(True)
     domain_right_edge = MutableAttribute(True)
     domain_dimensions = MutableAttribute(True)
+    # the point in index space "domain_left_edge" doesn't necessarily
+    # map to (0, 0, 0)
+    domain_offset = np.zeros(3, dtype="int64")
     _periodicity = MutableAttribute()
     _force_periodicity = False
 

diff --git a/yt/frontends/athena/data_structures.py b/yt/frontends/athena/data_structures.py
@@ -1,4 +1,5 @@
 import os
+import re
 import weakref
 
 import numpy as np
@@ -632,12 +633,27 @@ def _parse_parameter_file(self):
 
     @classmethod
     def _is_valid(cls, filename, *args, **kwargs):
-        try:
-            if "vtk" in filename:
-                return True
-        except Exception:
-            pass
-        return False
+        if not filename.endswith(".vtk"):
+            return False
+
+        with open(filename, "rb") as fh:
+            if not re.match(b"# vtk DataFile Version \\d\\.\\d\n", fh.readline(256)):
+                return False
+            if (
+                re.search(
+                    b"at time= .*, level= \\d, domain= \\d\n",
+                    fh.readline(256),
+                )
+                is None
+            ):
+                # vtk Dumps headers start with either "CONSERVED vars" or "PRIMITIVE vars",
+                # while vtk output headers start with "Really cool Athena data", but
+                # we will consider this an implementation detail and not attempt to
+                # match it exactly here.
+                # See Athena's user guide for reference
+                # https://princetonuniversity.github.io/Athena-Cversion/AthenaDocsUGbtk
+                return False
+        return True
 
     @property
     def _skip_cache(self):

diff --git a/yt/frontends/boxlib/data_structures.py b/yt/frontends/boxlib/data_structures.py
@@ -743,19 +743,7 @@ def _parse_cparams(self):
                 param, vals = (s.strip() for s in line.split("="))
             except ValueError:
                 continue
-            if param == "amr.n_cell":
-                vals = self.domain_dimensions = np.array(vals.split(), dtype="int32")
-
-                # For 1D and 2D simulations in BoxLib usually only the relevant
-                # dimensions have a specified number of zones, but yt requires
-                # domain_dimensions to have three elements, with 1 in the additional
-                # slots if we're not in 3D, so append them as necessary.
-
-                if self.dimensionality == 1:
-                    vals = self.domain_dimensions = np.array([vals[0], 1, 1])
-                elif self.dimensionality == 2:
-                    vals = self.domain_dimensions = np.array([vals[0], vals[1], 1])
-            elif param == "amr.ref_ratio":
+            if param == "amr.ref_ratio":
                 vals = self.refine_by = int(vals[0])
             elif param == "Prob.lo_bc":
                 vals = tuple(p == "1" for p in vals.split())
@@ -881,6 +869,7 @@ def _parse_header_file(self):
         stop = np.array(root_space[1].split(","), dtype="int64")
         dd = np.ones(3, dtype="int64")
         dd[: self.dimensionality] = stop - start + 1
+        self.domain_offset[: self.dimensionality] = start
         self.domain_dimensions = dd
 
         # Skip timesteps per level

diff --git a/yt/frontends/boxlib/definitions.py b/yt/frontends/boxlib/definitions.py
@@ -1,47 +0,0 @@
-# TODO: get rid of enzo parameters we do not need
-parameterDict = {
-    "CosmologyCurrentRedshift": float,
-    "CosmologyComovingBoxSize": float,
-    "CosmologyOmegaMatterNow": float,
-    "CosmologyOmegaLambdaNow": float,
-    "CosmologyHubbleConstantNow": float,
-    "CosmologyInitialRedshift": float,
-    "DualEnergyFormalismEta1": float,
-    "DualEnergyFormalismEta2": float,
-    "MetaDataString": str,
-    "HydroMethod": int,
-    "DualEnergyFormalism": int,
-    "InitialTime": float,
-    "ComovingCoordinates": int,
-    "DensityUnits": float,
-    "LengthUnits": float,
-    "LengthUnit": float,
-    "TemperatureUnits": float,
-    "TimeUnits": float,
-    "GravitationalConstant": float,
-    "Gamma": float,
-    "MultiSpecies": int,
-    "CompilerPrecision": str,
-    "CurrentTimeIdentifier": int,
-    "RefineBy": int,
-    "BoundaryConditionName": str,
-    "TopGridRank": int,
-    "TopGridDimensions": int,
-    "EOSSoundSpeed": float,
-    "EOSType": int,
-    "NumberOfParticleAttributes": int,
-}
-
-
-# converts the Orion inputs file name to the Enzo/yt name expected
-# throughout the code. key is Orion name, value is Enzo/yt equivalent
-orion2enzoDict = {
-    "amr.n_cell": "TopGridDimensions",
-    "materials.gamma": "Gamma",
-    "amr.ref_ratio": "RefineBy",
-    "castro.use_comoving": "ComovingCoordinates",
-    "castro.redshift_in": "CosmologyInitialRedshift",
-    "comoving_OmL": "CosmologyOmegaLambdaNow",
-    "comoving_OmM": "CosmologyOmegaMatterNow",
-    "comoving_h": "CosmologyHubbleConstantNow",
-}

diff --git a/yt/geometry/coordinates/coordinate_handler.py b/yt/geometry/coordinates/coordinate_handler.py
@@ -1,3 +1,4 @@
+import abc
 import weakref
 from numbers import Number
 
@@ -61,47 +62,56 @@ def validate_sequence_width(width, ds, unit=None):
             )
 
 
-class CoordinateHandler:
+class CoordinateHandler(abc.ABC):
     name = None
 
     def __init__(self, ds, ordering):
         self.ds = weakref.proxy(ds)
         self.axis_order = ordering
 
+    @abc.abstractmethod
     def setup_fields(self):
         # This should return field definitions for x, y, z, r, theta, phi
-        raise NotImplementedError
+        pass
 
+    @abc.abstractmethod
     def pixelize(self, dimension, data_source, field, bounds, size, antialias=True):
         # This should *actually* be a pixelize call, not just returning the
         # pixelizer
-        raise NotImplementedError
+        pass
 
+    @abc.abstractmethod
     def pixelize_line(self, field, start_point, end_point, npoints):
-        raise NotImplementedError
+        pass
 
     def distance(self, start, end):
         p1 = self.convert_to_cartesian(start)
         p2 = self.convert_to_cartesian(end)
         return np.sqrt(((p1 - p2) ** 2.0).sum())
 
+    @abc.abstractmethod
     def convert_from_cartesian(self, coord):
-        raise NotImplementedError
+        pass
 
+    @abc.abstractmethod
     def convert_to_cartesian(self, coord):
-        raise NotImplementedError
+        pass
 
+    @abc.abstractmethod
     def convert_to_cylindrical(self, coord):
-        raise NotImplementedError
+        pass
 
+    @abc.abstractmethod
     def convert_from_cylindrical(self, coord):
-        raise NotImplementedError
+        pass
 
+    @abc.abstractmethod
     def convert_to_spherical(self, coord):
-        raise NotImplementedError
+        pass
 
+    @abc.abstractmethod
     def convert_from_spherical(self, coord):
-        raise NotImplementedError
+        pass
 
     _data_projection = None
 
@@ -194,8 +204,9 @@ def y_axis(self):
         return ya
 
     @property
+    @abc.abstractproperty
     def period(self):
-        raise NotImplementedError
+        pass
 
     def sanitize_depth(self, depth):
         if is_sequence(depth):

diff --git a/yt/geometry/coordinates/cylindrical_coordinates.py b/yt/geometry/coordinates/cylindrical_coordinates.py
@@ -165,6 +165,9 @@ def pixelize(
             # Pixelizing along a cylindrical surface is a bit tricky
             raise NotImplementedError
 
+    def pixelize_line(self, field, start_point, end_point, npoints):
+        raise NotImplementedError
+
     def _ortho_pixelize(
         self, data_source, field, bounds, size, antialias, dim, periodic
     ):

diff --git a/yt/geometry/coordinates/geographic_coordinates.py b/yt/geometry/coordinates/geographic_coordinates.py
@@ -245,6 +245,9 @@ def pixelize(
         else:
             raise NotImplementedError
 
+    def pixelize_line(self, field, start_point, end_point, npoints):
+        raise NotImplementedError
+
     def _ortho_pixelize(
         self, data_source, field, bounds, size, antialias, dimension, periodic
     ):

diff --git a/yt/geometry/coordinates/spherical_coordinates.py b/yt/geometry/coordinates/spherical_coordinates.py
@@ -164,6 +164,9 @@ def pixelize(
         else:
             raise NotImplementedError
 
+    def pixelize_line(self, field, start_point, end_point, npoints):
+        raise NotImplementedError
+
     def _ortho_pixelize(
         self, data_source, field, bounds, size, antialias, dim, periodic
     ):