Merge pull request yt-project#3913 from neutrinoceros/manual_bp_yt4.0.4

REL: backports for yt 4.0.4

.github/workflows/wheels.yaml

@@ -7,6 +7,9 @@ on:
       - stable
     tags:
       - 'yt-*'
+  pull_request:
+    paths:
+      - '.github/workflows/wheels.yaml'
   workflow_dispatch:
 
 jobs:
@@ -29,14 +32,14 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Build wheels for CPython
-        uses: pypa/cibuildwheel@v2.3.0
+        uses: pypa/cibuildwheel@v2.4.0
         with:
           output-dir: dist
         env:
           CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-* cp310-*"
           CIBW_SKIP: "*-musllinux_*"  #  numpy doesn't have wheels for musllinux so we can't build some quickly and without bloating
           CIBW_ARCHS_LINUX: "x86_64"
-          CIBW_ARCHS_MACOS: "x86_64"
+          CIBW_ARCHS_MACOS: x86_64 arm64
           CIBW_ARCHS_WINDOWS: "auto"
           CIBW_ENVIRONMENT: "LDFLAGS='-static-libstdc++'"
           CIBW_BUILD_VERBOSITY: 1

doc/source/conf.py

@@ -77,9 +77,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "4.0.3"
+version = "4.0"
 # The full version, including alpha/beta/rc tags.
-release = "4.0.3"
+release = "4.0.4"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = yt
-version = 4.0.3
+version = 4.0.4
 description = An analysis and visualization toolkit for volumetric data
 long_description = file: README.md
 long_description_content_type = text/markdown

setup.py

@@ -15,8 +15,6 @@
 
 install_ccompiler()
 
-VERSION = "4.0.3"
-
 if os.path.exists("MANIFEST"):
     os.remove("MANIFEST")
 

tests/ci_install.sh

@@ -34,7 +34,7 @@ if [[ "${RUNNER_OS}" == "Windows" ]] && [[ ${dependencies} != "minimal" ]]; then
     # keep in sync: setup.cfg
     while read requirement; do conda install --yes $requirement; done < tests/windows_conda_requirements.txt
 else
-    python -m pip install --upgrade pip
+    python -m pip install --upgrade "pip != 22.1"
     python -m pip install --upgrade wheel
 
     # // band aid

yt/__init__.py

@@ -7,7 +7,7 @@
 * Contribute: https://github.com/yt-project/yt
 
 """
-__version__ = "4.0.3"
+__version__ = "4.0.4"
 
 import yt.units as units
 import yt.utilities.physical_constants as physical_constants

yt/frontends/gadget/data_structures.py

@@ -424,7 +424,15 @@ def _parse_parameter_file(self):
         )
 
         if hvals["NumFiles"] > 1:
-            self.filename_template = f"{prefix}.%(num)s{self._suffix}"
+            for t in (
+                f"{prefix}.%(num)s{self._suffix}",
+                f"{prefix}.gad.%(num)s{self._suffix}",
+            ):
+                if os.path.isfile(t % {"num": 0}):
+                    self.filename_template = t
+                    break
+            else:
+                raise RuntimeError("Could not determine correct data file template.")
         else:
             self.filename_template = self.parameter_filename
 

yt/geometry/particle_geometry_handler.py

@@ -94,11 +94,12 @@ def _setup_filenames(self):
                     mylog.warning(
                         "Failed to load '%s' (missing file or directory)", _filename
                     )
+                    break
                 if max(df.total_particles.values()) == 0:
                     break
                 fi += 1
                 self.data_files.append(df)
-                if self.chunksize <= 0:
+                if end is None:
                     break
                 start = end
                 end += self.chunksize

yt/utilities/lib/geometry_utils.pyx

@@ -15,7 +15,7 @@ import numpy as np
 cimport cython
 cimport numpy as np
 from cython cimport floating
-from libc.math cimport copysign, fabs
+from libc.math cimport copysign, fabs, log2
 from libc.stdlib cimport free, malloc
 
 from yt.utilities.lib.fp_utils cimport fclip, i64clip
@@ -40,7 +40,6 @@ cdef extern from "math.h":
     double fabs(double x) nogil
 
 cdef extern from "platform_dep.h":
-    double log2(double x) nogil
     long int lrint(double x) nogil
 
 @cython.cdivision(True)

yt/utilities/lib/platform_dep.h

@@ -25,9 +25,6 @@ static __inline double fmax(double x, double y){
 static __inline double fmin(double x, double y){
     return (x < y) ? x : y;
 }
-static __inline double log2(double x) {
-    return log(x) * M_LOG2E;
-}
 
 /* adapted from http://www.johndcook.com/blog/cpp_erf/
    code is under public domain license */

yt/visualization/color_maps.py

@@ -8,6 +8,7 @@
 from packaging.version import Version
 
 from yt.funcs import get_brewer_cmap
+from yt.utilities.logger import ytLogger as mylog
 
 from . import _colormap_data as _cm
 from ._commons import MPL_VERSION
@@ -76,8 +77,6 @@ def register_yt_colormaps_from_cmyt():
     """
     from matplotlib.pyplot import get_cmap
 
-    from yt.utilities.logger import ytLogger as mylog
-
     for hist_name, alias in _HISTORICAL_ALIASES.items():
         if MPL_VERSION >= Version("3.4.0"):
             cmap = get_cmap(alias).copy()
@@ -91,25 +90,25 @@ def register_yt_colormaps_from_cmyt():
             # Matplotlib 3.4.0 hard-forbids name collisions, but more recent versions
             # will emit a warning instead, so we emulate this behaviour regardless.
             mylog.warning("cannot register colormap '%s' (naming collision)", hist_name)
-            continue
 
 
 register_yt_colormaps_from_cmyt()
 
 # Add colormaps in _colormap_data.py that weren't defined here
 _vs = np.linspace(0, 1, 256)
 for k, v in list(_cm.color_map_luts.items()):
+    if k in yt_colormaps:
+        continue
+    cdict = {
+        "red": np.transpose([_vs, v[0], v[0]]),
+        "green": np.transpose([_vs, v[1], v[1]]),
+        "blue": np.transpose([_vs, v[2], v[2]]),
+    }
     try:
-        colormaps = mcm._cmap_registry
-    except AttributeError:  # mpl < 3.3.0
-        colormaps = mcm.cmap_d
-    if k not in yt_colormaps and k not in colormaps:
-        cdict = {
-            "red": np.transpose([_vs, v[0], v[0]]),
-            "green": np.transpose([_vs, v[1], v[1]]),
-            "blue": np.transpose([_vs, v[2], v[2]]),
-        }
         add_colormap(k, cdict)
+    except ValueError:
+        # expected if another map with identical name was already registered
+        mylog.warning("cannot register colormap '%s' (naming collision)", k)
 
 
 def get_colormap_lut(cmap_id: Union[Tuple[str, str], str]):