Autofix

doc/extensions/pythonscript_sphinxext.py

@@ -42,7 +42,7 @@ def run(self):
         # Use sphinx logger?
         uid = uuid.uuid4().hex[:8]
         print("")
-        print(">> Contents of the script: %s" % uid)
+        print(f">> Contents of the script: {uid}")
         print(content)
         print("")
 
@@ -87,7 +87,7 @@ def get_image_tag(filename, image_dir, image_rel_dir):
     my_uuid = uuid.uuid4().hex
     shutil.move(filename, image_dir + os.path.sep + my_uuid + filename)
     relative_filename = image_rel_dir + os.path.sep + my_uuid + filename
-    return '<img src="%s" width="600"><br>' % relative_filename
+    return f'<img src="{relative_filename}" width="600"><br>'
 
 
 def make_image_dir(setup, rst_dir):

doc/extensions/yt_colormaps.py

@@ -58,9 +58,9 @@ def run(self):
         lines = []
         for im in images:
             im_name = os.path.join("_static", os.path.basename(im))
-            lines.append(".. image:: %s" % im_name)
+            lines.append(f".. image:: {im_name}")
             lines.append("   :width: 400")
-            lines.append("   :target: ../../_images/%s" % os.path.basename(im))
+            lines.append(f"   :target: ../../_images/{os.path.basename(im)}")
             lines.append("\n")
         lines.append("\n")
         self.state_machine.insert_input(lines, rst_file)

doc/extensions/yt_cookbook.py

@@ -58,19 +58,19 @@ def run(self):
         )
 
         im_path = os.path.join(rst_dir, "_static")
-        images = sorted(glob.glob(os.path.join(im_path, "%s__*.png" % script_name)))
+        images = sorted(glob.glob(os.path.join(im_path, f"{script_name}__*.png")))
         lines = []
         lines.append(f"(`{script_bn} <{script_fn}>`__)")
         lines.append("\n")
         lines.append("\n")
-        lines.append(".. literalinclude:: %s" % self.arguments[0])
+        lines.append(f".. literalinclude:: {self.arguments[0]}")
         lines.append("\n")
         lines.append("\n")
         for im in images:
             im_name = os.path.join("_static", os.path.basename(im))
-            lines.append(".. image:: %s" % im_name)
+            lines.append(f".. image:: {im_name}")
             lines.append("   :width: 400")
-            lines.append("   :target: ../_images/%s" % os.path.basename(im))
+            lines.append(f"   :target: ../_images/{os.path.basename(im)}")
             lines.append("\n")
         lines.append("\n")
         for ext in data_patterns:

setup.py

@@ -20,7 +20,7 @@ def get_version(filename):
         for line in f.readlines():
             if line.startswith("__version__"):
                 return line.split("=")[1].strip()[1:-1]
-    raise RuntimeError("Could not get version from %s." % filename)
+    raise RuntimeError(f"Could not get version from {filename}.")
 
 
 VERSION = get_version("yt_astro_analysis/__init__.py")

yt_astro_analysis/cosmological_observation/api.py

@@ -15,3 +15,5 @@
 
 from yt_astro_analysis.cosmological_observation.cosmology_splice import CosmologySplice
 from yt_astro_analysis.cosmological_observation.light_cone.api import LightCone
+
+__all__ = ["CosmologySplice", "LightCone"]

yt_astro_analysis/cosmological_observation/light_cone/api.py

@@ -14,3 +14,5 @@
 # -----------------------------------------------------------------------------
 
 from .light_cone import LightCone
+
+__all__ = ["LightCone"]

yt_astro_analysis/cosmological_observation/light_cone/light_cone.py

@@ -453,7 +453,7 @@ def _save_light_cone_solution(self, filename="light_cone.dat"):
         mylog.info("Saving light cone solution to %s.", filename)
 
         f = open(filename, "w")
-        f.write("# parameter_filename = %s\n" % self.parameter_filename)
+        f.write(f"# parameter_filename = {self.parameter_filename}\n")
         f.write("\n")
         f.write(
             "# Slice    Dataset    Redshift    depth/box    "
@@ -491,10 +491,10 @@ def _save_light_cone_stack(
         )
 
         field_node = f"{field}_{weight_field}"
-        weight_field_node = "weight_field_%s" % weight_field
+        weight_field_node = f"weight_field_{weight_field}"
 
         if filename is None:
-            filename = os.path.join(self.output_dir, "%s_data" % self.output_prefix)
+            filename = os.path.join(self.output_dir, f"{self.output_prefix}_data")
         if not (filename.endswith(".h5")):
             filename += ".h5"
 

yt_astro_analysis/cosmological_observation/light_cone/tests/test_light_cone.py

@@ -84,7 +84,7 @@ def run(self):
             punits = (
                 _funits[self.field] * _funits[self.weight_field] * _funits["length"]
             )
-            wunits = fh["weight_field_%s" % self.weight_field].attrs["units"]
+            wunits = fh[f"weight_field_{self.weight_field}"].attrs["units"]
             pwunits = _funits[self.weight_field] * _funits["length"]
             assert wunits == str(pwunits.units)
         assert units == str(punits.units)

yt_astro_analysis/halo_analysis/api.py

@@ -25,3 +25,12 @@
     VisibleDeprecationWarning,
     stacklevel=2,
 )
+
+__all__ = [
+    "add_quantity",
+    "add_callback",
+    "add_filter",
+    "add_finding_method",
+    "add_recipe",
+    "HaloCatalog",
+]

yt_astro_analysis/halo_analysis/halo_catalog/halo_callbacks.py

@@ -57,7 +57,7 @@ def halo_sphere(halo, radius_field="virial_radius", factor=1.0, field_parameters
     """
 
     dds = halo.halo_catalog.data_ds
-    center = dds.arr([halo.quantities["particle_position_%s" % axis] for axis in "xyz"])
+    center = dds.arr([halo.quantities[f"particle_position_{axis}"] for axis in "xyz"])
     radius = factor * halo.quantities[radius_field]
     if radius <= 0.0:
         halo.data_object = None
@@ -255,7 +255,7 @@ def profile(
             field: my_profile.standard_deviation[field]
             for field in my_profile.standard_deviation
         }
-        variance_storage = "%s_variance" % storage
+        variance_storage = f"{storage}_variance"
         if hasattr(halo, variance_storage):
             halo_variance_store = getattr(halo, variance_storage)
         else:
@@ -315,7 +315,7 @@ def save_profiles(halo, storage="profiles", filename=None, output_dir="."):
         if isinstance(my_profile[field], YTArray):
             my_profile[field].convert_to_cgs()
         _yt_array_hdf5(profile_group, str(field), my_profile[field])
-    variance_storage = "%s_variance" % storage
+    variance_storage = f"{storage}_variance"
     if hasattr(halo, variance_storage):
         my_profile = getattr(halo, variance_storage)
         variance_group = fh.create_group("variance")
@@ -364,7 +364,7 @@ def load_profiles(halo, storage="profiles", fields=None, filename=None, output_d
         "%s_%06d.h5" % (filename, halo.quantities["particle_identifier"]),
     )
     if not os.path.exists(output_file):
-        raise RuntimeError("Profile file not found: %s." % output_file)
+        raise RuntimeError(f"Profile file not found: {output_file}.")
     mylog.info(
         "Loading halo %d profile data from %s.",
         halo.quantities["particle_identifier"],
@@ -397,7 +397,7 @@ def load_profiles(halo, storage="profiles", fields=None, filename=None, output_d
             my_variance[field] = _hdf5_yt_array(
                 my_group, field, ds=halo.halo_catalog.halos_ds
             )
-        setattr(halo, "%s_variance" % storage, my_variance)
+        setattr(halo, f"{storage}_variance", my_variance)
 
     fh.close()
 
@@ -451,8 +451,7 @@ def virial_quantities(
 
     if overdensity_field not in profile_data:
         raise RuntimeError(
-            "virial_quantities callback requires profile of %s."
-            % str(overdensity_field)
+            f"virial_quantities callback requires profile of {str(overdensity_field)}."
         )
 
     overdensity = profile_data[overdensity_field]
@@ -630,7 +629,7 @@ def iterative_center_of_mass(
         )
 
     center_orig = halo.halo_catalog.data_ds.arr(
-        [halo.quantities["particle_position_%s" % axis] for axis in "xyz"]
+        [halo.quantities[f"particle_position_{axis}"] for axis in "xyz"]
     )
     sphere = halo.halo_catalog.data_ds.sphere(
         center_orig, outer_radius * halo.quantities[radius_field]
@@ -653,7 +652,7 @@ def iterative_center_of_mass(
     )
 
     for i, axis in enumerate("xyz"):
-        halo.quantities["particle_position_%s" % axis] = sphere.center[i]
+        halo.quantities[f"particle_position_{axis}"] = sphere.center[i]
     del sphere
 
 

yt_astro_analysis/halo_analysis/halo_catalog/halo_filters.py

@@ -31,7 +31,7 @@ def quantity_value(halo, field, operator, value, units):
     """
 
     if field not in halo.quantities:
-        raise RuntimeError("Halo object does not contain %s quantity." % field)
+        raise RuntimeError(f"Halo object does not contain {field} quantity.")
 
     h_value = halo.quantities[field].in_units(units).to_ndarray()
     return eval(f"{h_value} {operator} {value}")

yt_astro_analysis/halo_analysis/halo_finding/api.py

@@ -26,3 +26,5 @@
 )
 
 from yt_astro_analysis.halo_finding.halo_objects import FOFHaloFinder, HOPHaloFinder
+
+__all__ = ["FOFHaloFinder", "HOPHaloFinder"]

yt_astro_analysis/halo_analysis/halo_finding/halo_objects.py

@@ -573,7 +573,7 @@ def maximum_density_location(self):
 
 
 class HaloList:
-    _fields = ["particle_position_%s" % ax for ax in "xyz"]
+    _fields = [f"particle_position_{ax}" for ax in "xyz"]
 
     def __init__(self, data_source, redshift=-1, ptype="all"):
         """
@@ -627,7 +627,7 @@ def _parse_output(self):
             )
             md_i = np.argmax(dens[cp:cp_c])
             px, py, pz = (
-                self.particle_fields["particle_position_%s" % ax][group_indices]
+                self.particle_fields[f"particle_position_{ax}"][group_indices]
                 for ax in "xyz"
             )
             self._max_dens[i] = (dens[cp:cp_c][md_i], px[md_i], py[md_i], pz[md_i])
@@ -651,7 +651,7 @@ class HOPHaloList(HaloList):
 
     _name = "HOP"
     _halo_class = HOPHalo
-    _fields = ["particle_position_%s" % ax for ax in "xyz"] + ["particle_mass"]
+    _fields = [f"particle_position_{ax}" for ax in "xyz"] + ["particle_mass"]
 
     def __init__(self, data_source, threshold=160.0, ptype="all"):
         self.threshold = threshold
@@ -740,7 +740,7 @@ def _reposition_particles(self, bounds):
         LE, RE = bounds
         dw = self.ds.domain_right_edge - self.ds.domain_left_edge
         for i, ax in enumerate("xyz"):
-            arr = self._data_source[self.ptype, "particle_position_%s" % ax]
+            arr = self._data_source[self.ptype, f"particle_position_{ax}"]
             arr[arr < LE[i] - self.padding] += dw[i]
             arr[arr > RE[i] + self.padding] -= dw[i]
 

yt_astro_analysis/halo_analysis/halo_finding/rockstar/api.py

@@ -28,3 +28,6 @@
 from yt_astro_analysis.halo_analysis.halo_finding.rockstar.rockstar import (
     RockstarHaloFinder,
 )
+
+
+__all__ = ["RockstarHaloFinder"]

yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py

@@ -301,7 +301,7 @@ def _setup_parameters(self, ts):
         if ptype not in tds.particle_types and ptype != "all":
             has_particle_filter = tds.add_particle_filter(ptype)
             if not has_particle_filter:
-                raise RuntimeError("Particle type (filter) %s not found." % (ptype))
+                raise RuntimeError(f"Particle type (filter) {ptype} not found.")
 
         dd = tds.all_data()
         # Get DM particle mass.
@@ -370,7 +370,7 @@ def run(self, block_ratio=1, callbacks=None, restart=False):
         if restart:
             restart_file = os.path.join(self.outbase, "restart.cfg")
             if not os.path.exists(restart_file):
-                raise RuntimeError("Restart file %s not found" % (restart_file))
+                raise RuntimeError(f"Restart file {restart_file} not found")
             with open(restart_file) as restart_fh:
                 for par in restart_fh:
                     if par.startswith("RESTART_SNAP"):

yt_astro_analysis/halo_analysis/tests/test_halo_catalog.py

@@ -60,7 +60,7 @@ def run(self):
         hc.add_quantity("nstars")
         hc.create()
 
-        fn = os.path.join(tmpdir, str(dds), "%s.0.h5" % str(dds))
+        fn = os.path.join(tmpdir, str(dds), f"{str(dds)}.0.h5")
         ds = load(fn)
         ad = ds.all_data()
         mi, ma = ad.quantities.extrema("nstars")

yt_astro_analysis/ppv_cube/api.py

@@ -11,3 +11,5 @@
 # -----------------------------------------------------------------------------
 
 from yt_astro_analysis.ppv_cube.ppv_cube import PPVCube
+
+__all__ = ["PPVCube"]

yt_astro_analysis/ppv_cube/ppv_cube.py

@@ -39,7 +39,7 @@ def _v_los(field, data):
     elif isinstance(normal, str):
 
         def _v_los(field, data):
-            return -data["gas", "velocity_%s" % normal]
+            return -data["gas", f"velocity_{normal}"]
 
     else:
         orient = Orientation(normal)

yt_astro_analysis/radmc3d_export/RadMC3DInterface.py

@@ -376,7 +376,7 @@ def write_source_files(self, sources, wavelengths):
 
         # write wavelength information
         for wavelength in wavelengths:
-            fhandle.write("%f \n" % wavelength)
+            fhandle.write(f"{wavelength:f} \n")
 
         # finally write blackbody temperature for each source
         for source in sources:
@@ -394,7 +394,7 @@ def write_source_files(self, sources, wavelengths):
 
         fhandle.write("%d \n" % nlam)
         for wavelength in wavelengths:
-            fhandle.write("%f \n" % wavelength)
+            fhandle.write(f"{wavelength:f} \n")
 
         # done with both
         fhandle.close()

yt_astro_analysis/radmc3d_export/api.py

@@ -18,3 +18,5 @@
     RadMC3DSource,
     RadMC3DWriter,
 )
+
+__all__ = ["read_radmc3d_image", "RadMC3DSource", "RadMC3DWriter"]