Added and applied formatting script.

Author: Bert Vandenbroucke

docs/source/conf.py

@@ -86,9 +86,7 @@ def run_apidoc(_):
 
     api_doc_dir = os.path.join(cur_dir, "modules")
     module = os.path.join(cur_dir, "../..", "velociraptor")
-    ignore = [
-        os.path.join(cur_dir, "../..", "tests"),
-    ]
+    ignore = [os.path.join(cur_dir, "../..", "tests")]
 
     os.environ["SPHINX_APIDOC_OPTIONS"] = "members,undoc-members,show-inheritance"
     main(["-M", "-f", "-e", "-T", "-d 0", "-o", api_doc_dir, module, *ignore])

examples/auto_plotter.py

@@ -9,7 +9,9 @@
 from velociraptor.autoplotter.metadata import AutoPlotterMetadata
 from velociraptor import load
 
-catalogue = load("/Users/mphf18/Documents/science/halo_matching/ref/halo_2729.properties")
+catalogue = load(
+    "/Users/mphf18/Documents/science/halo_matching/ref/halo_2729.properties"
+)
 
 ap = AutoPlotter("auto_plotter_example.yml")
 
@@ -18,4 +20,3 @@
 
 metadata = AutoPlotterMetadata(auto_plotter=ap)
 metadata.write_metadata("test_auto_plotter/test_metadata.yml")
-

examples/swift_integration.py

@@ -70,4 +70,3 @@
         fig.savefig(f"{particle_type}_halo_image_{halo_id}.png")
 
         plt.close(fig)
-

format.sh

@@ -0,0 +1,79 @@
+#!/bin/bash
+
+# Check if we can run pip
+# This also serves as a check for python3
+python3 -m pip --version > /dev/null
+if [[ $? -ne 0 ]]
+then
+  echo "ERROR: cannot run 'python3 -m pip'"
+  exit 1
+fi
+
+# Check if the virtual environment with black exists
+if [ ! -d black_formatting_env ]
+then
+  echo "Formatting environment not found, installing it..."
+  python3 -m venv black_formatting_env
+  ./black_formatting_env/bin/python3 -m pip install click==8.0.4 black==19.3b0
+fi
+# Now we know exactly which black to use
+black="./black_formatting_env/bin/python3 -m black"
+
+# Formatting command
+cmd="$black -t py38 $(find . -name '*.py' -not -path './black_formatting_env/*')"
+
+# Print the help
+function show_help {
+    echo -e "This script formats all Python scripts using black"
+    echo -e "  -h, --help \t Show this help"
+    echo -e "  -c, --check \t Test if the Python scripts are well formatted"
+}
+
+# Parse arguments
+TEST=0
+while [[ $# -gt 0 ]]
+do
+    key="$1"
+
+    case $key in
+	# print the help and exit
+	-h|--help)
+	    show_help
+	    exit
+	    ;;
+	# check if the code is well formatted
+	-c|--check)
+	    TEST=1
+	    shift
+	    ;;
+	# unknown option
+	*)
+	    echo "Argument '$1' not implemented"
+	    show_help
+	    exit
+	    ;;
+    esac
+done
+
+# Run the required commands
+if [[ $TEST -eq 1 ]]
+then
+    # Note trapping the exit status from both commands in the pipe. Also note
+    # do not use -q in grep as that closes the pipe on first match and we get
+    # a SIGPIPE error.
+    echo "Testing if Python scripts are correctly formatted"
+    $cmd --check
+    status=$?
+
+    # Check formatting
+    if [[ ! ${status} -eq 0 ]]
+    then
+        echo "ERROR: needs formatting"
+        exit 1
+    else
+        echo "Everything is correctly formatted"
+    fi
+else
+    echo "Formatting all Python scripts"
+    $cmd
+fi

tests/test_observational_data.py

@@ -128,4 +128,3 @@ def test_multi_obs():
     assert new_multi_z.get_datasets_overlapping_with([0.4, 0.6])[0].redshift == 0.5
 
     os.remove("multi_z_test.hdf5")
-

velociraptor/__init__.py

@@ -37,7 +37,7 @@ def load(
     filename: str,
     disregard_units: bool = False,
     registration_file_path: Union[str, None] = None,
-    mask: slice = Ellipsis
+    mask: slice = Ellipsis,
 ) -> VelociraptorCatalogue:
     """
     Loads a velociraptor catalogue, producing a VelociraptorCatalogue
@@ -79,12 +79,10 @@ def load(
     """
 
     catalogue = VelociraptorCatalogue(
-        filename,
-        disregard_units=disregard_units,
-        mask=mask
+        filename, disregard_units=disregard_units, mask=mask
     )
 
     if registration_file_path is not None:
         catalogue.register_derived_quantities(registration_file_path)
-        
+
     return catalogue

velociraptor/autoplotter/objects.py

@@ -745,7 +745,7 @@ def _add_lines_to_axes(self, ax: Axes, x: unyt_array, y: unyt_array) -> None:
         return
 
     def get_quantity_from_catalogue_with_mask(
-            self, quantity: str, catalogue: VelociraptorCatalogue,
+        self, quantity: str, catalogue: VelociraptorCatalogue
     ) -> unyt_array:
         """
         Get a quantity from the catalogue using the mask.
@@ -755,17 +755,17 @@ def get_quantity_from_catalogue_with_mask(
         # We give each dataset a custom name, that gets ruined when masking
         # in versions of unyt less than 2.6.0
         name = x.name
-        
+
         if self.structure_mask is not None:
             # if structure_mask already set, mask and return
             x_mask = logical_and(self.global_mask, self.structure_mask)
             x = x[x_mask]
             x.name = name
             return x
-        
+
         # allow all entries by default
         self.structure_mask = ones(x.shape).astype(bool)
-        
+
         if self.selection_mask is not None:
             # Create mask
             self.structure_mask = reduce(
@@ -779,24 +779,22 @@ def get_quantity_from_catalogue_with_mask(
                 )
             self.structure_mask = logical_and(
                 self.structure_mask,
-                catalogue.structure_type.structuretype
-                == self.select_structure_type,
+                catalogue.structure_type.structuretype == self.select_structure_type,
             )
         if self.exclude_structure_type is not None:
             self.structure_mask = logical_and(
                 self.structure_mask,
-                catalogue.structure_type.structuretype
-                != self.exclude_structure_type,
+                catalogue.structure_type.structuretype != self.exclude_structure_type,
             )
-            
+
         # combine global and structure masks
         x_mask = logical_and(self.global_mask, self.structure_mask)
 
         # apply to the unyt array of values
         x = x[x_mask]
         x.name = name
         return x
-                
+
     def _make_plot_scatter(
         self, catalogue: VelociraptorCatalogue
     ) -> Tuple[Figure, Axes]:
@@ -962,7 +960,7 @@ def _make_plot_cumulative_histogram(
         return fig, ax
 
     def make_plot(
-        self, catalogue: VelociraptorCatalogue, directory: str, file_extension: str,
+        self, catalogue: VelociraptorCatalogue, directory: str, file_extension: str
     ):
         """
         Federates out data parsing to individual functions based on the
@@ -1048,7 +1046,7 @@ class AutoPlotter(object):
     created_successfully: List[bool]
     # global mask
     global_mask: Union[None, array]
-    
+
     def __init__(
         self,
         filename: Union[str, List[str]],
@@ -1113,7 +1111,9 @@ def parse_yaml(self):
 
         return
 
-    def link_catalogue(self, catalogue: VelociraptorCatalogue, global_mask_tag: Union[None, str]):
+    def link_catalogue(
+        self, catalogue: VelociraptorCatalogue, global_mask_tag: Union[None, str]
+    ):
         """
         Links a catalogue with this object so that the plots
         can actually be created.

velociraptor/catalogue/catalogue.py

@@ -88,13 +88,7 @@ def register_field_properties(self):
         return
 
 
-def generate_getter(
-        filename,
-        name: str,
-        field: str,
-        full_name: str,
-        unit
-):
+def generate_getter(filename, name: str, field: str, full_name: str, unit):
     """
     Generates a function that:
 
@@ -122,7 +116,9 @@ def getter(self):
             with h5py.File(filename, "r") as handle:
                 try:
                     mask = getattr(self, "mask")
-                    setattr(self, f"_{name}", unyt.unyt_array(handle[field][mask], unit))
+                    setattr(
+                        self, f"_{name}", unyt.unyt_array(handle[field][mask], unit)
+                    )
                     getattr(self, f"_{name}").name = full_name
                     getattr(self, f"_{name}").file = filename
                 except KeyError:
@@ -168,7 +164,7 @@ def generate_sub_catalogue(
     registration_function: Callable,
     units: VelociraptorUnits,
     field_metadata: List[VelociraptorFieldMetadata],
-    mask: slice = Ellipsis
+    mask: slice = Ellipsis,
 ):
     """
     Generates a sub-catalogue object with the correct properties set.
@@ -181,10 +177,7 @@ def generate_sub_catalogue(
     """
 
     # This creates a _copy_ of the _class_, not object.
-    this_sub_catalogue_bases = (
-        __VelociraptorSubCatalogue,
-        object,
-    )
+    this_sub_catalogue_bases = (__VelociraptorSubCatalogue, object)
     this_sub_catalogue_dict = {}
 
     valid_sub_paths = []
@@ -198,7 +191,7 @@ def generate_sub_catalogue(
                 metadata.snake_case,
                 metadata.path,
                 metadata.name,
-                metadata.unit
+                metadata.unit,
             ),
             generate_setter(metadata.snake_case),
             generate_deleter(metadata.snake_case),
@@ -411,7 +404,7 @@ def __create_sub_catalogues(self):
                     registration_function=self.registration_functions[attribute_name],
                     units=self.units,
                     field_metadata=field_metadata,
-                    mask=self.mask
+                    mask=self.mask,
                 ),
             )
 

velociraptor/catalogue/registration.py

@@ -37,8 +37,7 @@ def registration_fail_all(
     + name: A fancy (possibly LaTeX'd) name for the field.
     + snake_case: A correct snake_case name for the field.
     """
-    
-    
+
     if field_path == "ThisFieldPathWouldNeverExist":
         return (
             unit_system.length,
@@ -1042,10 +1041,10 @@ def registration_cold_dense_gas_properties(
         aperture_size = match.group(2)
 
         try:
-            long_quantity = {"DiffuseMetal": "Diffuse Metal", "Gas": "Gas",}[
+            long_quantity = {"DiffuseMetal": "Diffuse Metal", "Gas": "Gas"}[
                 quantity_key
             ]
-            short_quantity = {"DiffuseMetal": "diffuse_metal", "Gas": "gas",}[
+            short_quantity = {"DiffuseMetal": "diffuse_metal", "Gas": "gas"}[
                 quantity_key
             ]
         except KeyError:
@@ -1097,8 +1096,8 @@ def registration_log_element_ratios_times_masses(
                 "LogIronOverHydrogen": "Fe/H",
             }[long_species]
 
-            short_floortype = {"Lo": "lowfloor", "Hi": "highfloor",}[floor_type]
-            floor_value = {"Lo": "-4", "Hi": "-3",}[floor_type]
+            short_floortype = {"Lo": "lowfloor", "Hi": "highfloor"}[floor_type]
+            floor_value = {"Lo": "-4", "Hi": "-3"}[floor_type]
         except KeyError:
             raise RegistrationDoesNotMatchError
 
@@ -1482,7 +1481,7 @@ def registration_element_masses_in_stars(
 
     return
 
-    
+
 # TODO
 # lambda_B
 # q