Black-formatted all files

sdi/__init__.py

@@ -9,7 +9,7 @@
 from .ref import ref
 from .secid import secid
 from .collate import collate
-from .snr_function import snr #New
+from .snr_function import snr  # New
 from . import test
 
 # in order to test click commands
@@ -20,7 +20,7 @@
 from .extract import extract_cmd as _extract_cmd
 from .subtract import subtract_cmd as _subtract_cmd
 from .collate import collate_cmd as _collate_cmd
-from .snr_function import snr_cmd as _snr_cmd #New
+from .snr_function import snr_cmd as _snr_cmd  # New
 from . import test_cmd
 
 _scidir = os.path.join(os.path.dirname(__file__), "test/fixtures/science")

sdi/_cli.py

@@ -5,12 +5,14 @@
 from functools import update_wrapper
 import click
 
+
 @click.group(chain=True)
 def cli():
     """
     Chains together pipeline commands.
     """
 
+
 @cli.resultcallback()
 def run_pipeline(operators):
     """
@@ -26,29 +28,35 @@ def run_pipeline(operators):
         # do necessary things on overall outputs
         pass
 
+
 def operator(func):
     """
     Decorator which wraps commands so that they return functions after being
     run by click.
     All of the returned functions are passed as an iterable
     into run_pipeline.
     """
+
     def new_func(*args, **kwargs):
         def operator(hduls):
             # args and kwargs are subcommand-specific
             return func(hduls, *args, **kwargs)
+
         return operator
 
     # basically return new_func, but better
     return update_wrapper(new_func, func)
 
+
 def generator(func):
     """
     Does what operator does, but for the first thing in the series, like
     opening the hduls.
     Works with sub-funcs that do not have 'hduls' as the first argument.
     """
+
     def new_func(hduls, *args, **kwargs):
         yield from hduls
         yield from func(*args, **kwargs)
+
     return operator(update_wrapper(new_func, func))

sdi/align.py

@@ -10,72 +10,84 @@
 import click
 import numpy as np
 from astropy.io.fits import CompImageHDU
-#from sources import Source
+
+# from sources import Source
 import astroalign
-from .snr_function import snr 
-#from _scripts import snr
+from .snr_function import snr
+
+# from _scripts import snr
 from . import _cli as cli
 
+
 def align(hduls, name="SCI", ref=None):
     """
     Aligns the source astronomical image(s) to the reference astronomical image
     \b
     :param hduls: list of fitsfiles
     :param name: header containing image data.
-    :param reference: index of desired 
+    :param reference: index of desired
     :return: list of FITS files with <name> HDU aligned
     """
 
     hduls_list = [hdul for hdul in hduls]
     outputs = []
 
-    hduls_list = snr(hduls_list,name) #SNR function appends snr to each hdul's "CAT" table.
-    hduls_list = list(hduls_list) #convert generator to list.
+    hduls_list = snr(
+        hduls_list, name
+    )  # SNR function appends snr to each hdul's "CAT" table.
+    hduls_list = list(hduls_list)  # convert generator to list.
 
-    if ref is None: #No reference index given. we establish reference based on best signal to noise ratio
+    if (
+        ref is None
+    ):  # No reference index given. we establish reference based on best signal to noise ratio
 
-        reference = hduls_list[0][name] #0th index reference is used by default
+        reference = hduls_list[0][name]  # 0th index reference is used by default
         ref_SNR = hduls_list[0]["CAT"].header["SNR"]
 
-        for hdul in hduls_list: #loops though hdul lists finding the hdul with greatest snr
-            if hdul["CAT"].header["SNR"] > ref_SNR: #compares SNR value of current hdul to ref
+        for (
+            hdul
+        ) in hduls_list:  # loops though hdul lists finding the hdul with greatest snr
+            if (
+                hdul["CAT"].header["SNR"] > ref_SNR
+            ):  # compares SNR value of current hdul to ref
                 ref_SNR = hdul["CAT"].header["SNR"]
         reference = hdul[name]
 
-    else: #ref index is provided
+    else:  # ref index is provided
         reference = hduls_list[ref][name]
 
     try:
         ref_data = reference.data
     except AttributeError:
-        print("The reference file have doesn't have Attribute: Data") 
+        print("The reference file have doesn't have Attribute: Data")
         pass
 
-    for i,hdul in enumerate(hduls_list):
+    for i, hdul in enumerate(hduls_list):
         np_src = hdul[name]
-         
+
         # possibly unneccessary but unsure about scoping
         output = np.array([])
-        
+
         try:
-            output = astroalign.register(np_src,ref_data)[0]
+            output = astroalign.register(np_src, ref_data)[0]
         except ValueError:
             np_src = hdul[name].data.byteswap().newbyteorder()
             output = astroalign.register(np_src, ref_data)[0]
             pass
 
-        if hasattr(hdul[name], "data"): 
+        if hasattr(hdul[name], "data"):
             idx = hdul.index_of(name)
             hdul[idx].data = output
-            hdul[idx].header['EXTNAME'] = ("ALGN    ")
-            hdul[idx].header = reference.header #hdul['sci'].header = reference.header
-            
+            hdul[idx].header["EXTNAME"] = "ALGN    "
+            hdul[idx].header = reference.header  # hdul['sci'].header = reference.header
+
     return (hdul for hdul in hduls_list)
 
+
 @cli.cli.command("align")
 @click.option("-n", "--name", default="SCI", help="The HDU to be aligned.")
 @cli.operator
-#TODO use CAT sources if they exist
+# TODO use CAT sources if they exist
 
 ## align function wrapper
 def align_cmd(hduls, name="SCI", ref=None):