skpkg: apply black line-length 115 to all files in the project directory by dabeycorn · Pull Request #35 · diffpy/diffpy.nmf_mapping · GitHub
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skpkg: apply black line-length 115 to all files in the project directory #35

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Merged
sbillinge merged 2 commits into from
Jun 28, 2025
Merged

skpkg: apply black line-length 115 to all files in the project directory #35

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a20d312
skpkg: apply black to all files in the project dir
dabeycorn Jun 27, 2025
1eb4bd6
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Jun 27, 2025
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31 changes: 21 additions & 10 deletions .github/ISSUE_TEMPLATE/release_checklist.md
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18 changes: 16 additions & 2 deletions doc/source/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -221,7 +221,13 @@
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
("index", "diffpy.nmf_mapping.tex", "diffpy.nmf_mapping Documentation", ab_authors, "manual"),
(
"index",
"diffpy.nmf_mapping.tex",
"diffpy.nmf_mapping Documentation",
ab_authors,
"manual",
),
]

# The name of an image file (relative to this directory) to place at the top of
Expand Down Expand Up @@ -249,7 +255,15 @@

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [("index", "diffpy.nmf_mapping", "diffpy.nmf_mapping Documentation", ab_authors, 1)]
man_pages = [
(
"index",
"diffpy.nmf_mapping",
"diffpy.nmf_mapping Documentation",
ab_authors,
1,
)
]

# If true, show URL addresses after external links.
# man_show_urls = False
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3 changes: 1 addition & 2 deletions src/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,7 @@
#
##############################################################################

"""nmf_mapping - tools for performing NMF on PDF and XRD data.
"""
"""nmf_mapping - tools for performing NMF on PDF and XRD data."""


__import__("pkg_resources").declare_namespace(__name__)
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65 changes: 48 additions & 17 deletions src/diffpy/nmf_mapping/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,11 @@ def main(args=None):
as well as the reconstruction error as a fxn of component
"""

parser = ArgumentParser(prog="nmf_mapping", description=_BANNER, formatter_class=RawTextHelpFormatter)
parser = ArgumentParser(
prog="nmf_mapping",
description=_BANNER,
formatter_class=RawTextHelpFormatter,
)

def tup(s):
if not isinstance(s, str):
Expand All @@ -45,7 +49,10 @@ def tup(s):

# args
parser.add_argument(
"directory", default=None, type=str, help="a directory of PDFs to calculate NMF decomposition"
"directory",
default=None,
type=str,
help="a directory of PDFs to calculate NMF decomposition",
)
group = parser.add_mutually_exclusive_group()
parser.add_argument(
Expand Down Expand Up @@ -105,25 +112,37 @@ def tup(s):
nargs="*",
help="the x-range over which to calculate NMF, can be multiple ranges (e.g. --xrange 5,10 12,15)",
)
parser.add_argument("--show", default=True, type=boolean_string, help="whether to show the plot")
parser.add_argument(
"--show",
default=True,
type=boolean_string,
help="whether to show the plot",
)
args0 = Namespace()
args1, _ = parser.parse_known_args(args, namespace=args0)

input_list, data_list = nmf.load_data(args1.directory, args1.xrd)
if args1.pca_thresh:
df_components, df_component_weight_timeseries, df_reconstruction_error, df_explained_var_ratio = (
nmf.NMF_decomposition(
input_list,
args1.xrange,
args1.threshold,
additional_comp=False,
improve_thresh=args1.improve_thresh,
n_iter=args1.n_iter,
pca_thresh=args1.pca_thresh,
)
(
df_components,
df_component_weight_timeseries,
df_reconstruction_error,
df_explained_var_ratio,
) = nmf.NMF_decomposition(
input_list,
args1.xrange,
args1.threshold,
additional_comp=False,
improve_thresh=args1.improve_thresh,
n_iter=args1.n_iter,
pca_thresh=args1.pca_thresh,
)
else:
df_components, df_component_weight_timeseries, df_reconstruction_error = nmf.NMF_decomposition(
(
df_components,
df_component_weight_timeseries,
df_reconstruction_error,
) = nmf.NMF_decomposition(
input_list,
args1.xrange,
args1.threshold,
Expand All @@ -149,7 +168,11 @@ def tup(s):
os.path.join(os.getcwd(), "nmf_result", "component_index_vs_pratio_col.json")
)
df_component_weight_timeseries.to_csv(
os.path.join(os.getcwd(), "nmf_result", output_fn + "component_row_pratio_col.txt"),
os.path.join(
os.getcwd(),
"nmf_result",
output_fn + "component_row_pratio_col.txt",
),
header=None,
index=False,
sep=" ",
Expand Down Expand Up @@ -196,7 +219,11 @@ def tup(s):

if args1.xrd:
np.savetxt(
os.path.join(os.getcwd(), "nmf_result", output_fn + f"_comp{i}" + ".xy"),
os.path.join(
os.getcwd(),
"nmf_result",
output_fn + f"_comp{i}" + ".xy",
),
data,
header=f"NMF Generated XRD\nSource = nmfMapping\n"
f"Date = {output_fn}\n{args1.x_units} Intensity\n",
Expand All @@ -205,7 +232,11 @@ def tup(s):
)
else:
np.savetxt(
os.path.join(os.getcwd(), "nmf_result", output_fn + f"_comp{i}" + ".cgr"),
os.path.join(
os.getcwd(),
"nmf_result",
output_fn + f"_comp{i}" + ".cgr",
),
data,
header=f"NMF Generated PDF\nSource: nmfMapping\n" f"Date: {output_fn}\nr g",
fmt="%s",
Expand Down
27 changes: 23 additions & 4 deletions src/diffpy/nmf_mapping/nmf_mapping_code.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,13 @@ def load_data(dir, xrd=False):

# TODO Add regularization on the frobenius norm in order to prevent creation of an excessive number of components
def NMF_decomposition(
data_arr, x_range=None, thresh=None, additional_comp=False, improve_thresh=None, n_iter=None, pca_thresh=None
data_arr,
x_range=None,
thresh=None,
additional_comp=False,
improve_thresh=None,
n_iter=None,
pca_thresh=None,
):
"""
Takes a 3D array of PDFs and returns the structurally significant
Expand Down Expand Up @@ -208,8 +214,17 @@ def NMF_decomposition(
df_component_weight_timeseries = pd.DataFrame(nmf_weight, index=range(n_comp))

if pca_thresh:
return df_components, df_component_weight_timeseries, df_reconstruction_error, df_explained_var_ratio
return df_components, df_component_weight_timeseries, df_reconstruction_error
return (
df_components,
df_component_weight_timeseries,
df_reconstruction_error,
df_explained_var_ratio,
)
return (
df_components,
df_component_weight_timeseries,
df_reconstruction_error,
)


def component_plot(df_components, xrd=False, x_units=None, show=True):
Expand Down Expand Up @@ -244,7 +259,11 @@ def component_plot(df_components, xrd=False, x_units=None, show=True):
shift = max_range
# seq to align with input phase
for i, s in enumerate(data_list):
ax.plot(df.index.to_numpy(dtype=np.single), df[s].to_numpy() + i * shift, label=s)
ax.plot(
df.index.to_numpy(dtype=np.single),
df[s].to_numpy() + i * shift,
label=s,
)
ax.legend(loc="best")
if xrd:
if x_units == "twotheta" or x_units == "ttheta":
Expand Down
3 changes: 1 addition & 2 deletions src/diffpy/version.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,7 @@
#
##############################################################################

"""Definition of __version__ and __date__ for diffpy.nmf_mapping.
"""
"""Definition of __version__ and __date__ for diffpy.nmf_mapping."""

__id__ = "$Id$"

Expand Down
6 changes: 5 additions & 1 deletion tests/test_NMF_analysis_code.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,11 @@
test_map = [
([data_dir, "--xrange", "5,10"], "output_1", "Number of components: 3\n"),
([data_dir], "output_2", "Number of components: 3\n"),
([data_dir, "--xrange", "5,10", "12,15"], "output_3", "Number of components: 3\n"),
(
[data_dir, "--xrange", "5,10", "12,15"],
"output_3",
"Number of components: 3\n",
),
]


Expand Down
3 changes: 1 addition & 2 deletions tests/test_version.py
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