Merge pull request #2 from bobleesj/flake8

Cookiecutter pre-commit workflow (except flake8)

.gitignore

@@ -20,4 +20,4 @@ lib
 lib64
 eggs
 parts
-.installed.cfg
+.installed.cfg

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+default_language_version:
+    python: python3
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit hooks
+    autofix_prs: true
+    autoupdate_branch: 'pre-commit-autoupdate'
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+    skip: [no-commit-to-branch]
+    submodules: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: '\.(rst|txt)$'
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        name: Prevent Commit to Main Branch
+        args: ["--branch", "main"]
+        stages: [pre-commit]

.travis.yml

@@ -33,4 +33,3 @@ script:
 
 notifications:
   email: false
-

AUTHORS.txt

@@ -1,2 +1,2 @@
 Simon J. L. Billinge <[email protected]>
-Zachary A. Thatcher<[email protected]>
+Zachary A. Thatcher<[email protected]>

CHANGELOG.rst

@@ -1 +0,0 @@
-

LICENSE.txt

@@ -30,4 +30,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -23,36 +23,36 @@ Input:
     - format: string (filepath)
         - eg: '/Users/zthatcher/Desktop/Data/nmf_mapping/time_data/' or . for cwd
 
-- save-files (optional): boolean as to whether or not you would like to save the dataframes, plots, and 
+- save-files (optional): boolean as to whether or not you would like to save the dataframes, plots, and
 components (note: pdf data saves as .cgr and xrd data saves as .xy)
     - format: boolean
         - eg: --save-files False
     - default: True
-    
+
 - threshold (optional and mut-exc to other thresholds): a threshold for the number of structural phases graphed (NMF components returned)
     - format as: integer
         - eg: --threshold 2
     - default: 10
-    
+
 - improve-thresh (optional and mut-exc to other thresholds): a threshold (between 0 and 1) for the relative improvement ratio necessary to
   add an additional component. Default is 0.001. 0.1 Recommended for real data.
     - format: float
         - eg: --improve-thresh 0.1
     - default = 0.001
-    
+
 - pca-thresh (optional and mut-exc to other thresholds): explained variance threshold for PCA component counting cutoff
     - format: float
         - eg: --pca-thresh 0.95
     - default = None
-    
+
 - n-iter (optional): total number of iterations to run NMF algo. Defaults to 1000. 10000 typical to publish.
     - format: int
         - eg: --n-iter 10000
     - default: 1000
 
-- x-range (optional): the active x-range over which to run the NMF analysis (must be between shortest and 
+- x-range (optional): the active x-range over which to run the NMF analysis (must be between shortest and
 longest range in the set of files)
-    - format: pair of integers representing the lower r bound and the upper r bound with a comma between 
+    - format: pair of integers representing the lower r bound and the upper r bound with a comma between
     the lower and upper bound
         -  eg: --xrange 5,10 12,15
     - default: entire range
@@ -71,7 +71,7 @@ longest range in the set of files)
     - format: boolean
         - eg: --show False
     - default: True
-    
+
 Returns:
 - Figure One: PDF or XRD pattern of structural phase components contributing to the NMF reconstruction
 - Figure Two: Weights of the phase components plotted in Figure One
@@ -81,4 +81,3 @@ Returns:
 Example:
 
 nmf_mapping . --threshold 3 --xrange 5,10 --show True
-

diffpy/nmf_mapping/nmf_mapping/main.py

@@ -1,12 +1,13 @@
 import os
 import sys
-from argparse import ArgumentParser, RawTextHelpFormatter, Namespace
 import time
+from argparse import ArgumentParser, Namespace, RawTextHelpFormatter
 from datetime import datetime
 
-from diffpy.nmf_mapping import nmf
 import numpy as np
 
+from diffpy.nmf_mapping import nmf
+
 
 def boolean_string(s):
     try:
@@ -24,9 +25,9 @@ def main(args=None):
     """
 
     _BANNER = """
-    This is a package which takes a directory of 1D diffraction files 
-    (xrd or pdf) and returns json files containing the decomposed components, 
-    the phase fraction of these components from file to file, 
+    This is a package which takes a directory of 1D diffraction files
+    (xrd or pdf) and returns json files containing the decomposed components,
+    the phase fraction of these components from file to file,
     as well as the reconstruction error as a fxn of component
     """
 

diffpy/nmf_mapping/nmf_mapping/nmf_mapping_code.py

@@ -3,22 +3,23 @@
 Local NMF Analysis of PDFs for PDFitc.
 """
 
-import numpy as np
-import pandas as pd
 from pathlib import Path
+
 import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
 
 try:
     from bg_mpl_stylesheet.bg_mpl_stylesheet import bg_mpl_style
 except ImportError:
     print("bg_mpl_style not found. Using generic matplotlib style.")
+import re
+import warnings
+
 from diffpy.utils.parsers.loaddata import loadData
 from scipy import interpolate
 from sklearn.decomposition import NMF, PCA
 from sklearn.exceptions import ConvergenceWarning
-import re
-
-import warnings
 
 warnings.filterwarnings("ignore", category=FutureWarning)
 warnings.filterwarnings("ignore", category=ConvergenceWarning)

diffpy/nmf_mapping/tests/data/different_r_grid/DIPA-H2O_3mmglass_20190908-061431_e3086a_0001_dark_corrected_img.gr

@@ -3,7 +3,7 @@
 wavelength = 0.1845
 dataformat = QA
 inputfile = DIPA-H2O_3mmglass_20190908-061431_e3086a_0001_dark_corrected_img.chi
-backgroundfile = 
+backgroundfile =
 mode = xray
 bgscale = 0.0
 composition = C6N
@@ -19,7 +19,7 @@ rpoly = 0.9
 [Misc]
 inputdir = /Users/sst/project/cal_and_int/int_20190906/chi
 savedir = /Users/sst/project/analysis/19st_amine/data/DIPA-H2O_3temp
-backgroundfilefull = 
+backgroundfilefull =
 
 #### start data
 #S 1

diffpy/nmf_mapping/tests/data/example_phases/LiO2.cif

@@ -255,4 +255,4 @@ _atom_site_occupancy
 _atom_site_attached_hydrogens
 O1 O2- 4 a 0 0 0 0.40(1) 1. 0
 Li1 Li1+ 8 c 0.25 0.25 0.25 0.74(2) 1. 0
-#End of TTdata_54368-ICSD
+#End of TTdata_54368-ICSD

diffpy/nmf_mapping/tests/data/example_phases/RuO2_tetragonal.cif

@@ -69,4 +69,4 @@ _atom_site_occupancy
 _atom_site_attached_hydrogens
 Ru1 Ru4+ 2 a 0 0 0 0.384 1. 0
 O1 O2- 4 f 0.3058(16) 0.3058(16) 0 0.517 1. 0
-#End of TTdata_15071-ICSD
+#End of TTdata_15071-ICSD

diffpy/nmf_mapping/tests/output/output_1/component_index_vs_RE_value.json

@@ -1 +1 @@
-{"0":{"1":297.2320764418,"2":99.3169152025,"3":0.1930209752,"4":0.1930209752,"5":0.1930209752,"6":0.1930209752,"7":0.1930209752,"8":0.1930209752,"9":0.1930209752,"10":0.1930209752}}
+{"0":{"1":297.2320764418,"2":99.3169152025,"3":0.1930209752,"4":0.1930209752,"5":0.1930209752,"6":0.1930209752,"7":0.1930209752,"8":0.1930209752,"9":0.1930209752,"10":0.1930209752}}

diffpy/nmf_mapping/tests/output/output_1/component_index_vs_pratio_col.json

@@ -1 +1 @@
-{"0":{"0":0.1012347369,"1":0.0761357385,"2":0.8226295245},"1":{"0":0.1010235873,"1":0.0779591956,"2":0.8210172171},"2":{"0":0.0994416662,"1":0.0916204305,"2":0.8089379033},"3":{"0":0.0887636744,"1":0.1838339774,"2":0.7274023482},"4":{"0":0.0474476951,"1":0.5411997046,"2":0.4113526004},"5":{"0":0.0087175609,"1":0.8962651575,"2":0.0950172816},"6":{"0":0.0010510094,"1":0.9857832857,"2":0.0131657049},"7":{"0":0.0037712798,"1":0.9949611562,"2":0.0012675641},"8":{"0":0.0098830598,"1":0.9901169402,"2":0.0},"9":{"0":0.0189903523,"1":0.9810096477,"2":0.0},"10":{"0":0.0316610363,"1":0.9683389637,"2":0.0},"11":{"0":0.0486184937,"1":0.9513815063,"2":0.0},"12":{"0":0.070690848,"1":0.929309152,"2":0.0},"13":{"0":0.0987468127,"1":0.9012531873,"2":0.0},"14":{"0":0.1336502636,"1":0.8663497364,"2":0.0},"15":{"0":0.1761934011,"1":0.8238065989,"2":0.0},"16":{"0":0.2269939584,"1":0.7730060416,"2":0.0},"17":{"0":0.2863470819,"1":0.7136529181,"2":0.0},"18":{"0":0.3540301731,"1":0.6459659981,"2":0.0000038288},"19":{"0":0.4290746918,"1":0.5708935987,"2":0.0000317095},"20":{"0":0.5095924913,"1":0.4903292057,"2":0.000078303},"21":{"0":0.5927003213,"1":0.4071615954,"2":0.0001380833},"22":{"0":0.6746779849,"1":0.3251164016,"2":0.0002056135},"23":{"0":0.7514333455,"1":0.2482910397,"2":0.0002756149},"24":{"0":0.8192174853,"1":0.1804393879,"2":0.0003431268},"25":{"0":0.875377344,"1":0.1242187716,"2":0.0004038844},"26":{"0":0.9188519755,"1":0.0806931319,"2":0.0004548926},"27":{"0":0.9502096756,"1":0.0492958216,"2":0.0004945028},"28":{"0":0.9712444548,"1":0.0282325552,"2":0.00052299},"29":{"0":0.9843478389,"1":0.0151103201,"2":0.000541841},"30":{"0":0.9919161267,"1":0.0075306698,"2":0.0005532035},"31":{"0":0.9959607838,"1":0.0034798433,"2":0.0005593729},"32":{"0":0.9979554044,"1":0.0014823242,"2":0.0005622714},"33":{"0":0.9988599149,"1":0.0005766909,"2":0.0005633941},"34":{"0":0.9992355861,"1":0.0002007286,"2":0.0005636853},"35":{"0":0.9993777604,"1":0.0000584775,"2":0.0005637622},"36":{"0":0.9994265484,"1":0.0000096631,"2":0.0005637886},"37":{"0":0.9994402459,"1":0.0,"2":0.0005597541},"38":{"0":0.9994430456,"1":0.0,"2":0.0005569544},"39":{"0":0.9994437327,"1":0.0,"2":0.0005562673},"40":{"0":0.9994438838,"1":0.0,"2":0.0005561162},"41":{"0":0.9994439131,"1":0.0,"2":0.0005560869},"42":{"0":0.9994439181,"1":0.0,"2":0.0005560819},"43":{"0":0.9994439188,"1":0.0,"2":0.0005560812},"44":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"45":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"46":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"47":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"48":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"49":{"0":0.9994439189,"1":0.0,"2":0.0005560811}}
+{"0":{"0":0.1012347369,"1":0.0761357385,"2":0.8226295245},"1":{"0":0.1010235873,"1":0.0779591956,"2":0.8210172171},"2":{"0":0.0994416662,"1":0.0916204305,"2":0.8089379033},"3":{"0":0.0887636744,"1":0.1838339774,"2":0.7274023482},"4":{"0":0.0474476951,"1":0.5411997046,"2":0.4113526004},"5":{"0":0.0087175609,"1":0.8962651575,"2":0.0950172816},"6":{"0":0.0010510094,"1":0.9857832857,"2":0.0131657049},"7":{"0":0.0037712798,"1":0.9949611562,"2":0.0012675641},"8":{"0":0.0098830598,"1":0.9901169402,"2":0.0},"9":{"0":0.0189903523,"1":0.9810096477,"2":0.0},"10":{"0":0.0316610363,"1":0.9683389637,"2":0.0},"11":{"0":0.0486184937,"1":0.9513815063,"2":0.0},"12":{"0":0.070690848,"1":0.929309152,"2":0.0},"13":{"0":0.0987468127,"1":0.9012531873,"2":0.0},"14":{"0":0.1336502636,"1":0.8663497364,"2":0.0},"15":{"0":0.1761934011,"1":0.8238065989,"2":0.0},"16":{"0":0.2269939584,"1":0.7730060416,"2":0.0},"17":{"0":0.2863470819,"1":0.7136529181,"2":0.0},"18":{"0":0.3540301731,"1":0.6459659981,"2":0.0000038288},"19":{"0":0.4290746918,"1":0.5708935987,"2":0.0000317095},"20":{"0":0.5095924913,"1":0.4903292057,"2":0.000078303},"21":{"0":0.5927003213,"1":0.4071615954,"2":0.0001380833},"22":{"0":0.6746779849,"1":0.3251164016,"2":0.0002056135},"23":{"0":0.7514333455,"1":0.2482910397,"2":0.0002756149},"24":{"0":0.8192174853,"1":0.1804393879,"2":0.0003431268},"25":{"0":0.875377344,"1":0.1242187716,"2":0.0004038844},"26":{"0":0.9188519755,"1":0.0806931319,"2":0.0004548926},"27":{"0":0.9502096756,"1":0.0492958216,"2":0.0004945028},"28":{"0":0.9712444548,"1":0.0282325552,"2":0.00052299},"29":{"0":0.9843478389,"1":0.0151103201,"2":0.000541841},"30":{"0":0.9919161267,"1":0.0075306698,"2":0.0005532035},"31":{"0":0.9959607838,"1":0.0034798433,"2":0.0005593729},"32":{"0":0.9979554044,"1":0.0014823242,"2":0.0005622714},"33":{"0":0.9988599149,"1":0.0005766909,"2":0.0005633941},"34":{"0":0.9992355861,"1":0.0002007286,"2":0.0005636853},"35":{"0":0.9993777604,"1":0.0000584775,"2":0.0005637622},"36":{"0":0.9994265484,"1":0.0000096631,"2":0.0005637886},"37":{"0":0.9994402459,"1":0.0,"2":0.0005597541},"38":{"0":0.9994430456,"1":0.0,"2":0.0005569544},"39":{"0":0.9994437327,"1":0.0,"2":0.0005562673},"40":{"0":0.9994438838,"1":0.0,"2":0.0005561162},"41":{"0":0.9994439131,"1":0.0,"2":0.0005560869},"42":{"0":0.9994439181,"1":0.0,"2":0.0005560819},"43":{"0":0.9994439188,"1":0.0,"2":0.0005560812},"44":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"45":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"46":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"47":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"48":{"0":0.9994439189,"1":0.0,"2":0.0005560811},"49":{"0":0.9994439189,"1":0.0,"2":0.0005560811}}

diffpy/nmf_mapping/tests/output/output_2/component_index_vs_RE_value.json

@@ -1 +1 @@
-{"0":{"1":477.1151575591,"2":181.8950165697,"3":0.5234417462,"4":0.5234417462,"5":0.5234417462,"6":0.5234417462,"7":0.5234417462,"8":0.5234417462,"9":0.5234417462,"10":0.5234417462}}
+{"0":{"1":477.1151575591,"2":181.8950165697,"3":0.5234417462,"4":0.5234417462,"5":0.5234417462,"6":0.5234417462,"7":0.5234417462,"8":0.5234417462,"9":0.5234417462,"10":0.5234417462}}

diffpy/nmf_mapping/tests/output/output_2/component_index_vs_pratio_col.json

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