search script NO_JIRA #82

kback-ccdc · 2025-07-18T15:22:09Z

Adding Chris Kingsbury's Void Search script to the opensource repo for next week's webinar

github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

flake8

🚫 [flake8] <302> _{reported by reviewdog 🐶}
expected 2 blank lines, found 1

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 134 in 92a57c4

def run_search(interface=None):

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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## open a GUI dialog asking for the search query.

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trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

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           interface.show_script_error('''Nothing was given to search for. Please enter either one number

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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query_report += f"Pore Total Surface Area (Å^2) {tsa[0]}-{tsa[1]} "

⚠️ [flake8] <293> _{reported by reviewdog 🐶}
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csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 182 in 92a57c4

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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           query_report +=  f"Pore Total Geometric Volume (&#8491;^3): {tgv[0]}-{tgv[1]} <br>"

🚫 [flake8] <231> _{reported by reviewdog 🐶}
missing whitespace after ','

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 189 in 92a57c4

pld = query_string_to_tuple(void_search_dict["pore_limiting_diameter"],200.0)

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multiple spaces after operator

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 190 in 92a57c4

query_report += f"Pore Limiting Diameter (Å): {pld[0]}-{pld[1]} "

🚫 [flake8] <231> _{reported by reviewdog 🐶}
missing whitespace after ','

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 194 in 92a57c4

pmd = query_string_to_tuple(void_search_dict["max_pore_diameter"],200.0)

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multiple spaces after operator

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 195 in 92a57c4

query_report += f"Pore Maximum Diameter (Å): {pmd[0]}-{pmd[1]} "

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missing whitespace after ','

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 199 in 92a57c4

npd = query_string_to_tuple(void_search_dict["num_percolated_dimensions"],3.1)

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multiple spaces after operator

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 200 in 92a57c4

query_report += f"Number of Percolated Dimensions: {npd[0]}-{npd[1]} "

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trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 211 in 92a57c4

"Pore Total Surface Area (\u212b^2)",

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trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

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'Chemical Name(s)',

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trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 230 in 92a57c4

tsv_file.write_row([h.identifier,

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csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 237 in 92a57c4

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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title="Voids_search",

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trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 251 in 92a57c4

More information on the pore calculations is available here:

[flake8] <401> _{reported by reviewdog 🐶}
'tkinter.Tk' imported but unused

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 34 in 92a57c4

from tkinter import Tk, Text, TOP, BOTH, X, N, LEFT, RIGHT

[flake8] <401> _{reported by reviewdog 🐶}
'tkinter.Text' imported but unused

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 34 in 92a57c4

from tkinter import Tk, Text, TOP, BOTH, X, N, LEFT, RIGHT

[flake8] <401> _{reported by reviewdog 🐶}
'tkinter.TOP' imported but unused

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 34 in 92a57c4

from tkinter import Tk, Text, TOP, BOTH, X, N, LEFT, RIGHT

[flake8] <401> _{reported by reviewdog 🐶}
'tkinter.N' imported but unused

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 34 in 92a57c4

from tkinter import Tk, Text, TOP, BOTH, X, N, LEFT, RIGHT

[flake8] <401> _{reported by reviewdog 🐶}
'tkinter.RIGHT' imported but unused

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 34 in 92a57c4

from tkinter import Tk, Text, TOP, BOTH, X, N, LEFT, RIGHT

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continuation line under-indented for visual indent

csd-python-api-scripts/scripts/voids_search/voids_search.py

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"total_geometric_volume": "Pore Total Geometric Volume (Å^3)",

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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"pore_limiting_diameter": "Pore Limiting Diameter (Å)",

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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"pore_limiting_diameter": "Pore Limiting Diameter (Å)",

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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"max_pore_diameter":"Pore Maximum Diameter (Å)",

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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"max_pore_diameter":"Pore Maximum Diameter (Å)",

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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"max_pore_diameter":"Pore Maximum Diameter (Å)",

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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"num_percolated_dimensions":"Number of Percolated Dimensions"}

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missing whitespace after ':'

csd-python-api-scripts/scripts/voids_search/voids_search.py

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"num_percolated_dimensions":"Number of Percolated Dimensions"}

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csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 43 in 92a57c4

class VoidDialog(Frame):

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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           [self.generate_entry(text, output) for text,output in zip(pore_query_dict.values(), self.outputs)]

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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vars = {k:v for k,v in zip(pore_query_dict.keys(), app.outputs)}

🚫 [flake8] <231> _{reported by reviewdog 🐶}
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csd-python-api-scripts/scripts/voids_search/voids_search.py

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vars = {k:v for k,v in zip(pore_query_dict.keys(), app.outputs)}

🚫 [flake8] <722> _{reported by reviewdog 🐶}
do not use bare 'except'

csd-python-api-scripts/scripts/voids_search/voids_search.py

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except:

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unexpected spaces around keyword / parameter equals

csd-python-api-scripts/scripts/voids_search/voids_search.py

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def query_string_to_tuple(query_string, default_upper_limit = 9999.9):

🚫 [flake8] <251> _{reported by reviewdog 🐶}
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csd-python-api-scripts/scripts/voids_search/voids_search.py

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def query_string_to_tuple(query_string, default_upper_limit = 9999.9):

🚫 [flake8] <231> _{reported by reviewdog 🐶}
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csd-python-api-scripts/scripts/voids_search/voids_search.py

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elif query_string in ("0","0.0"):

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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🚫 [flake8] <225> _{reported by reviewdog 🐶}
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csd-python-api-scripts/scripts/voids_search/voids_search.py

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if ll!="":

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trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

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lower_limit = 0.0

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csd-python-api-scripts/scripts/voids_search/voids_search.py

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if ul!="":

⚠️ [flake8] <293> _{reported by reviewdog 🐶}
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csd-python-api-scripts/scripts/voids_search/voids_search.py

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🚫 [flake8] <302> _{reported by reviewdog 🐶}
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csd-python-api-scripts/scripts/voids_search/voids_search.py

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def convert_to_ascii(text):

🚫 [flake8] <302> _{reported by reviewdog 🐶}
expected 2 blank lines, found 1

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 134 in 92a57c4

def run_search(interface=None):

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csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 163 in 92a57c4

🚫 [flake8] <266> _{reported by reviewdog 🐶}
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csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 164 in 92a57c4

## open a GUI dialog asking for the search query.

⚠️ [flake8] <291> _{reported by reviewdog 🐶}
trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

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           interface.show_script_error('''Nothing was given to search for. Please enter either one number

⚠️ [flake8] <293> _{reported by reviewdog 🐶}
blank line contains whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 176 in 92a57c4

🚫 [flake8] <222> _{reported by reviewdog 🐶}
multiple spaces after operator

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 180 in 92a57c4

query_report += f"Pore Total Surface Area (Å^2) {tsa[0]}-{tsa[1]} "

⚠️ [flake8] <293> _{reported by reviewdog 🐶}
blank line contains whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 182 in 92a57c4

🚫 [flake8] <222> _{reported by reviewdog 🐶}
multiple spaces after operator

csd-python-api-scripts/scripts/voids_search/voids_search.py

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           query_report +=  f"Pore Total Geometric Volume (&#8491;^3): {tgv[0]}-{tgv[1]} <br>"

🚫 [flake8] <231> _{reported by reviewdog 🐶}
missing whitespace after ','

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 189 in 92a57c4

pld = query_string_to_tuple(void_search_dict["pore_limiting_diameter"],200.0)

🚫 [flake8] <222> _{reported by reviewdog 🐶}
multiple spaces after operator

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 190 in 92a57c4

query_report += f"Pore Limiting Diameter (Å): {pld[0]}-{pld[1]} "

🚫 [flake8] <231> _{reported by reviewdog 🐶}
missing whitespace after ','

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 194 in 92a57c4

pmd = query_string_to_tuple(void_search_dict["max_pore_diameter"],200.0)

🚫 [flake8] <222> _{reported by reviewdog 🐶}
multiple spaces after operator

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 195 in 92a57c4

query_report += f"Pore Maximum Diameter (Å): {pmd[0]}-{pmd[1]} "

🚫 [flake8] <231> _{reported by reviewdog 🐶}
missing whitespace after ','

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 199 in 92a57c4

npd = query_string_to_tuple(void_search_dict["num_percolated_dimensions"],3.1)

🚫 [flake8] <222> _{reported by reviewdog 🐶}
multiple spaces after operator

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 200 in 92a57c4

query_report += f"Number of Percolated Dimensions: {npd[0]}-{npd[1]} "

⚠️ [flake8] <291> _{reported by reviewdog 🐶}
trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 211 in 92a57c4

"Pore Total Surface Area (\u212b^2)",

⚠️ [flake8] <291> _{reported by reviewdog 🐶}
trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 216 in 92a57c4

'Chemical Name(s)',

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trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 230 in 92a57c4

tsv_file.write_row([h.identifier,

⚠️ [flake8] <293> _{reported by reviewdog 🐶}
blank line contains whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 237 in 92a57c4

⚠️ [flake8] <291> _{reported by reviewdog 🐶}
trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 247 in 92a57c4

title="Voids_search",

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trailing whitespace

csd-python-api-scripts/scripts/voids_search/voids_search.py

Line 251 in 92a57c4

More information on the pore calculations is available here:

pmbulit · 2025-07-18T15:45:59Z

@kback-ccdc could you add a ReadMe.md to this folder so it follows the same requirements as the rest of the scripts on this repo and then also edit https://github.com/ccdc-opensource/csd-python-api-scripts/blob/main/scripts/ReadMe.md with a short description please?

pmbulit · 2025-07-18T15:51:12Z

scripts/voids_search/voids_search.py

+    elif query_string in ("0","0.0"):
+        ll, ul = 0.0, 0.1
+    else:
+        ll, ul = float(query_string)*0.95, float(query_string)*1.05


I think this shouldn't apply to percolated dimensions

Agree - I'll add something. It's still going to be that way under the hood - just makes it easier than figuring out inclusive / exclusive ranges in sql, but the report will be clean

pmbulit

One minor request for now. If the ReadMe has additional info on expected behaviour I might have more comments

…ou check this is what you were try/excepting for, testing seems fine NO_JIRA

basic Readme added, Pablo, please have a look and feel free to raise request again

lines 201 - 204 , searches the right field now, and all have rounding included

sonarqubecloud · 2025-07-21T12:49:43Z

Quality Gate passed

Issues
3 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

IsaacSugden

Looks good and fairly well tested by me. CK says he wants to add something for percolated dimensions at Pablo's request, but I'd be happy to merge before the webinar and add stuff like that later

search script NO_JIRA

92a57c4

kback-ccdc requested review from Alex-AMC, IsaacSugden and pmbulit July 18, 2025 15:22

kback-ccdc self-assigned this Jul 18, 2025

github-actions bot reviewed Jul 18, 2025

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kback-ccdc assigned ckingsbury-ccdc Jul 18, 2025

SonarCloud nagging about order NO_JIRA

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pmbulit reviewed Jul 18, 2025

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pmbulit previously requested changes Jul 18, 2025

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IsaacSugden added 6 commits July 18, 2025 16:55

Robots NO_JIRA

045beda

SonarCloud medium issue NO_JIRA

fdbe8c0

changing bare except to checking if destroy is necessary, Chris can y…

c50822d

…ou check this is what you were try/excepting for, testing seems fine NO_JIRA

SonarCloud NO_JIRA

e6b697c

basic Readme added NO_JIRA

97a5edc

updating top Readme.md NO_JIRA

2a30699

ckingsbury-ccdc and others added 2 commits July 20, 2025 23:18

Update voids_search.py CJK fixes for Pablo NO_JIRA

8b0bb9b

lines 201 - 204 , searches the right field now, and all have rounding included

Robots and typo NO_JIRA

8a8dfef

IsaacSugden approved these changes Jul 21, 2025

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kback-ccdc merged commit 741178f into main Jul 21, 2025
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