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report on repo #56

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merged 13 commits into from
Apr 17, 2024
Merged

report on repo #56

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8bd36ed
report on repo
abhicodes369 Mar 8, 2024
6d210a0
created wrapper column
abhicodes369 Mar 10, 2024
58a423e
Delete local.env.example
abhicodes369 Mar 10, 2024
6c1b907
Delete .gitignore
abhicodes369 Mar 10, 2024
321fa55
Adding recovered .gitignore file
abhicodes369 Mar 10, 2024
cf05312
added a new column in the csv file . please tell me if there are any …
abhicodes369 Mar 15, 2024
baf5d4a
added a new column in the csv file please tell me if there are any mo…
abhicodes369 Mar 15, 2024
d7df0ca
added a new column to csv and modified python file
abhicodes369 Mar 15, 2024
992147d
Refactor column names in repostatus.py and combined_report.html
abhicodes369 Apr 11, 2024
6ab39b5
Add zenodo-get, sphinx, and sphinx_rtd_theme to requirements.txt
abhicodes369 Apr 16, 2024
06167e7
Merge branch 'main' into created_repostatus/statistics
abhicodes369 Apr 16, 2024
4a148b8
wrap the html into a function
abhicodes369 Apr 16, 2024
e17a3e7
Merge branch 'created_repostatus/statistics' of https://github.com/ab…
abhicodes369 Apr 16, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -16,3 +16,4 @@ bvals.txt
nosetests.xml
coverage.xml
*.pyc
local.env
126 changes: 126 additions & 0 deletions combined_report.html
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This should go into the website folder. Another PR is also creating files there.

Original file line number Diff line number Diff line change
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<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th>Technique</th>
<th>Subfolder</th>
<th>Contributors</th>
<th>Tested</th>
</tr>
</thead>
<tbody>
<tr>
<td>IVIM</td>
<td>OGC_AmsterdamUMC</td>
<td>Oliver Gurney-Champion</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>OGC_AmsterdamUMC</td>
<td>Oliver Gurney-Champion</td>
<td>Yes</td>
</tr>
<tr>
<td>Tri-exponential</td>
<td>OGC_AmsterdamUMC</td>
<td>Oliver Gurney-Champion</td>
<td>Yes</td>
</tr>
<tr>
<td>Tri-exponential</td>
<td>OGC_AmsterdamUMC</td>
<td>Oliver Gurney-Champion</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>OGC_AmsterdamUMC</td>
<td>Oliver Gurney-Champion/Sebastiano Barbieri</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>PvH_KB_NKI</td>
<td>Petra van Houdt/Stefan Zijlema/Koen Baas</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>PV_MUMC</td>
<td>Paulien Voorter</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>IAR_LundUniversity</td>
<td>Ivan A. Rashid</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>IAR_LundUniversity</td>
<td>Ivan A. Rashid</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>IAR_LundUniversity</td>
<td>Ivan A. Rashid</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>IAR_LundUniversity</td>
<td>Ivan A. Rashid</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>IAR_LundUniversity</td>
<td>Farooq et al. Modified by Ivan A. Rashid</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>IAR_LundUniversity</td>
<td>Fadnavis et al. Modified by Ivan A. Rashid</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>IAR_LundUniversity</td>
<td>Modified by Ivan A. Rashid</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>IAR_LundUniversity</td>
<td>Modified by Ivan A. Rashid</td>
<td>Yes</td>
</tr>
<tr>
<td>IVIM</td>
<td>OJ_GU</td>
<td>Oscar Jalnefjord</td>
<td>No</td>
</tr>
<tr>
<td>IVIM</td>
<td>OJ_GU</td>
<td>Oscar Jalnefjord</td>
<td>No</td>
</tr>
<tr>
<td>IVIM</td>
<td>OJ_GU</td>
<td>Oscar Jalnefjord</td>
<td>No</td>
</tr>
<tr>
<td>IVIM</td>
<td>ETP_SRI</td>
<td>Eric Peterson</td>
<td>Yes</td>
</tr>
</tbody>
</table>
3 changes: 3 additions & 0 deletions local.env.example
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What is the idea behind setting these variables? You should be able to get the repository location from the location of the file, e.g. using the __file__ variable.

Original file line number Diff line number Diff line change
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REPO_DIR=/path/to/your/repo
CODE_CONTRIBUTIONS_FILE=/path/to/your/code_contributions_record.csv
ALGORITHMS_FILE=/path/to/your/algorithms.json
37 changes: 37 additions & 0 deletions repostatus.py
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This should move somewhere else. Probably utilities/repository or something.

Original file line number Diff line number Diff line change
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import os
import pandas as pd
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Pandas caused the test failure. It should be in the requirements.

from dotenv import load_dotenv
import json

# Load environment variables
load_dotenv(r'C:\Users\home\tf2.4\TF2.4_IVIM-MRI_CodeCollection\local.env')
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We should be able to get around hard coding paths. This won't work for me, for example.


# Read the CSV file
csv_file_path = os.getenv('CODE_CONTRIBUTIONS_FILE')
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Looking through the code I realize that your table is missing a column, wrapped. In the issue thread I mentioned parsing the files in the folders which isn't being done here, and that's what is missing. It should parse the wrapper folder to find which algorithms are wrapped.

And there I also mentioned double checking the code contributions against what is in the source folder.

So the source code folder and code contribution file should match. If not it would be nice to note that. That should be a superset of the wrapped code list. And that should be a superset of the tested code list. If anything doesn't match that logic then we should note it in the html or printing a message.

df = pd.read_csv(csv_file_path)

unique_subfolders = df['subfolder'].unique().tolist()

# Read the JSON file
algorithms_file_path = os.getenv('ALGORITHMS_FILE')
with open(algorithms_file_path, 'r') as f:
algorithms_data = json.load(f)

# Get a list of all algorithms from the JSON file
all_algorithms = algorithms_data['algorithms']

# Add a new column 'Tested' to the DataFrame if it starts with that of subfolder
df['Tested'] = df.apply(lambda row: 'Yes' if any(algorithm.startswith(row['subfolder'].split('_')[0]) for algorithm in all_algorithms) else 'No', axis=1)

# Select the desired columns
df_selected = df[['Technique', 'subfolder', 'Authors', 'Tested']]
df_selected.columns = ['Technique', 'Subfolder', 'Contributors', 'Tested']

# Convert the DataFrame to HTML
html_string = df_selected.to_html(index=False)

# Save the HTML to a file
with open('combined_report.html', 'w') as f:
f.write(html_string)
# printing message that report have been succesfully generated
print("Combined HTML report generated successfully.")
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