[GSoC] Objective 1: Add metadata integration notebook and script #441

adel3li · 2025-03-27T06:14:37Z

✏️ Description

Type: 🚀 feature

This PR contributes a demonstration of Objective 1 from the GSoC 2025 project: Metadata Integration for Atomic Data in Carsus.

Simulates a Carsus-style levels DataFrame
Adds a metadata table with:
- DOI reference
- Units (eV)
- Timestamp
- Git commit hash
- Notes
Adds a citation table for A_ij and Υ_ij
Exports all to HDF5 using pandas.HDFStore
Includes both a notebook and a Python script version

🔖 Submitted as part of the GSoC application for the Carsus/TARDIS project.
I’m happy to iterate based on mentor feedback.

📎 Resources

notebooks/gsoc2025_metadata_objective1.ipynb – walkthrough notebook
examples/generate_metadata.py – script version
README.md – project context and summary

✅ Testing

Manual test: Executed both the notebook and script successfully
Verified HDF5 outputs and structure
Pipeline tests not applicable at this stage

✅ Checklist

I requested two reviewers for this pull request
I updated the documentation (README.md) with context
I am not authorized to build documentation, but can revise if needed

Please let me know if you'd like me to adapt this code structure to Carsus conventions or expand to other data tables.

review-notebook-app · 2025-03-27T06:14:42Z

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github-actions · 2025-03-27T06:15:04Z

*beep* *bop*
Hi human,
I ran ruff on the latest commit (c5787cb).
Here are the outputs produced.
Results can also be downloaded as artifacts here.
Summarised output:

90	    	[ ] syntax-error
5	E402	[ ] module-import-not-at-top-of-file
4	F401	[*] unused-import
3	F821	[ ] undefined-name
2	E722	[ ] bare-except

Complete output(might be large):

README.md:3:6: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:3:26: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:3:38: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:3:42: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:3:48: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:3:58: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:3:61: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:3:72: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:3:87: SyntaxError: Compound statements are not allowed on the same line as simple statements
README.md:3:95: SyntaxError: Expected 'in', found name
README.md:3:102: SyntaxError: Expected ':', found name
README.md:3:115: SyntaxError: Expected an expression
README.md:4:1: SyntaxError: Expected an expression
README.md:4:10: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:4:19: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:4:22: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:4:29: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:4:36: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:4:41: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:4:49: SyntaxError: Expected an identifier
README.md:4:51: SyntaxError: Expected an expression
README.md:8:3: SyntaxError: Expected an expression
README.md:8:5: SyntaxError: Got unexpected token `
README.md:8:50: SyntaxError: Got unexpected token `
README.md:8:51: SyntaxError: Expected an expression
README.md:8:55: SyntaxError: Expected an expression
README.md:9:1: SyntaxError: Unexpected indentation
README.md:9:5: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:9:13: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:9:22: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:9:30: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:9:34: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:9:37: SyntaxError: Expected an expression
README.md:10:14: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:10:21: SyntaxError: Got unexpected token `
README.md:10:28: SyntaxError: Got unexpected token `
README.md:11:12: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:11:21: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:11:31: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:11:54: SyntaxError: Expected ',', found 'and'
README.md:11:62: SyntaxError: Expected ',', found name
README.md:11:69: SyntaxError: Expected ',', found name
README.md:12:14: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:12:23: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:13:10: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:13:21: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:13:26: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:13:31: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:15:1: SyntaxError: Expected a statement
README.md:15:3: SyntaxError: Expected an expression
README.md:15:5: SyntaxError: Got unexpected token `
README.md:15:35: SyntaxError: Got unexpected token `
README.md:15:36: SyntaxError: Expected an expression
README.md:15:40: SyntaxError: Expected an expression
README.md:16:1: SyntaxError: Unexpected indentation
README.md:16:5: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:16:12: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:16:20: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:16:23: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:16:27: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:16:36: SyntaxError: Compound statements are not allowed on the same line as simple statements
README.md:16:76: SyntaxError: Expected ':', found name
README.md:16:85: SyntaxError: Expected an identifier
README.md:20:1: SyntaxError: Expected a statement
README.md:20:6: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:21:6: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:21:11: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:22:27: SyntaxError: Expected ',', found ':'
README.md:22:28: SyntaxError: Expected ',', found '//'
README.md:26:6: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:32: SyntaxError: Expected a statement
README.md:26:40: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:43: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:47: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:59: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:67: SyntaxError: Compound statements are not allowed on the same line as simple statements
README.md:26:78: SyntaxError: Expected 'in', found name
README.md:26:85: SyntaxError: Expected ':', found name
README.md:26:88: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:93: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:98: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:104: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:108: SyntaxError: Simple statements must be separated by newlines or semicolons
README.md:26:116: SyntaxError: Expected an expression
README.md:27:1: SyntaxError: Expected an expression
README.md:27:12: SyntaxError: Compound statements are not allowed on the same line as simple statements
README.md:27:23: SyntaxError: Expected 'in', found name
README.md:27:28: SyntaxError: Got unexpected token –
README.md:27:45: SyntaxError: Expected an expression
README.md:27:46: SyntaxError: Expected an identifier
examples/generate_metadata.py:16:1: F821 Undefined name `get_ipython`
examples/generate_metadata.py:17:1: F821 Undefined name `get_ipython`
examples/generate_metadata.py:23:1: E402 Module level import not at top of file
examples/generate_metadata.py:24:1: E402 Module level import not at top of file
examples/generate_metadata.py:25:1: E402 Module level import not at top of file
examples/generate_metadata.py:26:1: E402 Module level import not at top of file
examples/generate_metadata.py:26:8: F401 [*] `os` imported but unused
examples/generate_metadata.py:27:1: E402 Module level import not at top of file
examples/generate_metadata.py:27:21: F401 [*] `pathlib.Path` imported but unused
examples/generate_metadata.py:55:5: E722 Do not use bare `except`
examples/generate_metadata.py:113:5: F821 Undefined name `display`
notebooks/gsoc2025_metadata_objective1.ipynb:cell 3:4:8: F401 [*] `os` imported but unused
notebooks/gsoc2025_metadata_objective1.ipynb:cell 3:5:21: F401 [*] `pathlib.Path` imported but unused
notebooks/gsoc2025_metadata_objective1.ipynb:cell 5:5:5: E722 Do not use bare `except`
Found 104 errors.
[*] 4 fixable with the `--fix` option.

adel3li · 2025-03-27T06:29:19Z

Hi @afloers @andrewfullard 👋

Following up on your email, @afloers — I'm submitting this PR as part of the first objective for the GSoC 2025 project: Metadata Integration for Atomic Data in Carsus.

This contribution includes:

✅ A Jupyter notebook demonstrating metadata integration (DOI, physical units, git commit, timestamp, notes) and citation tables
✅ Export to HDF5 using pandas.HDFStore
✅ A script version for automation (examples/generate_metadata.py)
✅ A README with a quick project summary

I'd be grateful for your feedback on structure, completeness, or anything you'd like to see improved or extended.
Also happy to pick up further tasks or issues to help shape the next steps of the project.

Thanks again for the guidance and support!

— Adel Ali

andrewfullard · 2025-03-28T16:09:26Z

This looks sensible to me. Please make an application.

Copilot

Pull Request Overview

This PR demonstrates the first objective of the GSoC 2025 project by simulating a Carsus-like atomic levels DataFrame, attaching detailed metadata, and exporting the results to an HDF5 file both via a Jupyter notebook and a standalone Python script.

Adds an examples/generate_metadata.py script that builds a metadata and citation table for atomic data
Updates the README.md to document the new metadata integration feature

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 4 comments.

File	Description
examples/generate_metadata.py	Script demonstrating metadata integration and HDF5 export
README.md	Documentation update introducing the metadata integration

Copilot · 2025-04-01T14:03:09Z

examples/generate_metadata.py

+get_ipython().system('pip install git+https://github.com/tardis-sn/carsus.git')
+get_ipython().system('pip install gitpython uncertainties')


Using get_ipython() to execute system commands may lead to errors when running this script outside of a notebook environment. Consider using subprocess.run or subprocess.check_call for reliability in a standalone script.

Suggested change

get_ipython().system('pip install git+https://github.com/tardis-sn/carsus.git')

get_ipython().system('pip install gitpython uncertainties')

subprocess.run(['pip', 'install', 'git+https://github.com/tardis-sn/carsus.git'], check=True)

subprocess.run(['pip', 'install', 'gitpython', 'uncertainties'], check=True)

Copilot · 2025-04-01T14:03:10Z

examples/generate_metadata.py

+get_ipython().system('pip install git+https://github.com/tardis-sn/carsus.git')
+get_ipython().system('pip install gitpython uncertainties')


Using get_ipython() to run installation commands may fail in non-notebook environments. It is recommended to replace these with subprocess-based calls for a more robust script execution.

Suggested change

get_ipython().system('pip install git+https://github.com/tardis-sn/carsus.git')

get_ipython().system('pip install gitpython uncertainties')

subprocess.run(['pip', 'install', 'git+https://github.com/tardis-sn/carsus.git'], check=True)

subprocess.run(['pip', 'install', 'gitpython', 'uncertainties'], check=True)

Copilot · 2025-04-01T14:03:10Z

examples/generate_metadata.py

+def get_git_commit():
+    try:
+        return subprocess.check_output(["git", "rev-parse", "HEAD"]).decode().strip()
+    except:


Avoid using a bare except clause; catch specific exceptions, e.g. subprocess.CalledProcessError, to improve error handling and debugging.

Suggested change

except:

except subprocess.CalledProcessError:

Copilot · 2025-04-01T14:03:11Z

examples/generate_metadata.py

+    print("Available datasets:")
+    print(store.keys())
+    print("\nMetadata preview:")
+    display(store["levels_metadata"])


The use of display() is specific to interactive environments like notebooks; if this script is intended for standalone execution, consider using print() or an alternative method to output metadata.

Suggested change

display(store["levels_metadata"])

print(store["levels_metadata"])

adel3li · 2025-04-06T19:02:53Z

Hi @andrewfullard 👋

Just wanted to follow up and share my final GSoC proposal, now officially submitted!

📄 Proposal:
(It includes a summary of this PR and a link to a more detailed version inside)

This opportunity is deeply important to me. I had to step away from college to support my family and worked my way back through self-learning and experience. Contributing to Carsus through GSoC would be a huge milestone in that journey.

Thank you again for your guidance and support 🙏
— Adel Ali

adel3li · 2025-04-09T09:48:15Z

Dear @andrewfullard ,

Quick note: I submitted my GSoC application but mistakenly uploaded the wrong proposal file under the Carsus project slot. The selected project is correct, and this PR is part of it — but the file doesn’t match. I’ve contacted GSoC support and shared the correct proposal with you via email.

This project truly means a lot to me, and I hope the actual work done here can still be considered.

— Adel Ali

[GSoC] Objective 1: Add metadata integration notebook and script

c5787cb

andrewfullard added the gsoc label Mar 28, 2025

wkerzendorf requested a review from Copilot April 1, 2025 14:01

Copilot AI reviewed Apr 1, 2025

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[GSoC] Objective 1: Add metadata integration notebook and script #441

[GSoC] Objective 1: Add metadata integration notebook and script #441

adel3li commented Mar 27, 2025 •

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		get_ipython().system('pip install git+https://github.com/tardis-sn/carsus.git')
		get_ipython().system('pip install gitpython uncertainties')

	display(store["levels_metadata"])
	print(store["levels_metadata"])

[GSoC] Objective 1: Add metadata integration notebook and script #441

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[GSoC] Objective 1: Add metadata integration notebook and script #441

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adel3li commented Mar 27, 2025 • edited Loading

✏️ Description

📎 Resources

✅ Testing

✅ Checklist

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Pull Request Overview

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