support column format

[dodu94]

Description

Support column format in MCNP. Something like:

wwe:p    1.e-6 1.e-5 1.e-4 .001 .01 .1    16.
    #     wwn1:p    wwn2:p    wwn3:p    wwn4:p    wwn5:p    wwn6:p    wwn7:p
          1  3.54E+00  2.35E+00  7.93E-01  5.00E-01  5.58E-01  1.29E+00  5.00E-01
          2  4.00E+00  0.00E+00  1.18E+00  4.66E-01  6.17E-01  1.75E+00  4.00E+00
          3  4.00E+00  0.00E+00  1.21E+00  5.83E-01  5.82E-01  1.98E+00  4.00E+00

Type of change

Please select what type of change this is.

• Bug fix (non-breaking change which fixes an issue)
• New feature
  • Non-breaking change which adds functionality
  • Breaking change fix or feature that would cause existing functionality to not work as expected

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• General testing
  • New and existing unit tests pass locally with my changes
  • Coverage is >80%

Summary by CodeRabbit

• New Features

  • Support for column-formatted MCNP input lines; such blocks are now merged into their parent cards and processed correctly.

• Tests

  • Added test coverage for column-formatted input handling to ensure reliable round-trip output.

• Refactor

  • Updated the internal numerical integration used in ACE group-structure energy collapse (no change to user-facing behavior).

[coderabbitai]

Walkthrough

Detects column-formatted MCNP lines beginning with # and merges them into the preceding card by appending those lines and re-parsing the previous card; also updates an ACE integration call and adds a unit test for the column-format behavior.

Changes

Cohort / File(s)	Summary
MCNP Column-Format Parser Enhancement src/f4enix/input/MCNPinput.py	Adds PAT_COLUMN_FORMAT = re.compile(r"\s*\#") and logic in _to_dict to append column-formatted lines (starting with #) to the previous card, then re-parse that card to refresh its state and continue processing.
Column-Format Feature Test tests/MCNPinput_test.py	Adds test_column_format to verify that column-formatted lines are preserved through write/read and that a specific formatted comment line ( # wwn1:p) appears in output.
ACE integration function rename src/f4enix/input/ace.py	Replaces numpy.trapz(y, x) with numpy.trapezoid(y, x) in group-structure energy collapse integration (functionality unchanged).

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Poem

🐰 I nudge the hashes into line,
Cards re-parsed — they look divine,
A tiny hop, a gentle fix,
Comments nestled, neat and mixed. ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'support column format' directly and concisely describes the main change—adding support for MCNP column-formatted lines in card parsing and output.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

• 📝 Generate docstrings (stacked PR)
• 📝 Generate docstrings (commit on current branch)

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch support-column-format-for-cards

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[coderabbitai]

Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/f4enix/input/MCNPinput.py`:
- Around line 605-613: The code assumes previous_key is always set when handling
column-format continuations (PAT_COLUMN_FORMAT.match(card.lines[0]) branch),
which can raise if a fragment appears before any real card; modify the
conditional to guard that previous_key is not None and exists in new_cards
(e.g., check "previous_key is not None and previous_key in new_cards") before
accessing new_cards[previous_key], and if the guard fails either create a new
entry or skip/raise a controlled parse error; apply the same guard to the
similar merge at the later occurrence (the block around the other
PAT_COLUMN_FORMAT usage at ~line 628) and ensure subsequent calls to get_input()
and get_values() only run on a valid card object.

In `@tests/MCNPinput_test.py`:
- Line 928: The test assigns an unused variable inp2 from
Input.from_input(outfile) causing a lint F841; either remove the assignment or
replace inp2 with a throwaway name (e.g., _) to indicate the parse is executed
for side-effects only. Locate the call to Input.from_input in the test (the inp2
variable assignment) and change the left-hand variable to _ or drop the
assignment entirely so the parsing is still performed but no unused-variable
warning is emitted.

---

ℹ️ Review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 3cfeaa4 and 4a85eab.

📒 Files selected for processing (3)

• src/f4enix/input/MCNPinput.py
• tests/MCNPinput_test.py
• tests/resources/input/column_format.i

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Files with missing lines	Coverage Δ
src/f4enix/input/MCNPinput.py	95.22% <100.00%> (+0.03%)	⬆️
src/f4enix/input/ace.py	85.00% <100.00%> (ø)

... and 26 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/f4enix/input/ace.py`:
- Line 317: The call to np.trapezoid in the values.append(...) expression will
fail on NumPy <2.0.0; either add an explicit dependency numpy>=2.0.0 to
pyproject.toml, or add a local compatibility fallback before that call: resolve
a trapezoid function by checking getattr(np, "trapezoid", np.trapz) (or
try/except AttributeError) and then replace the direct np.trapezoid call with
the resolved function (e.g., trapezoid_fn(y, x) / (e - e_0)) so older NumPy
installations use np.trapz.

---

ℹ️ Review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 4a85eab and 7887ab1.

📒 Files selected for processing (1)

• src/f4enix/input/ace.py