Fix errors in make risk report function by wenh06 · Pull Request #20 · DeepPSP/DBCI

wenh06 · 2026-02-17T06:34:05Z

Fix errors in generating latex table for the risk report (function make_risk_report):

Escape special characters in LaTeX.
Fix the header for the generated LaTeX table.

updates: - https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror - [github.com/psf/black-pre-commit-mirror: 25.1.0 → 25.11.0](psf/black-pre-commit-mirror@25.1.0...25.11.0) - [github.com/pycqa/isort: 6.0.1 → 7.0.0](PyCQA/isort@6.0.1...7.0.0)

…e computation of difference of two proportions confidence intervals using wang method

… method

Copilot

Pull request overview

This PR aims to fix issues in LaTeX output generation for make_risk_report, and also includes updates to the Wang (“exactCIdiff”) CI implementation plus supporting test/tooling changes.

Changes:

Add LaTeX escaping and rebuild the LaTeX table header in make_risk_report, and raise on unsupported return_type.
Adjust Wang CI internals (stable sorting, plateau handling, output conversion) and relax related test assertions.
Update developer tooling (flake8 ignores, devcontainer post-create setup) and document fixes in the changelog.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
`diff_binom_confint/_applications.py`	Adds LaTeX escaping helper, rewrites LaTeX header generation, fixes use of `diff_method`, adds unsupported `return_type` error.
`test/test_applications.py`	Adds a test asserting unsupported `return_type` raises `ValueError`.
`diff_binom_confint/_specials/_wang.py`	Forwards `verbose`, uses stable sorts, refines plateau/bounds logic, tweaks output conversion.
`test/test_specials.py`	Adds warning-based fallback to looser tolerances for Wang CI comparisons.
`CHANGELOG.rst`	Records the fixes for Wang edge cases and risk report LaTeX generation.
`.pre-commit-config.yaml`	Broadens flake8 ignore list to include E251/E202.
`.devcontainer/devcontainer.json`	Adds a post-create command to install dev deps and pre-commit hooks.

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diff_binom_confint/_applications.py

Copilot · 2026-02-17T06:42:36Z

diff_binom_confint/_applications.py

+                \begin{{tabular}}{{@{{\extracolsep{{6pt}}}}llllllll@{{}}}}
+                \toprule
+                \multicolumn{{2}}{{l}}{{Feature}} &
+                \multicolumn{{3}}{{l}}{{Affected}} &
+                \multicolumn{{2}}{{l}}{{{risk_name} Risk (${int(conf_level*100)}\%$ CI)}} &
+                {risk_name} Risk Difference (${int(conf_level*100)}\%$ CI) \\
+                \cmidrule(lr){{1-2}}\cmidrule(lr){{3-5}}\cmidrule(lr){{6-7}}\cmidrule(lr){{8-8}}
+                & & n & \% & t/v & n & \% & \\ \midrule


The generated LaTeX header uses \toprule, \midrule, and \cmidrule, which require the LaTeX booktabs package. Since make_risk_report(..., return_type='latex') returns only the tabular environment, this introduces an implicit dependency that may cause compilation failures for consumers not already using booktabs. Either avoid booktabs commands (use \hline/\cline), or document this requirement in the function docstring/output contract.

Copilot · 2026-02-17T06:42:36Z

diff_binom_confint/_applications.py

+        body = "\n".join(_latex_escape(line) for line in body_lines[5:-1])
+


body_lines[5:-1] relies on a hard-coded pandas DataFrame.to_latex() line layout. That layout varies across pandas versions and options (e.g., whether \midrule is emitted when header=False), so this slice can accidentally drop data rows or include rule lines unexpectedly. Prefer locating/removing wrapper/rule lines by content (e.g., stripping \begin{tabular}, \toprule, \midrule, \bottomrule, \end{tabular}) or generating the body from df_risk_table.iloc[2:] directly instead of slicing by index.

Suggested change

body = "\n".join(_latex_escape(line) for line in body_lines[5:-1])

# Keep only data rows from the pandas-generated LaTeX, dropping wrapper/rule lines

filtered_body_lines = []

for line in body_lines:

stripped = line.strip()

if not stripped:

continue

if stripped.startswith(r"\begin{tabular}"):

continue

if stripped.startswith(r"\end{tabular}"):

continue

if stripped.startswith(r"\toprule"):

continue

if stripped.startswith(r"\midrule"):

continue

if stripped.startswith(r"\bottomrule"):

continue

filtered_body_lines.append(_latex_escape(line))

body = "\n".join(filtered_body_lines)

Copilot · 2026-02-17T06:42:37Z

diff_binom_confint/_specials/_wang.py

 def binomial_ci_one_sided(
    n_positive: int,
    n_total: int,
    ref_positive: int,
    ref_total: int,
    conf_level: float,
    sides: str,
    precision: float,
    grid_one: int,
    grid_two: int,
+    verbose: bool = False,
 ) -> List[float]:


binomial_ci_one_sided now accepts a verbose parameter, but it is not used anywhere inside the function body (there are no debug prints/branches). This adds API surface without effect. Either remove the parameter from binomial_ci_one_sided (and the forwarded arguments) or implement verbose-controlled debug logging where needed.

Copilot · 2026-02-17T06:42:37Z

.pre-commit-config.yaml

      - id: flake8
        additional_dependencies: [pycodestyle>=2.11.0]
-        args: [--max-line-length=128, '--exclude=./.*,build,dist', '--ignore=E501,W503,E231,E203', --count, --statistics, --show-source]
+        args: [--max-line-length=128, '--exclude=./.*,build,dist', '--ignore=E501,W503,E231,E203,E251,E202,E226', --count, --statistics, --show-source]


The flake8 config change globally ignores E251/E202, which reduces lint coverage repo-wide and can hide real formatting issues. If this was only needed for a small number of lines, prefer fixing the formatting or using targeted # noqa: E251 / # noqa: E202 on the specific lines triggering it instead of disabling the checks globally.

Suggested change

args: [--max-line-length=128, '--exclude=./.*,build,dist', '--ignore=E501,W503,E231,E203,E251,E202,E226', --count, --statistics, --show-source]

args: [--max-line-length=128, '--exclude=./.*,build,dist', '--ignore=E501,W503,E231,E203,E226', --count, --statistics, --show-source]

CHANGELOG.rst

Copilot · 2026-02-17T06:42:37Z

diff_binom_confint/_specials/_wang.py

    else:
        ci = binomial_ci_one_sided(
-            n_positive, n_total, ref_positive, ref_total, conf_level, sides_val, precision, grid_one, grid_two
+            n_positive, n_total, ref_positive, ref_total, conf_level, sides_val, precision, grid_one, grid_two, verbose
        )
        return ConfidenceInterval(ci[1], ci[2], ci[0], conf_level, "wang", sides_val)


The PR description focuses on make_risk_report LaTeX generation, but this PR also changes the Wang CI implementation (_specials/_wang.py), adjusts test tolerances, and loosens flake8 ignores. Please update the PR description (or split into separate PRs) so reviewers can evaluate the additional changes explicitly.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

codecov · 2026-02-17T13:09:11Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.19%. Comparing base (c02e90f) to head (0b13022).
⚠️ Report is 22 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #20      +/-   ##
==========================================
+ Coverage   97.17%   97.19%   +0.01%     
==========================================
  Files           9        9              
  Lines        1062     1069       +7     
==========================================
+ Hits         1032     1039       +7     
  Misses         30       30

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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

pre-commit-ci bot and others added 7 commits December 1, 2025 16:33

update test of special methods

bd72da6

fix conflict

175ad19

Fix errors in edge cases (mainly when n_total equals ref_total) in th…

e16579c

…e computation of difference of two proportions confidence intervals using wang method

update pre-commit configs

f4fd5b4

fix potential issue where lowerb could be greater than upperb in wang…

9dc245b

… method

Fix errors in generating the latex format risk table

7c83669

Copilot AI review requested due to automatic review settings February 17, 2026 06:34

wenh06 self-assigned this Feb 17, 2026

Copilot started reviewing on behalf of wenh06 February 17, 2026 06:34 View session

update pre-commit config

1621eb2

Copilot AI reviewed Feb 17, 2026

View reviewed changes

wenh06 and others added 3 commits February 17, 2026 19:12

revert changes made in the wang method

8267a97

fix errors in test_applications.py

14b5b67

Update diff_binom_confint/_applications.py

0b13022

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Apply suggestions from code review

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Fix errors in make risk report function#20

Fix errors in make risk report function#20
wenh06 wants to merge 12 commits intomasterfrom
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		body = "\n".join(_latex_escape(line) for line in body_lines[5:-1])

-        body = "\n".join(_latex_escape(line) for line in body_lines[5:-1])
+        # Keep only data rows from the pandas-generated LaTeX, dropping wrapper/rule lines
+        filtered_body_lines = []
+        for line in body_lines:
+            stripped = line.strip()
+            if not stripped:
+                continue
+            if stripped.startswith(r"\begin{tabular}"):
+                continue
+            if stripped.startswith(r"\end{tabular}"):
+                continue
+            if stripped.startswith(r"\toprule"):
+                continue
+            if stripped.startswith(r"\midrule"):
+                continue
+            if stripped.startswith(r"\bottomrule"):
+                continue
+            filtered_body_lines.append(_latex_escape(line))
+        body = "\n".join(filtered_body_lines)

	args: [--max-line-length=128, '--exclude=./.*,build,dist', '--ignore=E501,W503,E231,E203,E251,E202,E226', --count, --statistics, --show-source]
	args: [--max-line-length=128, '--exclude=./.*,build,dist', '--ignore=E501,W503,E231,E203,E226', --count, --statistics, --show-source]

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