Repo - MINOR - Format the repository and run the pre-commit check on every pull request

.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# Commits that only reformat; `git config blame.ignoreRevsFile .git-blame-ignore-revs` makes local blame skip them.
+# Format the repository with the pinned pre-commit hooks
+9e57323f9221755140cb818a03e033dc7a42a4b2

.github/workflows/format.yaml

@@ -3,18 +3,20 @@ name: Format and Hygiene
 # Runs the repository's pre-commit suite (JuliaFormatter + file hygiene) so that
 # contributors who have not run `pre-commit install` locally are still caught.
 #
-# DISABLED as a pull request gate for now: the repository has pre-existing
-# formatting drift that has to be cleaned up first. Until then, run this
-# manually from the Actions tab ("Run workflow") to see the current damage.
-#
-# To enable it as a gate, uncomment the `pull_request` trigger below. If the
-# test suite's `Tests` job is a required status check, add `pre-commit` too.
+# The `pre-commit` job fails whenever the hooks rewrite a tracked file, so it
+# reports whether the repository is clean under the formatter. The repository
+# was swept with `pre-commit run --all-files` when this check was enabled, so
+# `pre-commit` can be a required status check. Pushes to develop are checked too,
+# since two pull requests that are each clean can merge into unformatted code.
 on:
   workflow_dispatch:
-  # pull_request:
-  #   branches:
-  #     - main
-  #     - develop
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - main
+      - develop
 
 permissions:
   contents: read

CLAUDE.md

@@ -138,7 +138,7 @@ These rules apply to **every** Agent tool invocation, not just performance work.
 
 ### Code Formatting
 
-Pre-commit hooks enforce formatting via JuliaFormatter and general file hygiene. The hook runs the developer's globally installed JuliaFormatter (the version is not currently pinned), so previously untouched files may normalize wholesale on first edit; this churn is expected and should not be reverted. **All code you write or modify must already conform to these standards before committing**, so the hooks have nothing to fix. Failing to do this creates noisy diffs in PRs where formatting changes leak into unrelated files.
+Pre-commit hooks enforce formatting via JuliaFormatter and general file hygiene, and the same hooks run as the `pre-commit` CI check on every pull request. The hook runs the JuliaFormatter in the default Julia environment; CI pins **1.0.62** (`.pre-commit-config.yaml`, `.github/workflows/format.yaml`), so install exactly that version or the formatting will differ. The repository is clean under the hooks, so a file that changes when you run them changed because of your edit. **All code you write or modify must already conform to these standards before committing**, so the hooks have nothing to fix. Failing to do this creates noisy diffs in PRs where formatting changes leak into unrelated files.
 
 The project's `.JuliaFormatter.toml` settings:
 - **Line width**: 180 characters max (`margin = 180`)

Project.toml

@@ -73,5 +73,3 @@ Statistics = "1"
 TOML = "1"
 Test = "1"
 julia = "1.11"
-
-

benchmarks/benchmark_against_fortran_run.jl

@@ -538,17 +538,17 @@ function compare_phix(
 
     grid = ForcingTerms.sample_boundary_grid(equil, p.mtheta_coil, p.nzeta_coil; psi=psilim)
     nobs = p.mtheta_coil * p.nzeta_coil
-    obs_R = zeros(nobs);
-    obs_phi = zeros(nobs);
+    obs_R = zeros(nobs)
+    obs_phi = zeros(nobs)
     obs_Z = zeros(nobs)
     for j in 1:p.nzeta_coil, i in 1:p.mtheta_coil
         idx = i + (j - 1) * p.mtheta_coil
         obs_R[idx] = grid.R[i]
         obs_phi[idx] = grid.phi_grid[j] + grid.phi_offset[i]
         obs_Z[idx] = grid.Z[i]
     end
-    B_R = zeros(nobs);
-    B_phi = zeros(nobs);
+    B_R = zeros(nobs)
+    B_phi = zeros(nobs)
     B_Z = zeros(nobs)
     ForcingTerms.compute_biot_savart_boundary!(B_R, B_phi, B_Z, obs_R, obs_phi, obs_Z, coil_sets)
     bn = zeros(p.mtheta_coil, p.nzeta_coil)
@@ -584,9 +584,9 @@ end
 
 function build_comparison_table(fort, julia, fortran_dir, bench_dir, nn)
     lines = String[]
-    push!(lines, "=" ^ 72)
+    push!(lines, "="^72)
     push!(lines, "GPEC FORTRAN vs JULIA COMPARISON")
-    push!(lines, "=" ^ 72)
+    push!(lines, "="^72)
     push!(lines, "Fortran : $fortran_dir")
     push!(lines, "Julia   : $(joinpath(bench_dir, "gpec.h5"))")
     push!(lines, "Date    : $(Dates.format(Dates.now(), "yyyy-mm-dd HH:MM"))")
@@ -629,9 +629,9 @@ function build_comparison_table(fort, julia, fortran_dir, bench_dir, nn)
     push!(lines, "")
 
     push!(lines, "--- Mercier Criterion ---")
-    fdi = fort["di"];
+    fdi = fort["di"]
     fdr = fort["dr"]
-    jdi = julia["di"];
+    jdi = julia["di"]
     jdr = julia["dr"]
     if !isempty(jdi) && !isempty(fdi)
         jdi_on_fg = [_interp1(jq_psi, jdi, p) for p in fq_psi]
@@ -705,7 +705,7 @@ function build_comparison_table(fort, julia, fortran_dir, bench_dir, nn)
             m = i <= length(m_ctrl) ? m_ctrl[i] : i
             fl = abs(f_L[i, i])
             jl = abs(j_L[i, i])
-            ratio = fl > 0 ? jl/fl : NaN
+            ratio = fl > 0 ? jl / fl : NaN
             push!(lines, @sprintf("%-5d  %14.4e  %14.4e  %-6s  %10.3f", m, fl, jl, rel_pct(fl, jl), ratio))
         end
     else
@@ -724,7 +724,7 @@ function build_comparison_table(fort, julia, fortran_dir, bench_dir, nn)
             m = i <= length(m_ctrl) ? m_ctrl[i] : i
             fl = abs(f_LS[i, i])
             jl = abs(j_LS[i, i])
-            ratio = fl > 0 ? jl/fl : NaN
+            ratio = fl > 0 ? jl / fl : NaN
             push!(lines, @sprintf("%-5d  %14.4e  %14.4e  %-6s  %10.3f", m, fl, jl, rel_pct(fl, jl), ratio))
         end
     else
@@ -753,7 +753,7 @@ function build_comparison_table(fort, julia, fortran_dir, bench_dir, nn)
 
         jp_r = (row > 0 && !isempty(julia["rational_psi"])) ? julia["rational_psi"][row] : NaN
         j_phi = (row > 0 && !isempty(julia["resonant_area_weighted_field"])) ? abs(julia["resonant_area_weighted_field"][row]) : NaN
-        j_wisl = (row > 0 && !isempty(julia["island_half_width"])) ? 2*julia["island_half_width"][row] : NaN
+        j_wisl = (row > 0 && !isempty(julia["island_half_width"])) ? 2 * julia["island_half_width"][row] : NaN
         j_kch = (row > 0 && !isempty(julia["chirikov_parameter"])) ? julia["chirikov_parameter"][row] : NaN
 
         push!(
@@ -842,16 +842,16 @@ function build_comparison_table(fort, julia, fortran_dir, bench_dir, nn)
         )
     end
 
-    push!(lines, "=" ^ 72)
+    push!(lines, "="^72)
     return lines
 end
 
 function _interp1(x::AbstractVector, y::AbstractVector, xi::Real)
-    n = length(x);
+    n = length(x)
     n < 2 && return y[1]
     xi <= x[1] && return y[1]
     xi >= x[end] && return y[end]
-    i = clamp(searchsortedlast(x, xi), 1, n-1)
+    i = clamp(searchsortedlast(x, xi), 1, n - 1)
     t = (xi - x[i]) / (x[i+1] - x[i])
     return y[i] + t * (y[i+1] - y[i])
 end
@@ -924,12 +924,12 @@ function generate_plots(fort, julia, bench_dir, nn)
     p6 = plot(; xlabel="m", ylabel="|b̄| [T]", title="Phi_x & Phi_tot spectrum (n=$nn)",
         legend=:topright)
     if !isempty(j_fvec) && !isempty(f_phi_x)
-        jfx_amps = [abs(get(Dict(zip(j_mmodes, j_fvec)), m, NaN+0im)) for m in m_ctrl]
-        jft_amps = [abs(get(Dict(zip(j_mmodes, j_rvec)), m, NaN+0im)) for m in m_ctrl]
+        jfx_amps = [abs(get(Dict(zip(j_mmodes, j_fvec)), m, NaN + 0im)) for m in m_ctrl]
+        jft_amps = [abs(get(Dict(zip(j_mmodes, j_rvec)), m, NaN + 0im)) for m in m_ctrl]
         ffx_amps = abs.(f_phi_x)
         fft_amps = abs.(f_phi_tot)
-        me, jfe = step_series(m_ctrl, replace(jfx_amps, NaN=>0.0))
-        _, jte = step_series(m_ctrl, replace(jft_amps, NaN=>0.0))
+        me, jfe = step_series(m_ctrl, replace(jfx_amps, NaN => 0.0))
+        _, jte = step_series(m_ctrl, replace(jft_amps, NaN => 0.0))
         _, ffe = step_series(m_ctrl, ffx_amps)
         _, fte = step_series(m_ctrl, fft_amps)
         plot!(p6, me, ffe; seriestype=:steppre, lw=2, color=:steelblue, label="Φ_x Fortran")
@@ -1200,7 +1200,7 @@ function generate_plots(fort, julia, bench_dir, nn)
                 j_theta_data, _, _ = PerturbedEquilibriumModes.modes_to_theta(h5_path, h5_var; keep_sfl_phi=false)
                 j_fun = j_theta_data[:, :, 1]  # (npsi, ntheta) for n=1
             catch e
-                @warn "modes_to_theta failed for $h5_var" exception=e
+                @warn "modes_to_theta failed for $h5_var" exception = e
             end
         end
 
@@ -1349,11 +1349,11 @@ function main(argv=ARGS)
     coil_dat_dir = joinpath(@__DIR__, "..", "src", "ForcingTerms", "coil_geometries")
 
     forcing_mode = use_file_forcing ? "file (Fortran Phi_coil)" : "coil (Julia Biot-Savart)"
-    println("=" ^ 72)
+    println("="^72)
     println("GPEC Fortran vs Julia Benchmark")
     println("  Fortran dir  : $fortran_dir")
     println("  Forcing mode : $forcing_mode")
-    println("=" ^ 72)
+    println("="^72)
 
     println("\n[1/5] Parsing Fortran inputs ...")
     p = parse_fortran_run(fortran_dir)
@@ -1441,15 +1441,15 @@ function main(argv=ARGS)
     println()
     table_lines = build_comparison_table(fort, julia, fortran_dir, bench_dir, p.nn)
     for line in table_lines
-        ;
-        println(line);
+
+        println(line)
     end
 
     table_path = joinpath(bench_dir, "comparison_table.txt")
     open(table_path, "w") do io
         for line in table_lines
-            ;
-            println(io, line);
+
+            println(io, line)
         end
     end
     println("\nComparison table saved to: ", abspath(table_path))