merge: main into fix/pdf-scale-regression-985 to resolve conflicts in PDF coordinate transform

Author: krystophny

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,21 @@
+## Summary
+- Change: <concise one-liner>
+- Scope: <files/modules>
+- Fixes: #<issue>
+
+## Evidence (Verification-First)
+- Local tests: attach/paste `make test-ci` summary and timestamps
+- Coverage: attach `coverage.txt` or `gcovr` summary (with versions)
+- CI run URL(s): paste full Actions URLs for all required checks
+
+## Risk / Compatibility
+- Risk: <low/med/high>
+- Backward-compat: <yes/no>
+- Notes: <migration, deprecations, perf>
+
+## Reviewer Checklist
+- [ ] Commit title follows Conventional Commits
+- [ ] PR links issue and includes evidence
+- [ ] No skipped/disabled tests; scope is minimal and focused
+- [ ] CI green and reproducible locally
+

.github/workflows/ci.yml

@@ -12,6 +12,10 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
+    - name: Root artifact hygiene check (Issue #990)
+      run: |
+        bash scripts/check_root_artifacts.sh
+
     - name: Setup Fortran Package Manager
       run: |
         # Try multiple mirrors and retry mechanisms for resilient FPM installation
@@ -116,4 +120,4 @@ jobs:
 
   # CMAKE CI test disabled - CMAKE build system removed in artifact cleanup
   # Issue #613: Root CMakeLists.txt removed, CMAKE example needs rework  
-  # Re-enable after CMAKE example updated to work without root build system
+  # Re-enable after CMAKE example updated to work without root build system

.gitignore

@@ -94,6 +94,10 @@ vicky_*.pdf
 vicky_*.txt
 title_test_*.png
 
+# Stray compiled test binaries that must never be tracked
+/test_basic_user_workflow
+/test_readme_promises
+
 # Additional root directory artifact prevention
 debug_*.png
 debug_*.pdf

AGENTS.md

@@ -0,0 +1,40 @@
+# Repository Guidelines
+
+## Project Structure & Module Organization
+- `src/`: Fortran library sources (e.g., `backends/`, `figures/`, `utilities/`).
+- `test/`: FPM tests (`test_*.f90`) and artifacts under `test/output/`.
+- `example/`: Fortran and Python examples; generated media in `output/example/...`.
+- `python/fortplot/`: Python wrapper and helpers (`core.py`, `axes.py`, etc.).
+- `cmake/`, `Makefile`, `fpm.toml`: Build systems; docs in `doc/`, FORD config in `doc.md`.
+
+## Build, Test, and Development Commands
+- Build (FPM): `make build` or `fpm build`.
+- Run examples: `make example` (Fortran), `make example_python`, `make example_matplotlib`.
+- Debug apps: `make debug` or `fpm run --target <app>`.
+- Tests: `make test` or `fpm test`; CI-fast set: `make test-ci`.
+- Coverage: `make coverage` (gcov/gcovr; results in `coverage.txt`).
+- Docs: `make doc` (FORD → `build/doc/index.html`).
+- Clean: `make clean`.
+  Examples: `make test ARGS="--target test_public_api"`, `make example ARGS="basic_plots"`.
+
+## Coding Style & Naming Conventions
+- Fortran: free-form, no implicit typing (`fpm.toml` enforces), prefer `use fortplot, only: wp => real64`.
+- Indentation: spaces, keep modules under ~1000 lines; group by subfolders (`backends/`, `figures/`).
+- Names: tests `test_*.f90`; procedures snake_case; modules end with `_t` for derived types (e.g., `figure_t`).
+- Python: follow PEP 8; modules split into focused files (`core.py`, `axes.py`, `advanced.py`).
+- Tooling: pre-commit for whitespace/EOF/YAML/TOML checks (`.pre-commit-config.yaml`).
+
+## Testing Guidelines
+- Framework: FPM auto-discovers tests in `test/`. Name new tests `test_<topic>.f90` and keep output in `build/test/output/`.
+- Run subsets: `fpm test --target <name>`.
+- Env controls: `FORTPLOT_SUPPRESS_WARNINGS=1 make test` (quiet), `FORTPLOT_FORCE_WARNINGS=1 make test`.
+- Coverage: prefer `make coverage` before submitting significant changes.
+
+## Commit & Pull Request Guidelines
+- Commits: Conventional Commits style (`feat:`, `fix:`, `docs:`, `refactor:`, `cleanup:`). Example: `fix: resolve pcolormesh dimension validation (#600)`.
+- PRs: concise description, link issues, list user-facing changes, include before/after images for rendering changes, and note test targets run (e.g., `test-ci`).
+
+## Security & Configuration Tips
+- Animations require `ffmpeg` (optional). Verify with `ffprobe` if needed.
+- Hardened builds: trampoline checks via `fpm build --flag "-Wtrampolines -Werror=trampolines"`.
+- Verification: `make verify-functionality`, `make verify-size-compliance` for artifact integrity.

Makefile

@@ -6,7 +6,7 @@ FPM_FLAGS_LIB = --flag -fPIC
 FPM_FLAGS_TEST = 
 FPM_FLAGS_DEFAULT = $(FPM_FLAGS_LIB)
 
-.PHONY: all build example debug test clean help matplotlib example_python example_matplotlib doc coverage create_build_dirs create_test_dirs validate-output test-docs verify-functionality verify-setup verify-size-compliance
+.PHONY: all build example debug test clean help matplotlib example_python example_matplotlib doc coverage create_build_dirs create_test_dirs validate-output test-docs verify-functionality verify-setup verify-size-compliance issue-branch issue-open-pr pr-merge pr-cleanup issue-loop issue-loop-dry
 
 # Default target
 all: build
@@ -45,6 +45,8 @@ test-ci:
 	@fpm test $(FPM_FLAGS_TEST) --target test_scaling || exit 1
 	@fpm test $(FPM_FLAGS_TEST) --target test_scatter_enhanced || exit 1
 	@fpm test $(FPM_FLAGS_TEST) --target test_histogram_functionality || exit 1
+	@# Regression guard for Issue #985 (PDF coordinate mapping)
+	@fpm test $(FPM_FLAGS_TEST) --target test_pdf_coordinate_mapping_985 || exit 1
 	@echo "CI essential test suite completed successfully"
 
 # Run Python examples with fortplot (default mode)
@@ -196,6 +198,48 @@ verify-with-evidence: verify-functionality
 	@echo "Evidence directory: test/output/verification/evidence/"
 	@ls -la test/output/verification/evidence/ || true
 
+# --- GitHub issue/PR helpers for Codex loop ---
+issue-branch:
+	@if [ -z "$(ISSUE)" ]; then echo "ISSUE=<number> required"; exit 2; fi
+	@echo "Creating branch for issue #$(ISSUE)"
+	@./scripts/issue_branch.sh $(ISSUE)
+
+issue-open-pr:
+	@if [ -z "$(ISSUE)" ]; then echo "ISSUE=<number> required"; exit 2; fi
+	@./scripts/issue_open_pr.sh $(ISSUE)
+
+pr-merge:
+	@if [ -z "$(PR)" ]; then echo "PR=<number> required"; exit 2; fi
+	@./scripts/pr_merge.sh $(PR) $(ARGS)
+
+pr-cleanup:
+	@if [ -z "$(PR)" ]; then echo "PR=<number> required"; exit 2; fi
+	@./scripts/pr_cleanup.sh $(PR)
+
+issue-loop:
+	@label=$${LABEL-__all__}; \
+	if [ "$$label" = "__all__" ]; then \
+		./scripts/issue_loop.sh --all --limit $${LIMIT:-999999}; \
+	else \
+		./scripts/issue_loop.sh --label "$$label" --limit $${LIMIT:-999999}; \
+	fi
+
+issue-loop-dry:
+	@label=$${LABEL-__all__}; \
+	if [ "$$label" = "__all__" ]; then \
+		./scripts/issue_loop.sh --all --limit $${LIMIT:-999999} --dry-run; \
+	else \
+		./scripts/issue_loop.sh --label "$$label" --limit $${LIMIT:-999999} --dry-run; \
+	fi
+
+issue-loop-auto:
+	@label=$${LABEL-__all__}; \
+	if [ "$$label" = "__all__" ]; then \
+		CLEAN_FORCE=1 ./scripts/issue_orchestrate_auto.sh --all --limit $${LIMIT:-999999}; \
+	else \
+		CLEAN_FORCE=1 ./scripts/issue_orchestrate_auto.sh --label "$$label" --limit $${LIMIT:-999999}; \
+	fi
+
 # File size compliance verification - fraud prevention
 verify-size-compliance:
 	@echo "Running file size fraud prevention verification..."

scripts/check_root_artifacts.sh

@@ -0,0 +1,37 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Check for forbidden artifacts in repository root (Issue #990)
+# Allowed locations: build/, doc/, output/, example/, test/, .git/
+
+shopt -s nullglob
+
+violations=()
+
+while IFS= read -r -d '' file; do
+  # Skip allowed paths
+  case "$file" in
+    ./build/*|./doc/*|./output/*|./example/*|./test/*|./.git/*)
+      continue
+      ;;
+  esac
+  violations+=("$file")
+done < <(find . -type f \( \
+  -name "*.png" -o -name "*.pdf" -o -name "*.txt" -o -name "*.log" -o -name "*.ppm" \
+  -o -name "*.mp4" -o -name "*.avi" -o -name "*.mkv" \) -print0)
+
+# Also explicitly check for common stray executables in root
+for bin in ./test_basic_user_workflow ./test_readme_promises; do
+  if [[ -f "$bin" ]]; then
+    violations+=("$bin")
+  fi
+done
+
+if (( ${#violations[@]} > 0 )); then
+  echo "ERROR: Found forbidden artifacts in repository root (Issue #990):"
+  printf '  %s\n' "${violations[@]}" | sort -u
+  echo "\nPlease move test outputs to test/output/ or build/ and ensure .gitignore covers these patterns."
+  exit 1
+fi
+
+echo "Root artifact hygiene check passed."

scripts/issue_branch.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+exec "$script_dir/../../prompts/scripts/issue_branch.sh" "$@"

scripts/issue_check_relevance.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+exec "$script_dir/../../prompts/scripts/issue_check_relevance.sh" "$@"

scripts/issue_loop.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+exec "$script_dir/../../prompts/scripts/issue_loop.sh" "$@"

scripts/issue_open_pr.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -euo pipefail
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+exec "$script_dir/../../prompts/scripts/issue_open_pr.sh" "$@"