feat(openemr-cmd): wrap pre-commit tooling, add prek-in-container dispatch by bradymiller · Pull Request #718 · openemr/openemr-devops

bradymiller · 2026-05-13T16:58:53Z

Summary

Adds in-container access to every pre-commit hook from OpenEMR's .pre-commit-config.yaml so developers can git commit from the host without installing PHP, Node, Python, codespell, pre-commit, or actionlint locally. The openemr flex container becomes the execution environment; openemr-cmd is the bridge.

openemr-cmd wrappers for each pre-commit composer script: cps (codespell), ccc (conventional-commits-check), crc (require-checker), cv (composer-validate), cn (composer-normalize), cnf (composer-normalize-fix), cck (composer-checks), cq (code-quality). First five wired into clean-sweep so the existing aggregate stays comprehensive.
openemr-cmd prek <args>: passthrough to in-container pre-commit. Substitutes actionlint-docker → actionlint-system at invocation time (DinD isn't available from inside the container); the repo's .pre-commit-config.yaml is untouched and host-side prek/pre-commit usage continues to work unchanged. cwd-aware container resolution (wt_resolve_container_from_cwd) so a commit fired from worktree foo always dispatches to foo's container.
openemr-cmd pi / pu (prek-install / prek-uninstall): manage host-side .git/hooks/{pre-commit,commit-msg} shims. One install on the primary repo covers every linked worktree (current and future) via gitcommondir. Refuses to clobber non-managed hooks without --force. Runtime safeguard rejects invocation via -d <container> or worktree exec with a clear error.
Container packages relocated: chromium, chromium-chromedriver, py3-codespell, plus the new pre-commit and actionlint, now installed at top of openemr.sh under DEVELOPER_TOOLS=yes gate (idempotent via apk info -e guards). Previously inside NEED_COMPOSER_BUILD=true, which meant they didn't survive docker compose down --keep-volumes && up (vendor preserved → block skipped → packages missing on the recreated container).
Bumps openemr-cmd VERSION to 1.0.31. Fixes a stale openemr-cmd-h filter line count (was 9, now 23).

End-to-end workflow this unlocks

For a contributor with only Docker installed on their host:

openemr-cmd worktree add my-feature -b              # one-time per feature
openemr-cmd pi                                       # one-time per clone
# edit files
git add path/to/file.php
git commit -m "feat: ..."
# → host hook fires → openemr-cmd prek run --hook-stage pre-commit
# → cwd-aware resolution dispatches to my-feature's container
# → pre-commit runs inside container against staged files
# → commit aborts on any failure, succeeds otherwise

Manual invocation paths remain:

openemr-cmd prek run --all-files — full-codebase check
openemr-cmd cq — full composer code-quality suite (direct composer path, bypasses prek)
openemr-cmd worktree exec <branch> prek run --all-files — target a specific worktree from anywhere

Test plan

`openemr-cmd` smoke checks

openemr-cmd --version reports 1.0.31
openemr-cmd --help shows the pre-commit-management: section with prek, pi/prek-install, pu/prek-uninstall entries, plus the eight new short-form wrappers under php-management
openemr-cmd-h php displays all 23 php-management entries (was truncated before due to stale filter count)

Per-tool wrappers (run inside any DEVELOPER_TOOLS=yes container; `openemr-cmd` from host)

openemr-cmd cps → runs codespell, no crash on warnings
openemr-cmd cv → reports composer.json validation
openemr-cmd cn → dry-run normalization, reports diff or "already normalized"
openemr-cmd crc → composer-require-checker output
openemr-cmd cq → runs the full composer code-quality suite

prek dispatcher

openemr-cmd prek --version reports the in-container pre-commit version
openemr-cmd prek run --all-files executes the full hook suite; actionlint runs without DinD
openemr-cmd prek run phpstan runs the single hook
Inside the openemr container, /tmp/openemr-cmd-pre-commit-config.yaml shows actionlint-system (not -docker)
From inside worktree foo, openemr-cmd prek run dispatches to foo's container (verify via docker ps while it runs)

Hook installation

openemr-cmd pi from the primary repo writes pre-commit and commit-msg shims to <primary>/.git/hooks/
Both shim files contain the __openemr_cmd_prek_hook__ marker
git commit from a worktree fires the shim and dispatches into that worktree's container
git commit from the primary fires the shim and dispatches into the primary's container
openemr-cmd pi refuses to overwrite a non-managed pre-existing hook; pi --force backs it up to *.bak.<timestamp> and installs
openemr-cmd pu removes only marker-bearing hooks; skips non-managed ones with a notice

Runtime safeguards

openemr-cmd -d <any-container> pi exits 1 with "host-only command" error (does not enter container)
openemr-cmd worktree exec <branch> pi produces the same error transitively
Same for pu/prek-uninstall

Container package persistence (the NEED_COMPOSER_BUILD fix)

After openemr-cmd worktree down --keep-volumes <branch> && openemr-cmd worktree up <branch>, all of chromium-browser, codespell, pre-commit, and actionlint resolve to installed binaries inside the new container
On subsequent container starts with packages already present, no apk install runs (verify the apk info -e short-circuit)

Compatibility

Host-based prek install followed by git commit still works for users who haven't run openemr-cmd pi (no change to host workflow)
CI continues to pass; in particular composer code-quality and shellcheck don't regress

🤖 Generated with Claude Code

Copilot

Pull request overview

This PR extends openemr-cmd to act as a host-side bridge into the Flex container for pre-commit tooling, enabling contributors to run the repository’s pre-commit hooks (and related composer checks) without installing the underlying runtimes locally. It also adjusts the Flex container startup so required dev-only packages persist across container recreation scenarios.

Changes:

Add openemr-cmd prek dispatcher (in-container pre-commit) plus host-only prek-install/prek-uninstall hook shims; add short wrapper commands for several composer-based checks.
Extend the Flex devtools entrypoint to expose new composer commands and include key ones in clean-sweep.
Move installation of dev-only Alpine packages (chromium, codespell, pre-commit, actionlint) earlier in openemr.sh under the DEVELOPER_TOOLS=yes gate; update openemr-cmd-h filter count and bump openemr-cmd version.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
utilities/openemr-cmd/openemr-cmd-h	Updates php-management help filter line count to reflect additional commands.
utilities/openemr-cmd/openemr-cmd	Adds worktree-cwd-aware container resolution, pre-commit dispatch (`prek`), host hook install/uninstall commands, new PHP/composer wrappers, and bumps version.
docker/openemr/flex/utilities/devtools	Adds devtools commands for composer-based pre-commit checks and wires key ones into `clean-sweep`.
docker/openemr/flex/openemr.sh	Installs dev-only Alpine packages early (idempotent) to avoid missing tooling after container recreation.

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+                cfg=/tmp/openemr-cmd-pre-commit-config.yaml
+                if [ -f .pre-commit-config.yaml ]; then
+                    sed "s/actionlint-docker/actionlint-system/g" .pre-commit-config.yaml > "${cfg}"
+                    exec pre-commit "$@" --config "${cfg}"


+                cfg=/tmp/openemr-cmd-pre-commit-config.yaml
+                if [ -f .pre-commit-config.yaml ]; then
+                    sed "s/actionlint-docker/actionlint-system/g" .pre-commit-config.yaml > "${cfg}"
+                    exec pre-commit "$@" --config "${cfg}"


Copilot

Pull request overview

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

+    docker ps \
+        --filter "label=com.docker.compose.project=openemr-${slug}" \
+        --filter "label=com.docker.compose.service=openemr" \
+        --format "{{.ID}}" | head -n 1


+#!/bin/sh
+# openemr-cmd-managed commit-msg hook -- do not edit by hand
+# ${PREK_HOOK_MARKER}
+exec openemr-cmd prek run --hook-stage commit-msg --commit-msg-filename "\$1"
+HOOKEOF
+            ;;
+        *)
+            cat > "${target}" <<HOOKEOF
+#!/bin/sh
+# openemr-cmd-managed pre-commit hook -- do not edit by hand
+# ${PREK_HOOK_MARKER}
+exec openemr-cmd prek run --hook-stage pre-commit
+HOOKEOF


+            return 1
+        fi
+        local backup
+        backup="${target}.bak.$(date +%s)"


…patch Adds in-container access to every pre-commit hook from .pre-commit-config.yaml so developers can `git commit` from the host without installing PHP, Node, Python, codespell, pre-commit, or actionlint locally. The openemr flex container becomes the execution environment; openemr-cmd is the bridge. devtools subcommands and openemr-cmd wrappers for each pre-commit composer script: codespell (cps), conventional-commits-check (ccc), require-checker (crc), composer-validate (cv), composer-normalize (cn), composer-normalize-fix (cnf), composer-checks (cck), code-quality (cq). First five are also wired into clean-sweep so the existing aggregate stays comprehensive. prek dispatcher (`openemr-cmd prek <args>`) is a passthrough to in-container pre-commit. Substitutes actionlint-docker -> actionlint-system at invocation time so the actionlint hook works without DinD; the repo's .pre-commit-config.yaml is untouched and host-side prek/pre-commit usage is unaffected. Resolves the target container via cwd (wt_resolve_container_from_cwd) so a commit fired from worktree foo dispatches to foo's container, not whichever worktree container happens to be running. prek-install (pi) and prek-uninstall (pu) manage host-side .git/hooks/{pre-commit,commit-msg} shims. Linked worktrees share gitcommondir, so a single install on the primary covers every current and future worktree. Both refuse to clobber non-managed hooks without --force and reject invocation via '-d <container>' or 'worktree exec' with a clear error. Container packages (actionlint, pre-commit, py3-codespell, plus the existing chromium/chromium-chromedriver) now installed at top of openemr.sh under the DEVELOPER_TOOLS=yes gate. Previously these lived inside the NEED_COMPOSER_BUILD branch, so they did not survive `docker compose down --keep-volumes && up` (vendor preserved -> block skipped -> packages missing). Moved out and guarded with `apk info -e` so they re-install on container recreation but are no-ops on subsequent starts. Bumps openemr-cmd VERSION to 1.0.31. Updates openemr-cmd-h's php-management filter line count from a stale 9 to 23 so all entries display. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…atch * SC2312 (line 185): process substitution masked jq's return value; add explicit '|| true' so the helper's empty-state handling is unambiguous to readers and to shellcheck. * SC2155 (line 885): split 'local backup="..."' so the assignment's exit code isn't masked by the 'local' builtin. * SC2310 (four sites in cmd_prek_install / cmd_prek_uninstall): drop 'func || exit 1' and 'if ! func' patterns (both of which disable set -e inside the called function) in favor of bare assignments that propagate the function's exit code through the script's set -euo pipefail. * --config placement (Copilot): pre-commit parses '--config' at the top-level parser. Trailing placement (after the subcommand) gave "unrecognized arguments". Move to precede "$@". * /tmp config race (Copilot): parallel openemr-cmd prek invocations in the same container could clobber each other's substituted config mid-run. Use mktemp for a unique path per invocation and trap-clean up on EXIT/INT/TERM. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docker ps in wt_resolve_container_from_cwd swallows daemon-unreachable errors (2>/dev/null) and forces a zero exit (|| true) so the caller can see an empty result rather than having 'set -o pipefail' kill the script before the dispatcher's own "no running openemr container" handling can run. * Hook shims bake in the absolute path to the openemr-cmd binary that installed them ($0 resolved via realpath, with command -v fallback). Git frequently invokes hooks with a reduced PATH (especially from GUI clients), so 'exec openemr-cmd ...' could fail when openemr-cmd lives in a user-local bindir like ~/bin or ~/.local/bin. * Backup filename for clobbered hooks uses mktemp instead of date +%s, so rapid 'prek-install --force' re-runs within the same second don't overwrite each other's backups. mktemp is portable across macOS BSD and Linux GNU coreutils (date +%s%N is GNU-only). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

kojiromike · 2026-05-15T09:44:01Z

    composer phpstan-baseline
 fi

+if [ "$1" = "codespell" ] || [ "$1" = "clean-sweep" ]; then


Suggest case/esac for this section, instead of if. There also really ought to be a way to avoid duplicating that cd. A shell function perhaps?

done on both fronts (ending up converting entire 'CODE QUALITY & STYLING' section to case/esac)

kojiromike · 2026-05-15T09:46:50Z

+
+    while IFS=$'\t' read -r b d; do
+        [[ -z "${b}" ]] && continue
+        local d_real


Can hoist this declaration

kojiromike · 2026-05-15T09:48:17Z

+        [[ -z "${b}" ]] && continue
+        local d_real
+        d_real=$(realpath -m "${d}" 2>/dev/null) || continue
+        if [[ "${d_real}" == "${toplevel_real}" ]]; then


Recommend single equals. Just a style thing here, but double equals has subtle breakage when dealing with some shells. (Only time you need == in bash is in arithmetic context.)

…ygiene * devtools: factor out 'run_composer_at_root' helper so each new code-quality handler is one line instead of three. Removes nine duplicated 'cd /var/www/localhost/htdocs/openemr' lines. The helper guards with '|| exit 1' so a missing webroot aborts the script rather than silently running composer from a wrong cwd ('devtools' has no 'set -e'). * openemr-cmd / wt_resolve_container_from_cwd: hoist 'local d_real' to the function's top-of-body declaration alongside the other locals (was redeclared on every loop iteration) and switch '==' to '=' for string equality inside '[[ ]]' (POSIX-standard spelling; '==' is reserved for arithmetic context in shell style guides). Behavioral parity: no functional change; output of every affected command is identical. Shellcheck count on 'devtools' drops from 53 to 49. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Address kojiromike's suggestion for the full section, not just the new handlers. Converts 13 pre-existing cascading-if blocks plus the 8 new ones added by this PR into a uniform case/esac dispatch: * One do_<task>() helper per handler -- the "what does this do" half of dispatch is now a flat, named, greppable definition rather than embedded in if-test bodies. Multi-line layout (one statement per line in each function body) matches the prevailing style guide. * Two helpers at the top of the section -- run_at_openemr_root (cd + "$@") and run_composer_at_root (cd + composer "$@"). Replaces 13 duplicated 'cd /var/www/localhost/htdocs/openemr' lines in the section with a centralized cd that guards with '|| exit 1'. * Single case "$1" in ... esac with 22 branches: 20 single-task branches (including the psr2-* / psr12-* backward-compat aliases), plus clean-sweep and clean-sweep-tests that enumerate exactly which do_* helpers compose them. The '*) ;;' default lets unmatched input fall through to the TESTING COMMANDS section below, where its own if-cascade still matches clean-sweep / clean-sweep-tests for the test suites (preserving the existing whole-file composition). Behavior preserved bit-for-bit: same handlers fire on each input, same order, same echo strings (including trailing whitespace in a few that had it), same find/php-l redirect dance in do_php_parserror (wrapped in sh -c to preserve the '2>&1 >&-' pattern through a subshell). The pre-existing '}' typo in '.\/ccdaservice\/node_modules}\/*' is kept verbatim -- separate fix if intended. Quantitative effect: section drops ~37 lines; shellcheck findings on the file drop from 49 to 37 (driven by collapsing 13 cd lines into two helpers). Zero shellcheck findings on lines touched by this PR. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Copilot

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

+                    # mktemp for the substituted config: a fixed /tmp path would
+                    # race if two prek invocations run concurrently in the same
+                    # container (parallel CI steps, manual run alongside a hook).
+                    cfg=$(mktemp -t openemr-cmd-pre-commit-config.XXXXXX.yaml) \


+do_php_parserror() {
    echo "Generating PHP parse errors"
-    cd /var/www/localhost/htdocs/openemr
-    find . -type f \( -name "*.php" -or -name "*.inc" \) \( -not -path "./vendor/*" -and -not -path "./node_modules/*" -and -not -path "./ccdaservice/node_modules}/*" \) -exec php -d error_reporting=32767 -l {} \; 2>&1 >&- | grep "^"
-fi
+    run_at_openemr_root sh -c 'find . -type f \( -name "*.php" -or -name "*.inc" \) \( -not -path "./vendor/*" -and -not -path "./node_modules/*" -and -not -path "./ccdaservice/node_modules}/*" \) -exec php -d error_reporting=32767 -l {} \; 2>&1 >&- | grep "^"'
+}


* mktemp template: 'mktemp -t openemr-cmd-pre-commit-config.XXXXXX.yaml' in the in-container prek dispatcher fails under Alpine's BusyBox mktemp, which requires the X-group at the *end* of the template (no trailing extension). Switch to full-path form 'mktemp /tmp/...XXXXXX'. No '.yaml' suffix needed -- pre-commit accepts any filename via --config. This form is also portable across GNU coreutils, BSD mktemp, and BusyBox. * do_php_parserror find exclusion: pre-existing typo './ccdaservice/node_modules}/*' had a stray '}', so the -not -path exclusion silently never matched and php -l was run on every .php file under ccdaservice/node_modules. Corrected to the actual directory name. Significantly faster php-parserror and clean-sweep runs; less noise. Flagged by Copilot on a line touched by the case/esac migration. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…tures Two composer scripts that were previously unreachable through openemr-cmd get dedicated wrappers, completing the in-container coverage for the host-zero-deps validation workflow: * phpunit-isolated (alias 'pit') -- composer phpunit-isolated. Runs the PHP isolated test suite, which needs neither a database nor an external Docker service. Lets contributors validate isolated tests inside the openemr container without a host PHP toolchain. * update-twig-fixtures (alias 'utf') -- composer update-twig-fixtures. Regenerates the expected-output fixture files used by the Twig render tests under tests/Tests/Isolated/Common/Twig/fixtures/render/. Mutating maintenance command (not a test): the help text and the in-container 'echo' both flag that fixture files are overwritten and the diff should be reviewed before committing. Both wired into the existing TESTING section in devtools (if-cascade style to match its neighbors; clean-sweep / clean-sweep-tests do not include them since isolated tests run independently and twig-fixture regeneration is mutating). openemr-cmd dispatches via existing run_devtools_in_docker. openemr-cmd-h's test-management filter line count bumped 8 -> 12 so all twelve entries display. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Mirror the new 'phpstanvolume' named volume added to the base docker-compose.yml files in openemr (3 environments: easy, easy-light, easy-redis) so that each worktree's PHPStan cache lives in its own docker-managed volume ('openemr-<slug>_phpstan') rather than colliding across worktrees or spilling onto the bind-mounted host filesystem. The mount itself (phpstanvolume -> tmp-phpstan in the openemr workdir) is declared in the base compose; the override file just gives that named volume a worktree-scoped 'name:' field, same pattern used for the other per-worktree volumes (db, vendor, nodemodules, etc.). Requires the openemr-side compose change to be in the worktree's checkout. Bump VERSION to 1.0.32. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…punit-isolated to clean-sweep Migrates the 12 cascading-if blocks in the TESTING COMMANDS section into per-task functions and case-branches inside the existing dispatch block, finishing the migration kojiromike initially suggested for the code-quality section. The combined block now covers code quality, styling, and testing under one dispatcher; the standalone TESTING COMMANDS section is removed. * New do_* helpers: do_unit_test, do_javascript_unit_test, do_jut_reports_build, do_api_test, do_e2e_test, do_fixtures_test, do_services_test, do_validators_test, do_controllers_test, do_common_test, do_phpunit_isolated, do_update_twig_fixtures. (The last two were previously standalone if-blocks added during the phpunit-isolated / update-twig-fixtures wrappers commit; now folded into the unified scheme.) * clean-sweep gains do_phpunit_isolated at the end of the test block (12 -> 22 task list). Previously the isolated suite was excluded even though it's part of the project's full validation set; including it makes clean-sweep cover everything CI runs plus the isolated tests that don't require a database. * clean-sweep-tests gains the same do_phpunit_isolated entry (11 -> 12 task list). * jut-reports-build and update-twig-fixtures remain explicit-only. jut-reports-build is a coverage-report build step, not a check; update-twig-fixtures is a mutating maintenance command that rewrites checked-in files and should never run as part of an aggregate. * Section header renamed: 'CODE QUALITY & STYLING COMMANDS' -> 'CODE QUALITY, STYLING & TESTING COMMANDS' Mechanical side-effect: 12 more 'cd /var/www/localhost/htdocs/openemr' lines collapse into the existing helpers, dropping shellcheck findings on devtools from 37 to 27 (-10 SC2164 'cd should have || exit'). No new shellcheck findings on the changed lines; zero functional change to any individual command's behavior (echo strings, env exports, and phpunit/npm invocations preserved verbatim). The only behavior change is the intentional addition of phpunit-isolated to the two aggregates. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

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bradymiller force-pushed the devops-wt-sync-dev-tools-openemrcmd branch from 480537a to 0904563 Compare May 15, 2026 06:01

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docs: document docker-routed pre-commit workflow + isolate PHPStan tmpDir via named volume openemr/openemr#12147

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feat(openemr-cmd): wrap pre-commit tooling, add prek-in-container dispatch#718

feat(openemr-cmd): wrap pre-commit tooling, add prek-in-container dispatch#718
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bradymiller commented May 13, 2026

Summary

End-to-end workflow this unlocks

Test plan

openemr-cmd smoke checks

Per-tool wrappers (run inside any DEVELOPER_TOOLS=yes container; openemr-cmd from host)

prek dispatcher

Hook installation

Runtime safeguards

Container package persistence (the NEED_COMPOSER_BUILD fix)

Compatibility

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`openemr-cmd` smoke checks

Per-tool wrappers (run inside any DEVELOPER_TOOLS=yes container; `openemr-cmd` from host)