address codeql comments and simplify root level config files (#136)

* chore: update dependencies

* ci: improve checkout steps in ops workflow

* chore: codeql linting

* fix: update ci pre-commit checks to conditionally skip main branch protection when pushing to main branch

* fix: update command for root dependency audit in security workflow

* fix: simplify pre-commit checks command in validate workflow

* refactor: move contribution guidelines, code of conduct, security policy; and renovate, codecov, and trivyignore config to .github dir to declutter root dir

* chore: remove root level Python version file

* refactor: update CITATION.cff with author emails and affiliations; remove codemeta.json

* chore: remove auto-install-peers option from .npmrc

* refactor: update justfile scripts for consistency and clarity; remove echo statements

Co-authored-by: Copilot <copilot@github.com>

* feat: move installation and self-hosting documentation from repo root to docs site

* refactor: yml -> yaml where aligning with standard syntax

* test(docs): replace visual regression tests with structural regression tests and ARIA snapshots

* chore: update uvicorn version to 0.46.0 in uv.lock

* refactor: align spacing in prod_compose definition for consistency

* fix: address codeql

Author: simonvanlierde

.cspell.yml .cspell.yaml.cspell.yml renamed to .cspell.yaml

@@ -21,13 +21,13 @@ cache:
   useCache: true
   cacheStrategy: content
 ignorePaths:
-  - .cspell.yml
+  - .cspell.yaml
   - .cspellcache
   - .devcontainer
   - .dockerignore
   - .git
   - .gitignore
-  - .trivyignore
+  - .github/trivyignore
   - .vscode
   - package-lock.json
   - pnpm-lock.yaml
@@ -55,6 +55,7 @@ words:
   - shellcheck
   - subrepo
   - subrepos
+  - tootallnate
   - trivyignores
   - trixie
   - tsvector

.devcontainer/backend/devcontainer.json

@@ -1,6 +1,6 @@
 {
   "name": "relab-backend",
-  "dockerComposeFile": ["../../compose.yml", "../../compose.dev.yml"],
+  "dockerComposeFile": ["../../compose.yaml", "../../compose.dev.yaml"],
   "service": "api",
   "runServices": ["api", "redis", "postgres"],
   "workspaceFolder": "/opt/relab/backend",

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 {
   "name": "relab-fullstack",
-  "dockerComposeFile": ["../compose.yml", "../compose.dev.yml"],
+  "dockerComposeFile": ["../compose.yaml", "../compose.dev.yaml"],
   "service": "app-site",
   "runServices": ["api", "redis", "postgres", "docs-site", "web-site", "app-site"],
   "workspaceFolder": "/opt/relab",

.devcontainer/docs/devcontainer.json

@@ -1,6 +1,6 @@
 {
   "name": "relab-docs",
-  "dockerComposeFile": ["../../compose.yml", "../../compose.dev.yml"],
+  "dockerComposeFile": ["../../compose.yaml", "../../compose.dev.yaml"],
   "service": "docs-site",
   "runServices": ["docs-site"],
   "workspaceFolder": "/opt/relab/docs",

.devcontainer/frontend-app/devcontainer.json

@@ -1,6 +1,6 @@
 {
   "name": "relab-frontend-app",
-  "dockerComposeFile": ["../../compose.yml", "../../compose.dev.yml"],
+  "dockerComposeFile": ["../../compose.yaml", "../../compose.dev.yaml"],
   "service": "app-site",
   "runServices": ["app-site"],
   "workspaceFolder": "/opt/relab/frontend-app",

.devcontainer/frontend-web/devcontainer.json

@@ -1,6 +1,6 @@
 {
   "name": "relab-frontend-web",
-  "dockerComposeFile": ["../../compose.yml", "../../compose.dev.yml"],
+  "dockerComposeFile": ["../../compose.yaml", "../../compose.dev.yaml"],
   "service": "web-site",
   "runServices": ["web-site"],
   "workspaceFolder": "/opt/relab/frontend-web",

CODE_OF_CONDUCT.md .github/CODE_OF_CONDUCT.mdCODE_OF_CONDUCT.md renamed to .github/CODE_OF_CONDUCT.md

@@ -2,7 +2,7 @@
 
 Thanks for contributing. RELab is a research platform developed at CML, Leiden University. The goal of this document is simple: get you productive without making you dig through the repo first.
 
-This page is for code and documentation changes. If you mainly want to run or deploy the stack, use [INSTALL.md](INSTALL.md).
+This page is for code and documentation changes. If you mainly want to run or deploy the stack, see [Install & Self-Host](https://docs.cml-relab.org/architecture/install/).
 
 ## Start Here
 

CONTRIBUTING.md .github/CONTRIBUTING.mdCONTRIBUTING.md renamed to .github/CONTRIBUTING.md

@@ -1,5 +1,5 @@
 blank_issues_enabled: false
 contact_links:
   - name: Contribution guide
-    url: https://github.com/CMLPlatform/relab/blob/main/CONTRIBUTING.md
+    url: https://github.com/CMLPlatform/relab/blob/main/.github/CONTRIBUTING.md
     about: Read this first if you need repo conventions, setup help, or contribution guidance.

.github/ISSUE_TEMPLATE/config.yml

@@ -23,7 +23,7 @@ _What problem does this solve or why is it worth merging?_
 
 ## Checklist
 
-- [ ] I've read the [contributing guidelines](../CONTRIBUTING.md)
+- [ ] I've read the [contributing guidelines](CONTRIBUTING.md)
 - [ ] Code follows style guidelines and passes quality checks (`just ci`)
 - [ ] Unit tests added/updated and passing locally (`just test`)
 - [ ] Documentation updated (if applicable)