chore: update markdownlint configuration and CI workflows

- Added new markdownlint rule for padded style in `.markdownlint.jsonc`.
- Updated `.pre-commit-config.yaml` to include arguments for preserving double-space hard line breaks in markdown.
- Modified CI workflow to remove markdown validation steps and streamline job outputs.
- Adjusted markdown tables in documentation for consistency and clarity.
- Enhanced `.gitignore` and Docker Compose files for better resource management and organization.

Author: caviri

.github/workflows/ci.yml

@@ -59,8 +59,6 @@ jobs:
     timeout-minutes: 5
     outputs:
       src: ${{ steps.filter.outputs.src }}
-      markdown: ${{ steps.filter.outputs.markdown }}
-      markdown_files: ${{ steps.filter.outputs.markdown_files }}
       shell: ${{ steps.filter.outputs.shell }}
     steps:
       - name: Checkout repository
@@ -81,8 +79,6 @@ jobs:
               - "pyproject.toml"
               - "uv.lock"
               - ".github/workflows/ci.yml"
-            markdown:
-              - "**/*.md"
             shell:
               - "**/*.sh"
               - ".github/workflows/ci.yml"
@@ -158,23 +154,6 @@ jobs:
           path: coverage.xml
           if-no-files-found: warn
 
-  markdown-validation:
-    name: Markdown validation
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    needs: changes
-    if: needs.changes.outputs.markdown == 'true'
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v5
-
-      - name: Lint Markdown
-        uses: DavidAnson/markdownlint-cli2-action@992badcdf24e3b8eb7e87ff9287fe931bcb00c6e  # v20
-        with:
-          config: .markdownlint.jsonc
-          globs: ${{ needs.changes.outputs.markdown_files }}
-          separator: ","
-
   shell-script-sanity:
     name: Shell script sanity
     runs-on: ubuntu-latest

.markdownlint.jsonc

@@ -5,5 +5,6 @@
   "MD025": false,
   "MD031": false,
   "MD032": false,
-  "MD040": false
+  "MD040": false,
+  "MD060": { "style": "padded" }
 }

.pre-commit-config.yaml

@@ -3,6 +3,8 @@ repos:
     rev: v5.0.0
     hooks:
       - id: trailing-whitespace
+        # Preserve double-space hard line breaks in markdown (CommonMark).
+        args: [--markdown-linebreak-ext=md]
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-json
@@ -20,3 +22,9 @@ repos:
     hooks:
       - id: yamllint
         args: [-c, .yamllint]
+
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.22.1
+    hooks:
+      - id: markdownlint-cli2
+        args: ["--config", ".markdownlint.jsonc"]

AGENTS.md

@@ -180,7 +180,7 @@ docker compose -f infra/compose/docker-compose.yml -f infra/compose/docker-compo
 ### `deploy` — Docker infrastructure management
 
 | Sub-command | Description |
-|-------------|-------------|
+| --- | --- |
 | `open-pulse deploy up` | Deploy services via Docker Compose. Without `--profile` flags, opens an interactive selector. Creates `.env` from `infra/env/.env.example` if absent. |
 | `open-pulse deploy down` | Tear down deployed services. `--volumes` / `-v` also removes named volumes. |
 | `open-pulse deploy ps` | Show the status of deployed containers. |
@@ -210,7 +210,7 @@ docker compose -f infra/compose/docker-compose.yml -f infra/compose/docker-compo
 ### `quest` — Analysis pipeline execution
 
 | Sub-command | Description |
-|-------------|-------------|
+| --- | --- |
 | `open-pulse quest start` | Run the full four-step pipeline. Checkpoint files in `.quest-checkpoints/`. |
 | `open-pulse quest run <yaml>` | Run a quest YAML directly (synchronous; the hub Pipeline page invokes this). |
 | `open-pulse quest run-step <step>` | Run a single step. |
@@ -224,7 +224,7 @@ from `tentris` — the service is now technology-agnostic).
 ### `services grimoire` — GrimoireLab service tools
 
 | Sub-command | Description |
-|-------------|-------------|
+| --- | --- |
 | `open-pulse services grimoire prepare-config` | Run SPARQL queries and generate a `projects.json`. |
 | `open-pulse services grimoire apply` | Query SPARQL, build `projects.json`, POST to the applier sidecar (which writes the file and restarts mordred). |
 | `open-pulse services grimoire install-watcher` | Install a cron job that pulls a git repo and detects config changes (Linux/macOS only). |
@@ -235,7 +235,7 @@ the CLI and the hub `/api/projects/*` routes).
 ### `gui` — Interactive UIs
 
 | Sub-command | Description |
-|-------------|-------------|
+| --- | --- |
 | `open-pulse gui grimoire` | Launch the password-protected Streamlit Grimoire UI (requires `[grimoire-ui]`). |
 | `open-pulse gui hub serve` | Run the Open Pulse Hub dashboard. Requires `[hub]`. |
 
@@ -245,7 +245,7 @@ the compose `hub` service publishes 9090 → 8000.
 ### `health` — Service health checks
 
 | Usage | Description |
-|-------|-------------|
+| --- | --- |
 | `open-pulse health` | Docker reachability + container status + endpoint probes + smoke tests. |
 
 ## Open Pulse Hub
@@ -256,7 +256,7 @@ request → 12h cookie session. All Python ships with the package
 (hatchling auto-includes everything under `src/open_pulse/`).
 
 | Path | Purpose |
-|---|---|
+| --- | --- |
 | `/` | Stat cards (services healthy/total, longest uptime, SPARQL repos, Neo4j nodes/rels) · service tiles · quick links |
 | `/stack` | Profile checkboxes → `open-pulse deploy {up,down,ps}` exec'd inside the cli container |
 | `/services` | Per-container start / stop / restart + logs drawer |

README.md

@@ -67,7 +67,7 @@ leading-slash arguments).
 ### Profiles
 
 | Profile | What comes up |
-|---|---|
+| --- | --- |
 | `default` | Neo4j |
 | `crawler` | Open Pulse Crawler API |
 | `extractor` | GME metadata extractor + Selenium |

infra/compose/README.md

@@ -54,7 +54,7 @@ docker compose -f docker-compose.yml \
 ## Profiles
 
 | Profile | Adds |
-|---|---|
+| --- | --- |
 | `default` | Neo4j (always present; the implicit "no profile" set) |
 | `analysis` | Analysis notebook |
 | `crawler` | `open-pulse-crawler` |

infra/compose/docker-compose.yml

@@ -299,4 +299,3 @@ services:
       start_period: 10s
     mem_limit: ${HUB_MEM_LIMIT:-512m}
     cpus: ${HUB_CPUS:-1.0}
-

infra/services/grimoirelab/.gitignore

@@ -1,2 +1,2 @@
 cron_logs/
-config/setup.cfg
+config/setup.cfg

infra/services/grimoirelab/README.md

@@ -126,7 +126,7 @@ curl -u admin:YOUR_PASSWORD -X GET "http://localhost:5601/api/saved_objects/_fin
 
 ### Check the indexes and aliases
 
-This allows to confirm the Mordred extraction went well for all your projects in projects.json. You can also confirm by seeing `collection finished` in the Mordred docker logs. 
+This allows to confirm the Mordred extraction went well for all your projects in projects.json. You can also confirm by seeing `collection finished` in the Mordred docker logs.
 
 It can also be seen on OpenSearch UI under Index Management - Indexes.
 
@@ -145,6 +145,6 @@ curl -k -u admin:YOUR_PASSWORD -X GET "https://localhost:9200/_cat/aliases?v"
 It can also be seen on OpenSearch UI under Dashbaords Management - Saved Objects.
 
 ```bash
-curl -u admin:YOUR_PASSWORD -X GET "http://localhost:5601/api/saved_objects/_find?type=dashboard" \   
+curl -u admin:YOUR_PASSWORD -X GET "http://localhost:5601/api/saved_objects/_find?type=dashboard" \
   -H "osd-xsrf: true"
 ```

infra/services/grimoirelab/config/projects.json

@@ -999,7 +999,7 @@
           "EPFL-ENAC/vue-cli-preset",
           "EPFL-ENAC/web-app",
           "EPFL-ENAC/zarr_geospatial_playground"
-      ] 
+      ]
     },
     "eth": {
       "meta": {
@@ -1015,4 +1015,4 @@
         ]
       }
 
-  }
+  }