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skills/matmaster-dpa4-workflows/references/bundled-tools.md

@@ -3,12 +3,12 @@
 ## Contents
 
 1. Compatibility policy
-2. Environment inventory
-3. Job-spec generation
-4. Bohrium CLI adapter
-5. Read-only OpenAPI probe
-6. Job template
-7. Missing prerequisites
+1. Environment inventory
+1. Job-spec generation
+1. Bohrium CLI adapter
+1. Read-only OpenAPI probe
+1. Job template
+1. Missing prerequisites
 
 ## Compatibility policy
 
@@ -20,9 +20,9 @@ skill does not bundle the proprietary MatMaster UI, Bohrium credentials, the
 Use capabilities in this order:
 
 1. installed MatMaster built-in skill/tool;
-2. bundled helper using an installed `bohr` CLI;
-3. bundled read-only OpenAPI probe;
-4. explicit prerequisite installation or user/platform intervention.
+1. bundled helper using an installed `bohr` CLI;
+1. bundled read-only OpenAPI probe;
+1. explicit prerequisite installation or user/platform intervention.
 
 Never fabricate a missing submission API. The bundled OpenAPI helper is intentionally read-only.
 
@@ -51,13 +51,13 @@ Generate a concrete `job.json` without editing a placeholder manually:
 
 ```bash
 python scripts/make_job_spec.py case-0001 \
-  --output case-0001/job.json \
-  --project-id 123 \
-  --image registry.dp.tech/path/to/validated-dpa4:tag \
-  --machine 'CURRENT_VALID_GPU_SKU' \
-  --name dpa4-workflow-case-0001 \
-  --backward run.log --backward logs/ --backward results/ \
-  --max-run-time 1440 --max-reschedule-times 1
+    --output case-0001/job.json \
+    --project-id 123 \
+    --image registry.dp.tech/path/to/validated-dpa4:tag \
+    --machine 'CURRENT_VALID_GPU_SKU' \
+    --name dpa4-workflow-case-0001 \
+    --backward run.log --backward logs/ --backward results/ \
+    --max-run-time 1440 --max-reschedule-times 1
 ```
 
 The script rejects incomplete image addresses, guessed `/root/input` commands, missing case directories, and absent `run.sh` for the default command.
@@ -88,11 +88,11 @@ python scripts/bohr_cli.py group-create --name run-v1 --project-id 123
 python scripts/bohr_cli.py group-create --name run-v1 --project-id 123 --execute
 
 python scripts/bohr_cli.py job-submit \
-  --spec case-0001/job.json --input case-0001 --group-id GROUP_ID
+    --spec case-0001/job.json --input case-0001 --group-id GROUP_ID
 python scripts/bohr_cli.py job-submit \
-  --spec case-0001/job.json --input case-0001 --group-id GROUP_ID --validate
+    --spec case-0001/job.json --input case-0001 --group-id GROUP_ID --validate
 python scripts/bohr_cli.py job-submit \
-  --spec case-0001/job.json --input case-0001 --group-id GROUP_ID --execute
+    --spec case-0001/job.json --input case-0001 --group-id GROUP_ID --execute
 ```
 
 The first form only prints a copy-safe command, `--validate` invokes Bohrium's native dry run without submission, and `--execute` performs the submission. Local validation rejects unresolved placeholders in the job spec and default `run.sh`. The sibling skill owns validation of scientific input files referenced by that wrapper. `job-terminate` and `job-kill` also require `--execute`. Resolve exact job IDs and preserve outputs before lifecycle changes.

skills/matmaster-dpa4-workflows/references/matmaster-operations.md

@@ -3,23 +3,23 @@
 ## Contents
 
 1. Platform model
-2. Capability priority
-3. Session node and storage
-4. Images and resources
-5. Job packaging and submission
-6. Monitoring, collection, and lifecycle
-7. Authentication and safety
+1. Capability priority
+1. Session node and storage
+1. Images and resources
+1. Job packaging and submission
+1. Monitoring, collection, and lifecycle
+1. Authentication and safety
 
 ## Platform model
 
 Keep four layers distinct:
 
-| Layer | Purpose | Persistent? |
-|---|---|---|
-| MatMaster session node | prepare inputs, debug, inspect, and analyze | system disk: no guarantee; mounted data disks: yes |
-| `/personal` | user-scoped durable files | yes |
-| `/share` | project-shared durable files | yes, project permissions apply |
-| Bohrium container job | isolated production compute with chosen image/resource | job workspace is temporary; declared/downloaded outputs persist |
+| Layer                  | Purpose                                                | Persistent?                                                     |
+| ---------------------- | ------------------------------------------------------ | --------------------------------------------------------------- |
+| MatMaster session node | prepare inputs, debug, inspect, and analyze            | system disk: no guarantee; mounted data disks: yes              |
+| `/personal`            | user-scoped durable files                              | yes                                                             |
+| `/share`               | project-shared durable files                           | yes, project permissions apply                                  |
+| Bohrium container job  | isolated production compute with chosen image/resource | job workspace is temporary; declared/downloaded outputs persist |
 
 The session node and submitted job are different resources with different lifecycles and billing. Do not assume a package installed on the session node exists inside the job image.
 
@@ -28,21 +28,21 @@ The session node and submitted job are different resources with different lifecy
 Use this order:
 
 1. MatMaster built-in skill/tool for the exact operation;
-2. bundled helper scripts over an installed `bohr` CLI;
-3. bundled read-only OpenAPI probe for discovery;
-4. raw CLI/OpenAPI only when the packaged helpers lack the required operation.
+1. bundled helper scripts over an installed `bohr` CLI;
+1. bundled read-only OpenAPI probe for discovery;
+1. raw CLI/OpenAPI only when the packaged helpers lack the required operation.
 
 Expected MatMaster platform capability families:
 
-| Need | Capability |
-|---|---|
-| prepare/inspect files | workspace shell and file tools |
-| submit a job or batch | built-in `bohrium-submit` skill |
-| list/query jobs and groups | Bohrium query/list action |
-| view/download logs and results | Bohrium log/download action |
-| stop wrong work | Bohrium terminate/kill action after resolving exact IDs |
-| list machine/SKU availability | Bohrium resource-list action |
-| track long execution | planning/todo and monitoring capability |
+| Need                           | Capability                                              |
+| ------------------------------ | ------------------------------------------------------- |
+| prepare/inspect files          | workspace shell and file tools                          |
+| submit a job or batch          | built-in `bohrium-submit` skill                         |
+| list/query jobs and groups     | Bohrium query/list action                               |
+| view/download logs and results | Bohrium log/download action                             |
+| stop wrong work                | Bohrium terminate/kill action after resolving exact IDs |
+| list machine/SKU availability  | Bohrium resource-list action                            |
+| track long execution           | planning/todo and monitoring capability                 |
 
 Discover the installed schemas at runtime. Historical names are evidence, not an API contract.
 
@@ -82,7 +82,12 @@ Bohrium expands the uploaded input into an unpredictable work directory. Use rel
   "job_name": "dpa4-workflow-case-0001",
   "command": "bash run.sh",
   "log_file": "run.log",
-  "backward_files": ["run.log", "logs/", "results/", "provenance.json"],
+  "backward_files": [
+    "run.log",
+    "logs/",
+    "results/",
+    "provenance.json"
+  ],
   "project_id": 123,
   "machine_type": "CURRENT_VALID_GPU_SKU",
   "image_address": "registry.dp.tech/.../validated-dpa4:tag",
@@ -124,19 +129,19 @@ result.
 For every group:
 
 1. list all members and compare unique case IDs with the manifest;
-2. inspect logs for representative running and failed jobs;
-3. wait through expected image-cache/runtime-initialization startup before calling a job hung;
-4. download both finished and failed terminal jobs;
-5. audit platform/files, then route workflow-quality acceptance to the owning skill;
-6. retry only invalid cases.
+1. inspect logs for representative running and failed jobs;
+1. wait through expected image-cache/runtime-initialization startup before calling a job hung;
+1. download both finished and failed terminal jobs;
+1. audit platform/files, then route workflow-quality acceptance to the owning skill;
+1. retry only invalid cases.
 
 Actions differ:
 
-| Action | Outputs | Record | Use |
-|---|---|---|---|
-| terminate | normally retained | retained | stop while preserving recoverable state |
-| kill | may not be retained | retained | force-stop an unrecoverable run |
-| delete | removed | removed | destructive cleanup only when explicitly required |
+| Action    | Outputs             | Record   | Use                                               |
+| --------- | ------------------- | -------- | ------------------------------------------------- |
+| terminate | normally retained   | retained | stop while preserving recoverable state           |
+| kill      | may not be retained | retained | force-stop an unrecoverable run                   |
+| delete    | removed             | removed  | destructive cleanup only when explicitly required |
 
 Resolve exact individual job IDs before lifecycle actions. Web UI group IDs and CLI-created group IDs may differ.
 

skills/matmaster-dpa4-workflows/references/platform-validation.md

@@ -3,19 +3,19 @@
 ## Contents
 
 1. Acceptance boundary
-2. Platform and file checks
-3. Batch and attempt checks
-4. Failure routing
-5. Minimum ledger
+1. Platform and file checks
+1. Batch and attempt checks
+1. Failure routing
+1. Minimum ledger
 
 ## Acceptance boundary
 
 This skill accepts only the platform portion of a case:
 
 1. scheduler identity and terminal state are reconciled with the manifest;
-2. submitted inputs and runtime metadata are traceable;
-3. declared results and failure evidence are recovered;
-4. batch counts and retry lineage are internally consistent.
+1. submitted inputs and runtime metadata are traceable;
+1. declared results and failure evidence are recovered;
+1. batch counts and retry lineage are internally consistent.
 
 Training convergence and checkpoint selection, inference accuracy, model
 deployment, atom mapping, ensemble behavior, minimization/MD validity, and
@@ -68,6 +68,6 @@ Route to the owning DeepMD skill:
 
 ## Minimum ledger
 
-| Case | Attempt | Job/group | Terminal | Files | Platform verdict | Evidence |
-|---|---|---|---|---|---|---|
-| case_id | 0 | IDs | state | pass/fail | valid/retry/excluded | concise paths/log lines |
+| Case    | Attempt | Job/group | Terminal | Files     | Platform verdict     | Evidence                |
+| ------- | ------- | --------- | -------- | --------- | -------------------- | ----------------------- |
+| case_id | 0       | IDs       | state    | pass/fail | valid/retry/excluded | concise paths/log lines |

skills/matmaster-dpa4-workflows/references/workflow-handoffs.md

@@ -3,10 +3,10 @@
 ## Contents
 
 1. Common contract
-2. Training and fine-tuning
-3. Inference
-4. LAMMPS execution
-5. Handoff back to the owning skill
+1. Training and fine-tuning
+1. Inference
+1. LAMMPS execution
+1. Handoff back to the owning skill
 
 ## Common contract
 

skills/matmaster-dpa4-workflows/scripts/audit_cases.py

@@ -1,16 +1,20 @@
 #!/usr/bin/env python3
+# SPDX-License-Identifier: LGPL-3.0-or-later
 """Run a non-destructive first-pass audit of DPA4 workflow case folders."""
 
 # ruff: noqa: T201 -- stdout is this command-line tool's result interface.
 
-from __future__ import annotations
+from __future__ import (
+    annotations,
+)
 
 import argparse
 import json
 import math
 import re
-from pathlib import Path
-
+from pathlib import (
+    Path,
+)
 
 FATAL_PATTERNS = {
     "unknown_dpa4": re.compile(r"Unknown model type:\s*dpa4", re.I),

skills/matmaster-dpa4-workflows/scripts/bohr_cli.py

@@ -1,9 +1,12 @@
 #!/usr/bin/env python3
+# SPDX-License-Identifier: LGPL-3.0-or-later
 """Safe adapter for common Bohrium job and group operations."""
 
 # ruff: noqa: T201 -- stdout is this command-line tool's result interface.
 
-from __future__ import annotations
+from __future__ import (
+    annotations,
+)
 
 import argparse
 import json
@@ -12,7 +15,9 @@
 import shlex
 import shutil
 import subprocess
-from pathlib import Path
+from pathlib import (
+    Path,
+)
 
 
 def executable(required: bool = True) -> str:

skills/matmaster-dpa4-workflows/scripts/bohrium_readonly.py

@@ -1,9 +1,12 @@
 #!/usr/bin/env python3
+# SPDX-License-Identifier: LGPL-3.0-or-later
 """Read-only Bohrium OpenAPI probes using only Python's standard library."""
 
 # ruff: noqa: T201 -- stdout is this command-line tool's result interface.
 
-from __future__ import annotations
+from __future__ import (
+    annotations,
+)
 
 import argparse
 import json
@@ -12,7 +15,6 @@
 import urllib.parse
 import urllib.request
 
-
 BASE = os.environ.get("BOHR_OPENAPI_BASE", "https://open.bohrium.com/openapi").rstrip(
     "/"
 )

skills/matmaster-dpa4-workflows/scripts/check_environment.py

@@ -1,18 +1,22 @@
 #!/usr/bin/env python3
+# SPDX-License-Identifier: LGPL-3.0-or-later
 """Inventory a MatMaster/Bohrium job environment without exposing secrets."""
 
 # ruff: noqa: T201 -- stdout is this command-line tool's result interface.
 
-from __future__ import annotations
+from __future__ import (
+    annotations,
+)
 
 import argparse
 import hashlib
 import json
 import os
 import shutil
 import subprocess
-from pathlib import Path
-
+from pathlib import (
+    Path,
+)
 
 COMMANDS = {
     "bohr": ["bohr", "version"],

skills/matmaster-dpa4-workflows/scripts/make_job_spec.py

@@ -1,14 +1,19 @@
 #!/usr/bin/env python3
+# SPDX-License-Identifier: LGPL-3.0-or-later
 """Generate and validate a Bohrium container job specification."""
 
 # ruff: noqa: T201 -- stdout is this command-line tool's result interface.
 
-from __future__ import annotations
+from __future__ import (
+    annotations,
+)
 
 import argparse
 import json
 import shlex
-from pathlib import Path
+from pathlib import (
+    Path,
+)
 
 
 def main() -> int: