manage-project

Name: manage-project
Author: Aperivue

208stars53forks

How to install manage-project?

aperivue/medsci-skills/manage-project

$npx -y skills add Aperivue/medsci-skills --skill manage-project

Installs into the current project.

Summary

Research project management for medical manuscripts. Scaffold project structure, track writing progress across phases, maintain project memory files, generate submission checklists and backwards timelines. Commands: init, status, sync-memory, checklist, timeline.

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SKILL.md

1	# Manage-Project Skill -- Research Project Management
2
3	## Purpose
4
5	Scaffold new research projects, track manuscript writing progress, maintain lightweight project memory, generate pre-submission checklists, and create backwards submission timelines. Integrates with all other writing skills and the project-manager agent.
6
7	---
8
9	## Commands
10
11	### `/manage-project init {name} --type {type} --journal {journal} [--ssot] [--zotero-collection NAME]`
12
13	Create a complete project scaffold for a new research paper.
14
15	Parameters:
16	- `{name}` -- Project identifier (e.g., `nnunet-skull-fracture`, `rfa-meta-analysis`)
17	- `--type` -- Paper type: `original \| meta \| case \| animal \| technical \| ai_validation \| letter`
18	- `--journal` -- Target journal: `RYAI \| AJR \| Radiology \| European_Radiology \| KJR \| INSI \| AJNR \| generic`
19	- `--ssot` -- Emit `SSOT.yaml` (schema v1) from `templates/SSOT.yaml.template` instead of legacy `project.yaml`. Required for Phase 1C auto-enforce (the PostToolUse verify-refs hook blocks instead of warns). New projects should pass `--ssot`; legacy in-flight projects stay on `project.yaml` until `/manage-project migrate-ssot` is run.
20	- `--zotero-collection NAME` -- Optional. Create a Zotero collection via pyzotero and populate `library_id` + `collection_key` in the contract. Requires `ZOTERO_API_KEY` + `ZOTERO_LIBRARY_ID` (optionally `ZOTERO_LIBRARY_TYPE`, default `user`). Graceful degrade: with pyzotero missing or credentials absent, the contract is scaffolded with `library_id: null` / `collection_key: null` and a WARN is printed.
21
22	SSOT template substitutions: `{{PROJECT_ID}}` → `{name}`; `{{PROJECT_TYPE}}` → the SSOT
23	`project_type` enum mapped from `--type` (`original → original_research`, `meta → meta_analysis`,
24	`case → case_report`, `ai_validation → ai_validation`, else `other`). Without
25	`--zotero-collection`, `library_id` / `collection_key` stay `null` until the owner links an
26	existing collection.
27
28	Implementation: backed by `scripts/init_project.py`. Invoke it directly when running outside
29	the skill harness (from the `medsci-skills` repo root):
30
31	```bash
32	python3 scripts/init_project.py \
33	--name {name} --type {type} --journal {journal} [--ssot] \
34	--project-root {target_dir}
35	```
36
37	The helper writes the contract file (`SSOT.yaml` with `--ssot`, else legacy `project.yaml`), the
38	directory scaffold, the minimal stubs `scripts/validate_project_contract.py` requires
39	(`manuscript/index.qmd`, `artifact_manifest.json`, `qc/status.json`), the memory-file templates,
40	and `project_state.json`. `qc/migration_complete` is NOT written by init — that marker belongs
41	to the migrate pipeline.
42
43	Do not hand-build the scaffold. The script is the source of truth for the tree and for
44	`project_state.json`; a hand-built one drifts from what the contract validator expects.
45
46	Read on demand:
47
48	\| File \| Read it when \| Cost if read blindly \|
49	\|---\|---\|---\|
50	\| `references/init_scaffold.md` \| you need to know where a scaffolded file lands, or what a `project_state.json` field means \| ~1,400 tokens describing output the script already produces for you \|
51
52	---
53	### `/manage-project migrate-ssot [--no-mark-complete]`
54
55	Thin wrapper over `scripts/migrate_project_to_ssot.py` that converts a legacy `project.yaml` project into SSOT.yaml form and, by default, touches `qc/migration_complete` so Phase 1C `auto` mode switches from `warn` to `enforce`.
56
57	```bash
58	python3 scripts/migrate_project_to_ssot.py \
59	--project-root . --write --mark-complete
60	```
61
62	- Default: `--write --mark-complete` (enforce-ready).
63	- `--no-mark-complete` flag form: run with `--write` only. Use when the project still has open QC failures — enforcement is deferred until the migration is validated.
64	- The migrate script refuses to touch `qc/migration_complete` unless the generated SSOT.yaml passes `validate_project_contract.py` AND `contract_mode=ssot`. Do not `touch qc/migration_complete` manually.
65
66	Re-run after resolving failures; the script is idempotent.
67
68	---
69
70	### `/manage-project status`
71
72	Report current progress. Reads `project_state.json`, scans existing files, and checks whether key project memory files are present and aligned.
73
74	Output format:
75
76	```
77	## Project Status: {name}
78	Journal: {journal} \| Type: {type} \| Created: {date}
79	Target submission: {date or "not set"}
80
81	### Phase Progress
82	[check] Phase 0: Project Init (complete)
83	[check] Phase 1: Outline (complete)
84	[check] Phase 2: Tables & Figures (complete)
85	[work] Phase 3: Methods (IN PROGRESS)
86	[wait] Phase

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manage-project

208stars53forks

View on GitHub

How to install manage-project?

aperivue/medsci-skills/manage-project

$npx -y skills add Aperivue/medsci-skills --skill manage-project

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Manage-Project Skill -- Research Project Management
2
3	## Purpose
4
5	Scaffold new research projects, track manuscript writing progress, maintain lightweight project memory, generate pre-submission checklists, and create backwards submission timelines. Integrates with all other writing skills and the project-manager agent.
6
7	---
8
9	## Commands
10
11	### `/manage-project init {name} --type {type} --journal {journal} [--ssot] [--zotero-collection NAME]`
12
13	Create a complete project scaffold for a new research paper.
14
15	Parameters:
16	- `{name}` -- Project identifier (e.g., `nnunet-skull-fracture`, `rfa-meta-analysis`)
17	- `--type` -- Paper type: `original \| meta \| case \| animal \| technical \| ai_validation \| letter`
18	- `--journal` -- Target journal: `RYAI \| AJR \| Radiology \| European_Radiology \| KJR \| INSI \| AJNR \| generic`
19	- `--ssot` -- Emit `SSOT.yaml` (schema v1) from `templates/SSOT.yaml.template` instead of legacy `project.yaml`. Required for Phase 1C auto-enforce (the PostToolUse verify-refs hook blocks instead of warns). New projects should pass `--ssot`; legacy in-flight projects stay on `project.yaml` until `/manage-project migrate-ssot` is run.
20	- `--zotero-collection NAME` -- Optional. Create a Zotero collection via pyzotero and populate `library_id` + `collection_key` in the contract. Requires `ZOTERO_API_KEY` + `ZOTERO_LIBRARY_ID` (optionally `ZOTERO_LIBRARY_TYPE`, default `user`). Graceful degrade: with pyzotero missing or credentials absent, the contract is scaffolded with `library_id: null` / `collection_key: null` and a WARN is printed.
21
22	SSOT template substitutions: `{{PROJECT_ID}}` → `{name}`; `{{PROJECT_TYPE}}` → the SSOT
23	`project_type` enum mapped from `--type` (`original → original_research`, `meta → meta_analysis`,
24	`case → case_report`, `ai_validation → ai_validation`, else `other`). Without
25	`--zotero-collection`, `library_id` / `collection_key` stay `null` until the owner links an
26	existing collection.
27
28	Implementation: backed by `scripts/init_project.py`. Invoke it directly when running outside
29	the skill harness (from the `medsci-skills` repo root):
30
31	```bash
32	python3 scripts/init_project.py \
33	--name {name} --type {type} --journal {journal} [--ssot] \
34	--project-root {target_dir}
35	```
36
37	The helper writes the contract file (`SSOT.yaml` with `--ssot`, else legacy `project.yaml`), the
38	directory scaffold, the minimal stubs `scripts/validate_project_contract.py` requires
39	(`manuscript/index.qmd`, `artifact_manifest.json`, `qc/status.json`), the memory-file templates,
40	and `project_state.json`. `qc/migration_complete` is NOT written by init — that marker belongs
41	to the migrate pipeline.
42
43	Do not hand-build the scaffold. The script is the source of truth for the tree and for
44	`project_state.json`; a hand-built one drifts from what the contract validator expects.
45
46	Read on demand:
47
48	\| File \| Read it when \| Cost if read blindly \|
49	\|---\|---\|---\|
50	\| `references/init_scaffold.md` \| you need to know where a scaffolded file lands, or what a `project_state.json` field means \| ~1,400 tokens describing output the script already produces for you \|
51
52	---
53	### `/manage-project migrate-ssot [--no-mark-complete]`
54
55	Thin wrapper over `scripts/migrate_project_to_ssot.py` that converts a legacy `project.yaml` project into SSOT.yaml form and, by default, touches `qc/migration_complete` so Phase 1C `auto` mode switches from `warn` to `enforce`.
56
57	```bash
58	python3 scripts/migrate_project_to_ssot.py \
59	--project-root . --write --mark-complete
60	```
61
62	- Default: `--write --mark-complete` (enforce-ready).
63	- `--no-mark-complete` flag form: run with `--write` only. Use when the project still has open QC failures — enforcement is deferred until the migration is validated.
64	- The migrate script refuses to touch `qc/migration_complete` unless the generated SSOT.yaml passes `validate_project_contract.py` AND `contract_mode=ssot`. Do not `touch qc/migration_complete` manually.
65
66	Re-run after resolving failures; the script is idempotent.
67
68	---
69
70	### `/manage-project status`
71
72	Report current progress. Reads `project_state.json`, scans existing files, and checks whether key project memory files are present and aligned.
73
74	Output format:
75
76	```
77	## Project Status: {name}
78	Journal: {journal} \| Type: {type} \| Created: {date}
79	Target submission: {date or "not set"}
80
81	### Phase Progress
82	[check] Phase 0: Project Init (complete)
83	[check] Phase 1: Outline (complete)
84	[check] Phase 2: Tables & Figures (complete)
85	[work] Phase 3: Methods (IN PROGRESS)
86	[wait] Phase

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