software-documentation/myst.yml at main · jupyterhealth/software-documentation · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
# See docs at: https://mystmd.org/guide/frontmatter
version: 1
project:
  title: 'JupyterHealth Software'
  description: 'Documentation on JupyterHealth Software'
  keywords: []
  #authors: ['JupyterHealth Software Team']
  github: https://github.com/jupyterhealth/software-documentation
  references:
    jupyterhealth_client: https://jupyterhealth-client.readthedocs.io/en/latest
  # See https://mystmd.org/guide/table-of-contents
  toc:
    - file: index.md
    # Note: this toc should reflect _navigation_, not document type
    # document types are a placeholder for now
    - title: Jupyter Health Exchange
      children:
        - file: jhe/getting-started.md
        - file: jhe/upgrading.md
        - file: jhe/client-flow.md
        - file: jhe/auth.md
        - file: jhe/access-control.md
        - file: jhe/admin-api.md
        - title: FHIR
          children:
            - file: jhe/fhir/fhir-api.md
            - file: jhe/fhir/fhir-engine.md
            - file: jhe/fhir/r4-import.md
        - file: jhe/bruno-api-collection.md
        - file: jhe/data-model.md
        - file: jhe/patient-identifiers.md
        - file: jhe/ow-integration.md
        - file: jhe/patient-access-integration.md
        - file: jhe/provider-ehr-launch.md
        - file: jhe/mcp-server.md
        # - title: Deploy
        #   children:
        #     - file: jhe/deploy/kubernetes.md
        # - file: tutorial/local-exchange-deployment.md
        # - file: tutorial/exchange-on-kubernetes.md
        # - file: tutorial/openmhealth-bp.ipynb
        # - file: tutorial/tutorial-cgm.ipynb
    - title: Tutorials
      children:
        # - file: tutorial/local-exchange-deployment.md
        # - file: tutorial/exchange-on-kubernetes.md
        - file: tutorial/openmhealth-bp.ipynb
        - file: tutorial/tutorial-cgm.ipynb
        - file: tutorial/medplum-provider-dashboard.md
    # - title: How-To Guides
    #   children:
    #     - title: For Admins and Deployment
    #       children:
    #         - file: howto/admins-deployers/configuring-hipaa-storage.md
    #         - file: howto/admins-deployers/add-data-source-type.md
    #         - file: howto/admins-deployers/connecting-new-wearable-api.md
    #         - file: howto/admins-deployers/upgrading-jupyterhealth.md
    #         - file: howto/admins-deployers/troubleshooting-ingestion-errors.md
    #     - title: For Clinicians and Researchers
    #       children:
    #         - file: howto/practitioners/study-management.md
    #         - file: howto/practitioners/patient-management.md
    #         - file: howto/practitioners/fetching-exporting-data.md
    #         - file: howto/practitioners/using-rest-api.md
    # - title: Explanation
    #   children:
    #     - file: explanation/index.md
    #     - file: explanation/exchange-overview.md
    #     - file: explanation/fhir-interoperability.md
    #     # - file: explanation/openmhealth-standards.md
    #     - file: explanation/data-flow.md
    #     - file: explanation/consent-management.md
    #     - file: explanation/security-overview.md
    #     - file: explanation/rbac-governance.md
    #     - file: explanation/architecture.md
    # - title: Reference
    #   children:
    #     - pattern: reference/*
    - file: contributing/index.md
  error_rules:
    # check-links error ignores
    - rule: link-resolves
      severity: ignore
      keys:
        - "http://localhost:8000"
        - "http://localhost:8000/"
        - "http://localhost:8000/admin"
        - "http://localhost:8001"
        - "http://localhost:8010/smart/callback"
        # epic.com blocks automated requests (403), so the checker can't verify it
        - "https://www.epic.com/software/mychart/"
    # doi.org intermittently rate-limits CI runners; this citation lookup in
    # tutorial-cgm.ipynb has flaked repeatedly (2026-07-12, 2026-07-15).
    - rule: doi-link-valid
      severity: ignore
      keys:
        - "10.1371/journal.pbio.2005143.s010"
        - "doi:10.1371/journal.pbio.2005143.s010"
site:
  template: book-theme
  title: JupyterHealth Software
  options:
    logo: "assets/images/jupyterhealth-logo.png"
    logo_dark: "assets/images/jupyterhealth-logo.png"
    folders: true
    navigation:
      collapse: true
  actions:
    - title: Project Jupyter
      url: https://jupyter.org
    - title: CommonHealth
      url: https://www.commonhealth.org
    - title: 2i2c
      url: https://2i2c.org
  domains:
    - jupyterhealth.github.io