PhenEx/mkdocs.yml at main · Bayer-Group/PhenEx · 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
117
118
119
120
121
122
123
124
site_name: PhenEx - Automatic Electronic Phenotype Execution
nav:
  - Introduction: index.md
  - Installation: installation.md
  - Data Model: data_model.md
  - Roadmap: roadmap.md
  - Tutorials:
      - Phenex Study Tutorial: tutorials/PhenEx_Study_Tutorial.ipynb
      - CodelistPhenotype: tutorials/CodelistPhenotype_Tutorial.ipynb
      - MeasurementPhenotype: tutorials/MeasurementPhenotype_Tutorial.ipynb
      - ArithmeticPhenotype: tutorials/ArithmeticPhenotype_Tutorial.ipynb
      - LogicPhenotype: tutorials/LogicPhenotype_Tutorial.ipynb
      - Python For PhenEx Tutorial: tutorials/Python_For_Phenex_Tutorial.ipynb
      - Generating SQL: tutorials/generating_sql.md
  - API:
      - Core:
          - Cohort: api/core/cohort.md
          - Study: api/core/study.md
      - Phenotypes:
          - Phenotype: api/phenotypes/phenotype.md
          - EventPhenotype: api/phenotypes/event_phenotype.md
          - CodelistPhenotype: api/phenotypes/codelist_phenotype.md
          - MeasurementPhenotype: api/phenotypes/measurement_phenotype.md
          - FurtherValueFilterPhenotype: api/phenotypes/further_value_filter_phenotype.md
          - AgePhenotype: api/phenotypes/age_phenotype.md
          - SexPhenotype: api/phenotypes/sex_phenotype.md
          - DeathPhenotype: api/phenotypes/death_phenotype.md
          - TimeRangePhenotype: api/phenotypes/time_range_phenotype.md
          - TimeRangeCountPhenotype: api/phenotypes/time_range_count_phenotype.md
          - TimeRangeDaysToNextRange: api/phenotypes/time_range_days_to_next_range_phenotype.md
          - TimeShiftPhenotype: api/phenotypes/time_shift_phenotype.md
          - EventCountPhenotype: api/phenotypes/event_count_phenotype.md
          - WithinSameEncounterPhenotype: api/phenotypes/within_same_encounter_phenotype.md
          - UserDefinedPhenotype: api/phenotypes/user_defined_phenotype.md
          - BinPhenotype: api/phenotypes/bin_phenotype.md
          - ArithmeticPhenotype: api/phenotypes/arithmetic_phenotype.md
          - LogicPhenotype: api/phenotypes/logic_phenotype.md
          - ScorePhenotype: api/phenotypes/score_phenotype.md
          - Factory:
              - CHADSVASCPhenotype: api/phenotypes/factory/chadsvasc.md
              - ISTHMajorBleed: api/phenotypes/factory/isth_major_bleed.md
              - StackableRegimen: api/phenotypes/factory/stackable_regimen.md
              - OneInpatientTwoOutpatientPhenotype: api/phenotypes/factory/one_inpatient_two_outpatient.md
              - SmartCodelistPhenotype: api/phenotypes/factory/smart_codelist_phenotype.md
              - LiverDysfunctionPhenotype: api/phenotypes/factory/liver_dysfunction_phenotype.md
              - SexSplitMeasurementPhenotype: api/phenotypes/factory/sex_split_measurement_phenotype.md
      - Filters:
          - Filter: api/filters/filter.md
          - ValueFilter: api/filters/value_filter.md
          - DateFilter: api/filters/date_filter.md
          - RelativeTimeRangeFilter: api/filters/relative_time_range_filter.md
          - CodelistFilter: api/filters/codelist_filter.md
          - CategoricalFilter: api/filters/categorical_filter.md
      - Codelists:
          - Codelist: api/codelists/codelists.md
          - LocalCSVCodelistFactory: api/codelists/local_csv_codelist_factory.md
          - MedConBCollection: api/codelists/medconb_collection.md
      - Database connections mappers and tables:
          - Table: api/tables.md
      - DerivedTables:
          - CombineOverlappingPeriods: api/derived_tables/combine_overlapping_periods.md
          - EventsToTimeRange: api/derived_tables/events_to_time_range.md
          - MinMaxDatesToTimeRange: api/derived_tables/min_max_dates_to_time_range.md
      - Connectors:
          - Connectors: api/ibis_connect.md
          - Mappers: api/mappers.md
          - DomainsDictionary: api/domains_dictionary.md
      - Simulation:
          - DomainsMocker: api/sim.md
      - Reporting:
          - Report: api/reporting/reporter.md
          - Table1: api/reporting/table1.md
          - Table2: api/reporting/table2.md
          - Waterfall: api/reporting/waterfall.md
          - InExCounts: api/reporting/counts.md
          - TimeToEvent: api/reporting/time_to_event.md
          - ReportDrafter: api/reporting/report_drafter.md
      - Util:
          - Pipeline Utilities: api/pipe.md
          - Serialization: api/util/serialization.md
          - DatabaseSampler: api/util/database_sampler.md
  - License: LICENSE.md

site_url: https://bayer-group.github.io/PhenEx/
repo_url: https://github.com/bayer-group/PhenEx
edit_uri: edit/main/docs/

plugins:
  - search:
      lang: en
      separator: '[\s\-\.]'
  - mkdocstrings:
      handlers:
        python:
          paths: [../phenex] # search packages in the src folder
          options:
            docstring_style: "google" # or "numpy", "restructuredtext", etc.
            inherited_members: true
  - mkdocs-jupyter
theme:
  name: material
  palette:
    primary: deep orange
    accent: deep orange
  features:
    - content.code.copy
    - content.action.edit
    - search.suggest
    - search.highlight
    - search.share
  favicon: assets/bird_icon.png
  logo: assets/bird_icon_white.png
markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: false # Try setting this to false
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tilde

extra_css:
  - assets/style.css