diff --git a/COLLABORATORS.md b/COLLABORATORS.md index f2f9c05..369c165 100644 --- a/COLLABORATORS.md +++ b/COLLABORATORS.md @@ -1,4 +1,4 @@ -## Welcome to the Kids First Access Model 🚀 +## Welcome to the INCLUDE Access Model 🚀 This repository serves as a downstream model designed to specialize the [Common Access Model](https://github.com/include-dcc/common-access-model). A @@ -6,7 +6,7 @@ pinned version of this upstream model is captured in src/kf_access_model/schema/upstream-models/common_access_model*.yaml. The purpose of this model is to build out a program-specific extension (or -profile) by importing the core elements and layering the Kids First unique data +profile) by importing the core elements and layering the INCLUDE unique data requirements on top. ## Key Integration Guidelines diff --git a/mkdocs.yml b/mkdocs.yml index ef626b2..19f789e 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -21,6 +21,33 @@ plugins: # scripts: # - gen_pages.py # or any other name or path + +markdown_extensions: + - pymdownx.superfences: + # https://mkdocs-mermaid2.readthedocs.io/en/latest/superfences + # custom code highlighting rules + custom_fences: + - name: mermaid + # disable code highlighting to display diagrams + format: !!python/name:pymdownx.superfences.fence_code_format + class: mermaid + # https://facelessuser.github.io/pymdown-extensions/extensions/magiclink/ + # auto-link HTML, FTP, and email links + - pymdownx.magiclink + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#admonition + # support for call-outs + - admonition + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#tables + # create tables + - tables + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#attribute-lists + # enables use of HTML attributes and CSS classes to applicable elements + - attr_list + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#markdown-in-html + # write markdown inside of HTML + - md_in_html + + watch: - src/include_access_model/schema diff --git a/project.justfile b/project.justfile index 80989ca..8ddfc31 100644 --- a/project.justfile +++ b/project.justfile @@ -25,4 +25,4 @@ gen-dbtmodel: [group('model development')] update-cam: - uv run update-cam -d src/include_access_model/schema/upstream-models + uv run update-cam -l src/include_access_model/schema/include_access_model.yaml -d src/include_access_model/schema/upstream-models diff --git a/pyproject.toml b/pyproject.toml index a5ce4ed..1aafbff 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -91,3 +91,4 @@ extend-exclude = [ [tool.uv.sources] the-caddie = { git = "https://github.com/carrollaboratory/the-caddie" } +#the-caddie = { path = "/home/torstees/dev/the-caddie" } diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index df50d5f..be987b8 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -1,11 +1,10 @@ ---- id: https://includedcc.org/include-access-model name: include-access-model title: INCLUDE DCC Access Model description: LinkML Schema for the internal INCLUDE DCC Access Model license: MIT see_also: - - https://includedcc.github.io/include-access-model +- https://includedcc.github.io/include-access-model prefixes: includedcc: https://includedcc.org/include-access-model/ @@ -85,15 +84,14 @@ default_prefix: includedcc default_range: linkml:string imports: - - upstream-models/common_access_model - +- upstream-models/common_access_model-0.0.7 classes: IncludeParticipant: title: INCLUDE Participant description: Information specific to INCLUDE participants is_a: Demographics slots: - - down_syndrome_status + - down_syndrome_status slots: down_syndrome_status: diff --git a/src/include_access_model/schema/upstream-models/common_access_model.yaml b/src/include_access_model/schema/upstream-models/common_access_model.yaml deleted file mode 120000 index 3336df0..0000000 --- a/src/include_access_model/schema/upstream-models/common_access_model.yaml +++ /dev/null @@ -1 +0,0 @@ -common_access_model-0.0.7.yaml \ No newline at end of file diff --git a/uv.lock b/uv.lock index 32f88b6..027ce65 100644 --- a/uv.lock +++ b/uv.lock @@ -499,6 +499,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/84/d0/205d54408c08b13550c733c4b85429e7ead111c7f0014309637425520a9a/deprecated-1.3.1-py2.py3-none-any.whl", hash = "sha256:597bfef186b6f60181535a29fbe44865ce137a5079f295b479886c82729d5f3f", size = 11298, upload-time = "2025-10-30T08:19:00.758Z" }, ] +[[package]] +name = "distro" +version = "1.9.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/fc/f8/98eea607f65de6527f8a2e8885fc8015d3e6f5775df186e443e0964a11c3/distro-1.9.0.tar.gz", hash = "sha256:2fa77c6fd8940f116ee1d6b94a2f90b13b5ea8d019b98bc8bafdcabcdd9bdbed", size = 60722, upload-time = "2023-12-24T09:54:32.31Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/12/b3/231ffd4ab1fc9d679809f356cebee130ac7daa00d6d6f3206dd4fd137e9e/distro-1.9.0-py3-none-any.whl", hash = "sha256:7bffd925d65168f85027d8da9af6bddab658135b840670a223589bc0c8ef02b2", size = 20277, upload-time = "2023-12-24T09:54:30.421Z" }, +] + [[package]] name = "docutils" version = "0.21.2" @@ -2573,6 +2582,19 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/ed/d2/4a73b18821fd4669762c855fd1f4e80ceb66fb72d71162d14da58444a763/rpds_py-0.28.0-pp311-pypy311_pp73-musllinux_1_2_x86_64.whl", hash = "sha256:5d0145edba8abd3db0ab22b5300c99dc152f5c9021fab861be0f0544dc3cbc5f", size = 552199, upload-time = "2025-10-22T22:24:26.54Z" }, ] +[[package]] +name = "ruyaml" +version = "0.91.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "distro" }, + { name = "setuptools" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/4b/75/abbc7eab08bad7f47887a0555d3ac9e3947f89d2416678c08e025e449fdc/ruyaml-0.91.0.tar.gz", hash = "sha256:6ce9de9f4d082d696d3bde264664d1bcdca8f5a9dff9d1a1f1a127969ab871ab", size = 239075, upload-time = "2021-12-07T16:19:58.427Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/1e/9a/16ca152a04b231c179c626de40af1d5d0bc2bc57bc875c397706016ddb2b/ruyaml-0.91.0-py3-none-any.whl", hash = "sha256:50e0ee3389c77ad340e209472e0effd41ae0275246df00cdad0a067532171755", size = 108906, upload-time = "2021-12-07T16:19:56.798Z" }, +] + [[package]] name = "send2trash" version = "1.8.3" @@ -2881,14 +2903,15 @@ wheels = [ [[package]] name = "the-caddie" -version = "0.6.1.dev2" -source = { git = "https://github.com/carrollaboratory/the-caddie#c04ede34b96cf5fe9e64b4a173683f9634f702b1" } +version = "0.6.2.dev1" +source = { git = "https://github.com/carrollaboratory/the-caddie#82fe600dffd73421f72cfd4f6fd0860ea8455f2f" } dependencies = [ { name = "hatchling" }, { name = "httpx" }, { name = "linkml" }, { name = "linkml-runtime" }, { name = "rich" }, + { name = "ruyaml" }, { name = "tomli", marker = "python_full_version < '3.11'" }, ]