From 0747436e7134dad28db3a491b48c3b519ffb1b98 Mon Sep 17 00:00:00 2001 From: Paul Schmiedmayer Date: Sun, 30 Jul 2023 11:22:55 -0700 Subject: [PATCH] Support visionOS, watchOS, and macOS Builds (#17) --- .github/DISCUSSION_TEMPLATE/cardinalkit.yml | 2 +- .../DISCUSSION_TEMPLATE/healthkitonfhir.yml | 2 +- .github/DISCUSSION_TEMPLATE/ideas.yml | 2 +- .../DISCUSSION_TEMPLATE/researchkitonfhir.yml | 2 +- .github/DISCUSSION_TEMPLATE/show-and-tell.yml | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/ISSUE_TEMPLATE/config.yml | 2 +- .github/ISSUE_TEMPLATE/internal_change.yml | 2 +- .github/ISSUE_TEMPLATE/major_feature.yml | 2 +- .github/ISSUE_TEMPLATE/minor_feature.yml | 2 +- .github/codecov.yml | 2 +- .github/pull_request_template.md | 2 +- .github/release.yml | 2 +- .github/workflows/action-release-tag.yml | 2 +- .../create-and-upload-coverage-report.yml | 2 +- .github/workflows/release.yml | 2 +- .github/workflows/reuse.yml | 2 +- .github/workflows/swiftlint.yml | 2 +- .github/workflows/test.yml | 2 +- .github/workflows/xcodebuild-or-fastlane.yml | 27 ++++-- .gitignore | 2 +- CITATION.cff | 22 +++++ CODE_OF_CONDUCT.md | 2 +- CONTRIBUTING.md | 4 +- CONTRIBUTORS.md | 7 +- FUNDING.yml | 4 +- LICENSES/MIT.txt | 2 +- README.md | 94 ++++++++++++++++++- SECURITY.md | 2 +- SUPPORT.md | 2 +- assets/biodesign-footer-dark.png.license | 2 +- assets/biodesign-footer-light.png.license | 2 +- profile/README.md | 13 +-- 33 files changed, 175 insertions(+), 48 deletions(-) create mode 100644 CITATION.cff diff --git a/.github/DISCUSSION_TEMPLATE/cardinalkit.yml b/.github/DISCUSSION_TEMPLATE/cardinalkit.yml index 01f90ed..1c678e4 100644 --- a/.github/DISCUSSION_TEMPLATE/cardinalkit.yml +++ b/.github/DISCUSSION_TEMPLATE/cardinalkit.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/DISCUSSION_TEMPLATE/healthkitonfhir.yml b/.github/DISCUSSION_TEMPLATE/healthkitonfhir.yml index 4d5e865..46088e2 100644 --- a/.github/DISCUSSION_TEMPLATE/healthkitonfhir.yml +++ b/.github/DISCUSSION_TEMPLATE/healthkitonfhir.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/DISCUSSION_TEMPLATE/ideas.yml b/.github/DISCUSSION_TEMPLATE/ideas.yml index d25e26c..28627aa 100644 --- a/.github/DISCUSSION_TEMPLATE/ideas.yml +++ b/.github/DISCUSSION_TEMPLATE/ideas.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/DISCUSSION_TEMPLATE/researchkitonfhir.yml b/.github/DISCUSSION_TEMPLATE/researchkitonfhir.yml index 7bdf784..705de0c 100644 --- a/.github/DISCUSSION_TEMPLATE/researchkitonfhir.yml +++ b/.github/DISCUSSION_TEMPLATE/researchkitonfhir.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/DISCUSSION_TEMPLATE/show-and-tell.yml b/.github/DISCUSSION_TEMPLATE/show-and-tell.yml index 61ae402..1c7b57d 100644 --- a/.github/DISCUSSION_TEMPLATE/show-and-tell.yml +++ b/.github/DISCUSSION_TEMPLATE/show-and-tell.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 75800fe..f09e9d7 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 66fadb1..1a5602f 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/ISSUE_TEMPLATE/internal_change.yml b/.github/ISSUE_TEMPLATE/internal_change.yml index 26bd38a..bc6b336 100644 --- a/.github/ISSUE_TEMPLATE/internal_change.yml +++ b/.github/ISSUE_TEMPLATE/internal_change.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/ISSUE_TEMPLATE/major_feature.yml b/.github/ISSUE_TEMPLATE/major_feature.yml index 1790f2f..8c404a3 100644 --- a/.github/ISSUE_TEMPLATE/major_feature.yml +++ b/.github/ISSUE_TEMPLATE/major_feature.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/ISSUE_TEMPLATE/minor_feature.yml b/.github/ISSUE_TEMPLATE/minor_feature.yml index 38f2a8a..439f2a7 100644 --- a/.github/ISSUE_TEMPLATE/minor_feature.yml +++ b/.github/ISSUE_TEMPLATE/minor_feature.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/codecov.yml b/.github/codecov.yml index 8e0c2fe..b2694c7 100644 --- a/.github/codecov.yml +++ b/.github/codecov.yml @@ -1,5 +1,5 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index d30358d..a76a728 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,6 +1,6 @@ -# Stanford Biodesign for Digital Health .github Contributors +# Stanford Biodesign Digital Health Group .github Contributors -* [Vishnu Ravi](https://github.com/vishnuravi) * [Paul Schmiedmayer](https://github.com/PSchmiedmayer) +* [Vishnu Ravi](https://github.com/vishnuravi) +* [Oliver Aalami](https://github.com/aalami5) \ No newline at end of file diff --git a/FUNDING.yml b/FUNDING.yml index bf2f961..fef7966 100644 --- a/FUNDING.yml +++ b/FUNDING.yml @@ -1,9 +1,9 @@ # -# This source file is part of the Stanford Biodesign for Digital Health open-source project +# This source file is part of the Stanford Biodesign Digital Health Group open-source organization # # SPDX-FileCopyrightText: 2022 Stanford University and the project authors (see CONTRIBUTORS.md) # # SPDX-License-Identifier: MIT # -custom: [Stanford Biodesign for Digital Health.stanford.edu] \ No newline at end of file +custom: [Stanford Biodesign Digital Health Group.stanford.edu] \ No newline at end of file diff --git a/LICENSES/MIT.txt b/LICENSES/MIT.txt index 11e5a38..58de3a2 100644 --- a/LICENSES/MIT.txt +++ b/LICENSES/MIT.txt @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2022 Stanford Biodesign for Digital Health and the project authors (see CONTRIBUTORS.md) +Copyright (c) 2022 Stanford Biodesign Digital Health Group and the project authors (see CONTRIBUTORS.md) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: diff --git a/README.md b/README.md index fcf0180..111c8bb 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# .github +# Stanford Biodesign Digital Health Group + +This repository serves as a collection of default community health files, GitHub Action workflows, templates, and information for the Stanford Biodesign Digital Health Group organization. + + +## GitHub Actions + +This repository contains several GitHub Actions that automate and simplify the process of contributing to Stanford Biodesign Digital Health Group-related projects. + + +### Test Using Xcodebuild or Run Fastlane + +Allows GitHub Actions to build complex Swift Packages supporting Apple platforms as well as Xcode projects with a diverse set of requirements ranging from custom commands, xcodebuild, to using Fastlane. +You can learn more about the arguments in the [`xcodebuild-or-fastlane.yml` GitHub Action file](https://github.com/StanfordBDHG/.github/blob/main/.github/workflows/xcodebuild-or-fastlane.yml). + +```yml +jobs: + buildandtest: + name: Build and Test Swift Package + uses: StanfordBDHG/.github/.github/workflows/xcodebuild-or-fastlane.yml@v2 + with: + artifactname: TemplatePackage.xcresult + runsonlabels: '["macOS", "self-hosted"]' + scheme: TemplatePackage +``` + +### Merge and Upload Coverage Report + +Merge and upload code coverage reports to display them on codecov.io. +You can learn more about the arguments in the [`create-and-upload-coverage-report.yml` GitHub Action file](https://github.com/StanfordBDHG/.github/blob/main/.github/workflows/create-and-upload-coverage-report.yml). + +```yml +jobs: + uploadcoveragereport: + name: Upload Coverage Report + uses: StanfordBDHG/.github/.github/workflows/create-and-upload-coverage-report.yml@v2 + with: + coveragereports: ResultBundle1.xcresult ResultBundle2.xcresult +``` + +### REUSE + +Check that all your source files conform to the REUSE specification. +You can learn more about the arguments in the [`reuse.yml` GitHub Action file](https://github.com/StanfordBDHG/.github/blob/main/.github/workflows/reuse.yml). + +```yml +jobs: + reuse_action: + name: REUSE Compliance Check + uses: StanfordBDHG/.github/.github/workflows/reuse.yml@v2 +``` + +### SwiftLint + +Ensure that all Swift files conform to the defined style guide. +You can learn more about the arguments in the [`swiftlint.yml` GitHub Action file](https://github.com/StanfordBDHG/.github/blob/main/.github/workflows/swiftlint.yml). + +```yml + swiftlint: + name: SwiftLint + uses: StanfordBDHG/.github/.github/workflows/swiftlint.yml@v2 +``` + +### Action Tag Release + +Small GitHub Action that automatically tags releases based on semantic version tags, essential for GitHub Action repos. E.g., you tag a release for v2.4.2, and the action tags a v2 and v2.4). You can learn more about the arguments in the [`action-release-tag.yml` GitHub Action file](https://github.com/StanfordBDHG/.github/blob/main/.github/workflows/action-release-tag.yml). + +```yml +jobs: + releasetag: + name: Tag Release + uses: StanfordBDHG/.github/.github/workflows/action-release-tag.yml@v2 + secrets: + access-token: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + with: + user: PaulsAutomationBot +``` + + +## Continous Integration Setup + +The [ContinousIntegration](https://github.com/StanfordBDHG/ContinousIntegration) repository contains the setup and information about our self-hosted GitHub Action runners that is fitting the GitHub Actions found in this repository. + + +## Our Research + +For more information, check out our website at [biodesigndigitalhealth.stanford.edu](https://biodesigndigitalhealth.stanford.edu). + +![Stanford Byers Center for Biodesign Logo](https://raw.githubusercontent.com/StanfordBDHG/.github/main/assets/biodesign-footer-light.png#gh-light-mode-only) +![Stanford Byers Center for Biodesign Logo](https://raw.githubusercontent.com/StanfordBDHG/.github/main/assets/biodesign-footer-dark.png#gh-dark-mode-only) -This repository serves as a collection of default community health files, GitHub Action workflows, templates, and information for the Stanford Biodesign for Digital Health organization. diff --git a/SECURITY.md b/SECURITY.md index 3dc415e..30b9eae 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -1,6 +1,6 @@ -### Stanford Biodesign for Digital Health +### Stanford Biodesign Digital Health Group We empower the digital health community to rapidly prototype and build digital health solutions on a variety of platforms. -Our flagship project is [Spezi](https://github.com/StanfordSpezi), an open-source framework and ecosystem of modules for building modern, interoperable digital health applications -- the next generation of our original [CardinalKit](https://github.com/CardinalKit) framework. +Our flagship project is [Spezi](https://github.com/StanfordSpezi), an open-source framework and ecosystem of modules for building modern, interoperable digital health applications. Check out the [Spezi Template Application](https://github.com/StanfordSpezi/SpeziTemplateApplication) as a great way to get started. Other featured projects include: +- [LLMonFHIR](https://github.com/StanfordBDHG/LLMonFHIR) - using large language models to explain health data +- [HealthGPT](https://github.com/StanfordBDHG/HealthGPT) - querying Apple Health Data using natural language +- [Phoenix](https://github.com/StanfordBDHG/Phoenix) - web-based builder for FHIR surveys - [ResearchKitOnFHIR](https://github.com/StanfordBDHG/ResearchKitOnFHIR) - FHIR questionnaires on iOS with ResearchKit - [HealthKitOnFHIR](https://github.com/StanfordBDHG/HealthKitOnFHIR) - converting HealthKit data to FHIR resources -- [Phoenix](https://github.com/StanfordBDHG/Phoenix) - web-based builder for FHIR surveys -- [HealthGPT](https://github.com/StanfordBDHG/HealthGPT) - querying Apple Health Data using natural language -- [LLMonFHIR](https://github.com/StanfordBDHG/LLMonFHIR) - using large language models to explain health data For more information, check out our website at [biodesigndigitalhealth.stanford.edu](https://biodesigndigitalhealth.stanford.edu). + ![Stanford Byers Center for Biodesign Logo](https://raw.githubusercontent.com/StanfordBDHG/.github/main/assets/biodesign-footer-light.png#gh-light-mode-only) ![Stanford Byers Center for Biodesign Logo](https://raw.githubusercontent.com/StanfordBDHG/.github/main/assets/biodesign-footer-dark.png#gh-dark-mode-only)