diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index cf89bf2..540e64a 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -40,11 +40,15 @@ jobs: with: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} - use-public-rspm: true + # Use CRAN's macOS binaries with CRAN R's bundled OpenMP runtime. + # Keep Posit Package Manager enabled on Linux and Windows. + use-public-rspm: ${{ runner.os != 'macOS' }} - uses: r-lib/actions/setup-r-dependencies@v2 if: matrix.config.r == 'release' with: + # Do not restore macOS binaries from the previous repository setup. + cache-version: ${{ runner.os == 'macOS' && '2' || '1' }} extra-packages: any::rcmdcheck needs: check @@ -54,6 +58,17 @@ jobs: extra-packages: any::rcmdcheck, cran/ggrepel@0.9.6 needs: check + - name: Verify macOS dependencies load + if: runner.os == 'macOS' + shell: Rscript {0} + run: | + print(R.version) + print(getOption("repos")) + library(Rtsne) + library(dotCall64) + library(SeuratObject) + library(Seurat) + - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true diff --git a/DESCRIPTION b/DESCRIPTION index 7db99e2..184ba31 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,7 +4,7 @@ Version: 0.5.1 Description: CyteTypeR is the R version of CyteType python package. Authors@R: person("Nygen Analytics AB", , ,"contact@nygen.io", role = c("aut", "cre")) -License: MIT + file LICENSE +License: file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) Depends: diff --git a/LICENSE b/LICENSE index de4d7ba..bb21c42 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,445 @@ -YEAR: 2026 -COPYRIGHT HOLDER: CyteTypeR authors +Copyright (c) 2025 Nygen Analytics AB +Copyright (c) 2026 CyteTypeR authors + +CyteTypeR code and documentation are licensed under the Creative Commons +Attribution-NonCommercial-ShareAlike 4.0 International license +(CC BY-NC-SA 4.0). +https://creativecommons.org/licenses/by-nc-sa/4.0/ + +Attribution-NonCommercial-ShareAlike 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. 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If the provision + cannot be reformed, it shall be severed from this Public License + without affecting the enforceability of the remaining terms and + conditions. + + c. No term or condition of this Public License will be waived and no + failure to comply consented to unless expressly agreed to by the + Licensor. + + d. Nothing in this Public License constitutes or may be interpreted + as a limitation upon, or waiver of, any privileges and immunities + that apply to the Licensor or You, including from the legal + processes of any jurisdiction or authority. + +======================================================================= + +Creative Commons is not a party to its public +licenses. Notwithstanding, Creative Commons may elect to apply one of +its public licenses to material it publishes and in those instances +will be considered the “Licensor.” The text of the Creative Commons +public licenses is dedicated to the public domain under the CC0 Public +Domain Dedication. Except for the limited purpose of indicating that +material is shared under a Creative Commons public license or as +otherwise permitted by the Creative Commons policies published at +creativecommons.org/policies, Creative Commons does not authorize the +use of the trademark "Creative Commons" or any other trademark or logo +of Creative Commons without its prior written consent including, +without limitation, in connection with any unauthorized modifications +to any of its public licenses or any other arrangements, +understandings, or agreements concerning use of licensed material. For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. diff --git a/LICENSE.md b/LICENSE.md index 6c9924b..a0bc58e 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,31 +1,22 @@ -# MIT License +# License -Copyright (c) 2025 Nygen Analytics AB +## CyteTypeR (this repository) -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: +Copyright (c) 2025 Nygen Analytics AB +Copyright (c) 2026 CyteTypeR authors -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. +The code and documentation in this repository are licensed under the +Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International +license ([CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/)). -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +For commercial licensing, contact [contact@nygen.io](mailto:contact@nygen.io). ## CyteTypeR API ### Academic Use (Free) - Rate-limited API access for academic research and education - **No rate limits** when using your own LLM -- Generated data under [CC BY-SA-NC 4.0 (non-commercial)](https://creativecommons.org/licenses/by-nc-sa/4.0/) +- Generated data under [CC BY-NC-SA 4.0 (non-commercial)](https://creativecommons.org/licenses/by-nc-sa/4.0/) ### Commercial Use & Higher Rate Limits - Requires a commercial use license from Nygen Analytics AB @@ -35,3 +26,445 @@ SOFTWARE. ### Getting API Access 1. Academic users: Start with free rate-limited access 2. Need higher rates or commercial use: contact@nygen.io + +## Full license text + +```text +Attribution-NonCommercial-ShareAlike 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. Distribution of +Creative Commons public licenses does not create a lawyer-client or +other relationship. Creative Commons makes its licenses and related +information available on an "as-is" basis. Creative Commons gives no +warranties regarding its licenses, any material licensed under their +terms and conditions, or any related information. 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Licensors should read and understand the terms + and conditions of the license they choose before applying it. + Licensors should also secure all rights necessary before + applying our licenses so that the public can reuse the + material as expected. Licensors should clearly mark any + material not subject to the license. This includes other CC- + licensed material, or material used under an exception or + limitation to copyright. More considerations for licensors: + wiki.creativecommons.org/Considerations_for_licensors + + Considerations for the public: By using one of our public + licenses, a licensor grants the public permission to use the + licensed material under specified terms and conditions. If + the licensor's permission is not necessary for any reason--for + example, because of any applicable exception or limitation to + copyright--then that use is not regulated by the license. Our + licenses grant only permissions under copyright and certain + other rights that a licensor has authority to grant. Use of + the licensed material may still be restricted for other + reasons, including because others have copyright or other + rights in the material. A licensor may make special requests, + such as asking that all changes be marked or described. + Although not required by our licenses, you are encouraged to + respect those requests where reasonable. More considerations + for the public: + wiki.creativecommons.org/Considerations_for_licensees + +======================================================================= + +Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International +Public License + +By exercising the Licensed Rights (defined below), You accept and agree +to be bound by the terms and conditions of this Creative Commons +Attribution-NonCommercial-ShareAlike 4.0 International Public License +("Public License"). 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Adapter's License means the license You apply to Your Copyright + and Similar Rights in Your contributions to Adapted Material in + accordance with the terms and conditions of this Public License. + + c. BY-NC-SA Compatible License means a license listed at + creativecommons.org/compatiblelicenses, approved by Creative + Commons as essentially the equivalent of this Public License. + + d. Copyright and Similar Rights means copyright and/or similar rights + closely related to copyright including, without limitation, + performance, broadcast, sound recording, and Sui Generis Database + Rights, without regard to how the rights are labeled or + categorized. For purposes of this Public License, the rights + specified in Section 2(b)(1)-(2) are not Copyright and Similar + Rights. + + e. 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Share means to provide material to the public by any means or + process that requires permission under the Licensed Rights, such + as reproduction, public display, public performance, distribution, + dissemination, communication, or importation, and to make material + available to the public including in ways that members of the + public may access the material from a place and at a time + individually chosen by them. + + m. Sui Generis Database Rights means rights other than copyright + resulting from Directive 96/9/EC of the European Parliament and of + the Council of 11 March 1996 on the legal protection of databases, + as amended and/or succeeded, as well as other essentially + equivalent rights anywhere in the world. + + n. You means the individual or entity exercising the Licensed Rights + under this Public License. Your has a corresponding meaning. + + +Section 2 -- Scope. + + a. License grant. + + 1. 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Moral rights, such as the right of integrity, are not + licensed under this Public License, nor are publicity, + privacy, and/or other similar personality rights; however, to + the extent possible, the Licensor waives and/or agrees not to + assert any such rights held by the Licensor to the limited + extent necessary to allow You to exercise the Licensed + Rights, but not otherwise. + + 2. Patent and trademark rights are not licensed under this + Public License. + + 3. To the extent possible, the Licensor waives any right to + collect royalties from You for the exercise of the Licensed + Rights, whether directly or through a collecting society + under any voluntary or waivable statutory or compulsory + licensing scheme. 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@@ -146,6 +146,7 @@ Methods and full results are in the [preprint](https://www.biorxiv.org/content/1 ## License -CyteTypeR package code is available under the [MIT License](LICENSE.md). +CyteTypeR code and documentation are available under [CC BY-NC-SA 4.0](LICENSE.md). +For commercial licensing, contact [contact@nygen.io](mailto:contact@nygen.io). CyteType API access is free for academic and non-commercial research. Commercial API use and higher-rate access require a separate license from Nygen Analytics AB. Contact [contact@nygen.io](mailto:contact@nygen.io).