diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 000000000..418fa030e --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,17 @@ +## Related issue + + + +## Summary + + + +## Testing + + + +## Checklist + +- [ ] I added or updated tests, or this change does not require tests. +- [ ] I updated the documentation, or this change does not require documentation. +- [ ] I confirmed this change does not include confidential or sensitive information. diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 000000000..8ab6e3916 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,78 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, disability, ethnicity, sex characteristics, gender identity and expression, +level of experience, education, socio-economic status, nationality, personal +appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +- Using welcoming and inclusive language +- Being respectful of differing viewpoints and experiences +- Gracefully accepting constructive criticism +- Focusing on what is best for the community +- Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +- The use of sexualized language or imagery and unwelcome sexual attention or + advances +- Trolling, insulting/derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or electronic + address, without explicit permission +- Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies within all project spaces, and it also applies when +an individual is representing the project or its community in public spaces. +Examples of representing a project or community include using an official +project e-mail address, posting via an official social media account, or acting +as an appointed representative at an online or offline event. Representation of +a project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at +[opensource@biohub.org](mailto:opensource@biohub.org). All complaints will be +reviewed and investigated and will result in a response that is deemed +necessary and appropriate to the circumstances. The project team is obligated +to maintain confidentiality with regard to the reporter of an incident. Further +details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 1.4, available at +https://www.contributor-covenant.org/version/1/4/code-of-conduct.html. + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see +https://www.contributor-covenant.org/faq. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 892d749a1..791cb0d6b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -4,6 +4,12 @@ Thanks for your interest in contributing to VisCy! Please see the following steps for our workflow. +Participation in VisCy is governed by the +[Contributor Covenant Code of Conduct](./CODE_OF_CONDUCT.md). + +Do not report security vulnerabilities in public issues. Follow our +[security policy](./SECURITY.md) to report them privately. + ## Getting started Please read the [README](./README.md) for an overview of the project diff --git a/LICENSE b/LICENSE.md similarity index 97% rename from LICENSE rename to LICENSE.md index 4520d7a93..18f3286ff 100644 --- a/LICENSE +++ b/LICENSE.md @@ -1,6 +1,6 @@ BSD 3-Clause License -Copyright (c) 2023, CZ Biohub SF +Copyright (c) 2023, Biohub Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: diff --git a/README.md b/README.md index a73e4e6c1..73dc3fe75 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,9 @@ VisCy (blend of `vision` and `cyto`) is a deep learning pipeline for training and deploying computer vision models for image-based phenotyping at single-cell resolution. +> **Project status:** Active development. VisCy is beta software, and its APIs +> may change between releases. + ## Packages VisCy is organized as a [uv workspace](https://docs.astral.sh/uv/concepts/workspaces/) monorepo: @@ -69,6 +72,17 @@ Full documentation is hosted at . See [CONTRIBUTING.md](./CONTRIBUTING.md) for development setup and guidelines. +## Community + +Read the [contributing guide](CONTRIBUTING.md) before proposing a change. +Participation in VisCy is governed by the +[Contributor Covenant Code of Conduct](CODE_OF_CONDUCT.md). + +## Security + +Do not report security vulnerabilities in public issues. Follow our +[security policy](SECURITY.md) to report them privately. + ## License -[BSD-3-Clause](./LICENSE) +[BSD-3-Clause](./LICENSE.md) diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 000000000..937a8de2c --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,11 @@ +# Security Policy + +## Reporting a Vulnerability + +If you believe you have found a security vulnerability, please do not open a +public issue. Responsibly disclose it by contacting +[security@biohub.org](mailto:security@biohub.org). + +Include enough detail to reproduce and assess the issue, but do not include +sensitive information beyond what is necessary. The security team will +coordinate triage and next steps with the project maintainers. diff --git a/applications/airtable/LICENSE.md b/applications/airtable/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/applications/airtable/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/applications/cytoland/LICENSE.md b/applications/cytoland/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/applications/cytoland/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/applications/dynacell/LICENSE.md b/applications/dynacell/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/applications/dynacell/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/applications/dynaclr/LICENSE.md b/applications/dynaclr/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/applications/dynaclr/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/applications/qc/LICENSE.md b/applications/qc/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/applications/qc/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/packages/viscy-data/LICENSE.md b/packages/viscy-data/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/packages/viscy-data/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/packages/viscy-data/pyproject.toml b/packages/viscy-data/pyproject.toml index 959f9543e..3aac71bb2 100644 --- a/packages/viscy-data/pyproject.toml +++ b/packages/viscy-data/pyproject.toml @@ -38,7 +38,7 @@ dependencies = [ "pandas", "pyarrow", "pydantic>=2", - "torch>=2.10", + "torch>=2.13", "tqdm", "zarr", ] diff --git a/packages/viscy-models/LICENSE.md b/packages/viscy-models/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/packages/viscy-models/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/packages/viscy-models/README.md b/packages/viscy-models/README.md index 125c07e4b..2ac831f67 100644 --- a/packages/viscy-models/README.md +++ b/packages/viscy-models/README.md @@ -127,4 +127,4 @@ In the works! ## License -BSD-3-Clause - see [LICENSE](../../LICENSE) in repository root. +BSD-3-Clause - see [LICENSE](../../LICENSE.md) in repository root. diff --git a/packages/viscy-models/pyproject.toml b/packages/viscy-models/pyproject.toml index fe563943e..2d942b2e5 100644 --- a/packages/viscy-models/pyproject.toml +++ b/packages/viscy-models/pyproject.toml @@ -35,7 +35,7 @@ dependencies = [ "numpy>=2.4.1", "pytorch-metric-learning", "timm>=1.0.15", - "torch>=2.10", + "torch>=2.13", "transformers>=4.40", ] diff --git a/packages/viscy-transforms/LICENSE.md b/packages/viscy-transforms/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/packages/viscy-transforms/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/packages/viscy-transforms/README.md b/packages/viscy-transforms/README.md index 7fa08f72c..4bd100041 100644 --- a/packages/viscy-transforms/README.md +++ b/packages/viscy-transforms/README.md @@ -61,4 +61,4 @@ In the works! ## License -BSD-3-Clause - see [LICENSE](../../LICENSE) in repository root. +BSD-3-Clause - see [LICENSE](../../LICENSE.md) in repository root. diff --git a/packages/viscy-transforms/pyproject.toml b/packages/viscy-transforms/pyproject.toml index e2f75a028..46ea3c846 100644 --- a/packages/viscy-transforms/pyproject.toml +++ b/packages/viscy-transforms/pyproject.toml @@ -33,7 +33,7 @@ dependencies = [ "kornia>=0.8.2", "monai>=1.5.2", "numpy>=2.4.1", - "torch>=2.10", + "torch>=2.13", ] optional-dependencies.notebook = [ diff --git a/packages/viscy-utils/LICENSE.md b/packages/viscy-utils/LICENSE.md new file mode 100644 index 000000000..18f3286ff --- /dev/null +++ b/packages/viscy-utils/LICENSE.md @@ -0,0 +1,28 @@ +BSD 3-Clause License + +Copyright (c) 2023, Biohub + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/packages/viscy-utils/pyproject.toml b/packages/viscy-utils/pyproject.toml index 5ea32d75b..09e360b6f 100644 --- a/packages/viscy-utils/pyproject.toml +++ b/packages/viscy-utils/pyproject.toml @@ -42,7 +42,7 @@ dependencies = [ "scipy", "tensorboard", "tensorstore", - "torch>=2.10", + "torch>=2.13", "torchvision", "viscy-data", "wandb>=0.12.10", diff --git a/uv.lock b/uv.lock index bfd8cdd5a..dacfcf950 100644 --- a/uv.lock +++ b/uv.lock @@ -1,5 +1,5 @@ version = 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