@datagrok/bio 2.27.7 → 2.27.8

package/CREDITS.md

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+# Bio — Third-Party Libraries
+
+The `@datagrok/bio` package is distributed under the MIT license that covers the
+rest of the `public/` repository (see [`../../LICENSE.md`](../../LICENSE.md)). It
+incorporates the open-source components listed below; this file reproduces the
+attribution and notices required by their respective licenses.
+
+All runtime JavaScript dependencies bundled into the published artifact are
+under permissive licenses (MIT, Apache-2.0, BSD-3-Clause). No copyleft
+(GPL/LGPL/MPL) component is bundled into the published Bio plugin.
+
+---
+
+## 1. Bundled in the published artifact (`dist/`)
+
+### immunum (1.1.0)
+
+ENPICOM's antibody/TCR numbering library, compiled to WebAssembly. The
+WASM binary is bundled into `dist/`; the wasm-bindgen JS glue is reused from
+[`src/utils/antibody-numbering/immunum-glue.js`](src/utils/antibody-numbering/immunum-glue.js),
+which is a port of the upstream `node_modules/immunum/immunum.js` modified
+only to replace the Node-only `require('fs').readFileSync` top-level loader
+with an explicit `initImmunum(bytes)` entry point so it works in browsers and
+web workers. The modification is noted in the file header per MIT terms.
+
+- Upstream: https://github.com/ENPICOM/immunum — https://immunum.enpicom.com
+- License: **MIT**
+
+```
+MIT License
+
+Copyright (c) 2026 ENPICOM
+
+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:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+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.
+```
+
+### @biowasm/aioli (3.x)
+
+WebAssembly runtime that drives multiple sequence alignment (kalign). The
+aioli library itself is bundled; the kalign tool it loads is fetched at
+runtime — see Section 3 below.
+
+- Upstream: https://github.com/biowasm/aioli
+- License: **MIT**
+
+```
+MIT License
+
+Copyright (c) 2018 Robert Aboukhalil
+
+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:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+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.
+```
+
+### Ajv (8.x) and ajv-errors (3.x)
+
+JSON-schema validator used for monomer-library JSON validation.
+
+- Upstream: https://ajv.js.org/ — https://github.com/ajv-validator/ajv-errors
+- License: **MIT**
+
+```
+The MIT License (MIT)
+
+Copyright (c) 2015-2021 Evgeny Poberezkin
+
+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:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+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.
+```
+
+(`ajv-errors` carries an analogous MIT notice — *Copyright (c) 2017 Evgeny
+Poberezkin*.)
+
+### fastest-levenshtein (1.0.x)
+
+Levenshtein-distance implementation used in sequence comparison code paths.
+
+- Upstream: https://github.com/ka-weihe/fastest-levenshtein
+- License: **MIT**
+
+```
+MIT License
+
+Copyright (c) 2020 Kasper Unn Weihe
+
+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:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+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.
+```
+
+### umap-js (1.4.x)
+
+UMAP dimensionality reduction used by sequence-space and similarity viewers.
+The npm package metadata declares MIT but the LICENSE file shipped in the
+tarball is **Apache-2.0**, so we comply with the more conservative Apache-2.0
+terms (preserve copyright/attribution; mark modifications, of which there are
+none).
+
+- Upstream: https://github.com/PAIR-code/umap-js
+- Author: Andy Coenen (Google PAIR)
+- License: **Apache-2.0**
+
+> Licensed under the Apache License, Version 2.0 (the "License"); you may not
+> use this file except in compliance with the License. You may obtain a copy of
+> the License at http://www.apache.org/licenses/LICENSE-2.0
+>
+> Unless required by applicable law or agreed to in writing, software
+> distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
+> WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
+> License for the specific language governing permissions and limitations
+> under the License.
+
+The full Apache-2.0 license text is available at the URL above and in
+`node_modules/umap-js/LICENSE`.
+
+---
+
+## 2. Linked at runtime via the Datagrok platform (webpack externals)
+
+These libraries are not bundled into Bio's `dist/` — they are provided once
+by the platform host and shared across all packages.
+
+| Component                        | Version | License      | Upstream                                          |
+|----------------------------------|---------|--------------|---------------------------------------------------|
+| OpenChemLib JS                   | 7.x     | BSD-3-Clause | https://github.com/cheminfo/openchemlib-js        |
+| RxJS                             | 6.x     | Apache-2.0   | https://github.com/ReactiveX/rxjs                 |
+| cash-dom                         | 8.x     | MIT          | https://github.com/fabiospampinato/cash           |
+| Day.js                           | 1.x     | MIT          | https://github.com/iamkun/dayjs                   |
+| wu.js                            | 2.x     | MIT          | https://github.com/fitzgen/wu.js                  |
+
+OpenChemLib JS is also referenced by Bio's `package.json` `sources`. The
+upstream `openchemlib-js` npm package is distributed under BSD-3-Clause:
+*Copyright (c) 2015-2017, cheminfo.*
+
+---
+
+## 3. Fetched at runtime from third-party CDNs (not bundled)
+
+### kalign (via @biowasm/aioli)
+
+`@biowasm/aioli` loads the **kalign** multiple-sequence-alignment tool from
+the public biowasm CDN (`https://biowasm.com/cdn/v3/...`) on demand. kalign
+itself is **not** bundled into Bio's `dist/` and is **not** redistributed by
+the Datagrok platform. Users that load it transitively are subject to
+kalign's upstream license (GPLv3).
+
+- Upstream: https://github.com/TimoLassmann/kalign
+- License: GPLv3 (used as a runtime-fetched, non-bundled dependency)
+
+---
+
+## 4. Docker container (`dockerfiles/`) — PepSeA service
+
+The Bio package ships a single Docker image (`dockerfiles/Dockerfile`) that
+provides a PepSeA-based MSA service for HELM peptide sequences. The image is
+built from `datagrok/python` and pulls third-party software at build time:
+
+| Component     | Source                                          | License                |
+|---------------|-------------------------------------------------|------------------------|
+| PepSeA        | https://github.com/Merck/PepSeA (main branch)   | MIT (Merck & Co.)      |
+| MAFFT         | https://mafft.cbrc.jp/ (`mafft_7.520-1` .deb)   | MAFFT license (BSD-style, free for any use with attribution) |
+| FastAPI       | https://github.com/tiangolo/fastapi             | MIT                    |
+| uvicorn       | https://www.uvicorn.org/                        | BSD-3-Clause           |
+| ujson         | https://github.com/ultrajson/ultrajson          | BSD-3-Clause           |
+| Python stdlib | https://www.python.org/                         | PSF License            |
+
+The `Dockerfile` patches a few lines of PepSeA's `api.py` at build time to
+add a `/distout` endpoint and JSON error-handling middleware; per MIT terms
+those modifications are noted here.
+
+---
+
+## 5. Development-only dependencies
+
+Tools used during the build/test cycle (not in the runtime tree, not bundled):
+the `datagrok-tools` CLI transitively pulls in `puppeteer-screen-recorder`,
+which references `@ffmpeg-installer/ffmpeg` (LGPL-2.1) and
+`@ffmpeg-installer/win32-x64` (GPLv3). These binaries are **not**
+redistributed as part of the published Bio plugin and impose no obligation on
+users of the plugin.
+
+The peer/devDependencies on other Datagrok plugins (`@datagrok/chem`,
+`@datagrok/dendrogram`, `@datagrok/eda`, `@datagrok/helm`,
+`@datagrok/peptides`) are MIT — covered by the repo-wide `LICENSE.md`. Each
+of those plugins maintains its own `CREDITS.md` (or will) for its own
+third-party content.