Add Novae

README.md

@@ -15,9 +15,9 @@ It **does not** imply endorsement or that an in-depth review has been performed.
 
 Submit a pull-request adding a `meta.yaml` file for your package to the `packages` directory.
 
--   Please refer to other entries for examples
--   The full definition of available fields is available in [`schema.json`](schema.json)
--   Please copy the checklist from below into the pull request description and answer all questions.
+- Please refer to other entries for examples
+- The full definition of available fields is available in [`schema.json`](schema.json)
+- Please copy the checklist from below into the pull request description and answer all questions.
 
 ## What are the requirements for an ecosystem package?
 
@@ -37,25 +37,25 @@ Short description: XXX
 
 How does the package use scverse data structures (please describe in a few sentences): XXX
 
--   [ ] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license
--   [ ] The package provides versioned releases
--   [ ] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
--   [ ] Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1]
--   [ ] Continuous integration (CI) automatically executes these tests on each push or pull request [^2]
--   [ ] The package provides API documentation via a website or README[^3]
--   [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
--   [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website
+- [ ] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license
+- [ ] The package provides versioned releases
+- [ ] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
+- [ ] Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1]
+- [ ] Continuous integration (CI) automatically executes these tests on each push or pull request [^2]
+- [ ] The package provides API documentation via a website or README[^3]
+- [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
+- [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website
 
 ### Recommended
 
--   [ ] Please announce this package on scverse communication channels (zulip, discourse, twitter)
--   [ ] Please tag the author(s) these announcements. Handles (e.g. `@scverse_team`) to include are:
-    -   Twitter:
-    -   Zulip:
-    -   Discourse:
-    -   Mastodon:
--   [ ] The package provides tutorials (or "vignettes") that help getting users started quickly
--   [ ] The package uses the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse).
+- [ ] Please announce this package on scverse communication channels (zulip, discourse, twitter)
+- [ ] Please tag the author(s) these announcements. Handles (e.g. `@scverse_team`) to include are:
+    - Twitter:
+    - Zulip:
+    - Discourse:
+    - Mastodon:
+- [ ] The package provides tutorials (or "vignettes") that help getting users started quickly
+- [ ] The package uses the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse).
 
 [^1]: We recommend thtat tests cover at least all user facing (public) functions. Minimal tests ensure that the function does not fail on an example data set. Ideally, tests also ensure the correctness of the results, e.g. by comparing against a snapshot.
 

packages/novae/meta.yaml

@@ -0,0 +1,20 @@
+name: novae
+description: |
+  Graph-based foundation model for spatial transcriptomics data.
+  Zero-shot spatial domain inference, batch-effect correction, and many other features.
+project_home: https://github.com/MICS-Lab/novae
+documentation_home: https://mics-lab.github.io/novae/
+publications:
+  - 10.1101/2024.09.09.612009
+install:
+  pypi: novae
+tags:
+  - spatial-omics
+  - spatial-transcriptomics
+  - spatialdata
+  - deep learning
+license: BSD-3-Clause
+version: v0.2.1
+authors:
+  - quentinblampey
+test_command: pip install ".[dev]" && pytest

packages/sopa/meta.yaml

@@ -6,7 +6,7 @@ description: |
 project_home: https://github.com/gustaveroussy/sopa
 documentation_home: https://gustaveroussy.github.io/sopa/
 publications:
-  - 10.1101/2023.12.22.571863
+  - 10.1038/s41467-024-48981-z
 install:
   pypi: sopa
 tags: