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add Palantir to scvers #1

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@katosh katosh commented May 13, 2024

@ManuSetty this is a local PR just to discuss the changes. I only added the package description that is needed to make a submission for Palantir to be added to the scverse. Please let me know if I should make any further changes and what other authors besides you I should include.

@katosh katosh requested a review from ManuSetty May 13, 2024 20:22
@katosh katosh self-assigned this May 13, 2024
pre-commit-ci bot and others added 3 commits May 14, 2024 10:36
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#170)
8abdd64 
updates:
- [github.com/python-jsonschema/check-jsonschema: 0.28.2 → 0.28.3](python-jsonschema/check-jsonschema@0.28.2...0.28.3)
- [github.com/python-jsonschema/check-jsonschema: 0.28.2 → 0.28.3](python-jsonschema/check-jsonschema@0.28.2...0.28.3)
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](astral-sh/ruff-pre-commit@v0.4.3...v0.4.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@berombau
add flowsom meta.yaml (scverse#168)
b01c0f4
@katosh
add authors to palantir
a3aad87
@katosh katosh marked this pull request as draft May 15, 2024 18:14
katosh and others added 23 commits May 24, 2024 11:13
@katosh
Add palantir to the scverse (scverse#171)
5082626 
* add Palantir

* add authors to palantir
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#172)
02eb1f0 
updates:
- [github.com/python-jsonschema/check-jsonschema: 0.28.3 → 0.28.4](python-jsonschema/check-jsonschema@0.28.3...0.28.4)
- [github.com/python-jsonschema/check-jsonschema: 0.28.3 → 0.28.4](python-jsonschema/check-jsonschema@0.28.3...0.28.4)
- [github.com/astral-sh/ruff-pre-commit: v0.4.4 → v0.4.5](astral-sh/ruff-pre-commit@v0.4.4...v0.4.5)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#174)
4ec23f3 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.5 → v0.4.7](astral-sh/ruff-pre-commit@v0.4.5...v0.4.7)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@maltekuehl
Add pytximport (scverse#173)
f9d5694 
* Add pytximport

* Replace tab with spaces to fix prettier error
@Zethson
Add pertpy (scverse#175)
e92af1e 
* Add pertpy

Signed-off-by: zethson <lukas.heumos@posteo.net>

* rename file

Signed-off-by: zethson <lukas.heumos@posteo.net>

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#176)
39feb47 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
e5ba39f
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#178)
521e78c 
updates:
- [github.com/python-jsonschema/check-jsonschema: 0.28.4 → 0.28.5](python-jsonschema/check-jsonschema@0.28.4...0.28.5)
- [github.com/python-jsonschema/check-jsonschema: 0.28.4 → 0.28.5](python-jsonschema/check-jsonschema@0.28.4...0.28.5)
- [github.com/astral-sh/ruff-pre-commit: v0.4.8 → v0.4.9](astral-sh/ruff-pre-commit@v0.4.8...v0.4.9)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#179)
9b429e2 
updates:
- [github.com/python-jsonschema/check-jsonschema: 0.28.5 → 0.28.6](python-jsonschema/check-jsonschema@0.28.5...0.28.6)
- [github.com/python-jsonschema/check-jsonschema: 0.28.5 → 0.28.6](python-jsonschema/check-jsonschema@0.28.5...0.28.6)
- [github.com/astral-sh/ruff-pre-commit: v0.4.9 → v0.4.10](astral-sh/ruff-pre-commit@v0.4.9...v0.4.10)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
b128a83
@bernheder
Added meta.yaml for the Rectangle package (scverse#180)
314c8bb 
* Added meta.yaml for the Rectangle package

* Added meta.yaml for the Rectangle package

* added link to tutorial
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#181)
2cbe368 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.10 → v0.5.0](astral-sh/ruff-pre-commit@v0.4.10...v0.5.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#183)
5e8a4ff 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
b91a7a0
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#184)
89acb37 
updates:
- [github.com/python-jsonschema/check-jsonschema: 0.28.6 → 0.29.0](python-jsonschema/check-jsonschema@0.28.6...0.29.0)
- [github.com/python-jsonschema/check-jsonschema: 0.28.6 → 0.29.0](python-jsonschema/check-jsonschema@0.28.6...0.29.0)
- [github.com/astral-sh/ruff-pre-commit: v0.5.1 → v0.5.2](astral-sh/ruff-pre-commit@v0.5.1...v0.5.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#191)
49eda99 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.2 → v0.5.4](astral-sh/ruff-pre-commit@v0.5.2...v0.5.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@grst @pre-commit-ci
Be explicit about test coverage and add footnotes (scverse#190)
c9de2e1 
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for more information, see https://pre-commit.ci

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* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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[pre-commit.ci] pre-commit autoupdate (scverse#192)
98cef2c 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
137ce36
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#194)
c9b96a0 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#196)
7f14680 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@mehdijoodaki
Add PILOT (scverse#189)
45dac56 
* Add  PILOT

* Update meta.yaml
@huang-sh @pre-commit-ci
add GPTBioInsightor (scverse#193)
6bb4090 
* add GPTBioInsightor

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for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
pre-commit-ci bot and others added 29 commits June 3, 2025 10:56
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#251)
364a074 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@serjisa
Add a new package: scLiTr (scverse#246)
f6681ad 
Create meta.yaml
@earmingol @pre-commit-ci
Add scCellFie (scverse#248)
f859f03 
* Added meta.yaml for scCellFie

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---------

Co-authored-by: Erick Armingol <erickarmingol@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#252)
087d02f 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.11.12 → v0.11.13](astral-sh/ruff-pre-commit@v0.11.12...v0.11.13)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
d0cca3d
@scverse-bot
Updated template-repos.yml
0ca6fb6
@huang-sh @grst @mikkelnrasmussen
add scmcp (scverse#238)
bb7dd3c 
* add scanpy-mcp

* Rename meta.yml to meta.yaml

* Update meta.yaml

* rename to scmcp

* Delete packages/scanpy-mcp directory

* Create meta.yaml

* Update meta.yaml

---------

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com>
@Zethson
Remove core packages (scverse#257)
715b6a4 
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
@pre-commit-ci @flying-sheep
[pre-commit.ci] pre-commit autoupdate (scverse#255)
08fc058 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#260)
5b229e8 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#261)
7233fb5 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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[pre-commit.ci] pre-commit autoupdate (scverse#264)
e4be05a 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
32bb4c3
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#266)
773142c 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@annmoel @pre-commit-ci @mikkelnrasmussen
add scxmatch (scverse#256)
b2363d2 
* add scxmatch

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for more information, see https://pre-commit.ci

* Corrected DOI format

* Update meta.yaml

---------

Co-authored-by: Anna Moeller <je30bery@idea-ramses.aibe.uni-erlangen.de>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com>
@joschif @mikkelnrasmussen
Add delnx (scverse#259)
c6480db 
add meta

Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com>
@psl-schaefer @mikkelnrasmussen
adding partipy (scverse#265)
737908c 
* adding partipy

* fix typo

---------

Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#267)
cfe613c 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
cc18e54
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#268)
2b89c92 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@maltekuehl @mikkelnrasmussen
Add spatiomic (scverse#263)
da4521d 
Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com>
@PSSUN @pre-commit-ci @mikkelnrasmussen
add STMiner (scverse#254)
12b46a0 
* add STMiner

Name of the tool: STMiner

Short description: Gene-centric spatial transcriptomics for deciphering complex spatial omics data

How does the package use scverse data structures (please describe in a few sentences): STMiner uses AnnData as standardized input and output, and all operations are based on AnnData. STMiner also supports reading data in multiple formats (CSV, gem, etc.) and converting them into AnnData for unified operations.

- [x] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license
- [x] The package provides versioned releases
- [x] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
- [x] Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1]
- [x] Continuous integration (CI) automatically executes these tests on each push or pull request [^2]
- [x] The package provides API documentation via a website or README[^3]
- [x] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
- [x] I am an author or maintainer of the tool and agree on listing the package on the scverse website

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To add a new package to the list, please add a `meta.yaml` file to the `packages` directory and
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* [pre-commit.ci] auto fixes from pre-commit.com hooks

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#269)
3f1dcf2 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
dcad1e2
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#270)
76d605b 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#273)
e3daf0a 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@scverse-bot
Updated template-repos.yml
c4398e1
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (scverse#275)
e4e7357 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@katosh
Merge remote-tracking branch 'official/main' into main
80cbbab
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