init

add tests

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

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resolve comments

Squashed commit of the following:

commit 56888eb
Merge: d169628 9068a93
Author: Selman Özleyen <32667648+selmanozleyen@users.noreply.github.com>
Date:   Fri Jun 13 12:03:07 2025 +0200

    Merge pull request #235 from theislab/feature/predict_batch

    Feature and Speedup: `predict_batch`

commit d169628
Merge: f6cdf17 801adf0
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri Jun 13 11:28:18 2025 +0200

    Merge pull request #239 from theislab/feature/ooc-dataloading

    Feature: Out of Core Dataloading Option

commit 801adf0
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu Jun 12 15:31:53 2025 +0200

    add return types

commit 6d44054
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu Jun 12 13:56:48 2025 +0200

    update error message

commit 3bda128
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu Jun 12 13:56:20 2025 +0200

    document better

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Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Thu Jun 12 11:51:03 2025 +0000

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

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commit 8f18574
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu Jun 12 13:50:55 2025 +0200

    remove unused fixture

commit 8e808a9
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Thu Jun 12 11:17:33 2025 +0000

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commit 67e64e1
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu Jun 12 13:17:22 2025 +0200

    add tests

commit ab95081
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu Jun 12 12:08:48 2025 +0200

    throw error when there isn't any valid indices

commit 9068a93
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Thu Jun 12 09:38:43 2025 +0000

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commit d65151a
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu Jun 12 11:38:34 2025 +0200

    When using PredictionSampler we can't use batched mode

commit bb941ea
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu Jun 12 11:33:45 2025 +0200

    clarify documentation that this requires same number of cells

commit 7461dc3
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Sun Jun 1 16:07:15 2025 +0200

    Fix type error

commit 04566e7
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Tue May 27 17:11:02 2025 +0200

    Replace tree map

commit 4a9bbcd
Merge: 855c5d9 f6cdf17
Author: LeonStadelmann <169152764+LeonStadelmann@users.noreply.github.com>
Date:   Tue May 27 16:58:19 2025 +0200

    Merge branch 'main' into feature/predict_batch

commit f6cdf17
Merge: b4b7c96 70766f5
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Tue May 27 09:10:57 2025 +0200

    Merge pull request #246 from theislab/pre-commit-ci-update-config

    [pre-commit.ci] pre-commit autoupdate

commit b4b7c96
Merge: 7a69c5d b67804f
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Tue May 27 09:10:36 2025 +0200

    Merge pull request #245 from theislab/feature/stochastic_to_cellflow_class

    pass rng from cellflow.predict

commit 70766f5
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon May 26 18:56:02 2025 +0000

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    - [github.com/tox-dev/pyproject-fmt: v2.5.1 → v2.6.0](tox-dev/pyproject-fmt@v2.5.1...v2.6.0)
    - [github.com/astral-sh/ruff-pre-commit: v0.11.10 → v0.11.11](astral-sh/ruff-pre-commit@v0.11.10...v0.11.11)

commit b67804f
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Mon May 26 11:03:13 2025 +0200

    fix callback/

commit b9bc6c2
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Mon May 26 09:04:25 2025 +0200

    pass rng from cellflow.predict

commit 7a69c5d
Merge: ce064e3 50a3cc8
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 17:17:03 2025 +0200

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    [pre-commit.ci] pre-commit autoupdate

commit ce064e3
Merge: 6cb5540 b6c0bdb
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 17:14:53 2025 +0200

    Merge pull request #215 from theislab/add/solver_callback

    Add solver to callback call

commit 6cb5540
Merge: 0dbf90f 83db489
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 17:05:14 2025 +0200

    Merge pull request #233 from theislab/tutorial/combosciplex

    add combosciplex

commit 0dbf90f
Merge: d8ae659 69327d9
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 17:04:55 2025 +0200

    Merge pull request #244 from theislab/tests/find_failing2

    deprecation python 3.10

commit 69327d9
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 15:42:55 2025 +0200

    enable all tests

commit 83db489
Merge: 63c4966 d8ae659
Author: Dominik Klein <domin.klein@gmail.com>
Date:   Fri May 23 15:29:53 2025 +0200

    Merge branch 'main' into tutorial/combosciplex

commit 63c4966
Author: Dominik Klein <domin.klein@gmail.com>
Date:   Fri May 23 15:22:53 2025 +0200

    add combosciplex

commit 855c5d9
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Fri May 23 14:59:56 2025 +0200

    revert duplicate removal

commit 235bc0e
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Fri May 23 14:03:43 2025 +0200

    emove duplicate

commit 24ade1e
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Fri May 23 14:01:31 2025 +0200

    Add testing for genot predict

commit 340b696
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 12:23:15 2025 +0200

    only enable test_cellflow_with_validation

commit 9dfcd18
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 11:50:27 2025 +0200

    skip some tests again

commit f481dac
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 10:38:10 2025 +0200

    enable more tests again

commit 6bb6550
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 10:27:57 2025 +0200

    deprecate 3.10

commit 8e8d2ad
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 10:26:24 2025 +0200

    deprecate 3.10

commit 11d2f55
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 10:24:35 2025 +0200

    deprecate 3.10

commit 459f435
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 10:22:14 2025 +0200

    enable some more tests

commit 0b56b4c
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 10:05:24 2025 +0200

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commit 2e7aac9
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Fri May 23 09:48:30 2025 +0200

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commit d8ae659
Merge: 70eec9a f3c840c
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Thu May 22 16:27:36 2025 +0200

    Merge pull request #241 from theislab/fix/tokenattention

    fix TokenAttention

commit 0da9154
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Thu May 22 16:25:26 2025 +0200

    skip more tests

commit 7de55b3
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Thu May 22 15:06:36 2025 +0200

    skip more tests

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Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Thu May 22 11:17:07 2025 +0000

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commit 7840c80
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Thu May 22 13:16:42 2025 +0200

    skip gene emb tests

commit f3c840c
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Thu May 22 08:41:30 2025 +0200

    update scvi dependency

commit fd76f07
Author: selmanozleyen <syozleyen@gmail.com>
Date:   Wed May 21 13:15:15 2025 +0200

    add genot

commit e97edd2
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Wed May 21 12:41:07 2025 +0200

    Handle empty input

commit 454734e
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Tue May 20 19:31:39 2025 +0200

    revert previous precommit changes

commit 0884a8b
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Tue May 20 17:17:10 2025 +0200

    fix tests

commit 186bcaa
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Tue May 20 15:35:46 2025 +0200

    fix tests

commit c5c0494
Author: Dominik Klein <dominik.klein@helmholtz-munich.de>
Date:   Tue May 20 15:30:09 2025 +0200

    fix TokenAttention

commit 1e585cd
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Tue May 20 10:46:42 2025 +0000

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commit 5dc4a54
Author: selmanozleyen <syozleyen@gmail.com>
Date:   Tue May 20 12:45:24 2025 +0200

    support both dataloaders

commit dd098fa
Author: selmanozleyen <syozleyen@gmail.com>
Date:   Tue May 20 11:21:35 2025 +0200

    init

commit 50a3cc8
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon May 19 18:57:43 2025 +0000

    [pre-commit.ci] pre-commit autoupdate

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    - [github.com/astral-sh/ruff-pre-commit: v0.11.9 → v0.11.10](astral-sh/ruff-pre-commit@v0.11.9...v0.11.10)

commit 2ccb43d
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Sun May 18 12:33:32 2025 +0200

    Add batched predict test

commit 10edee2
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Sat May 17 20:11:45 2025 +0200

    Adjust docs

commit b6c0bdb
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Sat May 17 17:42:27 2025 +0200

    fix docs

commit 021aff0
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Thu May 15 12:42:30 2025 +0200

    update implementation so that two functions predict and predict batch are unified

commit 6bdbf5c
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Tue May 13 16:24:30 2025 +0000

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

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commit db6dc69
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Tue May 13 18:20:22 2025 +0200

    needs testing

commit a3c43d3
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Tue May 13 18:00:26 2025 +0200

    condition keys left to add

commit 03dfb2b
Author: selman.ozleyen <syozleyen@gmail.com>
Date:   Tue May 13 17:50:41 2025 +0200

    init

commit f1e8704
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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    [pre-commit.ci] auto fixes from pre-commit.com hooks

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commit facf52d
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Mon May 12 13:23:52 2025 +0200

    Added source data parameter + stochastic test

commit 04a1d2c
Author: Dominik Klein <domin.klein@gmail.com>
Date:   Fri May 9 13:35:02 2025 +0200

    add combosciplex

commit 54e2386
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Thu May 1 16:16:21 2025 +0200

    Rename flow

commit ac8d073
Merge: 5327a05 4970ad4
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Thu May 1 16:14:11 2025 +0200

    Merge branch 'main' into add/solver_callback

commit 5327a05
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Thu May 1 12:37:09 2025 +0200

    Added test for custom callbacks

commit e650031
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Thu Apr 24 18:09:57 2025 +0200

    Add typing and solver for on_train_end

commit 5e18f6e
Author: LeonStadelmann <leonstadlmnn@gmail.com>
Date:   Mon Apr 21 16:57:33 2025 +0200

    Add solver to callback call

Revert "resolve comments"

This reverts commit 1429cab.

Revert "Revert "resolve comments""

This reverts commit 6f0d747.

Revert "Squashed commit of the following:"

This reverts commit d850771.

Author: selmanozleyen

.github/workflows/build.yaml

@@ -15,10 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.11
+      - name: Set up Python 3.10
         uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
       - name: Install build dependencies

.github/workflows/lint.yml

@@ -25,10 +25,10 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: true
-      - name: Set up Python 3.11
+      - name: Set up Python 3.10
         uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.10"
 
       - name: Cache pre-commit
         uses: actions/cache@v3

.github/workflows/test.yaml

@@ -23,12 +23,12 @@ jobs:
       fail-fast: false
       matrix:
         include:
+          - os: ubuntu-latest
+            python: "3.10"
           - os: ubuntu-latest
             python: "3.11"
           - os: ubuntu-latest
             python: "3.12"
-          - os: ubuntu-latest
-            python: "3.13"
           - os: macos-latest
             python: "3.12"
 

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 repos:
   # Hooks that are run everywhere
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.0.0-beta.5
+    rev: v2.0.0-beta.3
     hooks:
       - id: biome-format
   # Hooks that are run for scripts
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.6.0
+    rev: v2.5.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.11
+    rev: v0.11.9
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.10"
 sphinx:
   configuration: docs/conf.py
   # disable this for more lenient docs builds

docs/installation.rst

@@ -1,6 +1,6 @@
 Installation
 ============
-:mod:`cellflow` requires Python version >= 3.11 to run.
+:mod:`cellflow` requires Python version >= 3.10 to run.
 
 PyPI
 ----