Merge branch 'main' into main

.github/workflows/build.yml

@@ -2,9 +2,9 @@ name: Build
 
 on:
   push:
-    branches: [main, 1.1.x]
+    branches: [main, 1.1.x, 1.2.x]
   pull_request:
-    branches: [main, 1.1.x]
+    branches: [main, 1.1.x, 1.2.x]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

.github/workflows/test_linux.yml

@@ -2,9 +2,9 @@ name: Test (Linux)
 
 on:
   push:
-    branches: [main, 1.1.x]
+    branches: [main, 1.1.x, 1.2.x]
   pull_request:
-    branches: [main, 1.1.x]
+    branches: [main, 1.1.x, 1.2.x]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -38,13 +38,10 @@ jobs:
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
 
-      - name: Install test dependencies
-        run: |
-          python -m pip install --upgrade pip wheel
-
       - name: Install dependencies
         run: |
-          pip install --pre ".[tests]"
+          python -m pip install --upgrade pip wheel uv
+          python -m uv pip install --system "scvi-tools[tests] @ ."
 
       - name: Test
         env:

.github/workflows/test_linux_cuda.yml

@@ -2,7 +2,7 @@ name: Test (Linux, CUDA)
 
 on:
   pull_request:
-    branches: [main, 1.1.x]
+    branches: [main, 1.1.x, 1.2.x]
     types: [labeled, synchronize, opened]
   schedule:
     - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
@@ -48,7 +48,8 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install ".[tests]"
+          python -m pip install --upgrade pip wheel uv
+          python -m uv pip install --system "scvi-tools[tests] @ ."
 
       - name: Test
         env:

.github/workflows/test_linux_pre.yml

@@ -2,7 +2,7 @@ name: Test (Linux, prereleases)
 
 on:
   pull_request:
-    branches: [main, 1.1.x]
+    branches: [main, 1.1.x, 1.2.x]
     types: [labeled, synchronize, opened]
   schedule:
     - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
@@ -48,13 +48,10 @@ jobs:
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
 
-      - name: Install test dependencies
-        run: |
-          python -m pip install --upgrade pip wheel
-
       - name: Install dependencies
         run: |
-          pip install --pre ".[tests]"
+          python -m pip install --upgrade pip wheel uv
+          python -m uv pip install --system "scvi-tools[tests] @ ."
 
       - name: Test
         env:

.github/workflows/test_linux_private.yml

@@ -2,10 +2,10 @@ name: Test (Linux, private)
 
 on:
   pull_request:
-    branches: [main, 1.1.x]
+    branches: [main, 1.1.x, 1.2.x]
     types: [labeled, synchronize, opened]
   push:
-    branches: [main, 1.1.x]
+    branches: [main, 1.1.x, 1.2.x]
   schedule:
     - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
   workflow_dispatch:
@@ -60,13 +60,10 @@ jobs:
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
 
-      - name: Install test dependencies
-        run: |
-          python -m pip install --upgrade pip wheel
-
       - name: Install dependencies
         run: |
-          pip install ".[tests]"
+          python -m pip install --upgrade pip wheel uv
+          python -m uv pip install --system "scvi-tools[tests] @ ."
 
       - name: Test
         env:

docs/api/developer.md

@@ -93,6 +93,7 @@ Parameterizable probability distributions.
    :toctree: reference/
    :nosignatures:
 
+   distributions.Poisson
    distributions.NegativeBinomial
    distributions.NegativeBinomialMixture
    distributions.ZeroInflatedNegativeBinomial
@@ -124,6 +125,7 @@ These classes should be used to construct user-facing model classes.
     model.base.PyroJitGuideWarmup
     model.base.PyroModelGuideWarmup
     model.base.DifferentialComputation
+    model.base.EmbeddingMixin
 ```
 
 ## Module
@@ -197,6 +199,7 @@ These classes should be used to construct module classes that define generative
    module.base.BaseMinifiedModeModuleClass
    module.base.PyroBaseModuleClass
    module.base.JaxBaseModuleClass
+   module.base.EmbeddingModuleMixin
    module.base.LossOutput
    module.base.auto_move_data
 
@@ -219,7 +222,9 @@ Basic neural network building blocks.
    nn.FCLayers
    nn.Encoder
    nn.Decoder
+   nn.DecoderSCVI
    nn.one_hot
+   nn.Embedding
 
 ```
 
@@ -252,25 +257,6 @@ TrainingPlans define train/test/val optimization steps for modules.
 
 ```
 
-## Model hyperparameter tuning
-
-`scvi-tools` supports automatic model hyperparameter tuning using [Ray Tune]. These
-classes allow for new model classes to be easily integrated with the module.
-
-```{eval-rst}
-.. currentmodule:: scvi
-```
-
-```{eval-rst}
-.. autosummary::
-   :toctree: reference/
-   :nosignatures:
-
-   autotune.TunerManager
-   autotune.Tunable
-   autotune.TunableMixin
-```
-
 ## Utilities
 
 ```{eval-rst}

docs/api/user.md

@@ -117,8 +117,8 @@ Here we maintain a few package specific utilities for feature selection, etc.
    :toctree: reference/
    :nosignatures:
 
-   autotune.ModelTuner
-   autotune.TuneAnalysis
+   autotune.run_autotune
+   autotune.AutotuneExperiment
 ```
 
 ## Model hub

docs/release_notes/index.md

@@ -7,7 +7,47 @@ is available in the [commit logs](https://github.com/scverse/scvi-tools/commits/
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-### 1.1.1 (unreleased)
+### 1.2.0 (unreleased)
+
+#### Added
+
+-   Add new experimental functional API for hyperparameter tuning with
+    {func}`scvi.autotune.run_autotune` and {class}`scvi.autotune.AutotuneExperiment` to replace
+    {class}`scvi.autotune.ModelTuner`, {class}`scvi.autotune.TunerManager`, and
+    {class}`scvi.autotune.TuneAnalysis` {pr}`2561`.
+-   Add experimental class {class}`scvi.nn.Embedding` implementing methods for extending embeddings
+    {pr}`2574`.
+-   Add experimental support for representing batches with continuously-valued embeddings by passing
+    in `batch_representation="embedding"` to {class}`scvi.model.SCVI` {pr}`2576`.
+-   Add experimental mixin classes {class}`scvi.model.base.EmbeddingMixin` and
+    {class}`scvi.module.base.EmbeddingModuleMixin` {pr}`2576`.
+-   Add option to generate synthetic spatial coordinates in {func}`scvi.data.synthetic_iid` with
+    argument `generate_coordinates` {pr}`2603`.
+-   Add experimental support for using custom {class}`lightning.pytorch.core.LightningDataModule`s
+    in {func}`scvi.autotune.run_autotune` {pr}`2605`.
+
+#### Changed
+
+-   Deprecate {func}`scvi.data.cellxgene`, to be removed in v1.3. Please directly use the
+    [cellxgene-census](https://chanzuckerberg.github.io/cellxgene-census/) instead {pr}`2542`.
+
+#### Removed
+
+-   Remove {class}`scvi.autotune.ModelTuner`, {class}`scvi.autotune.TunerManager`, and
+    {class}`scvi.autotune.TuneAnalysis` in favor of new experimental functional API with
+    {func}`scvi.autotune.run_autotune` and {class}`scvi.autotune.AutotuneExperiment` {pr}`2561`.
+
+### 1.1.2 (2024-03-01)
+
+#### Changed
+
+-   Address AnnData >= 0.10 deprecation warning for {func}`anndata.read` by replacing instances with
+    {func}`anndata.read_h5ad` {pr}`2531`.
+-   Address AnnData >= 0.10 deprecation warning for {class}`anndata._core.sparse_dataset.SparseDataset`
+    by replacing instances with {class}`anndata.experimental.CSCDataset` and
+    {class}`anndata.experimental.CSRDataset` {pr}`2531`.
+
+### 1.1.1 (2024-02-19)
 
 #### Fixed
 

pyproject.toml

@@ -5,7 +5,7 @@ requires = ["hatchling"]
 
 [project]
 name = "scvi-tools"
-version = "1.1.1"
+version = "1.1.2"
 description = "Deep probabilistic analysis of single-cell omics data."
 readme = "README.md"
 requires-python = ">=3.9"
@@ -59,7 +59,7 @@ dependencies = [
 [project.optional-dependencies]
 tests = [
     "pytest",
-    "pytest-cov",
+    "coverage",
     "scvi-tools[optional]"
 ]  # dependencies for running the test suite
 editing = [
@@ -89,8 +89,6 @@ docsbuild = ["scvi-tools[docs,optional]"]  # docs build dependencies
 autotune = [
     "hyperopt>=0.2",
     "ray[tune]>=2.5.0,<2.10.0",
-    "ipython",
-    "scib-metrics>=0.4.1",
     "tensorboard",
 ]  # scvi.autotune
 aws = ["boto3"] # scvi.hub.HubModel.pull_from_s3
@@ -182,10 +180,6 @@ select = [
     "RUF100",  # Report unused noqa directives
 ]
 ignore = [
-    # line too long -> we accept long comment lines; black gets rid of long code lines
-    "E501",
-    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
-    "E731",
     # allow I, O, l as variable names -> I is the identity matrix
     "E741",
     # Missing docstring in public package
@@ -207,10 +201,17 @@ ignore = [
     "D203",
     # We want docstrings to start immediately after the opening triple quote
     "D213",
-    # Missing argument description in the docstring TODO: enable
-    "D417",
 ]
 
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.per-file-ignores]
+"docs/*" = ["I", "BLE001"]
+"tests/*" = ["D"]
+"*/__init__.py" = ["F401"]
+"scvi/__init__.py" = ["I"]
+
 [tool.ruff.format]
 # Like Black, use double quotes for strings.
 quote-style = "double"
@@ -224,14 +225,7 @@ skip-magic-trailing-comma = false
 # Like Black, automatically detect the appropriate line ending.
 line-ending = "auto"
 
-[tool.ruff.pydocstyle]
-convention = "numpy"
 
-[tool.ruff.per-file-ignores]
-"docs/*" = ["I", "BLE001"]
-"tests/*" = ["D"]
-"*/__init__.py" = ["F401"]
-"scvi/__init__.py" = ["I"]
 
 [tool.jupytext]
 formats = "ipynb,md"

scvi/__init__.py

@@ -4,7 +4,7 @@
 import logging
 import warnings
 
-from ._constants import METRIC_KEYS, REGISTRY_KEYS
+from ._constants import REGISTRY_KEYS
 from ._settings import settings
 
 # this import needs to come after prior imports to prevent circular import
@@ -25,7 +25,6 @@
 __all__ = [
     "settings",
     "REGISTRY_KEYS",
-    "METRIC_KEYS",
     "data",
     "model",
     "external",

scvi/_constants.py

@@ -16,18 +16,4 @@ class _REGISTRY_KEYS_NT(NamedTuple):
     OBSERVED_LIB_SIZE: str = "observed_lib_size"
 
 
-class _METRIC_KEYS_NT(NamedTuple):
-    TRAINING_KEY: str = "training"
-    VALIDATION_KEY: str = "validation"
-    # classification
-    ACCURACY_KEY: str = "accuracy"
-    F1_SCORE_KEY: str = "f1_score"
-    CALIBRATION_ERROR_KEY: str = "calibration_error"
-    AUROC_KEY: str = "auroc"
-    CLASSIFICATION_LOSS_KEY: str = "classification_loss"
-    TRUE_LABELS_KEY: str = "true_labels"
-    LOGITS_KEY: str = "logits"
-
-
 REGISTRY_KEYS = _REGISTRY_KEYS_NT()
-METRIC_KEYS = _METRIC_KEYS_NT()