Merge branch 'main' into chex

.github/workflows/build.yml

@@ -9,17 +9,22 @@ on:
 jobs:
     package:
         runs-on: ubuntu-latest
+
         steps:
             - uses: actions/checkout@v3
-            - name: Set up Python 3.10
+
+            - name: Set up Python 3.11
               uses: actions/setup-python@v4
               with:
-                  python-version: "3.10"
+                  python-version: "3.11"
                   cache: "pip"
                   cache-dependency-path: "**/pyproject.toml"
+
             - name: Install build dependencies
               run: python -m pip install --upgrade pip wheel twine build
+
             - name: Build package
               run: python -m build
+
             - name: Check package
               run: twine check --strict dist/*.whl

.github/workflows/release.yml

@@ -9,19 +9,19 @@ jobs:
     release:
         name: Release
         runs-on: ubuntu-latest
+
         steps:
-            # will use ref/SHA that triggered it
             - name: Checkout code
               uses: actions/checkout@v3
 
-            - name: Set up Python 3.9
+            - name: Set up Python 3.11
               uses: actions/setup-python@v4
               with:
-                  python-version: "3.9"
+                  python-version: "3.11"
 
             - name: Install hatch
               run: |
-                  pip install hatch
+                  python -m pip install --upgrade hatch
 
             - name: Build project for distribution
               run: hatch build

.github/workflows/test_linux_cpu.yml

@@ -34,24 +34,29 @@ jobs:
 
         steps:
             - uses: actions/checkout@v3
+
             - name: Set up Python ${{ matrix.python }}
               uses: actions/setup-python@v4
               with:
                   python-version: ${{ matrix.python }}
                   cache: "pip"
                   cache-dependency-path: "**/pyproject.toml"
+
             - name: Install test dependencies
               run: |
                   python -m pip install --upgrade pip wheel
-            - name: Install dependencies
+
+            - name: Install scvi-tools test dependencies
               run: |
-                  pip install ".[dev,pymde,autotune,hub]"
+                  pip install ".[tests]"
+
             - name: Test
               env:
                   MPLBACKEND: agg
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
               run: |
                   pytest -v --cov --color=yes
+
             - name: Upload coverage
               uses: codecov/codecov-action@v3

.github/workflows/test_linux_cpu_pre.yml

@@ -36,24 +36,29 @@ jobs:
 
         steps:
             - uses: actions/checkout@v3
+
             - name: Set up Python ${{ matrix.python }}
               uses: actions/setup-python@v4
               with:
                   python-version: ${{ matrix.python }}
                   cache: "pip"
                   cache-dependency-path: "**/pyproject.toml"
+
             - name: Install test dependencies
               run: |
                   python -m pip install --upgrade pip wheel
-            - name: Install dependencies
+
+            - name: Install scvi-tools test dependencies
               run: |
-                  pip install --pre ".[dev,pymde,autotune,hub]"
+                  pip install --pre ".[tests]"
+
             - name: Test
               env:
                   MPLBACKEND: agg
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
               run: |
                   pytest -v --cov --color=yes
+
             - name: Upload coverage
               uses: codecov/codecov-action@v3

.github/workflows/test_linux_cuda.yml

@@ -15,13 +15,11 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                ubuntu: [latest]
-                mamba: [latest]
                 python: ["3.11"]
                 cuda: ["11"]
 
         container:
-            image: martinkim0/scvi-tools:ubuntu-${{ matrix.ubuntu }}-mamba-${{ matrix.mamba}}-python-${{ matrix.python }}-cuda-${{ matrix.cuda }}
+            image: martinkim0/scvi-tools:py${{ matrix.python }}-cu${{ matrix.cuda }}-base
             options: --user root --gpus all
 
         steps:
@@ -30,15 +28,15 @@ jobs:
 
             - name: Install dependencies
               run: |
-                  pip install ".[dev,pymde,autotune,hub]"
+                  pip install ".[tests]"
 
             - name: Test
               env:
                   MPLBACKEND: agg
                   PLATFORM: ubuntu
                   DISPLAY: :42
               run: |
-                  pytest -v --cov --color=yes --cuda
+                  pytest -v --cov --color=yes --accelerator cuda --devices auto
 
             - name: Upload coverage
               uses: codecov/codecov-action@v3

.github/workflows/test_macos_cpu.yml

@@ -36,24 +36,29 @@ jobs:
 
         steps:
             - uses: actions/checkout@v3
+
             - name: Set up Python ${{ matrix.python }}
               uses: actions/setup-python@v4
               with:
                   python-version: ${{ matrix.python }}
                   cache: "pip"
                   cache-dependency-path: "**/pyproject.toml"
+
             - name: Install test dependencies
               run: |
                   python -m pip install --upgrade pip wheel
-            - name: Install dependencies
+
+            - name: Install scvi-tools test dependencies
               run: |
-                  pip install ".[dev,pymde,autotune,hub]"
+                  pip install ".[tests]"
+
             - name: Test
               env:
                   MPLBACKEND: agg
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
               run: |
                   pytest -v --cov --color=yes
+
             - name: Upload coverage
               uses: codecov/codecov-action@v3

.github/workflows/test_windows_cpu.yml

@@ -36,24 +36,29 @@ jobs:
 
         steps:
             - uses: actions/checkout@v3
+
             - name: Set up Python ${{ matrix.python }}
               uses: actions/setup-python@v4
               with:
                   python-version: ${{ matrix.python }}
                   cache: "pip"
                   cache-dependency-path: "**/pyproject.toml"
+
             - name: Install test dependencies
               run: |
                   python -m pip install --upgrade pip wheel
-            - name: Install dependencies
+
+            - name: Install scvi-tools test dependencies
               run: |
-                  pip install ".[dev,pymde,autotune,hub]"
+                  pip install ".[tests]"
+
             - name: Test
               env:
                   MPLBACKEND: agg
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
               run: |
                   pytest -v --cov --color=yes
+
             - name: Upload coverage
               uses: codecov/codecov-action@v3

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
             # https://github.com/jupyterlab/jupyterlab/issues/12675
             language_version: "17.9.1"
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.0.278
+      rev: v0.0.280
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

README.md

@@ -1,15 +1,14 @@
 <img src="https://github.com/scverse/scvi-tools/blob/main/docs/_static/scvi-tools-horizontal.svg?raw=true" width="400" alt="scvi-tools">
 
-[![Stars](https://img.shields.io/github/stars/scverse/scvi-tools?logo=GitHub&color=yellow)](https://github.com/YosefLab/scvi-tools/stargazers)
+[![Stars](https://img.shields.io/github/stars/scverse/scvi-tools?logo=GitHub&color=yellow)](https://github.com/scverse/scvi-tools/stargazers)
 [![PyPI](https://img.shields.io/pypi/v/scvi-tools.svg)](https://pypi.org/project/scvi-tools)
-[![Documentation Status](https://readthedocs.org/projects/scvi/badge/?version=latest)](https://scvi.readthedocs.io/en/stable/?badge=stable)
-![Build
-Status](https://github.com/scverse/scvi-tools/workflows/scvi-tools/badge.svg)
-[![Coverage](https://codecov.io/gh/scverse/scvi-tools/branch/master/graph/badge.svg)](https://codecov.io/gh/YosefLab/scvi-tools)
-[![Code
-Style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
-[![Downloads](https://pepy.tech/badge/scvi-tools)](https://pepy.tech/project/scvi-tools)
-[![Project chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://scverse.zulipchat.com/)
+[![PyPIDownloads](https://pepy.tech/badge/scvi-tools)](https://pepy.tech/project/scvi-tools)
+[![CondaDownloads](https://img.shields.io/conda/dn/conda-forge/scvi-tools?logo=Anaconda)](https://anaconda.org/conda-forge/scvi-tools)
+[![Docs](https://readthedocs.org/projects/scvi/badge/?version=latest)](https://scvi.readthedocs.io/en/stable/?badge=stable)
+[![Build](https://github.com/scverse/scvi-tools/actions/workflows/build.yml/badge.svg)](https://github.com/scverse/scvi-tools/actions/workflows/build.yml/)
+[![Coverage](https://codecov.io/gh/scverse/scvi-tools/branch/main/graph/badge.svg)](https://codecov.io/gh/scverse/scvi-tools)
+[![Discourse](https://img.shields.io/discourse/posts?color=yellow&logo=discourse&server=https%3A%2F%2Fdiscourse.scverse.org)](https://discourse.scverse.org/)
+[![Chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://scverse.zulipchat.com/)
 
 [scvi-tools](https://scvi-tools.org/) (single-cell variational inference
 tools) is a package for probabilistic modeling and analysis of single-cell omics

docs/release_notes/index.md

@@ -22,11 +22,22 @@ is available in the [commit logs](https://github.com/YosefLab/scvi-tools/commits
 -   Add `load_sparse_tensor` argument in {class}`scvi.data.AnnTorchDataset` for directly
     loading SciPy CSR and CSC data structures to their PyTorch counterparts, leading to
     faster data loading depending on the sparsity of the data {pr}`2158`.
+-   Add per-group LFC information to the {meth}`scvi.criticism.PosteriorPredictiveCheck.differential_expression`
+    method {pr}`2173`. `metrics["diff_exp"]` is now a dictionary where the `summary`
+    stores the summary dataframe, and the `lfc_per_model_per_group` key stores the
+    per-group LFC.
+-   Expose {meth}`torch.save` keyword arguments in {class}`scvi.model.base.BaseModelClass.save`
+    and {class}`scvi.external.GIMVI.save` {pr}`2200`.
+-   Add `model_kwargs` and `train_kwargs` arguments to {meth}`scvi.autotune.ModelTuner.fit` {pr}`2203`.
 
 #### Changed
 
 -   Replace `sparse` with `sparse_format` argument in {meth}`scvi.data.synthetic_iid`
     for increased flexibility over dataset format {pr}`2163`.
+-   Add per-group LFC information to the {meth}`scvi.criticism.PosteriorPredictiveCheck.differential_expression`
+    method {pr}`2173`. `metrics["diff_exp"]` is now a dictionary where the `summary`
+    stores the summary dataframe, and the `lfc_per_model_per_group` key stores the
+    per-group LFC.
 
 #### Removed
 

pyproject.toml

@@ -60,50 +60,63 @@ dependencies = [
 
 
 [project.optional-dependencies]
-dev = [
-    "black",
+tests = [
     "pytest",
     "pytest-cov",
+    "scvi-tools[optional]"
+]  # dependencies for running the test suite
+editing = [
+    "black",
     "flake8",
-    "scanpy>=1.6",
-    "loompy>=3.0.6",
     "jupyter",
     "nbformat",
     "nbconvert",
     "pre-commit",
     "ruff",
-    "pymde",
-    "genomepy",
-    "cellxgene-census"
-]
+]  # dependencies for editing and committing code
+dev = ["scvi-tools[editing,tests]"]  # dependencies for dev work
+
 docs = [
-  "docutils>=0.8,!=0.18.*,!=0.19.*",
-  "sphinx>=4.1",
-  "ipython",
-  "sphinx-book-theme>=1.0.1",
-  "sphinx_copybutton",
-  "sphinx-design",
-  "sphinxext-opengraph",
-  "sphinx-hoverxref",
-  "sphinxcontrib-bibtex>=1.0.0",
-  "myst-parser",
-  "myst-nb",
-  "sphinx-autodoc-typehints",
-]
+    "docutils>=0.8,!=0.18.*,!=0.19.*", # see https://github.com/scverse/cookiecutter-scverse/pull/205
+    "sphinx>=4.1",
+    "ipython",
+    "sphinx-book-theme>=1.0.1",
+    "sphinx_copybutton",
+    "sphinx-design",
+    "sphinxext-opengraph",
+    "sphinx-hoverxref",
+    "sphinxcontrib-bibtex>=1.0.0",
+    "myst-parser",
+    "myst-nb",
+    "sphinx-autodoc-typehints",
+]  # basic docs dependencies
+docsbuild = ["scvi-tools[docs,optional]"]  # docs build dependencies
+
 autotune = [
-  "hyperopt>=0.2",
-  "ray[tune]>=2.5.0",
-  "ipython",
-  "scib-metrics>=0.3",
-]
-pymde = ["pymde"]
-tutorials = ["scanpy", "leidenalg", "python-igraph", "loompy", "scikit-misc", "pynndescent", "pymde", "huggingface_hub", "genomepy"]
-hub = ["huggingface_hub"]
-regseq = [
-    "biopython>=1.81",
-    "genomepy",
-]
-census = ["cellxgene-census"]
+    "hyperopt>=0.2",
+    "ray[tune]>=2.5.0",
+    "ipython",
+    "scib-metrics>=0.3",
+]  # scvi.autotune
+census = ["cellxgene-census"]  # scvi.data.cellxgene
+hub = ["huggingface_hub"]  # scvi.hub dependencies
+pymde = ["pymde"]  # scvi.model.utils.mde dependencies
+regseq = ["biopython>=1.81", "genomepy"]  # scvi.data.add_dna_sequence
+loompy = ["loompy>=3.0.6"]  # read loom
+scanpy = ["scanpy>=1.6"]  # scvi.criticism and read 10x
+optional = [
+    "scvi-tools[autotune,census,hub,loompy,pymde,regseq,scanpy]"
+]  # all optional user functionality
+
+tutorials = [
+    "leidenalg",
+    "pynndescent",
+    "igraph",
+    "scikit-misc",
+    "scvi-tools[optional]",
+]  # dependencies for all tutorials
+
+all = ["scvi-tools[dev,docs,tutorials]"]  # all dependencies
 
 [tool.hatch.build.targets.wheel]
 packages = ['scvi']

readthedocs.yml

@@ -10,10 +10,7 @@ python:
         - method: pip
           path: .
           extra_requirements:
-              - docs
-              - pymde
-              - hub
-              - autotune
+              - docsbuild
 submodules:
     include:
         - "docs/tutorials/notebooks"