Merge branch 'main' of https://github.com/Hrovatin/scvi-tools

.editorconfig

@@ -1,18 +1,15 @@
-# http://editorconfig.org
-
 root = true
 
 [*]
 indent_style = space
 indent_size = 4
+end_of_line = lf
+charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
-charset = utf-8
-end_of_line = lf
 
-[*.bat]
-indent_style = tab
-end_of_line = crlf
+[*.{yml,yaml}]
+indent_size = 2
 
 [LICENSE]
 insert_final_newline = false

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
 contact_links:
-    - name: Usage question
-      url: https://discourse.scvi-tools.org/
-      about: Please ask and answer non-development questions at https://discourse.scvi-tools.org/.
+  - name: Usage question
+    url: https://discourse.scvi-tools.org/
+    about: Please ask and answer non-development questions at https://discourse.scvi-tools.org/.

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -6,14 +6,13 @@ labels: releases
 assignees: ""
 ---
 
--   [ ] Bump version in `pyproject.toml`.
--   [ ] If patch release, backport version bump PR into the appropriate branch. Else, create a new branch off `main` with the appropriate rules.
--   [ ] Create a new GitHub draft release targeting the release branch with the same body as the previous release (don't release yet).
--   [ ] Trigger a Docker image build in [`scvi-tools-docker`](https://github.com/YosefLab/scvi-tools-docker) targeting the release branch.
--   [ ] After image builds and pushes to the registry, run the [tutorials](https://github.com/scverse/scvi-tutorials) using the new image.
+-   [ ] Bump version in `pyproject.toml`
+-   [ ] If patch release, backport version bump PR into the appropriate branch. Else, create a new branch off `main` with the appropriate rules
+-   [ ] Trigger a Docker image build in [`scvi-tools-docker`](https://github.com/YosefLab/scvi-tools-docker) targeting the release branch
+-   [ ] After image builds and pushes to the registry, run the [tutorials](https://github.com/scverse/scvi-tutorials) using the new image
 -   [ ] Publish a new release on the tutorials repo off `main` after all tutorials changes have been merged.
--   [ ] Create a new branch off `main` in the main repo and run `git submodule update --remote`, and then merge the PR, with an appropriate backport as needed.
--   [ ] Double check everything and then publish the draft release on the main repo.
--   [ ] Check that the [feedstock repo](https://github.com/conda-forge/scvi-tools-feedstock) updates correctly.
--   [ ] Check that the version updates correctly on [PyPI](https://pypi.org/project/scvi-tools/).
--   [ ] (Optional) Post threads on Discourse and Twitter!
+-   [ ] Create a new branch off `main` in the main repo and run `git submodule update --remote`, and then merge the PR, with an appropriate backport as needed
+-   [ ] Create a new GitHub release targeting the release branch with the same body as the previous release
+-   [ ] Check that the version updates correctly on [PyPI](https://pypi.org/project/scvi-tools/)
+-   [ ] Check that the [feedstock repo](https://github.com/conda-forge/scvi-tools-feedstock) updates correctly
+-   [ ] (Optional) Post threads on Discourse and Twitter

.github/pull_request_template.md

@@ -1,6 +0,0 @@
--   [ ] Closes #xxxx (Replace xxxx with the GitHub issue number)
--   [ ] Tests added and passed if fixing a bug or adding a new feature
--   [ ] All code checks passed
--   [ ] Added type annotations to new arguments/methods/functions
--   [ ] Added an entry in the latest `docs/release_notes/index.md` file if fixing a bug or adding a new feature
--   [ ] If the changes are patches for a version, I have added the `on-merge: backport to x.x.x` label

.github/workflows/build.yml

@@ -1,30 +1,31 @@
-name: Check Build
+name: Check build
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches:
+      [main, 0.15.x, 0.16.x, 0.17.x, 0.18.x, 0.19.x, 0.20.x, 1.0.x, 1.1.x]
+  pull_request:
+    branches:
+      [main, 0.15.x, 0.16.x, 0.17.x, 0.18.x, 0.19.x, 0.20.x, 1.0.x, 1.1.x]
 
-jobs:
-    package:
-        runs-on: ubuntu-latest
-
-        steps:
-            - uses: actions/checkout@v3
-
-            - name: Set up Python 3.11
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.11"
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
-            - 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
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          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

@@ -1,32 +1,29 @@
 name: Release
 
 on:
-    push:
-        tags:
-            - "*.*.*"
+  release:
+    types: [published]
 
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
 jobs:
-    release:
-        name: Release
-        runs-on: ubuntu-latest
-
-        steps:
-            - name: Checkout code
-              uses: actions/checkout@v3
-
-            - name: Set up Python 3.11
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.11"
-
-            - name: Install hatch
-              run: |
-                  python -m pip install --upgrade hatch
-
-            - name: Build project for distribution
-              run: hatch build
-
-            - name: Publish a Python distribution to PyPI
-              uses: pypa/gh-action-pypi-publish@release/v1
-              with:
-                  password: ${{ secrets.PYPI_TOKEN }}
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/scvi-tools
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test_linux.yml

@@ -0,0 +1,62 @@
+name: Test (Linux)
+
+on:
+  push:
+    branches:
+      [main, 0.15.x, 0.16.x, 0.17.x, 0.18.x, 0.19.x, 0.20.x, 1.0.x, 1.1.x]
+  pull_request:
+    branches:
+      [main, 0.15.x, 0.16.x, 0.17.x, 0.18.x, 0.19.x, 0.20.x, 1.0.x, 1.1.x]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.9", "3.10", "3.11"]
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - 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
+        run: |
+          pip install --pre ".[tests]"
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3