Merge branch 'main' into main

Hrovatin · Feb 5, 2024 · 3a67d1c · 3a67d1c
2 parents 3319fc8 + 0f560d5
commit 3a67d1c
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Showing 20 changed files with 184 additions and 82 deletions.
diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -1,12 +1,10 @@
-name: Check build
+name: Build
 
 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]
+    branches: [main, 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]
+    branches: [main, 1.1.x]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -18,9 +16,9 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
       - name: Install build dependencies

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -19,9 +19,9 @@ jobs:
         with:
           filter: blob:none
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.x"
+          python-version: "3.11"
           cache: "pip"
       - run: pip install build
       - run: python -m build

diff --git a/.github/workflows/test_linux.yml b/.github/workflows/test_linux.yml
@@ -2,11 +2,9 @@ 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]
+    branches: [main, 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]
+    branches: [main, 1.1.x]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -25,7 +23,7 @@ jobs:
         os: [ubuntu-latest]
         python: ["3.9", "3.10", "3.11"]
 
-    name: ${{ matrix.name }} Python ${{ matrix.python }}
+    name: Integration
 
     env:
       OS: ${{ matrix.os }}
@@ -34,7 +32,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: "pip"

diff --git a/.github/workflows/test_linux_cuda.yml b/.github/workflows/test_linux_cuda.yml
@@ -2,10 +2,10 @@ name: Test (Linux, CUDA)
 
 on:
   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]
+    branches: [main, 1.1.x]
+    types: [labeled, synchronize, opened]
   schedule:
-    - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
+    - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
   workflow_dispatch:
 
 concurrency:
@@ -14,6 +14,14 @@ concurrency:
 
 jobs:
   test:
+    # if PR has label "cuda tests" or "all tests" or if scheduled or manually triggered
+    if: >-
+      (
+        contains(github.event.pull_request.labels.*.name, 'cuda tests') ||
+        contains(github.event.pull_request.labels.*.name, 'all tests') ||
+        contains(github.event_name, 'schedule') ||
+        contains(github.event_name, 'workflow_dispatch')
+      )
     runs-on: [self-hosted, Linux, X64, CUDA]
     defaults:
       run:
@@ -26,13 +34,10 @@ jobs:
         cuda: ["11"]
 
     container:
-      image: martinkim0/scvi-tools:py${{ matrix.python }}-cu${{ matrix.cuda }}-base
+      image: scverse/scvi-tools:py${{ matrix.python }}-cu${{ matrix.cuda }}-base
       options: --user root --gpus all
 
-    environment:
-      name: private_test
-
-    name: ${{ matrix.name }} Python ${{ matrix.python }} CUDA
+    name: Integration (CUDA)
 
     env:
       OS: ${{ matrix.os }}

diff --git a/.github/workflows/test_linux_pre.yml b/.github/workflows/test_linux_pre.yml
@@ -1,8 +1,11 @@
-name: Test (Linux, prerelease)
+name: Test (Linux, prereleases)
 
 on:
+  pull_request:
+    branches: [main, 1.1.x]
+    types: [labeled, synchronize, opened]
   schedule:
-    - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
+    - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
   workflow_dispatch:
 
 concurrency:
@@ -11,6 +14,14 @@ concurrency:
 
 jobs:
   test:
+    # if PR has label "cuda tests" or "all tests" or if scheduled or manually triggered
+    if: >-
+      (
+        contains(github.event.pull_request.labels.*.name, 'prerelease tests') ||
+        contains(github.event.pull_request.labels.*.name, 'all tests') ||
+        contains(github.event_name, 'schedule') ||
+        contains(github.event_name, 'workflow_dispatch')
+      )
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -22,7 +33,7 @@ jobs:
         os: [ubuntu-latest]
         python: ["3.9", "3.10", "3.11", "3.12"]
 
-    name: ${{ matrix.name }} Python ${{ matrix.python }} prereleases
+    name: Integration (Prereleases)
 
     env:
       OS: ${{ matrix.os }}
@@ -31,7 +42,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: "pip"

diff --git a/.github/workflows/test_linux_private.yml b/.github/workflows/test_linux_private.yml
@@ -2,8 +2,12 @@ name: Test (Linux, private)
 
 on:
   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]
+    branches: [main, 1.1.x]
+    types: [labeled, synchronize, opened]
+  push:
+    branches: [main, 1.1.x]
+  schedule:
+    - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
   workflow_dispatch:
 
 concurrency:
@@ -12,6 +16,15 @@ concurrency:
 
 jobs:
   test:
+    # if PR has label "private tests" or "all tests" or if scheduled or manually triggered or on push
+    if: >-
+      (
+        contains(github.event.pull_request.labels.*.name, 'private tests') ||
+        contains(github.event.pull_request.labels.*.name, 'all tests') ||
+        contains(github.event_name, 'schedule') ||
+        contains(github.event_name, 'workflow_dispatch') ||
+        contains(github.event_name, 'push')
+      )
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -23,13 +36,10 @@ jobs:
         os: [ubuntu-latest]
         python: ["3.11"]
 
-    environment:
-      name: private_test
-
     permissions:
       id-token: write
 
-    name: ${{ matrix.name }} Python ${{ matrix.python }} private
+    name: Unit (Private)
 
     env:
       OS: ${{ matrix.os }}
@@ -44,7 +54,7 @@ jobs:
           aws-region: us-west-1
           role-duration-seconds: 3600
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: "pip"

diff --git a/.github/workflows/test_macos.yml b/.github/workflows/test_macos.yml
@@ -22,7 +22,7 @@ jobs:
         os: [macos-latest]
         python: ["3.9", "3.10", "3.11"]
 
-    name: ${{ matrix.name }} Python ${{ matrix.python }}
+    name: Integration
 
     env:
       OS: ${{ matrix.os }}
@@ -31,7 +31,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: "pip"

diff --git a/.github/workflows/test_macos_m1.yml b/.github/workflows/test_macos_m1.yml
@@ -0,0 +1,59 @@
+name: Test (MacOS M1)
+
+on:
+  schedule:
+    - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
+  workflow_dispatch:
+
+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: [macos-14]
+        python: ["3.9", "3.10", "3.11"]
+
+    name: Integration
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        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 ".[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
diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
@@ -2,7 +2,7 @@ name: Test (Windows)
 
 on:
   schedule:
-    - cron: "0 10 * * *" # runs at 10:00 UTC -> 03:00 PST every day
+    - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
   workflow_dispatch:
 
 concurrency:
@@ -22,7 +22,7 @@ jobs:
         os: [windows-latest]
         python: ["3.9", "3.10", "3.11"]
 
-    name: ${{ matrix.name }} Python ${{ matrix.python }}
+    name: Integration
 
     env:
       OS: ${{ matrix.os }}
@@ -31,7 +31,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
           cache: "pip"

diff --git a/codecov.yml b/codecov.yml
@@ -1,12 +1,16 @@
-# Run to check if valid
-# curl --data-binary @codecov.yml https://codecov.io/validate
+codecov:
+  require_ci_to_pass: no
+
 coverage:
   status:
     project:
       default:
         target: 85%
         threshold: 1%
-    patch: off
+    patch: false
+    changes: false
 
-ignore:
-  - "scvi/_compat.py"
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no
diff --git a/docs/release_notes/index.md b/docs/release_notes/index.md
@@ -7,7 +7,7 @@ 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
 
-### 1.1.0 (2023-12-DD)
+### 1.1.0 (2024-02-DD)
 
 #### Added
 
@@ -76,6 +76,7 @@ is available in the [commit logs](https://github.com/scverse/scvi-tools/commits/
 -   Fix initialization of {class}`scvi.distributions.NegativeBinomial` and
     {class}`scvi.distributions.ZeroInflatedNegativeBinomial` when `validate_args=True` and
     optional parameters not passed in {pr}`2395`.
+-   Fix error when re-initializing {class}`scvi.external.GIMVI` with the same datasets {pr}`2446`.
 
 #### Changed
 
@@ -110,7 +111,7 @@ is available in the [commit logs](https://github.com/scverse/scvi-tools/commits/
 
 ## Version 1.0
 
-### 1.0.4 (2023-10-xx)
+### 1.0.4 (2023-10-13)
 
 ### Added
 

diff --git a/docs/tutorials/index_scrna.md b/docs/tutorials/index_scrna.md
@@ -15,4 +15,5 @@ notebooks/scrna/cellassign_tutorial
 notebooks/scrna/amortized_lda
 notebooks/scrna/scVI_DE_worm
 notebooks/scrna/contrastiveVI_tutorial
+notebooks/scrna/scanvi_fix
 ```
diff --git a/docs/tutorials/notebooks b/docs/tutorials/notebooks