Update workflows, pre-commit, typing, and dependencies (#79)

* Update workflows and pre-commit * Update scvi-tools lower bound * Remove use_gpu * Switch to 3.10 typing * Remove future annotations from typing file * Fix typing * Fix typing * Fix typing * Fix tests * Fix tests and commment out * Fixes
YosefLab · Jan 31, 2024 · 3b47c90 · 3b47c90
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diff --git a/.codecov.yaml b/.codecov.yaml
@@ -1,16 +1,16 @@
 # Based on pydata/xarray
 codecov:
-    require_ci_to_pass: no
+  require_ci_to_pass: no
 
 coverage:
-    status:
-        project:
-            default:
-                target: 80%
-        patch: false
-        changes: false
+  status:
+    project:
+      default:
+        target: 80%
+    patch: false
+    changes: false
 
 comment:
-    layout: diff, flags, files
-    behavior: once
-    require_base: no
+  layout: diff, flags, files
+  behavior: once
+  require_base: no
diff --git a/.editorconfig b/.editorconfig
@@ -8,5 +8,11 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
+[*.{yml,yaml}]
+indent_size = 2
+
+[LICENSE]
+insert_final_newline = false
+
 [Makefile]
 indent_style = tab
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -1,23 +1,29 @@
-name: Check Build
+name: Build
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-    package:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v2
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.10"
-            - 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
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          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
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
diff --git a/.github/workflows/test_linux.yaml b/.github/workflows/test_linux.yaml
@@ -0,0 +1,60 @@
+name: Test (Linux)
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+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: 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 --pre ".[dev,test]"
+
+      - 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_linux_pre.yaml b/.github/workflows/test_linux_pre.yaml
@@ -0,0 +1,70 @@
+name: Test (Linux, prereleases)
+
+on:
+  pull_request:
+    branches: [main]
+    types: [labeled, synchronize, opened]
+  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:
+    # if PR has label "prerelease 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:
+        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: Integration (Prereleases)
+
+    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 --pre ".[dev,test]"
+
+      - 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/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,70 +1,49 @@
 fail_fast: false
 default_language_version:
-    python: python3
+  python: python3
 default_stages:
-    - commit
-    - push
+  - commit
+  - push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/psf/black
-      rev: 22.10.0
-      hooks:
-          - id: black
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.2
-      hooks:
-          - id: prettier
-    - repo: https://github.com/asottile/blacken-docs
-      rev: v1.12.1
-      hooks:
-          - id: blacken-docs
-    - repo: https://github.com/PyCQA/isort
-      rev: 5.11.5
-      hooks:
-          - id: isort
-    - repo: https://github.com/asottile/yesqa
-      rev: v1.4.0
-      hooks:
-          - id: yesqa
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0
-      hooks:
-          - id: detect-private-key
-          - id: check-ast
-          - id: end-of-file-fixer
-          - id: mixed-line-ending
-            args: [--fix=lf]
-          - id: trailing-whitespace
-          - id: check-case-conflict
-    - repo: https://github.com/myint/autoflake
-      rev: v1.7.6
-      hooks:
-          - id: autoflake
-            args:
-                - --in-place
-                - --remove-all-unused-imports
-                - --remove-unused-variable
-                - --ignore-init-module-imports
-    - repo: https://github.com/PyCQA/flake8
-      rev: 5.0.4
-      hooks:
-          - id: flake8
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v3.1.0
-      hooks:
-          - id: pyupgrade
-            args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
+    hooks:
+      - id: prettier
+        # Newer versions of node don't work on systems that have an older version of GLIBC
+        # (in particular Ubuntu 18.04 and Centos 7)
+        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+        # https://github.com/jupyterlab/jupyterlab/issues/12675
+        language_version: "17.9.1"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.11
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        types_or: [python, pyi, jupyter]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'