Initial commit

.codecov.yaml

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+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

.cruft.json

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+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "8a4b931453619c21ee88c66222d313b935e6e274",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "embedding-scvi",
+      "package_name": "embedding_scvi",
+      "project_description": "A very interesting piece of code",
+      "author_full_name": "Martin Kim",
+      "author_email": "[email protected]",
+      "github_user": "martinkim0",
+      "project_repo": "https://github.com/YosefLab/embedding-scvi",
+      "license": "MIT License",
+      "_copy_without_render": [
+        ".github/workflows/**.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
+}

.editorconfig

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+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[.cruft.json]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+            available datasets or to share a subset of your data.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Version information
+      description: |
+        Please paste below the output of
+
+        ```python
+        import session_info
+        session_info.show(html=False, dependencies=True)
+        ```
+      placeholder: |
+        -----
+        anndata             0.8.0rc2.dev27+ge524389
+        session_info        1.0.0
+        -----
+        asttokens           NA
+        awkward             1.8.0
+        backcall            0.2.0
+        cython_runtime      NA
+        dateutil            2.8.2
+        debugpy             1.6.0
+        decorator           5.1.1
+        entrypoints         0.4
+        executing           0.8.3
+        h5py                3.7.0
+        ipykernel           6.15.0
+        jedi                0.18.1
+        mpl_toolkits        NA
+        natsort             8.1.0
+        numpy               1.22.4
+        packaging           21.3
+        pandas              1.4.2
+        parso               0.8.3
+        pexpect             4.8.0
+        pickleshare         0.7.5
+        pkg_resources       NA
+        prompt_toolkit      3.0.29
+        psutil              5.9.1
+        ptyprocess          0.7.0
+        pure_eval           0.2.2
+        pydev_ipython       NA
+        pydevconsole        NA
+        pydevd              2.8.0
+        pydevd_file_utils   NA
+        pydevd_plugins      NA
+        pydevd_tracing      NA
+        pygments            2.12.0
+        pytz                2022.1
+        scipy               1.8.1
+        setuptools          62.5.0
+        setuptools_scm      NA
+        six                 1.16.0
+        stack_data          0.3.0
+        tornado             6.1
+        traitlets           5.3.0
+        wcwidth             0.2.5
+        zmq                 23.1.0
+        -----
+        IPython             8.4.0
+        jupyter_client      7.3.4
+        jupyter_core        4.10.0
+        -----
+        Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+        Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
+        -----
+        Session information updated at 2022-07-07 17:55

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Propose a new feature for embedding-scvi
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/workflows/build.yaml

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+name: Check Build
+
+on:
+  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@v3
+      - name: Set up Python 3.10
+        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.yaml

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+name: Release
+
+on:
+  push:
+    tags:
+      - "*.*.*"
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install hatch
+        run: pip install 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_API_TOKEN }}

.github/workflows/test.yaml

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+name: Test
+
+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:
+        include:
+          - os: ubuntu-latest
+            python: "3.9"
+          - os: ubuntu-latest
+            python: "3.10"
+          - os: ubuntu-latest
+            python: "3.10"
+            pip-flags: "--pre"
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    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
+        run: |
+          pip install ${{ matrix.pip-flags }} ".[dev,test]"
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          pytest -v --cov --color=yes
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3

.gitignore

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+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.mypy_cache/
+.ruff_cache/
+
+# Distribution / packaging
+/build/
+/dist/
+/*.egg-info/
+
+# Tests and coverage
+/.pytest_cache/
+/.cache/
+/data/
+
+# docs
+/docs/generated/
+/docs/_build/
+
+# IDEs
+/.idea/
+/.vscode/

.pre-commit-config.yaml

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+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/psf/black
+    rev: "23.9.1"
+    hooks:
+      - id: black
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.3
+    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: v0.0.289
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    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$'

.readthedocs.yaml

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+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+sphinx:
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: true
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc