Switch to scverse cookiecutter template (#402)

* Add tests for databases and fix IEDB

Despite sticking to v3 version number, IEDB have updated their file format

 * BCR and TCR are now in separate files
 * the csv header has changed. Names are different, and there are now *two* rows
   representing the header.

* rename to src

* update readme

* WIP

* update pyproject.toml

* add changelog

* fix tests

* apply pre-commit autofixes

* update pre-commit file

* clean up sphinx modules

* Switch to ipynb tutorials for now

* WIP docs

* WIP docs

* WIP docs

* update CI

* update conda deps

* Add action to test notebook

* add RTD config

* clean up imports in ddatasets

* add dependency for coverage

* CI

* CI

* doc fixes

* CI

* CI

* get rid of raw cells in IO tutorial

* CI

* convert raw cells in 3k tutorial

* bump tutorials

* debug rtd

* Revert "debug rtd"

This reverts commit 3b5ef86.

* debug rtd

* debug rtd

* fix spacing

* exclude a few ruff warnings

* update editorconfig

* fix blacken-docs pre-commit

* Add cruft.json

* update target versions for black/ruff

* update README

* sphinx fail on warning

* debug rtd

* debug rtd

* debug rtd

* debug RTD

.conda/meta.yaml

@@ -16,15 +16,12 @@ build:
 
 requirements:
   host:
-    - python >=3.8
-    - pip!=22.1 # https://github.com/pypa/pip/issues/11110
-    - flit
-    - setuptools_scm
-    - pytoml
-    - importlib_metadata
+    - python >=3.9
+    - hatchling
+    - hatch-vcs
 
   run:
-    - python >=3.8
+    - python >=3.9
     - anndata >=0.9
     - awkward >=2.1.0
     - mudata >=0.2.2
@@ -60,7 +57,6 @@ test:
     - scirpy
   commands:
     - pytest --pyargs scirpy -m "not extra"
-    - cd docs && jupytext --execute tutorials/tutorial_3k_tcr.md
 
 about:
   home: https://scverse.org/scirpy

.cruft.json

@@ -0,0 +1,23 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "6a4338030e0c83a9034d607ed66abeff83e18840",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "scirpy",
+      "package_name": "scirpy",
+      "project_description": "A very interesting piece of code",
+      "author_full_name": "Gregor Sturm",
+      "author_email": "[email protected]",
+      "github_user": "grst",
+      "project_repo": "https://github.com/scverse/scirpy",
+      "license": "BSD 3-Clause License",
+      "_copy_without_render": [
+        ".github/workflows/**.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
+}

.editorconfig

@@ -1,15 +1,18 @@
 root = true
 
 [*]
-charset = utf-8
+indent_style = space
+indent_size = 4
 end_of_line = lf
-insert_final_newline = true
+charset = utf-8
 trim_trailing_whitespace = true
-max_line_length = 88
+insert_final_newline = true
 
-[*.py]
-indent_size = 4
-indent_style = space
+[*.{yml,yaml}]
+indent_size = 2
+
+[.cruft.json]
+indent_size = 2
 
 [Makefile]
 indent_style = tab

.gitattributes

@@ -1,2 +1,2 @@
-# Pickle files (for testing) should always have UNIX line endings. 
+# Pickle files (for testing) should always have UNIX line endings.
 *.pkl text eol=lf

.github/ISSUE_TEMPLATE/bug_report.md

@@ -20,9 +20,9 @@ A clear and concise description of what you expected to happen.
 
 **System**
 
-- OS: [e.g. Windows 10]
-- Python version [e.g. 3.9]
-- Versions of libraries involved [e.g. AnnData 0.8.0, Scirpy 0.12.0]
+-   OS: [e.g. Windows 10]
+-   Python version [e.g. 3.9]
+-   Versions of libraries involved [e.g. AnnData 0.8.0, Scirpy 0.12.0]
 
 **Additional context**
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +1,5 @@
-blank_issues_enabled: true
-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.
+blank_issues_enabled: true
+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/workflows/build.yaml

@@ -0,0 +1,29 @@
+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/conda.yml → .github/workflows/conda.yaml

@@ -2,28 +2,34 @@ name: conda
 
 on:
   push:
-    branches: [master]
+    branches: [main]
   pull_request:
-    branches: [master]
+    branches: [main]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
-  tests:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
+  test:
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-        os: ["ubuntu-latest", "macos-latest"]
+        include:
+          - os: ubuntu-latest
+            python: "3.9"
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
 
     steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0 # required for setuptools-scm
+      - uses: actions/checkout@v3
 
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v2

.github/workflows/release.yaml

@@ -0,0 +1,30 @@
+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 }}