init repo

.bumpversion.cfg

@@ -0,0 +1,8 @@
+[bumpversion]
+current_version = 0.0.1
+tag = True
+commit = True
+
+[bumpversion:file:./pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"

.codecov.yaml

@@ -0,0 +1,17 @@
+# 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

@@ -0,0 +1,23 @@
+{
+    "template": "https://github.com/scverse/cookiecutter-scverse",
+    "commit": "1434c56aeae999b606cf30d7b8d57d491034afec",
+    "checkout": null,
+    "context": {
+        "cookiecutter": {
+            "project_name": "atlas_protocol",
+            "package_name": "atlas_protocol_scripts",
+            "project_description": "A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022). ",
+            "author_full_name": "Gregor Sturm",
+            "author_email": "[email protected]",
+            "github_user": "icbi-lab",
+            "project_repo": "https://github.com/icbi-lab/atlas_protocol",
+            "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

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[Makefile]
+indent_style = tab

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,89 @@
+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

@@ -0,0 +1,5 @@
+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

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for atlas_protocol
+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

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+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

.github/workflows/sync.yaml

@@ -0,0 +1,46 @@
+name: Sync Template
+
+on:
+    workflow_dispatch:
+    schedule:
+        - cron: "0 2 * * *" # every night at 2:00 UTC
+
+jobs:
+    sync:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.10"
+            - name: Install dependencies
+              # for now, pin cookiecutter version, due to https://github.com/cruft/cruft/issues/166
+              run: python -m pip install --upgrade cruft "cookiecutter<2" pre-commit toml
+            - name: Find Latest Tag
+              uses: oprypin/[email protected]
+              id: get-latest-tag
+              with:
+                  repository: scverse/cookiecutter-scverse
+                  releases-only: false
+                  sort-tags: true
+                  regex: '^v\d+\.\d+\.\d+$' # vX.X.X
+            - name: Sync
+              run: |
+                  cruft update --checkout ${{ steps.get-latest-tag.outputs.tag }} --skip-apply-ask --project-dir .
+            - name: Create Pull Request
+              uses: peter-evans/create-pull-request@v4
+              with:
+                  commit-message: Automated template update from cookiecutter-scverse
+                  branch: template-update
+                  title: Automated template update from cookiecutter-scverse
+                  body: |
+                      A new version of the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse/releases)
+                      got released. This PR adds all new changes to your repository and helps to to stay in sync with
+                      the latest best-practice template maintained by the scverse team.
+
+                      **If a merge conflict arised, a `.rej` file with the rejected patch is generated. You'll need to
+                      manually merge these changes.**
+
+                      For more information about the template sync, please refer to the
+                      [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).

.github/workflows/test.yaml

@@ -0,0 +1,62 @@
+name: Test
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+    test:
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -e {0} # -e to fail on error
+
+        strategy:
+            fail-fast: false
+            matrix:
+                python: ["3.8", "3.10"]
+                os: [ubuntu-latest]
+
+        env:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python ${{ matrix.python }}
+              uses: actions/setup-python@v2
+              with:
+                  python-version: ${{ matrix.python }}
+
+            - name: Get pip cache dir
+              id: pip-cache-dir
+              run: |
+                  echo "::set-output name=dir::$(pip cache dir)"
+            - name: Restore pip cache
+              uses: actions/cache@v2
+              with:
+                  path: ${{ steps.pip-cache-dir.outputs.dir }}
+                  key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
+                  restore-keys: |
+                      pip-${{ runner.os }}-${{ env.pythonLocation }}-
+            - name: Install test dependencies
+              run: |
+                  python -m pip install --upgrade pip wheel
+                  pip install codecov
+            - name: Install dependencies
+              run: |
+                  pip install ".[dev,test]"
+            - name: Test
+              env:
+                  MPLBACKEND: agg
+                  PLATFORM: ${{ matrix.os }}
+                  DISPLAY: :42
+              run: |
+                  pytest -v --cov --color=yes
+            - name: Upload coverage
+              env:
+                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
+              run: |
+                  codecov --required --flags=unittests

.gitignore

@@ -0,0 +1,28 @@
+# 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

@@ -0,0 +1,50 @@
+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: "23.1.0"
+      hooks:
+          - id: black
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.13.0
+      hooks:
+          - id: blacken-docs
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v3.0.0-alpha.6
+      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/charliermarsh/ruff-pre-commit
+      rev: v0.0.259
+      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$'