diff --git a/.codecov.yaml b/.codecov.yaml
new file mode 100644
index 0000000..d0c0e29
--- /dev/null
+++ b/.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
diff --git a/.cruft.json b/.cruft.json
new file mode 100644
index 0000000..7dd65b1
--- /dev/null
+++ b/.cruft.json
@@ -0,0 +1,30 @@
+{
+ "template": "https://github.com/scverse/cookiecutter-scverse",
+ "commit": "ab6df8677b2e65fc8ae7ae9b7425373b706af3ee",
+ "checkout": null,
+ "context": {
+ "cookiecutter": {
+ "project_name": "ehrdata",
+ "package_name": "ehrdata",
+ "project_description": "A Python package for EHR data",
+ "author_full_name": "Eljas Roellin, Lukas Heumos, Xinyue Zhang",
+ "author_email": "eljas.roellin@helmholtz-munich.de",
+ "github_user": "theislab",
+ "github_repo": "ehrdata",
+ "license": "Apache License Version 2.0",
+ "ide_integration": true,
+ "_copy_without_render": [
+ ".github/workflows/build.yaml",
+ ".github/workflows/test.yaml",
+ "docs/_templates/autosummary/**.rst"
+ ],
+ "_render_devdocs": false,
+ "_jinja2_env_vars": {
+ "lstrip_blocks": true,
+ "trim_blocks": true
+ },
+ "_template": "https://github.com/scverse/cookiecutter-scverse"
+ }
+ },
+ "directory": null
+}
diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000..66678e3
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,15 @@
+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,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 0000000..a5a20e6
--- /dev/null
+++ b/.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
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 0000000..5b62547
--- /dev/null
+++ b/.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.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 0000000..973ec26
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for ehrdata
+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
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
new file mode 100644
index 0000000..265a95e
--- /dev/null
+++ b/.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
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..e663f6e
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,29 @@
+name: Release
+
+on:
+ release:
+ types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+ release:
+ name: Upload release to PyPI
+ runs-on: ubuntu-latest
+ environment:
+ name: pypi
+ url: https://pypi.org/p/ehrdata
+ permissions:
+ id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+ steps:
+ - uses: actions/checkout@v4
+ with:
+ filter: blob:none
+ fetch-depth: 0
+ - uses: actions/setup-python@v4
+ with:
+ python-version: "3.x"
+ cache: "pip"
+ - run: pip install build
+ - run: python -m build
+ - name: Publish package distributions to PyPI
+ uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 0000000..2bfe232
--- /dev/null
+++ b/.github/workflows/test.yaml
@@ -0,0 +1,67 @@
+name: Test
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+ schedule:
+ - cron: "0 5 1,15 * *"
+
+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: "3.10"
+ - os: ubuntu-latest
+ python: "3.12"
+ - os: ubuntu-latest
+ python: "3.12"
+ pip-flags: "--pre"
+ name: PRE-RELEASE DEPENDENCIES
+
+ name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+ 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: ${{ matrix.os }}
+ DISPLAY: :42
+ run: |
+ coverage run -m pytest -v --color=yes
+ - name: Report coverage
+ run: |
+ coverage report
+ - name: Upload coverage
+ uses: codecov/codecov-action@v3
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..31e10b3
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,20 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.*cache/
+
+# Distribution / packaging
+/dist/
+
+# Tests and coverage
+/data/
+/node_modules/
+
+# docs
+/docs/generated/
+/docs/_build/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..3be6c20
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,46 @@
+fail_fast: false
+default_language_version:
+ python: python3
+default_stages:
+ - commit
+ - push
+minimum_pre_commit_version: 2.16.0
+repos:
+ - repo: https://github.com/pre-commit/mirrors-prettier
+ rev: v4.0.0-alpha.8
+ hooks:
+ - id: prettier
+ - repo: https://github.com/tox-dev/pyproject-fmt
+ rev: "2.2.4"
+ hooks:
+ - id: pyproject-fmt
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: v0.6.8
+ hooks:
+ - id: ruff
+ types_or: [python, pyi, jupyter]
+ args: [--fix, --exit-non-zero-on-fix]
+ - id: ruff-format
+ types_or: [python, pyi, jupyter]
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.6.0
+ hooks:
+ - id: detect-private-key
+ - id: check-ast
+ - id: end-of-file-fixer
+ - id: mixed-line-ending
+ args: [--fix=lf]
+ - id: trailing-whitespace
+ - id: check-case-conflict
+ # Check that there are no merge conflicts (could be generated by template sync)
+ - id: check-merge-conflict
+ args: [--assume-in-merge]
+ - repo: local
+ hooks:
+ - id: forbid-to-commit
+ name: Don't commit rej files
+ entry: |
+ Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+ Fix the merge conflicts manually and remove the .rej files.
+ language: fail
+ files: '.*\.rej$'
diff --git a/.prettierrc.yaml b/.prettierrc.yaml
new file mode 100644
index 0000000..9aaffcb
--- /dev/null
+++ b/.prettierrc.yaml
@@ -0,0 +1,7 @@
+overrides:
+ # JSON with comments and trailing commas
+ - files: .vscode/*.json
+ options:
+ parser: json5
+ quoteProps: preserve
+ singleQuote: false
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 0000000..69897c3
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,16 @@
+# 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
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 0000000..a6fa580
--- /dev/null
+++ b/.vscode/extensions.json
@@ -0,0 +1,18 @@
+{
+ "recommendations": [
+ // GitHub integration
+ "github.vscode-github-actions",
+ "github.vscode-pull-request-github",
+ // Language support
+ "ms-python.python",
+ "ms-python.vscode-pylance",
+ "ms-toolsai.jupyter",
+ "tamasfe.even-better-toml",
+ // Dependency management
+ "ninoseki.vscode-mogami",
+ // Linting and formatting
+ "editorconfig.editorconfig",
+ "charliermarsh.ruff",
+ "esbenp.prettier-vscode",
+ ],
+}
diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 0000000..36d1874
--- /dev/null
+++ b/.vscode/launch.json
@@ -0,0 +1,33 @@
+{
+ // Use IntelliSense to learn about possible attributes.
+ // Hover to view descriptions of existing attributes.
+ // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+ "version": "0.2.0",
+ "configurations": [
+ {
+ "name": "Python: Build Documentation",
+ "type": "debugpy",
+ "request": "launch",
+ "module": "sphinx",
+ "args": ["-M", "html", ".", "_build"],
+ "cwd": "${workspaceFolder}/docs",
+ "console": "internalConsole",
+ "justMyCode": false,
+ },
+ {
+ "name": "Python: Debug Test",
+ "type": "debugpy",
+ "request": "launch",
+ "program": "${file}",
+ "purpose": ["debug-test"],
+ "console": "internalConsole",
+ "justMyCode": false,
+ "env": {
+ "PYTEST_ADDOPTS": "--color=yes",
+ },
+ "presentation": {
+ "hidden": true,
+ },
+ },
+ ],
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..b6715d6
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,18 @@
+{
+ "[python][jsonc][yaml]": {
+ "editor.formatOnSave": true,
+ },
+ "[python]": {
+ "editor.defaultFormatter": "charliermarsh.ruff",
+ "editor.codeActionsOnSave": {
+ "source.fixAll": "always",
+ "source.organizeImports": "always",
+ },
+ },
+ "[jsonc][yaml]": {
+ "editor.defaultFormatter": "esbenp.prettier-vscode",
+ },
+ "python.analysis.typeCheckingMode": "basic",
+ "python.testing.pytestEnabled": true,
+ "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..e7b7808
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,15 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/en/1.0.0/
+[semantic versioning]: https://semver.org/spec/v2.0.0.html
+
+## [Unreleased]
+
+### Added
+
+- Basic tool, preprocessing and plotting functions
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..1768f6c
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,202 @@
+Apache License Version 2.0
+Version 2.0, January 2004
+http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
+ control with that entity. For the purposes of this definition,
+ "control" means (i) the power, direct or indirect, to cause the
+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
+ exercising permissions granted by this License.
+
+ "Source" form shall mean the preferred form for making modifications,
+ including but not limited to software source code, documentation
+ source, and configuration files.
+
+ "Object" form shall mean any form resulting from mechanical
+ transformation or translation of a Source form, including but
+ not limited to compiled object code, generated documentation,
+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
+ or by an individual or Legal Entity authorized to submit on behalf of
+ the copyright owner. For the purposes of this definition, "submitted"
+ means any form of electronic, verbal, or written communication sent
+ to the Licensor or its representatives, including but not limited to
+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
+
+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
+ subsequently incorporated within the Work.
+
+2. Grant of Copyright License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ copyright license to reproduce, prepare Derivative Works of,
+ publicly display, publicly perform, sublicense, and distribute the
+ Work and such Derivative Works in Source or Object form.
+
+3. Grant of Patent License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
+ where such license applies only to those patent claims licensable
+ by such Contributor that are necessarily infringed by their
+ Contribution(s) alone or by combination of their Contribution(s)
+ with the Work to which such Contribution(s) was submitted. If You
+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
+ or a Contribution incorporated within the Work constitutes direct
+ or contributory patent infringement, then any patent licenses
+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
+
+4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
+ attribution notices from the Source form of the Work,
+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
+
+ (d) If the Work includes a "NOTICE" text file as part of its
+ distribution, then any Derivative Works that You distribute must
+ include a readable copy of the attribution notices contained
+ within such NOTICE file, excluding those notices that do not
+ pertain to any part of the Derivative Works, in at least one
+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
+ documentation, if provided along with the Derivative Works; or,
+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS
+
+APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+Copyright (c) 2024, Eljas Roellin, Lukas Heumos, Xinyue Zhang
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..bba45d8
--- /dev/null
+++ b/README.md
@@ -0,0 +1,57 @@
+# ehrdata
+
+[![Tests][badge-tests]][tests]
+[![Documentation][badge-docs]][documentation]
+
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/ehrdata/test.yaml?branch=main
+[badge-docs]: https://img.shields.io/readthedocs/ehrdata
+
+A Python package for EHR data
+
+## Getting started
+
+Please refer to the [documentation][],
+in particular, the [API documentation][].
+
+## Installation
+
+You need to have Python 3.10 or newer installed on your system.
+If you don't have Python installed, we recommend installing [Mambaforge][].
+
+There are several alternative options to install ehrdata:
+
+
+
+1. Install the latest development version:
+
+```bash
+pip install git+https://github.com/theislab/ehrdata.git@main
+```
+
+## Release notes
+
+See the [changelog][].
+
+## Contact
+
+For questions and help requests, you can reach out in the [scverse discourse][].
+If you found a bug, please use the [issue tracker][].
+
+## Citation
+
+> t.b.a
+
+[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge
+[scverse discourse]: https://discourse.scverse.org/
+[issue tracker]: https://github.com/theislab/ehrdata/issues
+[tests]: https://github.com/theislab/ehrdata/actions/workflows/test.yml
+[documentation]: https://ehrdata.readthedocs.io
+[changelog]: https://ehrdata.readthedocs.io/en/latest/changelog.html
+[api documentation]: https://ehrdata.readthedocs.io/en/latest/api.html
+[pypi]: https://pypi.org/project/ehrdata
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..d4bb2cb
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_static/.gitkeep b/docs/_static/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
new file mode 100644
index 0000000..b8c8d47
--- /dev/null
+++ b/docs/_static/css/custom.css
@@ -0,0 +1,4 @@
+/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
+div.cell_output table.dataframe {
+ font-size: 0.8em;
+}
diff --git a/docs/_templates/.gitkeep b/docs/_templates/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
new file mode 100644
index 0000000..7b4a0cf
--- /dev/null
+++ b/docs/_templates/autosummary/class.rst
@@ -0,0 +1,61 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. add toctree option to make autodoc generate the pages
+
+.. autoclass:: {{ objname }}
+
+{% block attributes %}
+{% if attributes %}
+Attributes table
+~~~~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in attributes %}
+ ~{{ name }}.{{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block methods %}
+{% if methods %}
+Methods table
+~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in methods %}
+ {%- if item != '__init__' %}
+ ~{{ name }}.{{ item }}
+ {%- endif -%}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block attributes_documentation %}
+{% if attributes %}
+Attributes
+~~~~~~~~~~
+
+{% for item in attributes %}
+
+.. autoattribute:: {{ [objname, item] | join(".") }}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
+
+{% block methods_documentation %}
+{% if methods %}
+Methods
+~~~~~~~
+
+{% for item in methods %}
+{%- if item != '__init__' %}
+
+.. automethod:: {{ [objname, item] | join(".") }}
+{%- endif -%}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
diff --git a/docs/api.md b/docs/api.md
new file mode 100644
index 0000000..61b71f1
--- /dev/null
+++ b/docs/api.md
@@ -0,0 +1,38 @@
+# API
+
+## Preprocessing
+
+```{eval-rst}
+.. module:: ehrdata.pp
+.. currentmodule:: ehrdata
+
+.. autosummary::
+ :toctree: generated
+
+ pp.basic_preproc
+```
+
+## Tools
+
+```{eval-rst}
+.. module:: ehrdata.tl
+.. currentmodule:: ehrdata
+
+.. autosummary::
+ :toctree: generated
+
+ tl.basic_tool
+```
+
+## Plotting
+
+```{eval-rst}
+.. module:: ehrdata.pl
+.. currentmodule:: ehrdata
+
+.. autosummary::
+ :toctree: generated
+
+ pl.basic_plot
+ pl.BasicClass
+```
diff --git a/docs/changelog.md b/docs/changelog.md
new file mode 100644
index 0000000..d9e79ba
--- /dev/null
+++ b/docs/changelog.md
@@ -0,0 +1,3 @@
+```{include} ../CHANGELOG.md
+
+```
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..dd1206e
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,131 @@
+# Configuration file for the Sphinx documentation builder.
+
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+import sys
+from datetime import datetime
+from importlib.metadata import metadata
+from pathlib import Path
+
+HERE = Path(__file__).parent
+sys.path.insert(0, str(HERE / "extensions"))
+
+
+# -- Project information -----------------------------------------------------
+
+# NOTE: If you installed your project in editable mode, this might be stale.
+# If this is the case, reinstall it to refresh the metadata
+info = metadata("ehrdata")
+project_name = info["Name"]
+author = info["Author"]
+copyright = f"{datetime.now():%Y}, {author}."
+version = info["Version"]
+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
+repository_url = urls["Source"]
+
+# The full version, including alpha/beta/rc tags
+release = info["Version"]
+
+bibtex_bibfiles = ["references.bib"]
+templates_path = ["_templates"]
+nitpicky = True # Warn about broken links
+needs_sphinx = "4.0"
+
+html_context = {
+ "display_github": True, # Integrate GitHub
+ "github_user": "theislab",
+ "github_repo": project_name,
+ "github_version": "main",
+ "conf_py_path": "/docs/",
+}
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings.
+# They can be extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = [
+ "myst_nb",
+ "sphinx_copybutton",
+ "sphinx.ext.autodoc",
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.autosummary",
+ "sphinx.ext.napoleon",
+ "sphinxcontrib.bibtex",
+ "sphinx_autodoc_typehints",
+ "sphinx_tabs.tabs",
+ "sphinx.ext.mathjax",
+ "IPython.sphinxext.ipython_console_highlighting",
+ "sphinxext.opengraph",
+ *[p.stem for p in (HERE / "extensions").glob("*.py")],
+]
+
+autosummary_generate = True
+autodoc_member_order = "groupwise"
+default_role = "literal"
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_use_rtype = True # having a separate entry generally helps readability
+napoleon_use_param = True
+myst_heading_anchors = 6 # create anchors for h1-h6
+myst_enable_extensions = [
+ "amsmath",
+ "colon_fence",
+ "deflist",
+ "dollarmath",
+ "html_image",
+ "html_admonition",
+]
+myst_url_schemes = ("http", "https", "mailto")
+nb_output_stderr = "remove"
+nb_execution_mode = "off"
+nb_merge_streams = True
+typehints_defaults = "braces"
+
+source_suffix = {
+ ".rst": "restructuredtext",
+ ".ipynb": "myst-nb",
+ ".myst": "myst-nb",
+}
+
+intersphinx_mapping = {
+ "python": ("https://docs.python.org/3", None),
+ "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+ "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+ "numpy": ("https://numpy.org/doc/stable/", None),
+}
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_book_theme"
+html_static_path = ["_static"]
+html_css_files = ["css/custom.css"]
+
+html_title = project_name
+
+html_theme_options = {
+ "repository_url": repository_url,
+ "use_repository_button": True,
+ "path_to_docs": "docs/",
+ "navigation_with_keys": False,
+}
+
+pygments_style = "default"
+
+nitpick_ignore = [
+ # If building the documentation fails because of a missing link that is outside your control,
+ # you can add an exception to this list.
+ # ("py:class", "igraph.Graph"),
+]
diff --git a/docs/contributing.md b/docs/contributing.md
new file mode 100644
index 0000000..8a9b28d
--- /dev/null
+++ b/docs/contributing.md
@@ -0,0 +1,215 @@
+# Contributing guide
+
+Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
+This document will not reproduce the entire content from there.
+Instead, it aims at summarizing the most important information to get you started on contributing.
+
+We assume that you are already familiar with git and with making pull requests on GitHub.
+If not, please refer to the [scanpy developer guide][].
+
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+
+## Installing dev dependencies
+
+In addition to the packages needed to _use_ this package,
+you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
+
+:::::{tabs}
+::::{group-tab} Hatch
+The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+```bash
+hatch test # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
+hatch run docs:build # defined in the table [tool.hatch.envs.docs]
+```
+
+::::
+
+::::{group-tab} Pip
+If you prefer managing environments manually, you can use `pip`:
+
+```bash
+cd ehrdata
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev,test,doc]"
+```
+
+::::
+:::::
+
+[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+
+## Code-style
+
+This package uses [pre-commit][] to enforce consistent code-styles.
+On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message.
+
+To enable pre-commit locally, simply run
+
+```bash
+pre-commit install
+```
+
+in the root of the repository.
+Pre-commit will automatically download all dependencies when it is run for the first time.
+
+Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
+If you didn't run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+
+If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
+
+```bash
+git pull --rebase
+```
+
+to integrate the changes into yours.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
+
+Finally, most editors have an _autoformat on save_ feature.
+Consider enabling this option for [ruff][ruff-editors] and [prettier][prettier-editors].
+
+[pre-commit]: https://pre-commit.com/
+[pre-commit.ci]: https://pre-commit.ci/
+[ruff-editors]: https://docs.astral.sh/ruff/integrations/
+
+[prettier-editors]: https://prettier.io/docs/en/editors.html
+
+(writing-tests)=
+
+## Writing tests
+
+This package uses [pytest][] for automated testing.
+Please write {doc}`scanpy:dev/testing` for every function added to the package.
+
+Most IDEs integrate with pytest and provide a GUI to run tests.
+Just point yours to one of the environments returned by
+
+```bash
+hatch env create hatch-test # create test environments for all supported versions
+hatch env find hatch-test # list all possible test environment paths
+```
+
+Alternatively, you can run all tests from the command line by executing
+
+:::::{tabs}
+::::{group-tab} Hatch
+
+```bash
+hatch test # test with the highest supported Python version
+# or
+hatch test --all # test with all supported Python versions
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
+pytest
+```
+
+::::
+:::::
+
+in the root of the repository.
+
+[pytest]: https://docs.pytest.org/
+
+### Continuous integration
+
+Continuous integration will automatically run the tests on all pull requests and test
+against the minimum and maximum supported Python version.
+
+Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+The purpose of this check is to detect incompatibilities of new package versions early on and
+gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
+
+## Publishing a release
+
+### Updating the version number
+
+Before making a release, you need to update the version number in the `pyproject.toml` file.
+Please adhere to [Semantic Versioning][semver], in brief
+
+> Given a version number MAJOR.MINOR.PATCH, increment the:
+>
+> 1. MAJOR version when you make incompatible API changes,
+> 2. MINOR version when you add functionality in a backwards compatible manner, and
+> 3. PATCH version when you make backwards compatible bug fixes.
+>
+> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
+
+Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
+Specify `vX.X.X` as a tag name and create a release.
+For more information, see [managing GitHub releases][].
+This will automatically create a git tag and trigger a Github workflow that creates a release on [PyPI][].
+
+[semver]: https://semver.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
+[pypi]: https://pypi.org/
+
+## Writing documentation
+
+Please write documentation for new or changed features and use-cases.
+This project uses [sphinx][] with the following features:
+
+- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+
+See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
+
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
+
+### Tutorials with myst-nb and jupyter notebooks
+
+The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
+Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
+It is your responsibility to update and re-run the notebook whenever necessary.
+
+If you are interested in automatically running notebooks as part of the continuous integration,
+please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
+
+[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
+
+#### Hints
+
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`.
+ Only if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control,
+ you can add an entry to the `nitpick_ignore` list in `docs/conf.py`
+
+(docs-building)=
+
+#### Building the docs locally
+
+:::::{tabs}
+::::{group-tab} Hatch
+
+```bash
+hatch docs:build
+hatch docs:open
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
+cd docs
+make html
+(xdg-)open _build/html/index.html
+```
+
+::::
+:::::
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
new file mode 100644
index 0000000..1135204
--- /dev/null
+++ b/docs/extensions/typed_returns.py
@@ -0,0 +1,32 @@
+# code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
+# with some minor adjustment
+from __future__ import annotations
+
+import re
+from collections.abc import Generator, Iterable
+
+from sphinx.application import Sphinx
+from sphinx.ext.napoleon import NumpyDocstring
+
+
+def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
+ for line in lines:
+ if m := re.fullmatch(r"(?P\w+)\s+:\s+(?P[\w.]+)", line):
+ yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+ else:
+ yield line
+
+
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
+ lines_raw = self._dedent(self._consume_to_next_section())
+ if lines_raw[0] == ":":
+ del lines_raw[0]
+ lines = self._format_block(":returns: ", list(_process_return(lines_raw)))
+ if lines and lines[-1]:
+ lines.append("")
+ return lines
+
+
+def setup(app: Sphinx):
+ """Set app."""
+ NumpyDocstring._parse_returns_section = _parse_returns_section
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..8b5f298
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,15 @@
+```{include} ../README.md
+
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+
+api.md
+changelog.md
+contributing.md
+references.md
+
+notebooks/example
+```
diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb
new file mode 100644
index 0000000..6e77abe
--- /dev/null
+++ b/docs/notebooks/example.ipynb
@@ -0,0 +1,171 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Example notebook"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import numpy as np\n",
+ "from anndata import AnnData\n",
+ "import pandas as pd\n",
+ "import ehrdata"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "adata = AnnData(np.random.normal(size=(20, 10)))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "With myst it is possible to link in the text cell of a notebook such as this one the documentation of a function or a class.\n",
+ "\n",
+ "Let's take as an example the function {func}`ehrdata.pp.basic_preproc`. \n",
+ "You can see that by clicking on the text, the link redirects to the API documentation of the function. \n",
+ "Check the raw markdown of this cell to understand how this is specified.\n",
+ "\n",
+ "This works also for any package listed by `intersphinx`. Go to `docs/conf.py` and look for the `intersphinx_mapping` variable. \n",
+ "There, you will see a list of packages (that this package is dependent on) for which this functionality is supported. \n",
+ "\n",
+ "For instance, we can link to the class {class}`anndata.AnnData`, to the attribute {attr}`anndata.AnnData.obs` or the method {meth}`anndata.AnnData.write`.\n",
+ "\n",
+ "Again, check the raw markdown of this cell to see how each of these links are specified.\n",
+ "\n",
+ "You can read more about this in the [intersphinx page](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html) and the [myst page](https://myst-parser.readthedocs.io/en/v0.15.1/syntax/syntax.html#roles-an-in-line-extension-point)."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Implement a preprocessing function here."
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "0"
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "ehrdata.pp.basic_preproc(adata)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
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