migrate repo

.pre-commit-config.yaml

@@ -0,0 +1,54 @@
+ci:
+  autoupdate_schedule: quarterly
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+      - id: no-commit-to-branch
+        args: [--branch=main]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.9
+    hooks:
+      - id: ruff
+        args: [--fix]
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - "numpy"
+  - repo: https://github.com/doublify/pre-commit-rust
+    rev: v1.0
+    hooks:
+      - id: fmt
+      - id: cargo-check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.12.1
+    hooks:
+      - id: yamlfmt
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.17
+    hooks:
+      - id: mdformat

.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+sphinx:
+  configuration: docs/source/conf.py
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

Cargo.toml

@@ -0,0 +1,22 @@
+[package]
+name    = "_utils_rust"
+version = "0.1.0"
+edition = "2021"
+
+[lib]
+name       = "_utils_rust"
+crate-type = ["cdylib"]
+
+[dependencies]
+bincode       = { version = "1.3" }
+indexmap      = { version = "2.1.0", features = ["rayon"] }
+itertools     = { version = "0.12.1" }
+ndarray       = { version = "0.15.6", features = ["rayon"] }
+ndarray-stats = { version = "0.5.1" }
+num           = { version = "0.4.1" }
+numpy         = { version = "0.21.0" }
+polars        = { version = "0.39", features = ["partition_by", "dtype-categorical"] }
+pyo3          = { version = "0.21.0", features = ["extension-module"] }
+pyo3-polars   = { version = "0.13.0" }
+rayon         = { version = "1.8.0" }
+sprs          = { version = "0.11.1", features = ["serde"] }

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Niklas Müller-Bötticher, Naveed Ishaque, Roland Eils, Berlin Institute of Health @ Charité
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# sainsc
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+
+/ˈsaiəns/
+
+_"**S**egmentation-free **A**nalysis of **In S**itu **C**apture data"_
+or alternatively
+"_**S**tupid **A**cronyms **In Sc**ience_"
+
+`sainsc` is a segmentation-free analysis tool for spatial transcriptomics from in situ
+capture technologies (but also works for imaging-based technologies). It is easily
+integratable with the [scverse](https://github.com/scverse) (i.e. `scanpy` and `squidpy`)
+by exporting data in [`AnnData`](https://anndata.readthedocs.io/) or
+[`SpatialData`](https://spatialdata.scverse.org/) format.
+
+## Installation
+
+`sainsc` will be made available on [PyPI](https://pypi.org/) and
+[bioconda](https://bioconda.github.io/). For detailed installation instructions
+please refer to the [documentation](https://sainsc.readthedocs.io/en/stable/installation.html).
+
+## Documentation
+
+For an extensive documentation of the package please refer to the
+[ReadTheDocs page](https://sainsc.readthedocs.io)
+
+## Versioning
+
+This project follows the [SemVer](https://semver.org/) guidelines for versioning.
+
+## Citations
+
+## License
+
+This project is licensed under the MIT License - for details please refer to the
+[LICENSE](./LICENSE) file.

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     = source
+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)

docs/source/_templates/python/class.rst

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+{% if obj.display %}
+   {% if is_own_page %}
+{{ obj.id }}
+{{ "=" * obj.id | length }}
+
+   {% endif %}
+   {% set visible_children = obj.children|selectattr("display")|list %}
+   {% set own_page_children = visible_children|selectattr("type", "in", own_page_types)|list %}
+   {% if is_own_page and own_page_children %}
+.. toctree::
+   :hidden:
+
+      {% for child in own_page_children %}
+   {{ child.include_path }}
+      {% endfor %}
+
+   {% endif %}
+.. py:{{ obj.type }}:: {% if is_own_page %}{{ obj.id }}{% else %}{{ obj.short_name }}{% endif %}{% if obj.args %}({{ obj.args }}){% endif %}
+
+   {% for (args, return_annotation) in obj.overloads %}
+      {{ " " * (obj.type | length) }}   {{ obj.short_name }}{% if args %}({{ args }}){% endif %}
+
+   {% endfor %}
+   {% if obj.bases %}
+      {% if "show-inheritance" in autoapi_options %}
+
+   Bases: {% for base in obj.bases %}{{ base|link_objs }}{% if not loop.last %}, {% endif %}{% endfor %}
+      {% endif %}
+
+
+      {% if "show-inheritance-diagram" in autoapi_options and obj.bases != ["object"] %}
+   .. autoapi-inheritance-diagram:: {{ obj.obj["full_name"] }}
+      :parts: 1
+         {% if "private-members" in autoapi_options %}
+      :private-bases:
+         {% endif %}
+
+      {% endif %}
+   {% endif %}
+   {% if obj.docstring %}
+
+   {{ obj.docstring|indent(3) }}
+   {% endif %}
+   {% for obj_item in visible_children %}
+      {% if obj_item.type not in own_page_types %}
+
+   {{ obj_item.render()|indent(3) }}
+      {% endif %}
+   {% endfor %}
+   {% if is_own_page and own_page_children %}
+      {% set visible_attributes = own_page_children|selectattr("type", "equalto", "attribute")|list %}
+      {% if visible_attributes %}
+Attributes
+----------
+
+.. autoapisummary::
+
+         {% for attribute in visible_attributes %}
+   {{ attribute.id }}
+         {% endfor %}
+
+
+      {% endif %}
+      {% set visible_properties = own_page_children|selectattr("type", "equalto", "property")|list %}
+      {% if visible_properties %}
+Properties
+----------
+
+.. autoapisummary::
+
+         {% for property in visible_properties %}
+   {{ property.id }}
+         {% endfor %}
+
+
+      {% endif %}
+      {% set visible_exceptions = own_page_children|selectattr("type", "equalto", "exception")|list %}
+      {% if visible_exceptions %}
+Exceptions
+----------
+
+.. autoapisummary::
+
+         {% for exception in visible_exceptions %}
+   {{ exception.id }}
+         {% endfor %}
+
+
+      {% endif %}
+      {% set visible_classes = own_page_children|selectattr("type", "equalto", "class")|list %}
+      {% if visible_classes %}
+Classes
+-------
+
+.. autoapisummary::
+
+         {% for klass in visible_classes %}
+   {{ klass.id }}
+         {% endfor %}
+
+
+      {% endif %}
+      {% set visible_methods = own_page_children|selectattr("type", "equalto", "method")|list %}
+      {% if visible_methods %}
+Methods
+-------
+
+.. autoapisummary::
+
+            {% for method in visible_methods %}
+   {{ method.id }}
+            {% endfor %}
+
+
+      {% endif %}
+   {% endif %}
+{% endif %}

docs/source/conf.py

@@ -0,0 +1,90 @@
+import importlib.metadata
+import os
+import sys
+from datetime import datetime
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "sainsc"
+copyright = f"""
+{datetime.now():%Y}, Niklas Müller-Bötticher, Naveed Ishaque, Roland Eils,
+Berlin Institute of Health @ Charité"""
+author = "Niklas Müller-Bötticher"
+version = importlib.metadata.version("sainsc")
+release = version
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+
+extensions = [
+    "sphinx_copybutton",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "autoapi.extension",
+    "sphinx.ext.mathjax",
+]
+
+
+autodoc_typehints = "none"
+autodoc_typehints_format = "short"
+
+autoapi_dirs = ["../../sainsc"]
+autoapi_options = [
+    "members",
+    "undoc-members",
+    "show-inheritance",
+    "show-module-summary",
+    "imported-members",
+]
+autoapi_python_class_content = "both"
+autoapi_own_page_level = "attribute"
+autoapi_template_dir = "_templates"
+autoapi_member_order = "groupwise"
+
+python_use_unqualified_type_names = True  # still experimental
+
+autosummary_generate = True
+autosummary_imported_members = True
+
+nitpicky = True
+nitpick_ignore = [
+    ("py:class", "numpy.typing.DTypeLike"),
+    ("py:class", "numpy.typing.NDArray"),
+    ("py:mod", "polars"),
+    ("py:class", "polars.DataFrame"),
+    ("py:class", "optional"),
+]
+
+exclude_patterns: list[str] = ["_templates"]
+
+intersphinx_mapping = dict(
+    anndata=("https://anndata.readthedocs.io/en/stable/", None),
+    matplotlib=("https://matplotlib.org/stable/", None),
+    numpy=("https://numpy.org/doc/stable/", None),
+    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
+    polars=("https://docs.pola.rs/py-polars/html/", None),
+    python=("https://docs.python.org/3", None),
+    scipy=("https://docs.scipy.org/doc/scipy/", None),
+    seaborn=("https://seaborn.pydata.org/", None),
+    spatialdata=("https://spatialdata.scverse.org/en/stable/", None),
+)
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path: list[str] = []
+
+
+def skip_submodules(app, what, name, obj, skip, options):
+    if what == "module":
+        skip = True
+    return skip
+
+
+def setup(sphinx):
+    sphinx.connect("autoapi-skip-member", skip_submodules)