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..4b3c8d5 --- /dev/null +++ b/.cruft.json @@ -0,0 +1,30 @@ +{ + "template": "https://github.com/scverse/cookiecutter-scverse", + "commit": "cfdd468f3bf7967aca8f518268199370a475180a", + "checkout": null, + "context": { + "cookiecutter": { + "project_name": "pici-vitessce", + "package_name": "pici_vitessce", + "project_description": "A very interesting piece of code", + "author_full_name": "Sricharan Reddy Varra", + "author_email": "srivarra@stanford.edu", + "github_user": "angelolab", + "github_repo": "pici-vitessce", + "license": "MIT License", + "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..af64746 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -0,0 +1,11 @@ +name: Feature request +description: Propose a new feature for pici-vitessce +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..bfa2cf0 --- /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@v4 + - name: Set up Python 3.12 + uses: actions/setup-python@v5 + with: + python-version: "3.12" + 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..4277957 --- /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/pici_vitessce + 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@v5 + 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..841bd7c --- /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@v4 + - name: Set up Python ${{ matrix.python }} + uses: actions/setup-python@v5 + 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: ${{ matrix.os }} + DISPLAY: :42 + run: | + coverage run -m pytest -v --color=yes + - name: Report coverage + run: | + coverage report + - name: Upload coverage + uses: codecov/codecov-action@v3 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..57c89ef --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,46 @@ +fail_fast: false +default_language_version: + python: python3 +default_stages: + - pre-commit + - pre-push +minimum_pre_commit_version: 2.16.0 +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier + - repo: https://github.com/tox-dev/pyproject-fmt + rev: v2.5.0 + hooks: + - id: pyproject-fmt + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.7.3 + hooks: + - id: ruff + types_or: [python, pyi, jupyter] + args: [--fix, --exit-non-zero-on-fix] + - id: ruff-format + types_or: [python, pyi, jupyter] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 + hooks: + - id: detect-private-key + - id: check-ast + - id: end-of-file-fixer + - id: mixed-line-ending + args: [--fix=lf] + - id: trailing-whitespace + - id: check-case-conflict + # Check that there are no merge conflicts (could be generated by template sync) + - id: check-merge-conflict + args: [--assume-in-merge] + - repo: local + hooks: + - id: forbid-to-commit + name: Don't commit rej files + entry: | + Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates. + Fix the merge conflicts manually and remove the .rej files. + language: fail + files: '.*\.rej$' 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/.python-version b/.python-version new file mode 100644 index 0000000..2c07333 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 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/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..20b882b --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2024, Sricharan Reddy Varra + +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. diff --git a/README.md b/README.md new file mode 100644 index 0000000..08d927b --- /dev/null +++ b/README.md @@ -0,0 +1,57 @@ +# pici-vitessce + +[![Tests][badge-tests]][tests] +[![Documentation][badge-docs]][documentation] + +[badge-tests]: https://img.shields.io/github/actions/workflow/status/angelolab/pici-vitessce/test.yaml?branch=main +[badge-docs]: https://img.shields.io/readthedocs/pici-vitessce + +A very interesting piece of code + +## 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 pici-vitessce: + + + +1. Install the latest development version: + +```bash +pip install git+https://github.com/angelolab/pici-vitessce.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/angelolab/pici-vitessce/issues +[tests]: https://github.com/angelolab/pici-vitessce/actions/workflows/test.yml +[documentation]: https://pici-vitessce.readthedocs.io +[changelog]: https://pici-vitessce.readthedocs.io/en/latest/changelog.html +[api documentation]: https://pici-vitessce.readthedocs.io/en/latest/api.html +[pypi]: https://pypi.org/project/pici-vitessce 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..85b70a5 --- /dev/null +++ b/docs/api.md @@ -0,0 +1,38 @@ +# API + +## Preprocessing + +```{eval-rst} +.. module:: pici_vitessce.pp +.. currentmodule:: pici_vitessce + +.. autosummary:: + :toctree: generated + + pp.basic_preproc +``` + +## Tools + +```{eval-rst} +.. module:: pici_vitessce.tl +.. currentmodule:: pici_vitessce + +.. autosummary:: + :toctree: generated + + tl.basic_tool +``` + +## Plotting + +```{eval-rst} +.. module:: pici_vitessce.pl +.. currentmodule:: pici_vitessce + +.. 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..7dc8860 --- /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("pici-vitessce") +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": "angelolab", + "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..66f074e --- /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 pici-vitessce +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 run docs:build +hatch run 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..e4ac552 --- /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 pici_vitessce" + ] + }, + { + "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}`pici_vitessce.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": [ + "pici_vitessce.pp.basic_preproc(adata)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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Luecken and Fidel Ramirez and Jeffrey Regier and Sergei Rybakov and Anna C. Schaar and Valeh Valiollah Pour Amiri and Philipp Weiler and Galen Xing and Bonnie Berger and Dana Pe'er and Aviv Regev and Sarah A. Teichmann and Francesca Finotello and F. Alexander Wolf and Nir Yosef and Oliver Stegle and Fabian J. Theis and}, + title = {The scverse project provides a computational ecosystem for single-cell omics data analysis}, + journal = {Nature Biotechnology} +} diff --git a/docs/references.md b/docs/references.md new file mode 100644 index 0000000..00ad6a6 --- /dev/null +++ b/docs/references.md @@ -0,0 +1,5 @@ +# References + +```{bibliography} +:cited: +``` diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..9a80b3b --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,149 @@ +[build-system] +build-backend = "hatchling.build" +requires = [ "hatchling" ] + +[project] +name = "pici-vitessce" +version = "0.0.1" +description = "A very interesting piece of code" +readme = "README.md" +license = { file = "LICENSE" } +maintainers = [ + { name = "Sricharan Reddy Varra", email = "srivarra@stanford.edu" }, +] +authors = [ + { name = "Sricharan Reddy Varra" }, +] +requires-python = ">=3.10" +classifiers = [ + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", +] +dependencies = [ + "anndata", + "numpy", + "polars>=1.13.1", + "pyarrow>=18", + "pydantic>=2.9.2", + # for debug logging (referenced from the issue template) + "session-info", + "universal-pathlib>=0.2.5", + "vitessce[all]", +] +optional-dependencies.dev = [ + "pre-commit", + "twine>=4.0.2", +] +optional-dependencies.doc = [ + "docutils>=0.8,!=0.18.*,!=0.19.*", + "ipykernel", + "ipython", + "myst-nb>=1.1", + "pandas", + # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/ + "setuptools", + "sphinx>=4", + "sphinx-autodoc-typehints", + "sphinx-book-theme>=1", + "sphinx-copybutton", + "sphinx-tabs", + "sphinxcontrib-bibtex>=1", + "sphinxext-opengraph", +] +optional-dependencies.nb = [ + "ipywidgets>=8.1.5", + "jupyter>=1.1.1", + "tqdm>=4.67", +] +optional-dependencies.test = [ + "coverage", + "pytest", +] +# https://docs.pypi.org/project_metadata/#project-urls +urls.Documentation = "https://pici-vitessce.readthedocs.io/" +urls.Homepage = "https://github.com/angelolab/pici-vitessce" +urls.Source = "https://github.com/angelolab/pici-vitessce" + +[tool.hatch.envs.default] +installer = "uv" +features = [ "dev" ] + +[tool.hatch.envs.docs] +features = [ "doc" ] +scripts.build = "sphinx-build -M html docs docs/_build {args}" +scripts.open = "python -m webbrowser -t docs/_build/html/index.html" +scripts.clean = "git clean -fdX -- {args:docs}" + +[tool.hatch.envs.hatch-test] +features = [ "test" ] + +[tool.ruff] +line-length = 120 +src = [ "src" ] +extend-include = [ "*.ipynb" ] + +format.docstring-code-format = true + +lint.select = [ + "B", # flake8-bugbear + "BLE", # flake8-blind-except + "C4", # flake8-comprehensions + "D", # pydocstyle + "E", # Error detected by Pycodestyle + "F", # Errors detected by Pyflakes + "I", # isort + "RUF100", # Report unused noqa directives + "TID", # flake8-tidy-imports + "UP", # pyupgrade + "W", # Warning detected by Pycodestyle +] +lint.ignore = [ + "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable. + "D100", # Missing docstring in public module + "D104", # Missing docstring in public package + "D105", # __magic__ methods are often self-explanatory, allow missing docstrings + "D107", # Missing docstring in __init__ + # Disable one in each pair of mutually incompatible rules + "D203", # We don’t want a blank line before a class docstring + "D213", # <> We want docstrings to start immediately after the opening triple quote + "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings] + "D401", # First line should be in imperative mood; try rephrasing + "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines + "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient + "E741", # allow I, O, l as variable names -> I is the identity matrix +] +lint.per-file-ignores."*/__init__.py" = [ "F401" ] +lint.per-file-ignores."docs/*" = [ "I" ] +lint.per-file-ignores."tests/*" = [ "D" ] +lint.pydocstyle.convention = "numpy" + +[tool.pytest.ini_options] +testpaths = [ "tests" ] +xfail_strict = true +addopts = [ + "--import-mode=importlib", # allow using test files with same name +] + +[tool.coverage.run] +source = [ "pici_vitessce" ] +omit = [ + "**/test_*.py", +] + +[tool.cruft] +skip = [ + "tests", + "src/**/__init__.py", + "src/**/basic.py", + "docs/api.md", + "docs/changelog.md", + "docs/references.bib", + "docs/references.md", + "docs/notebooks/example.ipynb", +] + +[tool.uv.sources] +vitessce = { git = "https://github.com/vitessce/vitessce-python" } diff --git a/scripts/01_data_conversion.ipynb b/scripts/01_data_conversion.ipynb new file mode 100644 index 0000000..a66df7b --- /dev/null +++ b/scripts/01_data_conversion.ipynb @@ -0,0 +1,350 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from upath import UPath\n", + "\n", + "import pici_vitessce as pv" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Overview\n", + "\n", + "We will convert the data from the original format to an OME-Zarr format which works well with Vitessce and cloud storage. The configs will be generated in the $2^{nd}$ notebook.\n", + "
\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
Input Directory Structure Output Directory Structure
\n", + "\n", + "```sh\n", + "data/\n", + "└── processed/\n", + " ├── immune/\n", + " │ ├── cell_table/\n", + " │ │ └── cell_table_immune_thresholded.parquet\n", + " │ ├── image_data/\n", + " │ │ ├── fov1/\n", + " │ │ │ ├── chan1.tiff\n", + " │ │ │ ├── chan2.tiff\n", + " │ │ │ └── ...\n", + " │ │ └── ...\n", + " │ └── segmentation/\n", + " │ └── deepcell_output/\n", + " │ ├── fov1_whole_cell.tiff\n", + " │ └── ...\n", + " ├── tumor/\n", + " │ └── cell_table/\n", + " │ └── cell_table_tumor_thresholded.parquet\n", + " ├── image_data/\n", + " │ ├── fov1/\n", + " │ │ ├── chan1.tiff\n", + " │ │ ├── chan2.tiff\n", + " │ │ └── ...\n", + " │ └── ...\n", + " └── segmentation/\n", + " └── deepcell_output/\n", + " ├── fov1_whole_cell.tiff\n", + " └── ...\n", + "```\n", + "\n", + "\n", + "\n", + "```sh\n", + "data/\n", + "└── vitessce/\n", + " ├── fov1/\n", + " │ ├── immune/\n", + " │ │ ├── whole_cell_table.zarr\n", + " │ │ ├── image.ome.zarr\n", + " │ │ └── segmentation.ome.zarr\n", + " │ ├── tumor/\n", + " │ │ ├── whole_cell_table.zarr\n", + " │ │ ├── image.ome.zarr\n", + " │ │ └── segmentation.ome.zarr\n", + " │ └── configs/\n", + " │ ├── immune_config.json\n", + " │ ├── tumor_config.json\n", + " │ └── both_config.json\n", + " └── ...\n", + "```\n", + "\n", + "
\n", + "
" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Setup Data" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Set up Directories\n", + "\n", + "We set up the directories for ingestion and output here." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "processed_data_path = UPath(\"../data/processed\")\n", + "vitessce_path = UPath(\"../data/vitessce\")\n", + "\n", + "immune_data_path = processed_data_path / \"immune\"\n", + "immune_cell_table_path = immune_data_path / \"cell_table/cell_table_immune_thresholded.parquet\"\n", + "immune_fov_dir = immune_data_path / \"image_data\"\n", + "immune_fov_paths = immune_fov_dir.glob(\"[!.]*\")\n", + "immune_fov_names = [p.name for p in immune_fov_paths]\n", + "immune_segmentation_dir = immune_data_path / \"segmentation/deepcell_output\"\n", + "\n", + "\n", + "tumor_data_path = processed_data_path / \"tumor\"\n", + "tumor_cell_table_path = tumor_data_path / \"cell_table/cell_table_tumor_thresholded.parquet\"\n", + "tumor_fov_dir = tumor_data_path / \"image_data\"\n", + "tumor_fov_paths = tumor_fov_dir.glob(\"[!.]*\")\n", + "tumor_fov_names = [p.name for p in tumor_fov_paths]\n", + "tumor_segmentation_dir = tumor_data_path / \"segmentation/deepcell_output\"" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Set up AnnData column names" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "immune_markers = [\n", + " \"CD11b\",\n", + " \"CD14\",\n", + " \"CD141\",\n", + " \"CD163\",\n", + " \"CD206\",\n", + " \"CD209\",\n", + " \"CD3\",\n", + " \"CD38\",\n", + " \"CD4\",\n", + " \"CD45\",\n", + " \"CD68\",\n", + " \"CD8\",\n", + " \"CD86\",\n", + " \"Calprotectin\",\n", + " \"Chym_Tryp\",\n", + " \"FoxP3\",\n", + " \"GLUT1\",\n", + " \"HLA1\",\n", + " \"HLADR\",\n", + " \"ICOS\",\n", + " \"IDO1\",\n", + " \"Ki67\",\n", + " \"LAG3\",\n", + " \"PD1\",\n", + " \"PDL1\",\n", + " \"TIM3\",\n", + " \"TMEM119\",\n", + " \"Tox\",\n", + " \"Arginase1\",\n", + " \"Olig2\",\n", + "]\n", + "tumor_markers = [\n", + " \"HLA1\",\n", + " \"CD14\",\n", + " \"CD3\",\n", + " \"CD45\",\n", + " \"CD8\",\n", + " \"FOXP3\",\n", + " \"HLADR\",\n", + " \"ApoE\",\n", + " \"B7H3\",\n", + " \"CD133\",\n", + " \"EGFR\",\n", + " \"EGFRvIII\",\n", + " \"GFAP\",\n", + " \"GM2_GD2\",\n", + " \"GPC2\",\n", + " \"H3K27M\",\n", + " \"H3K27me3\",\n", + " \"HER2\",\n", + " \"IDH1_R132H\",\n", + " \"Ki67\",\n", + " \"NG2\",\n", + " \"Olig2\",\n", + " \"VISTA\",\n", + "]\n", + "obs_cols = [\n", + " \"fov\",\n", + " \"label\",\n", + " \"cell_meta_cluster_final_broad\",\n", + " \"cell_meta_cluster_final\",\n", + "]\n", + "obsm_cols = [\"centroid-0\", \"centroid-1\"]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Convert to Vitessce Accessible Formats" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Convert the Cell Table to AnnData" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pv.pp.process_cell_table_to_anndata(\n", + " cell_table_path=immune_cell_table_path,\n", + " fovs=immune_fov_names,\n", + " markers=immune_markers,\n", + " obs_cols=obs_cols,\n", + " obsm_cols=obsm_cols,\n", + " segmentation_dir=immune_segmentation_dir,\n", + " fov_category=\"immune\",\n", + " vitessce_path=vitessce_path,\n", + ")\n", + "\n", + "pv.pp.process_cell_table_to_anndata(\n", + " cell_table_path=tumor_cell_table_path,\n", + " fovs=tumor_fov_names,\n", + " markers=tumor_markers,\n", + " obs_cols=obs_cols,\n", + " obsm_cols=obsm_cols,\n", + " segmentation_dir=tumor_segmentation_dir,\n", + " fov_category=\"tumor\",\n", + " vitessce_path=vitessce_path,\n", + " rename_markers={\"FoxP3\": \"FOXP3\"},\n", + ")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Convert the FOVs to OME-Zarr Images" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pv.pp.convert_fovs_to_zarr(\n", + " fovs=immune_fov_names,\n", + " fov_category=\"immune\",\n", + " markers=immune_markers,\n", + " fovs_dir=immune_fov_dir,\n", + " vitessce_path=vitessce_path,\n", + ")\n", + "pv.pp.convert_fovs_to_zarr(\n", + " fovs=tumor_fov_names,\n", + " fov_category=\"tumor\",\n", + " markers=tumor_markers,\n", + " fovs_dir=tumor_fov_dir,\n", + " vitessce_path=vitessce_path,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Convert the Segmentation Masks to OME-Zarr Images" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pv.pp.convert_segmentations_to_zarr(\n", + " fovs=immune_fov_names,\n", + " fov_category=\"immune\",\n", + " segmentation_mask_suffixes=\"whole_cell\",\n", + " segmentation_dir=immune_segmentation_dir,\n", + " vitessce_path=vitessce_path,\n", + ")\n", + "pv.pp.convert_segmentations_to_zarr(\n", + " fovs=tumor_fov_names,\n", + " fov_category=\"tumor\",\n", + " segmentation_mask_suffixes=\"whole_cell\",\n", + " segmentation_dir=tumor_segmentation_dir,\n", + " vitessce_path=vitessce_path,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/scripts/02_vitessce_generation.ipynb b/scripts/02_vitessce_generation.ipynb new file mode 100644 index 0000000..c53984a --- /dev/null +++ b/scripts/02_vitessce_generation.ipynb @@ -0,0 +1,292 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from upath import UPath\n", + "from vitessce import (\n", + " VitessceConfig,\n", + ")\n", + "\n", + "import pici_vitessce as pv" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "vitessce_path = UPath(\"../data/vitessce\")\n", + "# tumor_data_dir = vitessce_path / \"tumor\"\n", + "# immune_data_dir = vitessce_path / \"immune\"" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "fov = \"Stanford_TA552_R1C1\"" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "immune_markers = [\n", + " \"CD11b\",\n", + " \"CD14\",\n", + " \"CD141\",\n", + " \"CD163\",\n", + " \"CD206\",\n", + " \"CD209\",\n", + " \"CD3\",\n", + " \"CD38\",\n", + " \"CD4\",\n", + " \"CD45\",\n", + " \"CD68\",\n", + " \"CD8\",\n", + " \"CD86\",\n", + " \"Calprotectin\",\n", + " \"Chym_Tryp\",\n", + " \"FoxP3\",\n", + " \"GLUT1\",\n", + " \"HLA1\",\n", + " \"HLADR\",\n", + " \"ICOS\",\n", + " \"IDO1\",\n", + " \"Ki67\",\n", + " \"LAG3\",\n", + " \"PD1\",\n", + " \"PDL1\",\n", + " \"TIM3\",\n", + " \"TMEM119\",\n", + " \"Tox\",\n", + " \"Arginase1\",\n", + " \"Olig2\",\n", + "]\n", + "tumor_markers = [\n", + " \"HLA1\",\n", + " \"CD14\",\n", + " \"CD3\",\n", + " \"CD45\",\n", + " \"CD8\",\n", + " \"FOXP3\",\n", + " \"HLADR\",\n", + " \"ApoE\",\n", + " \"B7H3\",\n", + " \"CD133\",\n", + " \"EGFR\",\n", + " \"EGFRvIII\",\n", + " \"GFAP\",\n", + " \"GM2_GD2\",\n", + " \"GPC2\",\n", + " \"H3K27M\",\n", + " \"H3K27me3\",\n", + " \"HER2\",\n", + " \"IDH1_R132H\",\n", + " \"Ki67\",\n", + " \"NG2\",\n", + " \"Olig2\",\n", + " \"VISTA\",\n", + "]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Create Vitessce Dataset config" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "vc = VitessceConfig(schema_version=\"1.0.17\", name=fov, base_dir=vitessce_path / fov)\n", + "tumor_dataset = pv.tl.add_vitessce_dataset(vc, fov=fov, dataset_name=\"tumor\")\n", + "# immune_dataset = pv.tl.add_vitessce_dataset(vc, vitessce_path=vitessce_path, fov=fov, dataset_name=\"immune\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Create Views and Configs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# immune_view = pv.tl.create_view(vc, immune_dataset, view_type=\"immune\")\n", + "tumor_view = pv.tl.create_view(vc, tumor_dataset, view_type=\"tumor\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### Scopes" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# immune_scope_config = pv.tl.setup_scopes(vc, immune_view)\n", + "tumor_scope_config = pv.tl.setup_scopes(vc, tumor_view)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### Coordination Setup" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Adjust the colors for the channels below, colors are from the [XKCD color survey](https://xkcd.com/color/rgb/). For Immune and Tumor images, we map the channel names to the colors." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "immune_color_map = {\n", + " \"CD14\": \"#650021\", # maroon\n", + " \"CD68\": \"#cb416b\", # dark pink\n", + " \"CD11b\": \"#840000\", # dark red\n", + " \"Olig2\": \"#014d4e\", # dark teal\n", + " \"GLUT1\": \"#b9a281\", # taupe\n", + "}\n", + "tumor_color_map = {\n", + " \"EGFR\": \"#fac205\", # goldenrod\n", + " \"B7H3\": \"#047495\", # sea blue\n", + " \"GFAP\": \"#1e488f\", # cobalt\n", + " \"H3K27me3\": \"#0a481e\", # pine green\n", + " \"HLADR\": \"#c0737a\", # dusty rose\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# pv.tl.link_views(\n", + "# vc,\n", + "# immune_view,\n", + "# immune_scope_config,\n", + "# vitessce_path=vitessce_path,\n", + "# dataset_name=\"immune\",\n", + "# fov=fov,\n", + "# channel_color_map=immune_color_map,\n", + "# )\n", + "pv.tl.link_views(\n", + " vc,\n", + " tumor_view,\n", + " tumor_scope_config,\n", + " vitessce_path=vitessce_path,\n", + " dataset_name=\"tumor\",\n", + " fov=fov,\n", + " channel_color_map=tumor_color_map,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# immune_layout = pv.tl.set_layout(immune_view)\n", + "tumor_layout = pv.tl.set_layout(tumor_view)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "vc.layout(tumor_layout)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "vc.web_app()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pv.tl.export_config(vc, tumor_view)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.7" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/src/pici_vitessce/__init__.py b/src/pici_vitessce/__init__.py new file mode 100644 index 0000000..04e65ae --- /dev/null +++ b/src/pici_vitessce/__init__.py @@ -0,0 +1,7 @@ +from importlib.metadata import version + +from . import pl, pp, tl + +__all__ = ["pl", "pp", "tl"] + +__version__ = version("pici-vitessce") diff --git a/src/pici_vitessce/pl/__init__.py b/src/pici_vitessce/pl/__init__.py new file mode 100644 index 0000000..c2315dd --- /dev/null +++ b/src/pici_vitessce/pl/__init__.py @@ -0,0 +1 @@ +from .basic import BasicClass, basic_plot diff --git a/src/pici_vitessce/pl/basic.py b/src/pici_vitessce/pl/basic.py new file mode 100644 index 0000000..ed390ef --- /dev/null +++ b/src/pici_vitessce/pl/basic.py @@ -0,0 +1,63 @@ +from anndata import AnnData + + +def basic_plot(adata: AnnData) -> int: + """Generate a basic plot for an AnnData object. + + Parameters + ---------- + adata + The AnnData object to preprocess. + + Returns + ------- + Some integer value. + """ + print("Import matplotlib and implement a plotting function here.") + return 0 + + +class BasicClass: + """A basic class. + + Parameters + ---------- + adata + The AnnData object to preprocess. + """ + + my_attribute: str = "Some attribute." + my_other_attribute: int = 0 + + def __init__(self, adata: AnnData): + print("Implement a class here.") + + def my_method(self, param: int) -> int: + """A basic method. + + Parameters + ---------- + param + A parameter. + + Returns + ------- + Some integer value. + """ + print("Implement a method here.") + return 0 + + def my_other_method(self, param: str) -> str: + """Another basic method. + + Parameters + ---------- + param + A parameter. + + Returns + ------- + Some integer value. + """ + print("Implement a method here.") + return "" diff --git a/src/pici_vitessce/pp/__init__.py b/src/pici_vitessce/pp/__init__.py new file mode 100644 index 0000000..2f3f3bb --- /dev/null +++ b/src/pici_vitessce/pp/__init__.py @@ -0,0 +1,7 @@ +from .basic import convert_fovs_to_zarr, convert_segmentations_to_zarr, process_cell_table_to_anndata + +__all__ = [ + "convert_fovs_to_zarr", + "convert_segmentations_to_zarr", + "process_cell_table_to_anndata", +] diff --git a/src/pici_vitessce/pp/basic.py b/src/pici_vitessce/pp/basic.py new file mode 100644 index 0000000..b829ffa --- /dev/null +++ b/src/pici_vitessce/pp/basic.py @@ -0,0 +1,197 @@ +import warnings + +import anndata as ad +import natsort as ns +import numpy as np +import polars as pl +from tifffile import imread +from tqdm.auto import tqdm +from upath import UPath +from vitessce.data_utils import VAR_CHUNK_SIZE, multiplex_img_to_ome_zarr, optimize_adata, optimize_arr +from zarr import DirectoryStore, consolidate_metadata + + +def process_cell_table_to_anndata( + cell_table_path: UPath, + fovs: list[str], + markers: list[str], + obs_cols: list[str], + obsm_cols: list[str], + segmentation_dir: UPath, + fov_category: str, + vitessce_path: UPath, + rename_markers: dict[str, str] | None = None, +) -> None: + """ + Conver the cell table to AnnData objects per FOV. + + Process the cell table to create AnnData objects for specified fields of view (FOVs), + specified markers, and specified observation variables. + Export them to Zarr stores. + + Parameters + ---------- + cell_table_path + Path to the parquet file containing cell data. + fovs + List of field of view identifiers to process. + markers + List of marker columns to include in the AnnData's X attribute. + obs_cols + List of observation columns to include in the AnnData's `obs` attribute. + obsm_cols + List of observation metadata columns to include in the AnnData's `obsm` attribute. + segmentation_dir + Path to the directory containing segmentation images. + fov_category + The category of the field of view (e.g., immune, tumor). + vitessce_path + Base output path for saving Vitessce-compatible data. + rename_markers, optional + Optional dictionary to rename markers in the cell table. + """ + # Read parquet files + cell_table = pl.read_parquet(source=cell_table_path) + if rename_markers is not None: + cell_table = cell_table.rename(rename_markers) + + for (_fov,), fov_ct in tqdm( + ns.natsorted( + cell_table.lazy() + .select(markers + obs_cols + obsm_cols) + .cast(dtypes={"label": pl.Int16}) + .filter(pl.col("fov").is_in(fovs)) + .collect() + .group_by("fov"), + key=lambda g: str(g[0]), + ) + ): + _fov = str(_fov) + fov_ct = fov_ct.sort("label") + + # Load unique labels from the segmentation image (filter on labels which are present in the image) + n_unique_labels = len(np.unique(imread(segmentation_dir / f"{_fov}_whole_cell.tiff"))) # type: ignore + fov_ct = fov_ct.lazy().filter(pl.col("label").is_in(range(1, n_unique_labels + 1))).collect() + + # Create AnnData object + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + fov_adata = ad.AnnData( + X=fov_ct[markers].to_pandas(), + obs=fov_ct[obs_cols].to_pandas(), + obsm={"spatial": fov_ct[obsm_cols].to_numpy()}, # type: ignore + ) + fov_adata.strings_to_categoricals() + + # Optimize the AnnData object + optimized_adata = optimize_adata( + fov_adata, + optimize_X=True, + ) + + # Define output path for Vitessce data + vitessce_fov_path = vitessce_path / _fov / fov_category + + if not vitessce_fov_path.exists(): + vitessce_fov_path.mkdir(parents=True, exist_ok=True) + + # Save the optimized AnnData to the Zarr format + store_path = DirectoryStore(vitessce_fov_path / "whole_cell_table.zarr") + optimized_adata.write_zarr(store=store_path, chunks=(fov_adata.shape[0], VAR_CHUNK_SIZE)) + consolidate_metadata(store=store_path) + + +def convert_fovs_to_zarr( + fovs: list[str], + fov_category: str, + fovs_dir: UPath, + markers: list[str], + vitessce_path: UPath, + marker_colormap: dict[str, str] | None = None, +) -> None: + """Converts multiple fields of view (folders of TIFFs) into Zarr Stores. + + Parameters + ---------- + fovs + The list of field of views to convert. + fov_category + The category of the field of view (e.g., immune, tumor). + fovs_dir + The directory containing all the field of views. + markers + The channels to convert. If `None`, all channels will be used. + vitessce_path + The output directory to place the converted field of views. + marker_colormap, optional + A colormap per channel. If `None`, colors will be auto-assigned. + """ + if isinstance(fovs, str): + fovs = [fovs] + + for fov in tqdm(fovs): + channel_paths = [fovs_dir / fov / f"{c}.tiff" for c in ns.natsorted(markers)] + fov_img = optimize_arr(arr=imread(files=channel_paths)) + + if not (vitessce_fov_path := vitessce_path / fov / fov_category).exists(): + vitessce_fov_path.mkdir(parents=True, exist_ok=True) + store_path = DirectoryStore(vitessce_fov_path / "image.ome.zarr") + + multiplex_img_to_ome_zarr( + img_arr=fov_img, + channel_names=markers, + img_name=fov, + axes="cyx", + chunks=(1, 256, 256), + channel_colors=marker_colormap, + output_path=store_path, + ) + consolidate_metadata(store=store_path) + + +def convert_segmentations_to_zarr( + fovs: list[str], + fov_category: str, + segmentation_mask_suffixes: str | list[str], + segmentation_dir: UPath, + vitessce_path: UPath, +) -> None: + """Converts TIFF cell segmentation masks or compartment segmentation masks to OME-ZARR files for multiple FOVs. + + Parameters + ---------- + fovs + A list of fields of view. + fov_category + The category of the field of view (e.g., immune, tumor). + segmentation_mask_suffixes + The suffixes of the segmentation masks to convert (e.g. "whole_cell", "nuclear") + segmentation_dir + The directory containing the specific segmentation masks. + vitessce_path + The output directory to place the converted segmentation masks. + """ + if isinstance(segmentation_mask_suffixes, str): + segmentation_mask_suffixes = [segmentation_mask_suffixes] + + for fov in tqdm(fovs): + segmentation_mask_paths = ns.natsorted( + [segmentation_dir / f"{fov}_{c}.tiff" for c in segmentation_mask_suffixes] + ) + segmentation_array = optimize_arr(arr=imread(files=segmentation_mask_paths).astype("int").squeeze()) # type: ignore + + if not (vitessce_seg_path := vitessce_path / fov / fov_category / "segmentation.ome.zarr").exists(): + vitessce_seg_path.mkdir(parents=True, exist_ok=True) + + store_path = DirectoryStore(vitessce_seg_path) + + multiplex_img_to_ome_zarr( + img_arr=segmentation_array, + channel_names=ns.natsorted(segmentation_mask_suffixes), + img_name=f"{fov}_segmentation", + axes="cyx" if segmentation_array.ndim == 3 else "yx", + chunks=(1, 256, 256) if segmentation_array.ndim == 3 else (256, 256), + channel_colors=None, + output_path=store_path, + ) + consolidate_metadata(store=store_path) diff --git a/src/pici_vitessce/tl/__init__.py b/src/pici_vitessce/tl/__init__.py new file mode 100644 index 0000000..0540fd9 --- /dev/null +++ b/src/pici_vitessce/tl/__init__.py @@ -0,0 +1,23 @@ +from .basic import ( + ScopeConfig, + VitessceViews, + _get_omero_channel_colors, + add_vitessce_dataset, + create_view, + export_config, + link_views, + set_layout, + setup_scopes, +) + +__all__ = [ + "VitessceViews", + "ScopeConfig", + "create_view", + "setup_scopes", + "link_views", + "add_vitessce_dataset", + "set_layout", + "export_config", + "_get_omero_channel_colors", +] diff --git a/src/pici_vitessce/tl/basic.py b/src/pici_vitessce/tl/basic.py new file mode 100644 index 0000000..ff1c23a --- /dev/null +++ b/src/pici_vitessce/tl/basic.py @@ -0,0 +1,398 @@ +import json +from collections.abc import Mapping +from typing import Any + +from matplotlib.colors import is_color_like, to_rgb +from ome_zarr.io import ZarrLocation +from ome_zarr.reader import Reader +from pydantic import BaseModel, ConfigDict +from upath import UPath +from vitessce import ( + AnnDataWrapper, + ImageOmeZarrWrapper, + ObsSegmentationsOmeZarrWrapper, + get_initial_coordination_scope_prefix, +) +from vitessce import CoordinationLevel as CL +from vitessce.config import ( + VitessceConfig, + VitessceConfigCoordinationScope, + VitessceConfigDataset, + VitessceConfigView, + VitessceConfigViewHConcat, + VitessceConfigViewVConcat, +) + + +class VitessceViews(BaseModel): + """Container for Vitessce configuration views.""" + + model_config = ConfigDict(arbitrary_types_allowed=True) + view_type: str + spatial_view: VitessceConfigView + layerController_view: VitessceConfigView + obsSets_view: VitessceConfigView + featureList_view: VitessceConfigView + obsSetSizes_view: VitessceConfigView + + +class ScopeConfig(BaseModel): + """Configuration for coordination scopes in Vitessce.""" + + model_config = ConfigDict(arbitrary_types_allowed=True) + + featureTypeScope: VitessceConfigCoordinationScope + featureValueTypeScope: VitessceConfigCoordinationScope + spatialSegmentationFilledScope: VitessceConfigCoordinationScope + spatialSegmentationStrokeWidthScope: VitessceConfigCoordinationScope + featureSelectionScope: VitessceConfigCoordinationScope + obsSetSelectionScope: VitessceConfigCoordinationScope + obsSetColorScope: VitessceConfigCoordinationScope + obsColorEncodingScope: VitessceConfigCoordinationScope + spatialChannelOpacityScope: VitessceConfigCoordinationScope + + +class OmeroChannelConfig(BaseModel): + """Configuration for channels in an Omero image.""" + + model_config = ConfigDict(arbitrary_types_allowed=True) + + channel_name: str + color: tuple[int, int, int] + omero_index: int + + +class OmeroImageConfig(BaseModel): + """Configuration for an Omero image.""" + + model_config = ConfigDict(arbitrary_types_allowed=True) + + channel_configs: list[OmeroChannelConfig] | list = [] + + def __add__(self, other: OmeroChannelConfig): + self.channel_configs.append(other) + return self + + def __iter__(self): + return iter(self.channel_configs) + + def __len__(self): + return len(self.channel_configs) + + def __getitem__(self, index): + return self.channel_configs[index] + + +def _validate_color(color) -> tuple[int, int, int]: + if not is_color_like(color): + raise ValueError(f"Color {color} is not a valid color") + else: + # Convert float RGB values (0-1) to integers (0-255) + color = tuple(int(c * 255) for c in to_rgb(color)) + return color + + +def _get_omero_channel_index(omero_channels: list[Mapping[str, Any]], channel: str) -> int: + for i, c in enumerate(omero_channels): + if c["label"] == channel: + return i + raise ValueError(f"Channel {channel} not found in omero channels") + + +def _get_omero_channel_colors(store: UPath, channel_color_map: Mapping[str, Any]) -> OmeroImageConfig: + reader = Reader(ZarrLocation(store)) + omero_channels = reader.zarr.root_attrs["omero"]["channels"] + omero_channel_configs = OmeroImageConfig() + for channel, color in channel_color_map.items(): + omero_index = _get_omero_channel_index(omero_channels, channel) + omero_channel_configs += OmeroChannelConfig( + channel_name=channel, + color=_validate_color(color), + omero_index=omero_index, + ) + return omero_channel_configs + + +def add_vitessce_dataset(vc: VitessceConfig, fov: str, dataset_name: str) -> VitessceConfigDataset: + """Add a datset to the Vitessce configuration. + + Parameters + ---------- + vc + The Vitessce configuration object. + fov + The name of the field of view. + dataset_name + The name of the dataset. + + Returns + ------- + The dataset object. + """ + dataset = vc.add_dataset(uid=f"{fov}-{dataset_name}", name=f"{fov}-{dataset_name}") + anndata_path = (vc.base_dir / dataset_name / "whole_cell_table.zarr").relative_to(vc.base_dir).as_posix() + segmentation_path = (vc.base_dir / dataset_name / "segmentation.ome.zarr").relative_to(vc.base_dir).as_posix() + image_path = (vc.base_dir / dataset_name / "image.ome.zarr").relative_to(vc.base_dir).as_posix() + + anndata_wrapper = AnnDataWrapper( + adata_path=anndata_path, + obs_set_paths=[["obs/cell_meta_cluster_final_broad", "obs/cell_meta_cluster_final"]], + obs_set_names=["Cell Cluster"], + obs_labels_paths=["obs/label"], + obs_labels_names=["obs/label"], + obs_locations_path="obsm/spatial", + obs_feature_matrix_path="X", + coordination_values={ + "fileUid": f"{dataset_name}-table", + "obsType": "cell", + "featureType": "gene", + "featureValueType": "expression", + }, + ) + + segmentation_wrapper = ObsSegmentationsOmeZarrWrapper( + img_path=segmentation_path, + obsTypesFromChannelNames=True, + coordination_values={ + "fileUid": f"{dataset_name}-segmentation", + "obsType": "cell", + }, + ) + + image_wrapper = ImageOmeZarrWrapper( + img_path=image_path, + coordination_values={"fileUid": f"{dataset_name}-image"}, + ) + + dataset = dataset.add_object(anndata_wrapper).add_object(segmentation_wrapper).add_object(image_wrapper) + + return dataset + + +def create_view(vc: VitessceConfig, dataset: VitessceConfigDataset, view_type: str) -> VitessceViews: + """Create a Vitessce view. + + Parameters + ---------- + vc + The Vitessce configuration object. + dataset + The Vitessce dataset object. + view_type + The type of view to create. Useful for differentiating between multiple sets of views. + + Returns + ------- + The view object. + """ + spatial_view = vc.add_view("spatialBeta", dataset=dataset).set_props( + title=f"Cell Segmentation | {view_type.capitalize()}" + ) + layerController_view = vc.add_view("layerControllerBeta", dataset=dataset).set_props( + title=f"Channels | {view_type.capitalize()}" + ) + obsSets_view = vc.add_view("obsSets", dataset=dataset).set_props(title=f"Cell Types | {view_type.capitalize()}") + obsSetSizes_view = vc.add_view("obsSetSizes", dataset=dataset).set_props( + title=f"Cell Cluster Sizes | {view_type.capitalize()}" + ) + featureList_view = vc.add_view("featureList", dataset=dataset).set_props( + title=f"Marker List | {view_type.capitalize()}", variablesLabelOverride="Marker" + ) + return VitessceViews( + view_type=view_type, + spatial_view=spatial_view, + layerController_view=layerController_view, + obsSets_view=obsSets_view, + featureList_view=featureList_view, + obsSetSizes_view=obsSetSizes_view, + ) + + +def setup_scopes(vc: VitessceConfig, views: VitessceViews) -> ScopeConfig: + """Setup coordination scopes for the Vitessce configuration. + + Parameters + ---------- + vc + The Vitessce configuration object. + views + The Vitessce views object. + + Returns + ------- + The coordination scopes object. + """ + # Create Scopes + (featureTypeScope, featureValueTypeScope, spatialSegmentationFilledScope, spatialSegmentationStrokeWidthScope) = ( + vc.add_coordination( + "featureType", "featureValueType", "spatialSegmentationFilled", "spatialSegmentationStrokeWidth" + ) + ) + + obsSetSelectionScope, obsSetColorScope, obsColorEncodingScope = vc.add_coordination( + "obsSetSelection", "obsSetColor", "obsColorEncoding" + ) + + (featureSelectionScope,) = vc.add_coordination("featureSelection") + + (spatialChannelOpacityScope,) = vc.add_coordination("spatialChannelOpacity") + + # Set Scopes + featureTypeScope.set_value("gene") + featureValueTypeScope.set_value("expression") + spatialSegmentationFilledScope.set_value(False) + spatialSegmentationStrokeWidthScope.set_value(0.1) + obsColorEncodingScope.set_value("cellSetSelection") + spatialChannelOpacityScope.set_value(0.3) + + views.featureList_view.use_coordination(featureSelectionScope) + views.obsSets_view.use_coordination(obsSetSelectionScope, obsSetColorScope, obsColorEncodingScope) + views.obsSetSizes_view.use_coordination(obsSetSelectionScope, obsSetColorScope) + + return ScopeConfig( + featureTypeScope=featureTypeScope, + featureValueTypeScope=featureValueTypeScope, + spatialSegmentationFilledScope=spatialSegmentationFilledScope, + spatialSegmentationStrokeWidthScope=spatialSegmentationStrokeWidthScope, + featureSelectionScope=featureSelectionScope, + obsSetSelectionScope=obsSetSelectionScope, + obsSetColorScope=obsSetColorScope, + obsColorEncodingScope=obsColorEncodingScope, + spatialChannelOpacityScope=spatialChannelOpacityScope, + ) + + +def link_views( + vc: VitessceConfig, + views: VitessceViews, + scopes: ScopeConfig, + vitessce_path: UPath, + dataset_name: str, + fov: str, + channel_color_map: Mapping[str, Any], +): + """Link views to coordination scopes. + + Parameters + ---------- + vc + The Vitessce configuration object. + views + The Vitessce views object. + scopes + The coordination scopes object. + fov + The name of the field of view. + n_vars + The number of variables in the dataset. + """ + omero_zarr_path = vitessce_path / fov / dataset_name / "image.ome.zarr" + omero_channel_configs = _get_omero_channel_colors(omero_zarr_path, channel_color_map) + + vc.link_views_by_dict( + views=[ + views.spatial_view, + views.layerController_view, + views.obsSets_view, + views.featureList_view, + views.obsSetSizes_view, + ], + input_val={ + "imageLayer": CL( + [ + { + "fileUid": f"{views.view_type}-image", + "photometricInterpretation": "BlackIsZero", + "spatialLayerVisible": True, + "spatialLayerOpacity": 1.0, + "featureValueColormapRange": [0, 1], + "spatialTargetResolution": None, + "imageChannel": CL( + [ + { + "spatialChannelOpacity": scopes.spatialChannelOpacityScope, + "spatialTargetC": o.omero_index, + "spatialChannelWindow": None, + "spatialChannelColor": list(o.color), + "spatialChannelVisible": True, + } + for o in omero_channel_configs + ] + ), + } + ] + ), + "segmentationLayer": CL( + [ + { + "fileUid": f"{views.view_type}-segmentation", + "spatialLayerVisible": True, + "spatialLayerOpacity": 1.0, + "segmentationChannel": CL( + [ + { + "obsType": "cell", + "obsSetSelection": scopes.obsSetSelectionScope, + "obsSetColor": scopes.obsSetColorScope, + "obsColorEncoding": scopes.obsColorEncodingScope, + "spatialTargetC": 0, + "spatialChannelVisible": True, + "featureType": scopes.featureTypeScope, + "featureValueType": scopes.featureValueTypeScope, + "featureSelection": scopes.featureSelectionScope, + "spatialSegmentationFilled": scopes.spatialSegmentationFilledScope, + "spatialSegmentationStrokeWidth": scopes.spatialSegmentationStrokeWidthScope, + "legendVisible": True, + "spatialChannelOpacity": 1.0, + } + ] + ), + } + ] + ), + }, + meta=True, + scope_prefix=get_initial_coordination_scope_prefix(f"{fov}-{views.view_type}", "image"), + ) + + +VitessceConcatView = VitessceConfigViewVConcat | VitessceConfigViewHConcat + + +def set_layout( + views: VitessceViews, +) -> VitessceConcatView: + """Set the layout of the Vitessce views. + + Parameters + ---------- + views + The Vitessce views object. + + Returns + ------- + The layout of the Vitessce visualization as an object. + """ + layout = views.spatial_view | ( + views.layerController_view / ((views.obsSets_view | views.obsSetSizes_view) / views.featureList_view) + ) + return layout + + +def export_config(vc: VitessceConfig, vc_view: VitessceConfigView): + """Export the Vitessce configuration to a JSON file. + + Parameters + ---------- + vc + The Vitessce configuration object. + vc_view + The Vitessce view object. + """ + config_dir = vc.base_dir / "configs" + config_dir.mkdir(exist_ok=True, parents=True) + + with open(vc.base_dir / "configs" / f"{vc_view.view_type}-config.json", "w") as f: + base_url = config_dir.relative_to(vc.base_dir).as_posix() + json.dump(vc.to_dict(base_url=base_url), f, indent=4) + # json.dump(vc.to_dict(base_url=vc.bae.resolve().absolute().as_posix()), f, indent=4) diff --git a/tests/test_basic.py b/tests/test_basic.py new file mode 100644 index 0000000..7e67395 --- /dev/null +++ b/tests/test_basic.py @@ -0,0 +1,12 @@ +import pytest + +import pici_vitessce + + +def test_package_has_version(): + assert pici_vitessce.__version__ is not None + + +@pytest.mark.skip(reason="This decorator should be removed when test passes.") +def test_example(): + assert 1 == 0 # This test is designed to fail. diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..08cbb01 --- /dev/null +++ b/uv.lock @@ -0,0 +1,4671 @@ +version = 1 +requires-python = ">=3.10" 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