From c3093b24973adcaff3b71271e7a758b3e80e23a2 Mon Sep 17 00:00:00 2001 From: Sricharan Reddy Varra Date: Fri, 19 Jul 2024 10:15:57 -0700 Subject: [PATCH] init --- .codecov.yaml | 17 + .cruft.json | 29 + .editorconfig | 18 + .github/ISSUE_TEMPLATE/bug_report.yml | 89 + .github/ISSUE_TEMPLATE/config.yml | 5 + .github/ISSUE_TEMPLATE/feature_request.yml | 11 + .github/workflows/build.yaml | 29 + .github/workflows/deploy.yaml | 39 + .github/workflows/release.yaml | 29 + .github/workflows/test.yaml | 67 + .gitignore | 34 + .pre-commit-config.yaml | 42 + .python-version | 1 + .readthedocs.yaml | 16 + CHANGELOG.md | 15 + LICENSE | 21 + README.md | 57 + docs/Makefile | 20 + docs/_static/.gitkeep | 0 docs/_static/css/custom.css | 4 + docs/_templates/.gitkeep | 0 docs/_templates/autosummary/class.rst | 61 + docs/api.md | 38 + docs/changelog.md | 3 + docs/conf.py | 129 + docs/contributing.md | 160 + docs/extensions/typed_returns.py | 32 + docs/index.md | 15 + docs/notebooks/example.ipynb | 171 + docs/references.bib | 10 + docs/references.md | 5 + ghpages-site/.gitignore | 24 + ghpages-site/.vscode/extensions.json | 4 + ghpages-site/.vscode/launch.json | 11 + ghpages-site/README.md | 47 + ghpages-site/astro.config.mjs | 10 + ghpages-site/biome.json | 38 + ghpages-site/components.json | 17 + ghpages-site/package.json | 43 + ghpages-site/pnpm-lock.yaml | 22791 ++++++++++++++++ ghpages-site/public/favicon.svg | 9 + ghpages-site/src/components/Footer.astro | 29 + ghpages-site/src/components/Header.astro | 0 ghpages-site/src/components/ModeToggle.tsx | 51 + ghpages-site/src/components/ui/badge.tsx | 36 + ghpages-site/src/components/ui/button.tsx | 58 + ghpages-site/src/components/ui/checkbox.tsx | 30 + ghpages-site/src/components/ui/command.tsx | 162 + ghpages-site/src/components/ui/dialog.tsx | 123 + .../src/components/ui/dropdown-menu.tsx | 209 + ghpages-site/src/components/ui/input.tsx | 25 + ghpages-site/src/components/ui/popover.tsx | 31 + ghpages-site/src/components/ui/select.tsx | 168 + ghpages-site/src/components/ui/separator.tsx | 31 + ghpages-site/src/components/ui/table.tsx | 133 + .../src/components/vitessce/FOVTable.tsx | 13 + .../src/components/vitessce/Tonic.tsx | 7 + .../src/components/vitessce/configs/tonic.ts | 232 + ghpages-site/src/env.d.ts | 2 + ghpages-site/src/lib/fovs.ts | 64 + ghpages-site/src/lib/table/columns.tsx | 89 + .../lib/table/data-table-column-header.tsx | 76 + .../lib/table/data-table-faceted-filter.tsx | 165 + .../src/lib/table/data-table-pagination.tsx | 106 + .../src/lib/table/data-table-toolbar.tsx | 67 + .../src/lib/table/data-table-view-options.tsx | 62 + ghpages-site/src/lib/table/data-table.tsx | 124 + ghpages-site/src/lib/table/definitions.ts | 92 + ghpages-site/src/lib/types.ts | 6 + ghpages-site/src/lib/utils.ts | 6 + ghpages-site/src/pages/[fov].astro | 30 + ghpages-site/src/pages/index.astro | 40 + ghpages-site/src/styles/globals.css | 98 + ghpages-site/tailwind.config.mjs | 72 + ghpages-site/tsconfig.json | 16 + package.json | 6 + pyproject.toml | 141 + requirements-dev.lock | 708 + requirements.lock | 708 + scripts/ingest_data_for_vitessce.ipynb | 563 + src/tonic_vitessce/__init__.py | 8 + src/tonic_vitessce/core/__init__.py | 8 + src/tonic_vitessce/core/constants.py | 124 + src/tonic_vitessce/pl/__init__.py | 1 + src/tonic_vitessce/pl/basic.py | 63 + src/tonic_vitessce/pp/__init__.py | 1 + src/tonic_vitessce/pp/basic.py | 17 + src/tonic_vitessce/tl/__init__.py | 3 + src/tonic_vitessce/tl/basic.py | 197 + tests/test_basic.py | 12 + 90 files changed, 29174 insertions(+) create mode 100644 .codecov.yaml create mode 100644 .cruft.json create mode 100644 .editorconfig create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml create mode 100644 .github/ISSUE_TEMPLATE/config.yml create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml create mode 100644 .github/workflows/build.yaml create mode 100644 .github/workflows/deploy.yaml create mode 100644 .github/workflows/release.yaml create mode 100644 .github/workflows/test.yaml create mode 100644 .gitignore create mode 100644 .pre-commit-config.yaml create mode 100644 .python-version create mode 100644 .readthedocs.yaml create mode 100644 CHANGELOG.md create mode 100644 LICENSE create mode 100644 README.md create mode 100644 docs/Makefile create mode 100644 docs/_static/.gitkeep create mode 100644 docs/_static/css/custom.css create mode 100644 docs/_templates/.gitkeep create mode 100644 docs/_templates/autosummary/class.rst create mode 100644 docs/api.md create mode 100644 docs/changelog.md create mode 100644 docs/conf.py create mode 100644 docs/contributing.md create mode 100644 docs/extensions/typed_returns.py create mode 100644 docs/index.md create mode 100644 docs/notebooks/example.ipynb create mode 100644 docs/references.bib create mode 100644 docs/references.md create mode 100644 ghpages-site/.gitignore create mode 100644 ghpages-site/.vscode/extensions.json create mode 100644 ghpages-site/.vscode/launch.json create mode 100644 ghpages-site/README.md create mode 100644 ghpages-site/astro.config.mjs create mode 100644 ghpages-site/biome.json create mode 100644 ghpages-site/components.json create mode 100644 ghpages-site/package.json create mode 100644 ghpages-site/pnpm-lock.yaml create mode 100644 ghpages-site/public/favicon.svg create mode 100644 ghpages-site/src/components/Footer.astro create mode 100644 ghpages-site/src/components/Header.astro create mode 100644 ghpages-site/src/components/ModeToggle.tsx create mode 100644 ghpages-site/src/components/ui/badge.tsx create mode 100644 ghpages-site/src/components/ui/button.tsx create mode 100644 ghpages-site/src/components/ui/checkbox.tsx create mode 100644 ghpages-site/src/components/ui/command.tsx create mode 100644 ghpages-site/src/components/ui/dialog.tsx create mode 100644 ghpages-site/src/components/ui/dropdown-menu.tsx create mode 100644 ghpages-site/src/components/ui/input.tsx create mode 100644 ghpages-site/src/components/ui/popover.tsx create mode 100644 ghpages-site/src/components/ui/select.tsx create mode 100644 ghpages-site/src/components/ui/separator.tsx create mode 100644 ghpages-site/src/components/ui/table.tsx create mode 100644 ghpages-site/src/components/vitessce/FOVTable.tsx create mode 100644 ghpages-site/src/components/vitessce/Tonic.tsx create mode 100644 ghpages-site/src/components/vitessce/configs/tonic.ts create mode 100644 ghpages-site/src/env.d.ts create mode 100644 ghpages-site/src/lib/fovs.ts create mode 100644 ghpages-site/src/lib/table/columns.tsx create mode 100644 ghpages-site/src/lib/table/data-table-column-header.tsx create mode 100644 ghpages-site/src/lib/table/data-table-faceted-filter.tsx create mode 100644 ghpages-site/src/lib/table/data-table-pagination.tsx create mode 100644 ghpages-site/src/lib/table/data-table-toolbar.tsx create mode 100644 ghpages-site/src/lib/table/data-table-view-options.tsx create mode 100644 ghpages-site/src/lib/table/data-table.tsx create mode 100644 ghpages-site/src/lib/table/definitions.ts create mode 100644 ghpages-site/src/lib/types.ts create mode 100644 ghpages-site/src/lib/utils.ts create mode 100644 ghpages-site/src/pages/[fov].astro create mode 100644 ghpages-site/src/pages/index.astro create mode 100644 ghpages-site/src/styles/globals.css create mode 100644 ghpages-site/tailwind.config.mjs create mode 100644 ghpages-site/tsconfig.json create mode 100644 package.json create mode 100644 pyproject.toml create mode 100644 requirements-dev.lock create mode 100644 requirements.lock create mode 100644 scripts/ingest_data_for_vitessce.ipynb create mode 100644 src/tonic_vitessce/__init__.py create mode 100644 src/tonic_vitessce/core/__init__.py create mode 100644 src/tonic_vitessce/core/constants.py create mode 100644 src/tonic_vitessce/pl/__init__.py create mode 100644 src/tonic_vitessce/pl/basic.py create mode 100644 src/tonic_vitessce/pp/__init__.py create mode 100644 src/tonic_vitessce/pp/basic.py create mode 100644 src/tonic_vitessce/tl/__init__.py create mode 100644 src/tonic_vitessce/tl/basic.py create mode 100644 tests/test_basic.py 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..3fa6f72 --- /dev/null +++ b/.cruft.json @@ -0,0 +1,29 @@ +{ + "template": "https://github.com/scverse/cookiecutter-scverse", + "commit": "de9fdc5884dce0450bad4fc4c3f67d07cdc15445", + "checkout": null, + "context": { + "cookiecutter": { + "project_name": "tonic-vitessce", + "package_name": "tonic_vitessce", + "project_description": "Vitessce Configs and Data Conversion for the dataset.", + "author_full_name": "Sricharan Reddy Varra", + "author_email": "srivarra@stanford.edu", + "github_user": "srivarra", + "project_repo": "https://github.com/angelolab/tonic-vitessce", + "license": "MIT License", + "_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..050f911 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,18 @@ +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}] +indent_size = 2 + +[.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 β€œHow 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..ff57a9e --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -0,0 +1,11 @@ +name: Feature request +description: Propose a new feature for tonic-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..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/deploy.yaml b/.github/workflows/deploy.yaml new file mode 100644 index 0000000..6826663 --- /dev/null +++ b/.github/workflows/deploy.yaml @@ -0,0 +1,39 @@ +name: Deploy to GitHub Pages + +on: + # Trigger the workflow every time you push to the `main` branch + # Using a different branch name? Replace `main` with your branch’s name + push: + branches: [main] + # Allows you to run this workflow manually from the Actions tab on GitHub. + workflow_dispatch: + +# Allow this job to clone the repo and create a page deployment +permissions: + contents: read + pages: write + id-token: write + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout your repository using git + uses: actions/checkout@v4.1.7 + - name: Install, build, and upload your site output + uses: withastro/action@v2.0.1 + with: + path: ./ghpages-site/ # The root location of your Astro project inside the repository. (optional) + # node-version: 20 # The specific version of Node that should be used to build your site. Defaults to 18. (optional) + # package-manager: pnpm@latest # The Node package manager that should be used to install dependencies and build your site. Automatically detected based on your lockfile. (optional) + + deploy: + needs: build + runs-on: ubuntu-latest + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4.0.5 diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml new file mode 100644 index 0000000..e64f059 --- /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/tonic_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@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: ${{ matrix.os }} + DISPLAY: :42 + run: | + coverage run -m pytest -v --color=yes + - name: Report coverage + run: | + coverage report + - name: Upload coverage + uses: codecov/codecov-action@v3 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b37a371 --- /dev/null +++ b/.gitignore @@ -0,0 +1,34 @@ +# Temp files +.DS_Store +*~ +buck-out/ + +# Compiled files +.venv/ +__pycache__/ +.mypy_cache/ +.ruff_cache/ + +# Distribution / packaging +/build/ +/dist/ +/*.egg-info/ + +# Tests and coverage +/.pytest_cache/ +/.cache/ +/data/ +/node_modules/ + +# docs +/docs/generated/ +/docs/_build/ + +# IDEs +/.idea/ +/.vscode/ + + +#Misc +/data/ +.astro/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..e3358a2 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,42 @@ +fail_fast: false +default_language_version: + python: python3 +default_stages: + - commit + - push +minimum_pre_commit_version: 2.16.0 +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.4.8 + hooks: + - id: ruff + types_or: [python, pyi, jupyter] + args: [--fix, --exit-non-zero-on-fix] + - id: ruff-format + types_or: [python, pyi, jupyter] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: detect-private-key + - id: check-ast + - id: end-of-file-fixer + - id: mixed-line-ending + args: [--fix=lf] + - id: trailing-whitespace + - id: check-case-conflict + # Check that there are no merge conflicts (could be generated by template sync) + - id: check-merge-conflict + args: [--assume-in-merge] + - repo: local + hooks: + - id: forbid-to-commit + name: Don't commit rej files + entry: | + Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates. + Fix the merge conflicts manually and remove the .rej files. + language: fail + files: '.*\.rej$' diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..d4b278f --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11.7 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..1870318 --- /dev/null +++ b/README.md @@ -0,0 +1,57 @@ +# tonic-vitessce + +[![Tests][badge-tests]][link-tests] +[![Documentation][badge-docs]][link-docs] + +[badge-tests]: https://img.shields.io/github/actions/workflow/status/srivarra/tonic-vitessce/test.yaml?branch=main +[link-tests]: https://github.com/angelolab/tonic-vitessce/actions/workflows/test.yml +[badge-docs]: https://img.shields.io/readthedocs/tonic-vitessce + +Vitessce Configs and Data Conversion for the dataset. + +## Getting started + +Please refer to the [documentation][link-docs]. In particular, the + +- [API documentation][link-api]. + +## 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](https://github.com/conda-forge/miniforge#mambaforge). + +There are several alternative options to install tonic-vitessce: + + + +1. Install the latest development version: + +```bash +pip install git+https://github.com/angelolab/tonic-vitessce.git@main +``` + +## Release notes + +See the [changelog][changelog]. + +## Contact + +For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse]. +If you found a bug, please use the [issue tracker][issue-tracker]. + +## Citation + +> t.b.a + +[scverse-discourse]: https://discourse.scverse.org/ +[issue-tracker]: https://github.com/srivarra/tonic-vitessce/issues +[changelog]: https://tonic-vitessce.readthedocs.io/latest/changelog.html +[link-docs]: https://tonic-vitessce.readthedocs.io +[link-api]: https://tonic-vitessce.readthedocs.io/latest/api.html +[link-pypi]: https://pypi.org/project/tonic-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..e4665df --- /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 %} + ~{{ fullname }}.{{ item }} +{%- endfor %} +{% endif %} +{% endblock %} + +{% block methods %} +{% if methods %} +Methods table +~~~~~~~~~~~~~ + +.. autosummary:: +{% for item in methods %} + {%- if item != '__init__' %} + ~{{ fullname }}.{{ 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..e333704 --- /dev/null +++ b/docs/api.md @@ -0,0 +1,38 @@ +# API + +## Preprocessing + +```{eval-rst} +.. module:: tonic_vitessce.pp +.. currentmodule:: tonic_vitessce + +.. autosummary:: + :toctree: generated + + pp.basic_preproc +``` + +## Tools + +```{eval-rst} +.. module:: tonic_vitessce.tl +.. currentmodule:: tonic_vitessce + +.. autosummary:: + :toctree: generated + + tl.basic_tool +``` + +## Plotting + +```{eval-rst} +.. module:: tonic_vitessce.pl +.. currentmodule:: tonic_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..9d51f2d --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,129 @@ +# 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("tonic-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": "srivarra", + "github_repo": "https://github.com/angelolab/tonic-vitessce", + "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.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), + "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..7af7039 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,160 @@ +# 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][]. + +## Installing dev dependencies + +In addition to the packages needed to _use_ this package, you need additional python packages to _run tests_ and _build +the documentation_. It's easy to install them using `pip`: + +```bash +cd tonic-vitessce +pip install -e ".[dev,test,doc]" +``` + +## 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]. + +[ruff-editors]: https://docs.astral.sh/ruff/integrations/ +[prettier-editors]: https://prettier.io/docs/en/editors.html + +## Writing tests + +```{note} +Remember to first install the package with `pip install -e '.[dev,test]'` +``` + +This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added +to the package. + +Most IDEs integrate with pytest and provide a GUI to run tests. Alternatively, you can run all tests from the +command line by executing + +```bash +pytest +``` + +in the root of the repository. + +### 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. + +[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests + +## 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. + +## 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 the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information +on how to write documentation. + +### 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](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse` +repository. + +#### 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` + +#### Building the docs locally + +```bash +cd docs +make html +open _build/html/index.html +``` + + + +[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html +[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html +[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui +[codecov]: https://about.codecov.io/sign-up/ +[codecov docs]: https://docs.codecov.com/docs +[codecov bot]: https://docs.codecov.com/docs/team-bot +[codecov app]: https://github.com/apps/codecov +[pre-commit.ci]: https://pre-commit.ci/ +[readthedocs.org]: https://readthedocs.org/ +[myst-nb]: https://myst-nb.readthedocs.io/en/latest/ +[jupytext]: https://jupytext.readthedocs.io/en/latest/ +[pre-commit]: https://pre-commit.com/ +[anndata]: https://github.com/scverse/anndata +[mudata]: https://github.com/scverse/mudata +[pytest]: https://docs.pytest.org/ +[semver]: https://semver.org/ +[sphinx]: https://www.sphinx-doc.org/en/master/ +[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html +[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 +[pypi]: https://pypi.org/ +[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository 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..bc19217 --- /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 tonic_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}`tonic_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": [ + "tonic_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/ghpages-site/.gitignore b/ghpages-site/.gitignore new file mode 100644 index 0000000..16d54bb --- /dev/null +++ b/ghpages-site/.gitignore @@ -0,0 +1,24 @@ +# build output +dist/ +# generated types +.astro/ + +# dependencies +node_modules/ + +# logs +npm-debug.log* +yarn-debug.log* +yarn-error.log* +pnpm-debug.log* + + +# environment variables +.env +.env.production + +# macOS-specific files +.DS_Store + +# jetbrains setting folder +.idea/ diff --git a/ghpages-site/.vscode/extensions.json b/ghpages-site/.vscode/extensions.json new file mode 100644 index 0000000..2592970 --- /dev/null +++ b/ghpages-site/.vscode/extensions.json @@ -0,0 +1,4 @@ +{ + "recommendations": ["astro-build.astro-vscode"], + "unwantedRecommendations": [] +} diff --git a/ghpages-site/.vscode/launch.json b/ghpages-site/.vscode/launch.json new file mode 100644 index 0000000..e368c54 --- /dev/null +++ b/ghpages-site/.vscode/launch.json @@ -0,0 +1,11 @@ +{ + "version": "0.2.0", + "configurations": [ + { + "command": "./node_modules/.bin/astro dev", + "name": "Development server", + "request": "launch", + "type": "node-terminal" + } + ] +} diff --git a/ghpages-site/README.md b/ghpages-site/README.md new file mode 100644 index 0000000..e34a99b --- /dev/null +++ b/ghpages-site/README.md @@ -0,0 +1,47 @@ +# Astro Starter Kit: Minimal + +```sh +npm create astro@latest -- --template minimal +``` + +[![Open in StackBlitz](https://developer.stackblitz.com/img/open_in_stackblitz.svg)](https://stackblitz.com/github/withastro/astro/tree/latest/examples/minimal) +[![Open with CodeSandbox](https://assets.codesandbox.io/github/button-edit-lime.svg)](https://codesandbox.io/p/sandbox/github/withastro/astro/tree/latest/examples/minimal) +[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/withastro/astro?devcontainer_path=.devcontainer/minimal/devcontainer.json) + +> πŸ§‘β€πŸš€ **Seasoned astronaut?** Delete this file. Have fun! + +## πŸš€ Project Structure + +Inside of your Astro project, you'll see the following folders and files: + +```text +/ +β”œβ”€β”€ public/ +β”œβ”€β”€ src/ +β”‚ └── pages/ +β”‚ └── index.astro +└── package.json +``` + +Astro looks for `.astro` or `.md` files in the `src/pages/` directory. Each page is exposed as a route based on its file name. + +There's nothing special about `src/components/`, but that's where we like to put any Astro/React/Vue/Svelte/Preact components. + +Any static assets, like images, can be placed in the `public/` directory. + +## 🧞 Commands + +All commands are run from the root of the project, from a terminal: + +| Command | Action | +| :------------------------ | :----------------------------------------------- | +| `npm install` | Installs dependencies | +| `npm run dev` | Starts local dev server at `localhost:4321` | +| `npm run build` | Build your production site to `./dist/` | +| `npm run preview` | Preview your build locally, before deploying | +| `npm run astro ...` | Run CLI commands like `astro add`, `astro check` | +| `npm run astro -- --help` | Get help using the Astro CLI | + +## πŸ‘€ Want to learn more? + +Feel free to check [our documentation](https://docs.astro.build) or jump into our [Discord server](https://astro.build/chat). diff --git a/ghpages-site/astro.config.mjs b/ghpages-site/astro.config.mjs new file mode 100644 index 0000000..f9a5013 --- /dev/null +++ b/ghpages-site/astro.config.mjs @@ -0,0 +1,10 @@ +import { defineConfig } from "astro/config"; +import react from "@astrojs/react"; +import tailwind from "@astrojs/tailwind"; + +// https://astro.build/config +export default defineConfig({ + integrations: [react(), tailwind({ applyBaseStyles: false })], + site: "https://angelolab.github.io", + base: "tonic-vitessce", +}); diff --git a/ghpages-site/biome.json b/ghpages-site/biome.json new file mode 100644 index 0000000..e1838ef --- /dev/null +++ b/ghpages-site/biome.json @@ -0,0 +1,38 @@ +{ + "$schema": "https://biomejs.dev/schemas/1.8.3/schema.json", + "organizeImports": { + "enabled": true + }, + "linter": { + "enabled": true, + "rules": { + "recommended": true + } + }, + "formatter": { + "enabled": true, + "formatWithErrors": true, + "ignore": [], + "attributePosition": "auto", + "indentStyle": "tab", + "indentWidth": 4, + "lineWidth": 120, + "lineEnding": "lf" + }, + "javascript": { + "formatter": { + "arrowParentheses": "always", + "bracketSameLine": false, + "bracketSpacing": true, + "jsxQuoteStyle": "double", + "quoteProperties": "asNeeded", + "semicolons": "always", + "trailingCommas": "all" + } + }, + "json": { + "formatter": { + "trailingCommas": "none" + } + } +} diff --git a/ghpages-site/components.json b/ghpages-site/components.json new file mode 100644 index 0000000..b75635b --- /dev/null +++ b/ghpages-site/components.json @@ -0,0 +1,17 @@ +{ + "$schema": "https://ui.shadcn.com/schema.json", + "style": "new-york", + "rsc": false, + "tsx": true, + "tailwind": { + "config": "tailwind.config.mjs", + "css": "./src/styles/globals.css", + "baseColor": "zinc", + "cssVariables": true, + "prefix": "tailwind.config.mjs" + }, + "aliases": { + "components": "@/components", + "utils": "@/lib/utils" + } +} diff --git a/ghpages-site/package.json b/ghpages-site/package.json new file mode 100644 index 0000000..f760338 --- /dev/null +++ b/ghpages-site/package.json @@ -0,0 +1,43 @@ +{ + "name": "ghpages-site", + "type": "module", + "version": "0.0.1", + "scripts": { + "dev": "astro dev", + "start": "astro dev", + "build": "astro check && astro build", + "preview": "astro preview", + "astro": "astro" + }, + "dependencies": { + "@astrojs/check": "^0.7.0", + "@astrojs/react": "^3.6.0", + "@astrojs/tailwind": "^5.1.0", + "@radix-ui/react-checkbox": "^1.1.1", + "@radix-ui/react-dialog": "^1.1.1", + "@radix-ui/react-dropdown-menu": "^2.1.1", + "@radix-ui/react-icons": "^1.3.0", + "@radix-ui/react-popover": "^1.1.1", + "@radix-ui/react-select": "^2.1.1", + "@radix-ui/react-separator": "^1.1.0", + "@radix-ui/react-slot": "^1.1.0", + "@tanstack/react-table": "^8.19.2", + "@types/react": "^18.3.3", + "@types/react-dom": "^18.3.0", + "astro": "^4.11.5", + "class-variance-authority": "^0.7.0", + "clsx": "^2.1.1", + "cmdk": "^1.0.0", + "lucide-react": "^0.399.0", + "react": "^18.3.1", 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use-sync-external-store: 1.2.0(react@18.3.1) + optionalDependencies: + "@types/react": 18.3.3 + react: 18.3.1 + + zwitch@2.0.4: {} diff --git a/ghpages-site/public/favicon.svg b/ghpages-site/public/favicon.svg new file mode 100644 index 0000000..f157bd1 --- /dev/null +++ b/ghpages-site/public/favicon.svg @@ -0,0 +1,9 @@ + + + + diff --git a/ghpages-site/src/components/Footer.astro b/ghpages-site/src/components/Footer.astro new file mode 100644 index 0000000..15ebdb0 --- /dev/null +++ b/ghpages-site/src/components/Footer.astro @@ -0,0 +1,29 @@ + diff --git a/ghpages-site/src/components/Header.astro b/ghpages-site/src/components/Header.astro new file mode 100644 index 0000000..e69de29 diff --git a/ghpages-site/src/components/ModeToggle.tsx b/ghpages-site/src/components/ModeToggle.tsx new file mode 100644 index 0000000..38af6f5 --- /dev/null +++ b/ghpages-site/src/components/ModeToggle.tsx @@ -0,0 +1,51 @@ +import * as React from "react"; +import { Moon, Sun } from "lucide-react"; + +import { Button } from "@ui/button"; +import { + DropdownMenu, + DropdownMenuContent, + DropdownMenuItem, + DropdownMenuTrigger, +} from "@ui/dropdown-menu"; + +export function ModeToggle() { + const [theme, setThemeState] = React.useState< + "theme-light" | "dark" | "system" + >("theme-light"); + + React.useEffect(() => { + const isDarkMode = document.documentElement.classList.contains("dark"); + setThemeState(isDarkMode ? "dark" : "theme-light"); + }, []); + + React.useEffect(() => { + const isDark = + theme === "dark" || + (theme === "system" && + window.matchMedia("(prefers-color-scheme: dark)").matches); + document.documentElement.classList[isDark ? "add" : "remove"]("dark"); + }, [theme]); + + return ( + + + + + + setThemeState("theme-light")}> + Light + + setThemeState("dark")}> + Dark + + setThemeState("system")}> + System + + + + ); +} diff --git a/ghpages-site/src/components/ui/badge.tsx b/ghpages-site/src/components/ui/badge.tsx new file mode 100644 index 0000000..2c89f2e --- /dev/null +++ b/ghpages-site/src/components/ui/badge.tsx @@ -0,0 +1,36 @@ +import * as React from "react"; +import { cva, type VariantProps } from "class-variance-authority"; + +import { cn } from "@/lib/utils"; + +const badgeVariants = cva( + "tailwind.config.mjsinline-flex tailwind.config.mjsitems-center tailwind.config.mjsrounded-md tailwind.config.mjsborder tailwind.config.mjspx-2.5 tailwind.config.mjspy-0.5 tailwind.config.mjstext-xs tailwind.config.mjsfont-semibold tailwind.config.mjstransition-colors focus:tailwind.config.mjsoutline-none focus:tailwind.config.mjsring-2 focus:tailwind.config.mjsring-ring focus:tailwind.config.mjsring-offset-2", + { + variants: { + variant: { + default: + "tailwind.config.mjsborder-transparent tailwind.config.mjsbg-primary tailwind.config.mjstext-primary-foreground tailwind.config.mjsshadow hover:tailwind.config.mjsbg-primary/80", + secondary: + "tailwind.config.mjsborder-transparent tailwind.config.mjsbg-secondary tailwind.config.mjstext-secondary-foreground hover:tailwind.config.mjsbg-secondary/80", + destructive: + "tailwind.config.mjsborder-transparent tailwind.config.mjsbg-destructive tailwind.config.mjstext-destructive-foreground tailwind.config.mjsshadow hover:tailwind.config.mjsbg-destructive/80", + outline: "tailwind.config.mjstext-foreground", + }, + }, + defaultVariants: { + variant: "default", + }, + }, +); + +export interface BadgeProps + extends React.HTMLAttributes, + VariantProps {} + +function Badge({ className, variant, ...props }: BadgeProps) { + return ( +
+ ); +} + +export { Badge, badgeVariants }; diff --git a/ghpages-site/src/components/ui/button.tsx b/ghpages-site/src/components/ui/button.tsx new file mode 100644 index 0000000..2365534 --- /dev/null +++ b/ghpages-site/src/components/ui/button.tsx @@ -0,0 +1,58 @@ +import * as React from "react"; +import { Slot } from "@radix-ui/react-slot"; +import { cva, type VariantProps } from "class-variance-authority"; + +import { cn } from "@/lib/utils"; + +const buttonVariants = cva( + "tailwind.config.mjsinline-flex tailwind.config.mjsitems-center tailwind.config.mjsjustify-center tailwind.config.mjswhitespace-nowrap tailwind.config.mjsrounded-md tailwind.config.mjstext-sm tailwind.config.mjsfont-medium tailwind.config.mjstransition-colors focus-visible:tailwind.config.mjsoutline-none focus-visible:tailwind.config.mjsring-1 focus-visible:tailwind.config.mjsring-ring disabled:tailwind.config.mjspointer-events-none disabled:tailwind.config.mjsopacity-50", + { + variants: { + variant: { + default: + "tailwind.config.mjsbg-primary tailwind.config.mjstext-primary-foreground tailwind.config.mjsshadow hover:tailwind.config.mjsbg-primary/90", + destructive: + "tailwind.config.mjsbg-destructive tailwind.config.mjstext-destructive-foreground tailwind.config.mjsshadow-sm hover:tailwind.config.mjsbg-destructive/90", + outline: + "tailwind.config.mjsborder tailwind.config.mjsborder-input tailwind.config.mjsbg-background tailwind.config.mjsshadow-sm hover:tailwind.config.mjsbg-accent hover:tailwind.config.mjstext-accent-foreground", + secondary: + "tailwind.config.mjsbg-secondary tailwind.config.mjstext-secondary-foreground tailwind.config.mjsshadow-sm hover:tailwind.config.mjsbg-secondary/80", + ghost: "hover:tailwind.config.mjsbg-accent hover:tailwind.config.mjstext-accent-foreground", + link: "tailwind.config.mjstext-primary tailwind.config.mjsunderline-offset-4 hover:tailwind.config.mjsunderline", + }, + size: { + default: + "tailwind.config.mjsh-9 tailwind.config.mjspx-4 tailwind.config.mjspy-2", + sm: "tailwind.config.mjsh-8 tailwind.config.mjsrounded-md tailwind.config.mjspx-3 tailwind.config.mjstext-xs", + lg: "tailwind.config.mjsh-10 tailwind.config.mjsrounded-md tailwind.config.mjspx-8", + icon: "tailwind.config.mjsh-9 tailwind.config.mjsw-9", + }, + }, + defaultVariants: { + variant: "default", + size: "default", + }, + }, +); + +export interface ButtonProps + extends React.ButtonHTMLAttributes, + VariantProps { + asChild?: boolean; +} + +const Button = React.forwardRef( + ({ className, variant, size, asChild = false, ...props }, ref) => { + const Comp = asChild ? Slot : "button"; + return ( + + ); + }, +); +Button.displayName = "Button"; + +export { Button, buttonVariants }; diff --git a/ghpages-site/src/components/ui/checkbox.tsx b/ghpages-site/src/components/ui/checkbox.tsx new file mode 100644 index 0000000..b444400 --- /dev/null +++ b/ghpages-site/src/components/ui/checkbox.tsx @@ -0,0 +1,30 @@ +import * as React from "react"; +import * as CheckboxPrimitive from "@radix-ui/react-checkbox"; +import { CheckIcon } from "@radix-ui/react-icons"; + +import { cn } from "@/lib/utils"; + +const Checkbox = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + + + + + +)); +Checkbox.displayName = CheckboxPrimitive.Root.displayName; + +export { Checkbox }; diff --git a/ghpages-site/src/components/ui/command.tsx b/ghpages-site/src/components/ui/command.tsx new file mode 100644 index 0000000..ce71db9 --- /dev/null +++ b/ghpages-site/src/components/ui/command.tsx @@ -0,0 +1,162 @@ +import * as React from "react"; +import { type DialogProps } from "@radix-ui/react-dialog"; +import { MagnifyingGlassIcon } from "@radix-ui/react-icons"; +import { Command as CommandPrimitive } from "cmdk"; + +import { cn } from "@/lib/utils"; +import { Dialog, DialogContent } from "@/components/ui/dialog"; + +const Command = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +Command.displayName = CommandPrimitive.displayName; + +interface CommandDialogProps extends DialogProps {} + +const CommandDialog = ({ children, ...props }: CommandDialogProps) => { + return ( + + + + {children} + + + + ); +}; + +const CommandInput = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( +
+ + +
+)); + +CommandInput.displayName = CommandPrimitive.Input.displayName; + +const CommandList = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); + +CommandList.displayName = CommandPrimitive.List.displayName; + +const CommandEmpty = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>((props, ref) => ( + +)); + +CommandEmpty.displayName = CommandPrimitive.Empty.displayName; + +const CommandGroup = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); + +CommandGroup.displayName = CommandPrimitive.Group.displayName; + +const CommandSeparator = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +CommandSeparator.displayName = CommandPrimitive.Separator.displayName; + +const CommandItem = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); + +CommandItem.displayName = CommandPrimitive.Item.displayName; + +const CommandShortcut = ({ + className, + ...props +}: React.HTMLAttributes) => { + return ( + + ); +}; +CommandShortcut.displayName = "CommandShortcut"; + +export { + Command, + CommandDialog, + CommandInput, + CommandList, + CommandEmpty, + CommandGroup, + CommandItem, + CommandShortcut, + CommandSeparator, +}; diff --git a/ghpages-site/src/components/ui/dialog.tsx b/ghpages-site/src/components/ui/dialog.tsx new file mode 100644 index 0000000..0c69b01 --- /dev/null +++ b/ghpages-site/src/components/ui/dialog.tsx @@ -0,0 +1,123 @@ +import * as React from "react"; +import * as DialogPrimitive from "@radix-ui/react-dialog"; +import { Cross2Icon } from "@radix-ui/react-icons"; + +import { cn } from "@/lib/utils"; + +const Dialog = DialogPrimitive.Root; + +const DialogTrigger = DialogPrimitive.Trigger; + +const DialogPortal = DialogPrimitive.Portal; + +const DialogClose = DialogPrimitive.Close; + +const DialogOverlay = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +DialogOverlay.displayName = DialogPrimitive.Overlay.displayName; + +const DialogContent = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, children, ...props }, ref) => ( + + + + {children} + + + Close + + + +)); +DialogContent.displayName = DialogPrimitive.Content.displayName; + +const DialogHeader = ({ + className, + ...props +}: React.HTMLAttributes) => ( +
+); +DialogHeader.displayName = "DialogHeader"; + +const DialogFooter = ({ + className, + ...props +}: React.HTMLAttributes) => ( +
+); +DialogFooter.displayName = "DialogFooter"; + +const DialogTitle = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +DialogTitle.displayName = DialogPrimitive.Title.displayName; + +const DialogDescription = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +DialogDescription.displayName = DialogPrimitive.Description.displayName; + +export { + Dialog, + DialogPortal, + DialogOverlay, + DialogTrigger, + DialogClose, + DialogContent, + DialogHeader, + DialogFooter, + DialogTitle, + DialogDescription, +}; diff --git a/ghpages-site/src/components/ui/dropdown-menu.tsx b/ghpages-site/src/components/ui/dropdown-menu.tsx new file mode 100644 index 0000000..227927b --- /dev/null +++ b/ghpages-site/src/components/ui/dropdown-menu.tsx @@ -0,0 +1,209 @@ +import * as React from "react"; +import * as DropdownMenuPrimitive from "@radix-ui/react-dropdown-menu"; +import { + CheckIcon, + ChevronRightIcon, + DotFilledIcon, +} from "@radix-ui/react-icons"; + +import { cn } from "@/lib/utils"; + +const DropdownMenu = DropdownMenuPrimitive.Root; + +const DropdownMenuTrigger = DropdownMenuPrimitive.Trigger; + +const DropdownMenuGroup = DropdownMenuPrimitive.Group; + +const DropdownMenuPortal = DropdownMenuPrimitive.Portal; + +const DropdownMenuSub = DropdownMenuPrimitive.Sub; + +const DropdownMenuRadioGroup = DropdownMenuPrimitive.RadioGroup; + +const DropdownMenuSubTrigger = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef & { + inset?: boolean; + } +>(({ className, inset, children, ...props }, ref) => ( + + {children} + + +)); +DropdownMenuSubTrigger.displayName = + DropdownMenuPrimitive.SubTrigger.displayName; + +const DropdownMenuSubContent = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +DropdownMenuSubContent.displayName = + DropdownMenuPrimitive.SubContent.displayName; + +const DropdownMenuContent = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, sideOffset = 4, ...props }, ref) => ( + + + +)); +DropdownMenuContent.displayName = DropdownMenuPrimitive.Content.displayName; + +const DropdownMenuItem = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef & { + inset?: boolean; + } +>(({ className, inset, ...props }, ref) => ( + +)); +DropdownMenuItem.displayName = DropdownMenuPrimitive.Item.displayName; + +const DropdownMenuCheckboxItem = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, children, checked, ...props }, ref) => ( + + + + + + + {children} + +)); +DropdownMenuCheckboxItem.displayName = + DropdownMenuPrimitive.CheckboxItem.displayName; + +const DropdownMenuRadioItem = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, children, ...props }, ref) => ( + + + + + + + {children} + +)); +DropdownMenuRadioItem.displayName = DropdownMenuPrimitive.RadioItem.displayName; + +const DropdownMenuLabel = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef & { + inset?: boolean; + } +>(({ className, inset, ...props }, ref) => ( + +)); +DropdownMenuLabel.displayName = DropdownMenuPrimitive.Label.displayName; + +const DropdownMenuSeparator = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +DropdownMenuSeparator.displayName = DropdownMenuPrimitive.Separator.displayName; + +const DropdownMenuShortcut = ({ + className, + ...props +}: React.HTMLAttributes) => { + return ( + + ); +}; +DropdownMenuShortcut.displayName = "DropdownMenuShortcut"; + +export { + DropdownMenu, + DropdownMenuTrigger, + DropdownMenuContent, + DropdownMenuItem, + DropdownMenuCheckboxItem, + DropdownMenuRadioItem, + DropdownMenuLabel, + DropdownMenuSeparator, + DropdownMenuShortcut, + DropdownMenuGroup, + DropdownMenuPortal, + DropdownMenuSub, + DropdownMenuSubContent, + DropdownMenuSubTrigger, + DropdownMenuRadioGroup, +}; diff --git a/ghpages-site/src/components/ui/input.tsx b/ghpages-site/src/components/ui/input.tsx new file mode 100644 index 0000000..2e4a337 --- /dev/null +++ b/ghpages-site/src/components/ui/input.tsx @@ -0,0 +1,25 @@ +import * as React from "react"; + +import { cn } from "@/lib/utils"; + +export interface InputProps + extends React.InputHTMLAttributes {} + +const Input = React.forwardRef( + ({ className, type, ...props }, ref) => { + return ( + + ); + }, +); +Input.displayName = "Input"; + +export { Input }; diff --git a/ghpages-site/src/components/ui/popover.tsx b/ghpages-site/src/components/ui/popover.tsx new file mode 100644 index 0000000..25fcd80 --- /dev/null +++ b/ghpages-site/src/components/ui/popover.tsx @@ -0,0 +1,31 @@ +import * as React from "react"; +import * as PopoverPrimitive from "@radix-ui/react-popover"; + +import { cn } from "@/lib/utils"; + +const Popover = PopoverPrimitive.Root; + +const PopoverTrigger = PopoverPrimitive.Trigger; + +const PopoverAnchor = PopoverPrimitive.Anchor; + +const PopoverContent = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, align = "center", sideOffset = 4, ...props }, ref) => ( + + + +)); +PopoverContent.displayName = PopoverPrimitive.Content.displayName; + +export { Popover, PopoverTrigger, PopoverContent, PopoverAnchor }; diff --git a/ghpages-site/src/components/ui/select.tsx b/ghpages-site/src/components/ui/select.tsx new file mode 100644 index 0000000..cf867cc --- /dev/null +++ b/ghpages-site/src/components/ui/select.tsx @@ -0,0 +1,168 @@ +import * as React from "react"; +import { + CaretSortIcon, + CheckIcon, + ChevronDownIcon, + ChevronUpIcon, +} from "@radix-ui/react-icons"; +import * as SelectPrimitive from "@radix-ui/react-select"; + +import { cn } from "@/lib/utils"; + +const Select = SelectPrimitive.Root; + +const SelectGroup = SelectPrimitive.Group; + +const SelectValue = SelectPrimitive.Value; + +const SelectTrigger = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, children, ...props }, ref) => ( + span]:tailwind.config.mjsline-clamp-1", + className, + )} + {...props} + > + {children} + + + + +)); +SelectTrigger.displayName = SelectPrimitive.Trigger.displayName; + +const SelectScrollUpButton = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + + + +)); +SelectScrollUpButton.displayName = SelectPrimitive.ScrollUpButton.displayName; + +const SelectScrollDownButton = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + + + +)); +SelectScrollDownButton.displayName = + SelectPrimitive.ScrollDownButton.displayName; + +const SelectContent = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, children, position = "popper", ...props }, ref) => ( + + + + + {children} + + + + +)); +SelectContent.displayName = SelectPrimitive.Content.displayName; + +const SelectLabel = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +SelectLabel.displayName = SelectPrimitive.Label.displayName; + +const SelectItem = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, children, ...props }, ref) => ( + + + + + + + {children} + +)); +SelectItem.displayName = SelectPrimitive.Item.displayName; + +const SelectSeparator = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>(({ className, ...props }, ref) => ( + +)); +SelectSeparator.displayName = SelectPrimitive.Separator.displayName; + +export { + Select, + SelectGroup, + SelectValue, + SelectTrigger, + SelectContent, + SelectLabel, + SelectItem, + SelectSeparator, + SelectScrollUpButton, + SelectScrollDownButton, +}; diff --git a/ghpages-site/src/components/ui/separator.tsx b/ghpages-site/src/components/ui/separator.tsx new file mode 100644 index 0000000..504ad6b --- /dev/null +++ b/ghpages-site/src/components/ui/separator.tsx @@ -0,0 +1,31 @@ +import * as React from "react"; +import * as SeparatorPrimitive from "@radix-ui/react-separator"; + +import { cn } from "@/lib/utils"; + +const Separator = React.forwardRef< + React.ElementRef, + React.ComponentPropsWithoutRef +>( + ( + { className, orientation = "horizontal", decorative = true, ...props }, + ref, + ) => ( + + ), +); +Separator.displayName = SeparatorPrimitive.Root.displayName; + +export { Separator }; diff --git a/ghpages-site/src/components/ui/table.tsx b/ghpages-site/src/components/ui/table.tsx new file mode 100644 index 0000000..c2932b3 --- /dev/null +++ b/ghpages-site/src/components/ui/table.tsx @@ -0,0 +1,133 @@ +import * as React from "react"; + +import { cn } from "@/lib/utils"; + +const Table = React.forwardRef< + HTMLTableElement, + React.HTMLAttributes +>(({ className, ...props }, ref) => ( +
+ + +)); +Table.displayName = "Table"; + +const TableHeader = React.forwardRef< + HTMLTableSectionElement, + React.HTMLAttributes +>(({ className, ...props }, ref) => ( + +)); +TableHeader.displayName = "TableHeader"; + +const TableBody = React.forwardRef< + HTMLTableSectionElement, + React.HTMLAttributes +>(({ className, ...props }, ref) => ( + +)); +TableBody.displayName = "TableBody"; + +const TableFooter = React.forwardRef< + HTMLTableSectionElement, + React.HTMLAttributes +>(({ className, ...props }, ref) => ( + tr]:last:tailwind.config.mjsborder-b-0", + className, + )} + {...props} + /> +)); +TableFooter.displayName = "TableFooter"; + +const TableRow = React.forwardRef< + HTMLTableRowElement, + React.HTMLAttributes +>(({ className, ...props }, ref) => ( + +)); +TableRow.displayName = "TableRow"; + +const TableHead = React.forwardRef< + HTMLTableCellElement, + React.ThHTMLAttributes +>(({ className, ...props }, ref) => ( +
[role=checkbox]]:tailwind.config.mjstranslate-y-[2px]", + className, + )} + {...props} + /> +)); +TableHead.displayName = "TableHead"; + +const TableCell = React.forwardRef< + HTMLTableCellElement, + React.TdHTMLAttributes +>(({ className, ...props }, ref) => ( + [role=checkbox]]:tailwind.config.mjstranslate-y-[2px]", + className, + )} + {...props} + /> +)); +TableCell.displayName = "TableCell"; + +const TableCaption = React.forwardRef< + HTMLTableCaptionElement, + React.HTMLAttributes +>(({ className, ...props }, ref) => ( +
+)); +TableCaption.displayName = "TableCaption"; + +export { + Table, + TableHeader, + TableBody, + TableFooter, + TableHead, + TableRow, + TableCell, + TableCaption, +}; diff --git a/ghpages-site/src/components/vitessce/FOVTable.tsx b/ghpages-site/src/components/vitessce/FOVTable.tsx new file mode 100644 index 0000000..26e89d9 --- /dev/null +++ b/ghpages-site/src/components/vitessce/FOVTable.tsx @@ -0,0 +1,13 @@ +import DataTable from "@/lib/table/data-table"; +import { fovs } from "@/lib/fovs"; +import { columns } from "@/lib/table/columns"; + +export default function FOVTable() { + const data = fovs; + + return ( +
+ +
+ ); +} diff --git a/ghpages-site/src/components/vitessce/Tonic.tsx b/ghpages-site/src/components/vitessce/Tonic.tsx new file mode 100644 index 0000000..499ee4f --- /dev/null +++ b/ghpages-site/src/components/vitessce/Tonic.tsx @@ -0,0 +1,7 @@ +import { Vitessce } from "vitessce"; +import generateTonicConfig from "@/components/vitessce/configs/tonic"; + +export default function Tonic({ fov }: { fov: string }) { + const tonic_config = generateTonicConfig(fov); + return ; +} diff --git a/ghpages-site/src/components/vitessce/configs/tonic.ts b/ghpages-site/src/components/vitessce/configs/tonic.ts new file mode 100644 index 0000000..922aeba --- /dev/null +++ b/ghpages-site/src/components/vitessce/configs/tonic.ts @@ -0,0 +1,232 @@ +import { + VitessceConfig, + CoordinationLevel as CL, + hconcat, + vconcat, + FileType as ft, + CoordinationType as ct, +} from "vitessce"; + +function generateTonicConfig(fov: string) { + const config = new VitessceConfig({ + schemaVersion: "1.0.16", + name: fov, + description: "Example", + }); + const fov_path = `https://angelolab-vitessce-vizualizations.s3.amazonaws.com/tonic/${fov.toUpperCase()}`; + + const dataset = config + .addDataset(fov) + .addFile({ + fileType: ft.IMAGE_OME_ZARR, + url: `${fov_path}/image.ome.zarr`, + coordinationValues: { + fileUid: "fov-image", + }, + options: undefined, + }) + .addFile({ + fileType: "anndata.zarr", + url: `${fov_path}/whole_cell_table.anndata.zarr`, + coordinationValues: { + fileUid: "adata", + obsType: "cell", + featureType: "gene", + featureValuetype: "expression", + }, + options: { + obsFeatureMatrix: { + path: "X", + }, + obsLocations: { + path: "obsm/spatial", + }, + obsSets: [ + { + name: "Cell Type", + path: [ + "obs/cell_cluster_broad", + "obs/cell_cluster", + "obs/cell_meta_cluster", + ], + }, + { + name: "Compartment", + path: "obs/compartment", + }, + ], + }, + }) + .addFile({ + fileType: "obsSegmentations.ome-zarr", + url: `${fov_path}/cell_segmentation.ome.zarr`, + coordinationValues: { + fileUid: "segmentation", + obsType: "cell", + }, + // options: undefined + options: { + obsTypesFromChannelNames: true, + }, + }); + + // Create Views + const spatialView = config + .addView(dataset, "spatialBeta") + .setProps({ title: "Cell Segmentation" }); + const lcView = config + .addView(dataset, "layerControllerBeta") + .setProps({ title: "Layers" }); + const obsSetsView = config + .addView(dataset, "obsSets") + .setProps({ title: "Cell Types" }); + const featureListView = config + .addView(dataset, "featureList") + .setProps({ title: "Marker List", variablesLabelOverride: "Markers" }); + const obsSetsSizesView = config.addView(dataset, "obsSetSizes"); + + // Cell Segmentation Scopes + const [ + cellFeatureTypeScope, + cellFeatureValueTypeScope, + cellSpatialSegmentationFilledScope, + cellSpatialSegmentationStrokeWidthScope, + ] = config.addCoordination( + ct.FEATURE_TYPE, + ct.FEATURE_VALUE_TYPE, + ct.SPATIAL_SEGMENTATION_FILLED, + ct.SPATIAL_SEGMENTATION_STROKE_WIDTH, + ); + cellFeatureTypeScope.setValue("gene"); + cellFeatureValueTypeScope.setValue("expression"); + cellSpatialSegmentationFilledScope.setValue(false); + cellSpatialSegmentationStrokeWidthScope.setValue(0.09); + + // Feature Selection + const [featureSelectionScope] = config.addCoordination( + ct.FEATURE_SELECTION, + ); + featureListView.useCoordination(featureSelectionScope); + + // Channel Scopes + const [spatialChannelOpacityScope] = config.addCoordination( + "spatialChannelOpacity", + ); + spatialChannelOpacityScope.setValue(0.3); + + // obs Scopes + const [obsSetSelectionScope, obsSetColorScope] = config.addCoordination( + "obsSetSelection", + "obsSetColor", + ); + obsSetsView.useCoordination(obsSetSelectionScope, obsSetColorScope); + + config.linkViewsByObject( + [spatialView, lcView, obsSetsView, featureListView, obsSetsSizesView], + { + imageLayer: CL([ + { + fileUid: "fov-image", + spatialLayerOpacity: 1, + spatialLayerVisible: true, + photometricInterpretation: "BlackIsZero", + spatialTargetResolution: null, + featureValueColormapRange: [0, 1], + imageChannel: CL([ + // CD8 + { + spatialTargetC: 2, + spatialChannelColor: [ + 172, 191, 105, + ] /* dark orange */, + spatialChannelVisible: true, + spatialChannelOpacity: spatialChannelOpacityScope, + spatialChannelWindow: null, + }, + // CD45 + { + spatialTargetC: 7, + spatialChannelColor: [ + 213, 182, 10, + ] /* dark yellow*/, + spatialChannelVisible: true, + spatialChannelOpacity: spatialChannelOpacityScope, + spatialChannelWindow: null, + }, + // ECAD + { + spatialTargetC: 15, + spatialChannelColor: [255, 255, 212] /* eggshell */, + spatialChannelVisible: true, + spatialChannelOpacity: spatialChannelOpacityScope, + spatialChannelWindow: null, + }, + // SMA + { + spatialTargetC: 22, + spatialChannelColor: [166, 129, 76] /* brown */, + spatialChannelVisible: true, + spatialChannelOpacity: spatialChannelOpacityScope, + spatialChannelWindow: null, + }, + // H3K9ac + { + spatialTargetC: 19, + spatialChannelColor: [4, 133, 209] /* cerulean */, + spatialChannelVisible: true, + spatialChannelOpacity: spatialChannelOpacityScope, + spatialChannelWindow: null, + }, + // H3K27me3 + { + spatialTargetC: 20, + spatialChannelColor: [4, 116, 149] /* cerulean */, + spatialChannelVisible: true, + spatialChannelOpacity: spatialChannelOpacityScope, + spatialChannelWindow: null, + }, + ]), + }, + ]), + segmentationLayer: CL([ + { + fileUid: "segmentation", + spatialLayerVisible: true, + spatialLayerOpacity: 1.0, + segmentationChannel: CL([ + { + obsType: "cell", + obsSetSelection: obsSetSelectionScope, + obsSetColor: obsSetColorScope, + spatialTargetC: 1, + spatialChannelVisible: true, + spatialChannelOpacity: 1.0, + featureType: cellFeatureTypeScope, + featureValueType: cellFeatureValueTypeScope, + featureSelection: featureSelectionScope, + spatialSegmentationFilled: + cellSpatialSegmentationFilledScope, + spatialSegmentationStrokeWidth: + cellSpatialSegmentationStrokeWidthScope, + legendVisible: true, + tooltipsVisible: true, + tooltipCrosshairsVisible: true, + }, + ]), + }, + ]), + }, + ); + + const legend = vconcat( + hconcat(obsSetsView, featureListView), + obsSetsSizesView, + ); + + config.layout(hconcat(spatialView, vconcat(lcView, legend))); + + const configJSON = config.toJSON(); + return configJSON; +} + +export default generateTonicConfig; diff --git a/ghpages-site/src/env.d.ts b/ghpages-site/src/env.d.ts new file mode 100644 index 0000000..acef35f --- /dev/null +++ b/ghpages-site/src/env.d.ts @@ -0,0 +1,2 @@ +/// +/// diff --git a/ghpages-site/src/lib/fovs.ts b/ghpages-site/src/lib/fovs.ts new file mode 100644 index 0000000..aa31286 --- /dev/null +++ b/ghpages-site/src/lib/fovs.ts @@ -0,0 +1,64 @@ +import type { FieldofView } from "./types"; + +export const fovs: FieldofView[] = [ + { + fov: "TONIC_TMA5_R1C2", + id: "1", + timepoint: "baseline", + localization: "Lymphnode", + }, + { + fov: "TONIC_TMA5_R5C1", + id: "2", + timepoint: "baseline", + localization: "Other", + }, + { + fov: "TONIC_TMA7_R4C6", + id: "3", + timepoint: "primary", + localization: "Breast", + }, + { + fov: "TONIC_TMA9_R4C6", + id: "4", + timepoint: "on_nivo", + localization: "Liver", + }, + { + fov: "TONIC_TMA14_R7C6", + id: "5", + timepoint: "baseline", + localization: "Skin", + }, + { + fov: "TONIC_TMA15_R7C2", + id: "6", + timepoint: "primary", + localization: "Breast", + }, + { + fov: "TONIC_TMA15_R10C1", + id: "7", + timepoint: "primary", + localization: "Breast", + }, + { + fov: "TONIC_TMA17_R12C4", + id: "8", + timepoint: "primary", + localization: "Breast", + }, + { + fov: "TONIC_TMA18_R2C3", + id: "9", + timepoint: "on_nivo", + localization: "Lymphnode", + }, + { + fov: "TONIC_TMA23_R10C1", + id: "10", + timepoint: "primary", + localization: "Breast", + }, +]; diff --git a/ghpages-site/src/lib/table/columns.tsx b/ghpages-site/src/lib/table/columns.tsx new file mode 100644 index 0000000..9280908 --- /dev/null +++ b/ghpages-site/src/lib/table/columns.tsx @@ -0,0 +1,89 @@ +"use client"; + +import type { ColumnDef } from "@tanstack/react-table"; +import clsx from "clsx"; + +import { + localizationOptions, + timepointOptions, + fovRefs, +} from "@/lib/table/definitions"; +import { DataTableColumnHeader } from "@/lib/table/data-table-column-header"; +// import { DataTableRowActions } from "@/lib/table/data-table-row-actions"; +import type { FieldofView } from "@/lib/types"; + +export const columns: ColumnDef[] = [ + { + accessorKey: "fov", + header: ({ column }) => ( + + ), + cell: ({ row }) => { + const fovhref = fovRefs.find( + (fov) => fov.value === row.getValue("fov"), + ); + if (!fovhref) { + return null; + } + return ( + + ); + }, + }, + { + accessorKey: "localization", + header: ({ column }) => ( + + ), + cell: ({ row }) => { + const localization = localizationOptions.find( + (localization) => + localization.value === row.getValue("localization"), + ); + if (!localization) { + return null; + } + + return ( +
+ {localization.label} +
+ ); + }, + filterFn: (row, id, value) => { + return value.includes(row.getValue(id)); + }, + }, + { + accessorKey: "timepoint", + header: ({ column }) => ( + + ), + cell: ({ row }) => { + const timepoint = timepointOptions.find( + (timepoint) => timepoint.value === row.getValue("timepoint"), + ); + if (!timepoint) { + return null; + } + + return ( +
+ {timepoint.label} +
+ ); + }, + filterFn: (row, id, value) => { + return value.includes(row.getValue(id)); + }, + }, + // { + // id: "actions", + // cell: ({ row }) => + // } +]; diff --git a/ghpages-site/src/lib/table/data-table-column-header.tsx b/ghpages-site/src/lib/table/data-table-column-header.tsx new file mode 100644 index 0000000..92d4367 --- /dev/null +++ b/ghpages-site/src/lib/table/data-table-column-header.tsx @@ -0,0 +1,76 @@ +import { + ArrowDownIcon, + ArrowUpIcon, + CaretSortIcon, + EyeNoneIcon, +} from "@radix-ui/react-icons"; +import { type Column } from "@tanstack/react-table"; + +import { cn } from "@/lib/utils"; +import { Button } from "@ui/button"; +import { + DropdownMenu, + DropdownMenuContent, + DropdownMenuItem, + DropdownMenuSeparator, + DropdownMenuTrigger, +} from "@ui/dropdown-menu"; + +interface DataTableColumnHeaderProps + extends React.HTMLAttributes { + column: Column; + title: string; +} + +export function DataTableColumnHeader({ + column, + title, + className, +}: DataTableColumnHeaderProps) { + if (!column.getCanSort()) { + return
{title}
; + } + return ( +
+ + + + + + column.toggleSorting(false)} + > + + {"Asc"} + + column.toggleSorting(true)} + > + + {"Desc"} + + + column.toggleVisibility(false)} + > + + {"Hide"} + + + +
+ ); +} diff --git a/ghpages-site/src/lib/table/data-table-faceted-filter.tsx b/ghpages-site/src/lib/table/data-table-faceted-filter.tsx new file mode 100644 index 0000000..cca569f --- /dev/null +++ b/ghpages-site/src/lib/table/data-table-faceted-filter.tsx @@ -0,0 +1,165 @@ +import * as React from "react"; +import { CheckIcon, PlusCircledIcon } from "@radix-ui/react-icons"; +import { type Column } from "@tanstack/react-table"; + +import { cn } from "@/lib/utils"; +import { Badge } from "@/components/ui/badge"; +import { Button } from "@/components/ui/button"; +import { + Command, + CommandEmpty, + CommandGroup, + CommandInput, + CommandItem, + CommandList, + CommandSeparator, +} from "@ui/command"; +import { Popover, PopoverContent, PopoverTrigger } from "@ui/popover"; +import { Separator } from "@ui/separator"; + +interface DataTableFacetedFilterProps { + column?: Column; + title?: string; + options: { + label: string; + value: string; + icon?: React.ComponentType<{ className?: string }>; + }[]; +} + +export function DataTableFacetedFilter({ + column, + title, + options, +}: DataTableFacetedFilterProps) { + const facets = column?.getFacetedUniqueValues(); + const selectedValues = new Set(column?.getFilterValue() as string[]); + + return ( + + + + + + + + + {"No Filter results"} + + {options.map((option) => { + const isSelected = selectedValues.has( + option.value, + ); + return ( + { + if (isSelected) { + selectedValues.delete( + option.value, + ); + } else { + selectedValues.add( + option.value, + ); + } + const filterValues = + Array.from(selectedValues); + column?.setFilterValue( + filterValues.length + ? filterValues + : undefined, + ); + }} + > +
+ +
+ {option.icon && ( + + )} + {option.label} + {facets?.get(option.value) && ( + + {facets.get(option.value)} + + )} + + ); + })} + + {selectedValues.size > 0 && ( + <> + + + + column?.setFilterValue(undefined) + } + className="justify-center text-center" + > + {"Clean Filters"} + + + + )} + + + + + ); +} diff --git a/ghpages-site/src/lib/table/data-table-pagination.tsx b/ghpages-site/src/lib/table/data-table-pagination.tsx new file mode 100644 index 0000000..0e1f095 --- /dev/null +++ b/ghpages-site/src/lib/table/data-table-pagination.tsx @@ -0,0 +1,106 @@ +import { + ChevronLeftIcon, + ChevronRightIcon, + DoubleArrowLeftIcon, + DoubleArrowRightIcon, +} from "@radix-ui/react-icons"; +import { type Table } from "@tanstack/react-table"; + +import { Button } from "@/components/ui/button"; +import { + Select, + SelectContent, + SelectItem, + SelectTrigger, + SelectValue, +} from "@ui/select"; + +interface DataTablePaginationProps { + table: Table; +} + +export function DataTablePagination({ + table, +}: DataTablePaginationProps) { + return ( +
+
+ {table.getFilteredSelectedRowModel().rows.length} of{" "} + {table.getFilteredRowModel().rows.length} {"row(s) selected"}. +
+
+
+

{"Rows per page"}

+ +
+
+ {"Page"} {table.getState().pagination.pageIndex + 1} of{" "} + {table.getPageCount()} +
+
+ + + + +
+
+
+ ); +} diff --git a/ghpages-site/src/lib/table/data-table-toolbar.tsx b/ghpages-site/src/lib/table/data-table-toolbar.tsx new file mode 100644 index 0000000..b67503b --- /dev/null +++ b/ghpages-site/src/lib/table/data-table-toolbar.tsx @@ -0,0 +1,67 @@ +"use client"; + +import { Cross2Icon } from "@radix-ui/react-icons"; +import type { Table } from "@tanstack/react-table"; + +import { Button } from "@/components/ui/button"; +import { Input } from "@/components/ui/input"; + +import { DataTableFacetedFilter } from "@/lib/table/data-table-faceted-filter"; +import { DataTableViewOptions } from "@/lib/table/data-table-view-options"; +import { localizationOptions, timepointOptions } from "./definitions"; + +interface DataTableToolbarProps { + table: Table; +} + +export function DataTableToolbar({ + table, +}: DataTableToolbarProps) { + const isFiltered = table.getState().columnFilters.length > 0; + + return ( +
+
+ + table + .getColumn("fov") + ?.setFilterValue(event.target.value) + } + className="h-8 w-[150px] lg:w-[250px]" + /> + + {table.getColumn("timepoint") && ( + + )} + {table.getColumn("localization") && ( + + )} + {isFiltered && ( + + )} +
+ +
+ ); +} diff --git a/ghpages-site/src/lib/table/data-table-view-options.tsx b/ghpages-site/src/lib/table/data-table-view-options.tsx new file mode 100644 index 0000000..8a45667 --- /dev/null +++ b/ghpages-site/src/lib/table/data-table-view-options.tsx @@ -0,0 +1,62 @@ +"use client"; + +import { DropdownMenuTrigger } from "@radix-ui/react-dropdown-menu"; +import { MixerHorizontalIcon } from "@radix-ui/react-icons"; +import { type Table } from "@tanstack/react-table"; + +import { Button } from "@/components/ui/button"; +import { + DropdownMenu, + DropdownMenuCheckboxItem, + DropdownMenuContent, + DropdownMenuLabel, + DropdownMenuSeparator, +} from "@/components/ui/dropdown-menu"; + +interface DataTableViewOptionsProps { + table: Table; +} + +export function DataTableViewOptions({ + table, +}: DataTableViewOptionsProps) { + return ( + + + + + + {"Edit Columns"} + + {table + .getAllColumns() + .filter( + (column) => + typeof column.accessorFn !== "undefined" && + column.getCanHide(), + ) + .map((column) => { + return ( + + column.toggleVisibility(!!value) + } + > + {column.id} + + ); + })} + + + ); +} diff --git a/ghpages-site/src/lib/table/data-table.tsx b/ghpages-site/src/lib/table/data-table.tsx new file mode 100644 index 0000000..c6eab27 --- /dev/null +++ b/ghpages-site/src/lib/table/data-table.tsx @@ -0,0 +1,124 @@ +"use client"; + +import React from "react"; +import { + type ColumnDef, + type ColumnFiltersState, + flexRender, + getCoreRowModel, + getFilteredRowModel, + getPaginationRowModel, + getSortedRowModel, + type SortingState, + useReactTable, + type VisibilityState, +} from "@tanstack/react-table"; + +import { + Table, + TableBody, + TableCell, + TableHead, + TableHeader, + TableRow, +} from "@/components/ui/table"; + +import { DataTablePagination } from "./data-table-pagination"; +import { DataTableToolbar } from "./data-table-toolbar"; + +interface DataTableProps { + columns: ColumnDef[]; + data: TData[]; +} + +export default function DataTable({ + columns, + data, +}: DataTableProps) { + const [sorting, setSorting] = React.useState([]); + const [columnVisibility, setColumnVisibility] = + React.useState({ + location: false, + otherInformation: false, + }); + const [columnFilters, setColumnFilters] = + React.useState([]); + + const table = useReactTable({ + data, + columns, + state: { + sorting, + columnVisibility, + columnFilters, + }, + enableRowSelection: true, + getCoreRowModel: getCoreRowModel(), + onSortingChange: setSorting, + getSortedRowModel: getSortedRowModel(), + onColumnVisibilityChange: setColumnVisibility, + getFilteredRowModel: getFilteredRowModel(), + getPaginationRowModel: getPaginationRowModel(), + onColumnFiltersChange: setColumnFilters, + }); + + return ( +
+ +
+ + + {table.getHeaderGroups().map((headerGroup) => ( + + {headerGroup.headers.map((header) => { + return ( + + {header.isPlaceholder + ? null + : flexRender( + header.column.columnDef + .header, + header.getContext(), + )} + + ); + })} + + ))} + + + {table.getRowModel().rows?.length ? ( + table.getRowModel().rows.map((row) => ( + + {row.getVisibleCells().map((cell) => ( + + {flexRender( + cell.column.columnDef.cell, + cell.getContext(), + )} + + ))} + + )) + ) : ( + + + {"No data results"} + + + )} + +
+
+ +
+ ); +} diff --git a/ghpages-site/src/lib/table/definitions.ts b/ghpages-site/src/lib/table/definitions.ts new file mode 100644 index 0000000..4ebbf42 --- /dev/null +++ b/ghpages-site/src/lib/table/definitions.ts @@ -0,0 +1,92 @@ +export const timepointOptions = [ + { + value: "baseline", + label: "Baseline", + }, + { + value: "primary", + label: "Primary", + }, + { + value: "on_nivo", + label: "On Nivo", + }, + { + value: "pre_nivo", + label: "Pre Nivo", + }, +]; +export const localizationOptions = [ + { + value: "Other", + label: "Other", + }, + { + value: "Lymphnode", + label: "Lymphnode", + }, + { + value: "Breast", + label: "Breast", + }, + { + value: "Liver", + label: "Liver", + }, + { + value: "Skin", + label: "Skin", + }, +]; +export const fovRefs = [ + { + value: "TONIC_TMA5_R1C2", + label: "TONIC TMA5 R1C2", + href: "/tonic-vitessce/tonic_tma5_r1c2", + }, + { + value: "TONIC_TMA5_R5C1", + label: "TONIC TMA5 R5C1", + href: "/tonic-vitessce/tonic_tma5_r5c1", + }, + { + value: "TONIC_TMA7_R4C6", + label: "TONIC TMA7 R4C6", + href: "/tonic-vitessce/tonic_tma7_r4c6", + }, + { + value: "TONIC_TMA9_R4C6", + label: "TONIC TMA9 R4C6", + href: "/tonic-vitessce/tonic_tma9_r4c6", + }, + { + value: "TONIC_TMA14_R7C6", + label: "TONIC TMA14 R7C6", + href: "/tonic-vitessce/tonic_tma14_r7c6", + }, + { + value: "TONIC_TMA15_R7C2", + label: "TONIC TMA15 R7C2", + href: "/tonic-vitessce/tonic_tma15_r7c2", + }, + { + value: "TONIC_TMA15_R10C1", + label: "TONIC TMA15 R10C1", + href: "/tonic-vitessce/tonic_tma15_r10c1", + }, + { + value: "TONIC_TMA17_R12C4", + label: "TONIC TMA17 R12C4", + href: "/tonic-vitessce/tonic_tma17_r12c4", + }, + { + value: "TONIC_TMA18_R2C3", + label: "TONIC TMA18 R2C3", + href: "/tonic-vitessce/tonic_tma18_r2c3", + }, + { + value: "TONIC_TMA23_R10C1", + label: "TONIC TMA23 R10C1", + href: "/tonic-vitessce/tonic_tma23_r10c1", + }, +]; diff --git a/ghpages-site/src/lib/types.ts b/ghpages-site/src/lib/types.ts new file mode 100644 index 0000000..0ed6999 --- /dev/null +++ b/ghpages-site/src/lib/types.ts @@ -0,0 +1,6 @@ +export interface FieldofView { + fov: string; + id: string; + timepoint: string; + localization: string; +} diff --git a/ghpages-site/src/lib/utils.ts b/ghpages-site/src/lib/utils.ts new file mode 100644 index 0000000..e644794 --- /dev/null +++ b/ghpages-site/src/lib/utils.ts @@ -0,0 +1,6 @@ +import { type ClassValue, clsx } from "clsx"; +import { twMerge } from "tailwind-merge"; + +export function cn(...inputs: ClassValue[]) { + return twMerge(clsx(inputs)); +} diff --git a/ghpages-site/src/pages/[fov].astro b/ghpages-site/src/pages/[fov].astro new file mode 100644 index 0000000..d94dcdb --- /dev/null +++ b/ghpages-site/src/pages/[fov].astro @@ -0,0 +1,30 @@ +--- +export function getStaticPaths() { + return [ + { params: { fov: "tonic_tma5_r1c2" } }, + { params: { fov: "tonic_tma5_r5c1" } }, + { params: { fov: "tonic_tma7_r4c6" } }, + { params: { fov: "tonic_tma9_r4c6" } }, + { params: { fov: "tonic_tma14_r7c6" } }, + { params: { fov: "tonic_tma15_r7c2" } }, + { params: { fov: "tonic_tma15_r10c1" } }, + { params: { fov: "tonic_tma17_r12c4" } }, + { params: { fov: "tonic_tma18_r2c3" } }, + { params: { fov: "tonic_tma23_r10c1" } }, + ]; +} + +const { fov } = Astro.params; + +import "@/styles/globals.css"; +import Tonic from "@vitessce_components/Tonic"; + +--- + + + + {fov} + + + + diff --git a/ghpages-site/src/pages/index.astro b/ghpages-site/src/pages/index.astro new file mode 100644 index 0000000..da182f5 --- /dev/null +++ b/ghpages-site/src/pages/index.astro @@ -0,0 +1,40 @@ +--- +import "@/styles/globals.css"; +import { ModeToggle } from "@/components/ModeToggle"; +import FOVTable from "@vitessce_components/FOVTable"; +--- + + + + + + TONIC FOVs + + + + diff --git a/ghpages-site/src/styles/globals.css b/ghpages-site/src/styles/globals.css new file mode 100644 index 0000000..0f3bb7b --- /dev/null +++ b/ghpages-site/src/styles/globals.css @@ -0,0 +1,98 @@ +@tailwind base; +@tailwind components; +@tailwind utilities; + +@layer base { + :root { + --background: 0 0% 100%; + --foreground: 240 10% 3.9%; + + --card: 0 0% 100%; + --card-foreground: 240 10% 3.9%; + + --popover: 0 0% 100%; + --popover-foreground: 240 10% 3.9%; + + --primary: 240 5.9% 10%; + --primary-foreground: 0 0% 98%; + + --secondary: 240 4.8% 95.9%; + --secondary-foreground: 240 5.9% 10%; + + --muted: 240 4.8% 95.9%; + --muted-foreground: 240 3.8% 46.1%; + + --accent: 240 4.8% 95.9%; + --accent-foreground: 240 5.9% 10%; + + --destructive: 0 84.2% 60.2%; + --destructive-foreground: 0 0% 98%; + + --border: 240 5.9% 90%; + --input: 240 5.9% 90%; + --ring: 240 10% 3.9%; + + --radius: 0.5rem; + } + + .dark { + --background: 240 10% 3.9%; + --foreground: 0 0% 98%; + + --card: 240 10% 3.9%; + --card-foreground: 0 0% 98%; + + --popover: 240 10% 3.9%; + --popover-foreground: 0 0% 98%; + + --primary: 0 0% 98%; + --primary-foreground: 240 5.9% 10%; + + --secondary: 240 3.7% 15.9%; + --secondary-foreground: 0 0% 98%; + + --muted: 240 3.7% 15.9%; + --muted-foreground: 240 5% 64.9%; + + --accent: 240 3.7% 15.9%; + --accent-foreground: 0 0% 98%; + + --destructive: 0 62.8% 30.6%; + --destructive-foreground: 0 0% 98%; + + --border: 240 3.7% 15.9%; + --input: 240 3.7% 15.9%; + --ring: 240 4.9% 83.9%; + } +} + +@layer base { + * { + @apply tailwind.config.mjsborder-border; + } + body { + @apply tailwind.config.mjsbg-background tailwind.config.mjstext-foreground; + } +} + +html { + height: 100%; +} + +body { + font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", "Roboto", + "Oxygen", "Ubuntu", "Cantarell", "Fira Sans", "Droid Sans", + "Helvetica Neue", sans-serif; + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; + display: flex; + flex-direction: column; + flex: 1; + height: 100%; + margin: 0; +} + +.vitessce-container { + height: max(100%, 100vh); + width: 100%; +} diff --git a/ghpages-site/tailwind.config.mjs b/ghpages-site/tailwind.config.mjs new file mode 100644 index 0000000..04b0e81 --- /dev/null +++ b/ghpages-site/tailwind.config.mjs @@ -0,0 +1,72 @@ +/** @type {import('tailwindcss').Config} */ +module.exports = { + darkMode: ["class"], + content: ["./src/**/*.{astro,html,js,jsx,md,mdx,ts,tsx}"], + prefix: "tailwind.config.mjs", + theme: { + container: { + center: true, + padding: "2rem", + screens: { + "2xl": "1400px", + }, + }, + extend: { + colors: { + border: "hsl(var(--border))", + input: "hsl(var(--input))", + ring: "hsl(var(--ring))", + background: "hsl(var(--background))", + foreground: "hsl(var(--foreground))", + primary: { + DEFAULT: "hsl(var(--primary))", + foreground: "hsl(var(--primary-foreground))", + }, + secondary: { + DEFAULT: "hsl(var(--secondary))", + foreground: "hsl(var(--secondary-foreground))", + }, + destructive: { + DEFAULT: "hsl(var(--destructive))", + foreground: "hsl(var(--destructive-foreground))", + }, + muted: { + DEFAULT: "hsl(var(--muted))", + foreground: "hsl(var(--muted-foreground))", + }, + accent: { + DEFAULT: "hsl(var(--accent))", + foreground: "hsl(var(--accent-foreground))", + }, + popover: { + DEFAULT: "hsl(var(--popover))", + foreground: "hsl(var(--popover-foreground))", + }, + card: { + DEFAULT: "hsl(var(--card))", + foreground: "hsl(var(--card-foreground))", + }, + }, + borderRadius: { + lg: "var(--radius)", + md: "calc(var(--radius) - 2px)", + sm: "calc(var(--radius) - 4px)", + }, + keyframes: { + "accordion-down": { + from: { height: "0" }, + to: { height: "var(--radix-accordion-content-height)" }, + }, + "accordion-up": { + from: { height: "var(--radix-accordion-content-height)" }, + to: { height: "0" }, + }, + }, + animation: { + "accordion-down": "accordion-down 0.2s ease-out", + "accordion-up": "accordion-up 0.2s ease-out", + }, + }, + }, + plugins: [require("tailwindcss-animate")], +}; diff --git a/ghpages-site/tsconfig.json b/ghpages-site/tsconfig.json new file mode 100644 index 0000000..569937b --- /dev/null +++ b/ghpages-site/tsconfig.json @@ -0,0 +1,16 @@ +{ + "extends": "astro/tsconfigs/strict", + "compilerOptions": { + "jsx": "react-jsx", + "jsxImportSource": "react", + "verbatimModuleSyntax": true, + "baseUrl": ".", + "paths": { + "@/*": ["src/*"], + "@ui/*": ["src/components/ui/*"], + "@vitessce_configs/*": ["src/components/vitessce/configs/*"], + "@vitessce_components/*": ["src/components/vitessce/*"], + "@custom_components/*": ["src/components/custom/*"] + } + } +} diff --git a/package.json b/package.json new file mode 100644 index 0000000..963ac2f --- /dev/null +++ b/package.json @@ -0,0 +1,6 @@ +{ + "dependencies": { + "@biomejs/biome": "^1.8.3", + "@tanstack/react-table": "^8.19.2" + } +} diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..0f87aaf --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,141 @@ +[build-system] +build-backend = "hatchling.build" +requires = ["hatchling"] + +[project] +name = "tonic-vitessce" +version = "0.0.1" +description = "Vitessce Configs and Data Conversion for the dataset." +readme = "README.md" +requires-python = ">=3.10" +license = {file = "LICENSE"} +authors = [ + {name = "Sricharan Reddy Varra"}, +] +maintainers = [ + {name = "Sricharan Reddy Varra", email = "srivarra@stanford.edu"}, +] +urls.Documentation = "https://tonic-vitessce.readthedocs.io/" +urls.Source = "https://github.com/angelolab/tonic-vitessce" +urls.Home-page = "https://github.com/angelolab/tonic-vitessce" +dependencies = [ + "anndata", + # for debug logging (referenced from the issue template) + "session-info", + "vitessce[all]>=3.2.6", +] + +[project.optional-dependencies] +dev = [ + "pre-commit", + "twine>=4.0.2", +] +doc = [ + "docutils>=0.8,!=0.18.*,!=0.19.*", + "sphinx>=4", + "sphinx-book-theme>=1.0.0", + "myst-nb>=1.1.0", + "sphinxcontrib-bibtex>=1.0.0", + "setuptools", # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/ + "sphinx-autodoc-typehints", + "sphinxext-opengraph", + # For notebooks + "ipykernel", + "ipython", + "sphinx-copybutton", + "pandas", +] +test = [ + "pytest", + "coverage", +] +dask = [ + "dask[complete]>=2024.5.2", + "dask-image>=2024.5.3", +] +nb = [ + "buckaroo>=0.6.11", +] + +[tool.coverage.run] +source = ["tonic_vitessce"] +omit = [ + "**/test_*.py", +] + +[tool.pytest.ini_options] +testpaths = ["tests"] +xfail_strict = true +addopts = [ + "--import-mode=importlib", # allow using test files with same name +] + +[tool.ruff] +line-length = 120 +src = ["src"] +extend-include = ["*.ipynb"] + +[tool.ruff.format] +docstring-code-format = true + +[tool.ruff.lint] +select = [ + "F", # Errors detected by Pyflakes + "E", # Error detected by Pycodestyle + "W", # Warning detected by Pycodestyle + "I", # isort + "D", # pydocstyle + "B", # flake8-bugbear + "TID", # flake8-tidy-imports + "C4", # flake8-comprehensions + "BLE", # flake8-blind-except + "UP", # pyupgrade + "RUF100", # Report unused noqa directives +] +ignore = [ + # line too long -> we accept long comment lines; formatter gets rid of long code lines + "E501", + # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient + "E731", + # allow I, O, l as variable names -> I is the identity matrix + "E741", + # Missing docstring in public package + "D104", + # Missing docstring in public module + "D100", + # Missing docstring in __init__ + "D107", + # Errors from function calls in argument defaults. These are fine when the result is immutable. + "B008", + # __magic__ methods are often self-explanatory, allow missing docstrings + "D105", + # first line should end with a period [Bug: doesn't work with single-line docstrings] + "D400", + # First line should be in imperative mood; try rephrasing + "D401", + ## Disable one in each pair of mutually incompatible rules + # We don’t want a blank line before a class docstring + "D203", + # We want docstrings to start immediately after the opening triple quote + "D213", +] + +[tool.ruff.lint.pydocstyle] +convention = "numpy" + +[tool.ruff.lint.per-file-ignores] +"docs/*" = ["I"] +"tests/*" = ["D"] +"*/__init__.py" = ["F401"] + +[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", +] diff --git a/requirements-dev.lock b/requirements-dev.lock new file mode 100644 index 0000000..0ff5145 --- /dev/null +++ b/requirements-dev.lock @@ -0,0 +1,708 @@ +# generated by rye +# use `rye lock` or `rye sync` to update this lockfile +# +# last locked with the following flags: +# pre: false +# features: [] +# all-features: true +# with-sources: false +# generate-hashes: false +# universal: false + +-e file:. +accessible-pygments==0.0.5 + # via pydata-sphinx-theme +aiobotocore==2.13.1 + # via s3fs +aiofiles==24.1.0 + # via vitessce +aiohttp==3.9.5 + # via aiobotocore + # via jupyter-server-proxy + # via ome-zarr + # via s3fs +aioitertools==0.11.0 + # via aiobotocore +aiosignal==1.3.1 + # via aiohttp +alabaster==0.7.16 + # via sphinx +anndata==0.10.8 + # via scanpy + # via tonic-vitessce + # via vitessce +anyio==4.4.0 + # via jupyter-server +anywidget==0.9.13 + # via vitessce +appnope==0.1.4 + # via ipykernel +argon2-cffi==23.1.0 + # via jupyter-server +argon2-cffi-bindings==21.2.0 + # via argon2-cffi +array-api-compat==1.7.1 + # via anndata +arrow==1.3.0 + # via isoduration +asciitree==0.3.3 + # via zarr +asttokens==2.4.1 + # via stack-data +attrs==23.2.0 + # via aiohttp + # via jsonschema + # via jupyter-cache + # via referencing +babel==2.15.0 + # via pydata-sphinx-theme + # via sphinx +backports-tarfile==1.2.0 + # via jaraco-context +beautifulsoup4==4.12.3 + # via nbconvert + # via pydata-sphinx-theme +black==24.4.2 + # via vitessce +bleach==6.1.0 + # via nbconvert +bokeh==3.5.0 + # via dask +botocore==1.34.131 + # via aiobotocore +buckaroo==0.6.11 + # via tonic-vitessce +certifi==2024.7.4 + # via requests +cffi==1.16.0 + # via argon2-cffi-bindings +cfgv==3.4.0 + # via pre-commit +charset-normalizer==3.3.2 + # via requests +click==8.1.7 + # via black + # via dask + # via distributed + # via jupyter-cache + # via uvicorn +cloudpickle==3.0.0 + # via dask + # via distributed +comm==0.2.2 + # via ipykernel + # via ipywidgets +contourpy==1.2.1 + # via bokeh + # via matplotlib +coverage==7.6.0 + # via tonic-vitessce +cycler==0.12.1 + # via matplotlib +dask==2024.7.0 + # via dask-expr + # via dask-image + # via distributed + # via ome-zarr + # via tonic-vitessce +dask-expr==1.1.7 + # via dask +dask-image==2024.5.3 + # via tonic-vitessce +debugpy==1.8.2 + # via ipykernel +decorator==5.1.1 + # via ipython +defusedxml==0.7.1 + # via nbconvert +distlib==0.3.8 + # via virtualenv +distributed==2024.7.0 + # via dask + # via ome-zarr +docutils==0.21.2 + # via myst-parser + # via pybtex-docutils + # via pydata-sphinx-theme + # via readme-renderer + # via sphinx + # via sphinxcontrib-bibtex + # via tonic-vitessce +esbuild-py==0.1.5 + # via vitessce +executing==2.0.1 + # via stack-data +fasteners==0.19 + # via zarr +fastjsonschema==2.20.0 + # via nbformat +filelock==3.15.4 + # via virtualenv +fonttools==4.53.1 + # via matplotlib +fqdn==1.5.1 + # via jsonschema +frozenlist==1.4.1 + # via aiohttp + # via aiosignal +fsspec==2024.6.1 + # via dask + # via ome-zarr + # via s3fs +generate-tiff-offsets==0.1.7 + # via vitessce +graphlib-backport==1.1.0 + # via buckaroo +h11==0.14.0 + # via uvicorn +h5py==3.11.0 + # via anndata + # via scanpy +identify==2.6.0 + # via pre-commit +idna==3.7 + # via anyio + # via jsonschema + # via requests + # via yarl +imageio==2.34.2 + # via pims + # via scikit-image +imagesize==1.4.1 + # via sphinx +importlib-metadata==8.0.0 + # via dask + # via jupyter-cache + # via keyring + # via myst-nb + # via twine +iniconfig==2.0.0 + # via pytest +ipykernel==6.29.5 + # via myst-nb + # via tonic-vitessce +ipython==8.26.0 + # via ipykernel + # via ipywidgets + # via myst-nb + # via tonic-vitessce +ipywidgets==8.1.3 + # via anywidget + # via buckaroo +isoduration==20.11.0 + # via jsonschema +jaraco-classes==3.4.0 + # via keyring +jaraco-context==5.3.0 + # via keyring +jaraco-functools==4.0.1 + # via keyring +jedi==0.19.1 + # via ipython +jinja2==3.1.4 + # via bokeh + # via dask + # via distributed + # via jupyter-server + # via myst-parser + # via nbconvert + # via sphinx +jmespath==1.0.1 + # via botocore +joblib==1.4.2 + # via pynndescent + # via scanpy + # via scikit-learn +jsonpointer==3.0.0 + # via jsonschema +jsonschema==4.23.0 + # via jupyter-events + # via nbformat + # via vitessce +jsonschema-specifications==2023.12.1 + # via jsonschema +jupyter-cache==1.0.0 + # via myst-nb +jupyter-client==8.6.2 + # via ipykernel + # via jupyter-server + # via nbclient +jupyter-core==5.7.2 + # via ipykernel + # via jupyter-client + # via jupyter-server + # via nbclient + # via nbconvert + # via nbformat +jupyter-events==0.10.0 + # via jupyter-server +jupyter-server==2.14.1 + # via jupyter-server-proxy +jupyter-server-proxy==4.3.0 + # via vitessce +jupyter-server-terminals==0.5.3 + # via jupyter-server +jupyterlab-pygments==0.3.0 + # via nbconvert +jupyterlab-widgets==3.0.11 + # via ipywidgets +keyring==25.2.1 + # via twine +kiwisolver==1.4.5 + # via matplotlib +latexcodec==3.0.0 + # via pybtex +lazy-loader==0.4 + # via scikit-image +legacy-api-wrap==1.4 + # via scanpy +llvmlite==0.43.0 + # via numba + # via pynndescent +locket==1.0.0 + # via distributed + # via partd +lz4==4.3.3 + # via dask +markdown-it-py==3.0.0 + # via mdit-py-plugins + # via myst-parser + # via rich +markupsafe==2.1.5 + # via jinja2 + # via nbconvert +matplotlib==3.9.1 + # via scanpy + # via seaborn +matplotlib-inline==0.1.7 + # via ipykernel + # via ipython +mdit-py-plugins==0.4.1 + # via myst-parser +mdurl==0.1.2 + # via markdown-it-py +mistune==3.0.2 + # via nbconvert +more-itertools==10.3.0 + # via jaraco-classes + # via jaraco-functools +msgpack==1.0.8 + # via distributed +multidict==6.0.5 + # via aiohttp + # via yarl +mypy-extensions==1.0.0 + # via black +myst-nb==1.1.1 + # via tonic-vitessce +myst-parser==3.0.1 + # via myst-nb +natsort==8.4.0 + # via anndata + # via scanpy +nbclient==0.10.0 + # via jupyter-cache + # via myst-nb + # via nbconvert +nbconvert==7.16.4 + # via jupyter-server +nbformat==5.10.4 + # via jupyter-cache + # via jupyter-server + # via myst-nb + # via nbclient + # via nbconvert +negspy==0.2.24 + # via vitessce +nest-asyncio==1.6.0 + # via ipykernel +networkx==3.3 + # via scanpy + # via scikit-image +nh3==0.2.18 + # via readme-renderer +nodeenv==1.9.1 + # via pre-commit +numba==0.60.0 + # via pynndescent + # via scanpy + # via umap-learn +numcodecs==0.12.1 + # via vitessce + # via zarr +numpy==1.26.4 + # via anndata + # via bokeh + # via contourpy + # via dask + # via dask-image + # via h5py + # via imageio + # via matplotlib + # via numba + # via numcodecs + # via ome-zarr + # via pandas + # via patsy + # via pims + # via pyarrow + # via pywavelets + # via scanpy + # via scikit-image + # via scikit-learn + # via scipy + # via seaborn + # via statsmodels + # via tifffile + # via umap-learn + # via vitessce + # via zarr +ome-zarr==0.8.3 + # via vitessce +overrides==7.7.0 + # via jupyter-server +packaging==24.1 + # via anndata + # via black + # via bokeh + # via dask + # via distributed + # via ipykernel + # via jupyter-server + # via lazy-loader + # via matplotlib + # via nbconvert + # via pims + # via pydata-sphinx-theme + # via pytest + # via scanpy + # via scikit-image + # via sphinx + # via statsmodels +pandas==2.2.2 + # via anndata + # via bokeh + # via dask + # via dask-expr + # via dask-image + # via scanpy + # via seaborn + # via statsmodels + # via tonic-vitessce + # via vitessce +pandocfilters==1.5.1 + # via nbconvert +parso==0.8.4 + # via jedi +partd==1.4.2 + # via dask +pathspec==0.12.1 + # via black +patsy==0.5.6 + # via scanpy + # via statsmodels +pexpect==4.9.0 + # via ipython +pillow==10.4.0 + # via bokeh + # via imageio + # via matplotlib + # via scikit-image +pims==0.7 + # via dask-image +pkginfo==1.10.0 + # via twine +platformdirs==4.2.2 + # via black + # via jupyter-core + # via virtualenv +pluggy==1.5.0 + # via pytest +pre-commit==3.7.1 + # via tonic-vitessce +prometheus-client==0.20.0 + # via jupyter-server +prompt-toolkit==3.0.47 + # via ipython +psutil==6.0.0 + # via distributed + # via ipykernel +psygnal==0.11.1 + # via anywidget +ptyprocess==0.7.0 + # via pexpect + # via terminado +pure-eval==0.2.2 + # via stack-data +pyarrow==16.1.0 + # via dask + # via dask-expr +pyarrow-hotfix==0.6 + # via dask +pybtex==0.24.0 + # via pybtex-docutils + # via sphinxcontrib-bibtex +pybtex-docutils==1.0.3 + # via sphinxcontrib-bibtex +pycparser==2.22 + # via cffi +pydata-sphinx-theme==0.15.4 + # via sphinx-book-theme +pygments==2.18.0 + # via accessible-pygments + # via ipython + # via nbconvert + # via pydata-sphinx-theme + # via readme-renderer + # via rich + # via sphinx +pynndescent==0.5.13 + # via scanpy + # via umap-learn +pyparsing==3.1.2 + # via matplotlib +pytest==8.2.2 + # via tonic-vitessce +python-dateutil==2.9.0.post0 + # via arrow + # via botocore + # via jupyter-client + # via matplotlib + # via pandas +python-json-logger==2.0.7 + # via jupyter-events +pytz==2024.1 + # via pandas +pywavelets==1.6.0 + # via scikit-image +pyyaml==6.0.1 + # via bokeh + # via dask + # via distributed + # via jupyter-cache + # via jupyter-events + # via myst-nb + # via myst-parser + # via pre-commit + # via pybtex +pyzmq==26.0.3 + # via ipykernel + # via jupyter-client + # via jupyter-server +readme-renderer==44.0 + # via twine +referencing==0.35.1 + # via jsonschema + # via jsonschema-specifications + # via jupyter-events +requests==2.32.3 + # via ome-zarr + # via requests-toolbelt + # via sphinx + # via twine +requests-toolbelt==1.0.0 + # via twine +rfc3339-validator==0.1.4 + # via jsonschema + # via jupyter-events +rfc3986==2.0.0 + # via twine +rfc3986-validator==0.1.1 + # via jsonschema + # via jupyter-events +rich==13.7.1 + # via twine +rpds-py==0.19.0 + # via jsonschema + # via referencing +s3fs==2024.6.1 + # via fsspec +scanpy==1.10.2 + # via vitessce +scikit-image==0.20.0 + # via ome-zarr +scikit-learn==1.5.1 + # via pynndescent + # via scanpy + # via umap-learn +scipy==1.14.0 + # via anndata + # via dask-image + # via pynndescent + # via scanpy + # via scikit-image + # via scikit-learn + # via statsmodels + # via umap-learn + # via vitessce +seaborn==0.13.2 + # via scanpy +send2trash==1.8.3 + # via jupyter-server +session-info==1.0.0 + # via scanpy + # via tonic-vitessce +setuptools==70.3.0 + # via tonic-vitessce +simpervisor==1.0.0 + # via jupyter-server-proxy +six==1.16.0 + # via asttokens + # via bleach + # via patsy + # via pybtex + # via python-dateutil + # via rfc3339-validator +slicerator==1.1.0 + # via pims +sniffio==1.3.1 + # via anyio +snowballstemmer==2.2.0 + # via sphinx +sortedcontainers==2.4.0 + # via distributed +soupsieve==2.5 + # via beautifulsoup4 +sphinx==7.3.7 + # via myst-nb + # via myst-parser + # via pydata-sphinx-theme + # via sphinx-autodoc-typehints + # via sphinx-book-theme + # via sphinx-copybutton + # via sphinxcontrib-bibtex + # via sphinxext-opengraph + # via tonic-vitessce +sphinx-autodoc-typehints==2.2.2 + # via tonic-vitessce +sphinx-book-theme==1.1.3 + # via tonic-vitessce +sphinx-copybutton==0.5.2 + # via tonic-vitessce +sphinxcontrib-applehelp==1.0.8 + # via sphinx +sphinxcontrib-bibtex==2.6.2 + # via tonic-vitessce +sphinxcontrib-devhelp==1.0.6 + # via sphinx +sphinxcontrib-htmlhelp==2.0.5 + # via sphinx +sphinxcontrib-jsmath==1.0.1 + # via sphinx +sphinxcontrib-qthelp==1.0.7 + # via sphinx +sphinxcontrib-serializinghtml==1.1.10 + # via sphinx +sphinxext-opengraph==0.9.1 + # via tonic-vitessce +sqlalchemy==2.0.31 + # via jupyter-cache +stack-data==0.6.3 + # via ipython +starlette==0.14.0 + # via vitessce +statsmodels==0.14.2 + # via scanpy +stdlib-list==0.10.0 + # via session-info +tabulate==0.9.0 + # via jupyter-cache +tblib==3.0.0 + # via distributed +terminado==0.18.1 + # via jupyter-server + # via jupyter-server-terminals +threadpoolctl==3.5.0 + # via scikit-learn +tifffile==2020.10.1 + # via dask-image + # via generate-tiff-offsets + # via pims + # via scikit-image + # via vitessce +tinycss2==1.3.0 + # via nbconvert +toolz==0.12.1 + # via dask + # via distributed + # via ome-zarr + # via partd +tornado==6.4.1 + # via bokeh + # via distributed + # via ipykernel + # via jupyter-client + # via jupyter-server + # via jupyter-server-proxy + # via terminado +tqdm==4.66.4 + # via scanpy + # via umap-learn + # via vitessce +traitlets==5.14.3 + # via comm + # via ipykernel + # via ipython + # via ipywidgets + # via jupyter-client + # via jupyter-core + # via jupyter-events + # via jupyter-server + # via jupyter-server-proxy + # via matplotlib-inline + # via nbclient + # via nbconvert + # via nbformat +twine==5.1.1 + # via tonic-vitessce +types-python-dateutil==2.9.0.20240316 + # via arrow +typing-extensions==4.12.2 + # via anywidget + # via ipython + # via myst-nb + # via pydata-sphinx-theme + # via sqlalchemy +tzdata==2024.1 + # via pandas +ujson==5.10.0 + # via vitessce +umap-learn==0.5.6 + # via scanpy +uri-template==1.3.0 + # via jsonschema +urllib3==2.2.2 + # via botocore + # via distributed + # via requests + # via twine +uvicorn==0.30.1 + # via vitessce +virtualenv==20.26.3 + # via pre-commit +vitessce==3.2.7 + # via tonic-vitessce +wcwidth==0.2.13 + # via prompt-toolkit +webcolors==24.6.0 + # via jsonschema +webencodings==0.5.1 + # via bleach + # via tinycss2 +websocket-client==1.8.0 + # via jupyter-server +widgetsnbextension==4.0.11 + # via ipywidgets +wrapt==1.16.0 + # via aiobotocore +xyzservices==2024.6.0 + # via bokeh +yarl==1.9.4 + # via aiohttp +zarr==2.18.2 + # via ome-zarr + # via vitessce +zict==3.0.0 + # via distributed +zipp==3.19.2 + # via importlib-metadata diff --git a/requirements.lock b/requirements.lock new file mode 100644 index 0000000..0ff5145 --- /dev/null +++ b/requirements.lock @@ -0,0 +1,708 @@ +# generated by rye +# use `rye lock` or `rye sync` to update this lockfile +# +# last locked with the following flags: +# pre: false +# features: [] +# all-features: true +# with-sources: false +# generate-hashes: false +# universal: false + +-e file:. +accessible-pygments==0.0.5 + # via pydata-sphinx-theme +aiobotocore==2.13.1 + # via s3fs +aiofiles==24.1.0 + # via vitessce +aiohttp==3.9.5 + # via aiobotocore + # via jupyter-server-proxy + # via ome-zarr + # via s3fs +aioitertools==0.11.0 + # via aiobotocore +aiosignal==1.3.1 + # via aiohttp +alabaster==0.7.16 + # via sphinx +anndata==0.10.8 + # via scanpy + # via tonic-vitessce + # via vitessce +anyio==4.4.0 + # via jupyter-server +anywidget==0.9.13 + # via vitessce +appnope==0.1.4 + # via ipykernel +argon2-cffi==23.1.0 + # via jupyter-server +argon2-cffi-bindings==21.2.0 + # via argon2-cffi +array-api-compat==1.7.1 + # via anndata +arrow==1.3.0 + # via isoduration +asciitree==0.3.3 + # via zarr +asttokens==2.4.1 + # via stack-data +attrs==23.2.0 + # via aiohttp + # via jsonschema + # via jupyter-cache + # via referencing +babel==2.15.0 + # via pydata-sphinx-theme + # via sphinx +backports-tarfile==1.2.0 + # via jaraco-context +beautifulsoup4==4.12.3 + # via nbconvert + # via pydata-sphinx-theme +black==24.4.2 + # via vitessce +bleach==6.1.0 + # via nbconvert +bokeh==3.5.0 + # via dask +botocore==1.34.131 + # via aiobotocore +buckaroo==0.6.11 + # via tonic-vitessce +certifi==2024.7.4 + # via requests +cffi==1.16.0 + # via argon2-cffi-bindings +cfgv==3.4.0 + # via pre-commit +charset-normalizer==3.3.2 + # via requests +click==8.1.7 + # via black + # via dask + # via distributed + # via jupyter-cache + # via uvicorn +cloudpickle==3.0.0 + # via dask + # via distributed +comm==0.2.2 + # via ipykernel + # via ipywidgets +contourpy==1.2.1 + # via bokeh + # via matplotlib +coverage==7.6.0 + # via tonic-vitessce +cycler==0.12.1 + # via matplotlib +dask==2024.7.0 + # via dask-expr + # via dask-image + # via distributed + # via ome-zarr + # via tonic-vitessce +dask-expr==1.1.7 + # via dask +dask-image==2024.5.3 + # via tonic-vitessce +debugpy==1.8.2 + # via ipykernel +decorator==5.1.1 + # via ipython +defusedxml==0.7.1 + # via nbconvert +distlib==0.3.8 + # via virtualenv +distributed==2024.7.0 + # via dask + # via ome-zarr +docutils==0.21.2 + # via myst-parser + # via pybtex-docutils + # via pydata-sphinx-theme + # via readme-renderer + # via sphinx + # via sphinxcontrib-bibtex + # via tonic-vitessce +esbuild-py==0.1.5 + # via vitessce +executing==2.0.1 + # via stack-data +fasteners==0.19 + # via zarr +fastjsonschema==2.20.0 + # via nbformat +filelock==3.15.4 + # via virtualenv +fonttools==4.53.1 + # via matplotlib +fqdn==1.5.1 + # via jsonschema +frozenlist==1.4.1 + # via aiohttp + # via aiosignal +fsspec==2024.6.1 + # via dask + # via ome-zarr + # via s3fs +generate-tiff-offsets==0.1.7 + # via vitessce +graphlib-backport==1.1.0 + # via buckaroo +h11==0.14.0 + # via uvicorn +h5py==3.11.0 + # via anndata + # via scanpy +identify==2.6.0 + # via pre-commit +idna==3.7 + # via anyio + # via jsonschema + # via requests + # via yarl +imageio==2.34.2 + # via pims + # via scikit-image +imagesize==1.4.1 + # via sphinx +importlib-metadata==8.0.0 + # via dask + # via jupyter-cache + # via keyring + # via myst-nb + # via twine +iniconfig==2.0.0 + # via pytest +ipykernel==6.29.5 + # via myst-nb + # via tonic-vitessce +ipython==8.26.0 + # via ipykernel + # via ipywidgets + # via myst-nb + # via tonic-vitessce +ipywidgets==8.1.3 + # via anywidget + # via buckaroo +isoduration==20.11.0 + # via jsonschema +jaraco-classes==3.4.0 + # via keyring +jaraco-context==5.3.0 + # via keyring +jaraco-functools==4.0.1 + # via keyring +jedi==0.19.1 + # via ipython +jinja2==3.1.4 + # via bokeh + # via dask + # via distributed + # via jupyter-server + # via myst-parser + # via nbconvert + # via sphinx +jmespath==1.0.1 + # via botocore +joblib==1.4.2 + # via pynndescent + # via scanpy + # via scikit-learn +jsonpointer==3.0.0 + # via jsonschema +jsonschema==4.23.0 + # via jupyter-events + # via nbformat + # via vitessce +jsonschema-specifications==2023.12.1 + # via jsonschema +jupyter-cache==1.0.0 + # via myst-nb +jupyter-client==8.6.2 + # via ipykernel + # via jupyter-server + # via nbclient +jupyter-core==5.7.2 + # via ipykernel + # via jupyter-client + # via jupyter-server + # via nbclient + # via nbconvert + # via nbformat +jupyter-events==0.10.0 + # via jupyter-server +jupyter-server==2.14.1 + # via jupyter-server-proxy +jupyter-server-proxy==4.3.0 + # via vitessce +jupyter-server-terminals==0.5.3 + # via jupyter-server +jupyterlab-pygments==0.3.0 + # via nbconvert +jupyterlab-widgets==3.0.11 + # via ipywidgets +keyring==25.2.1 + # via twine +kiwisolver==1.4.5 + # via matplotlib +latexcodec==3.0.0 + # via pybtex +lazy-loader==0.4 + # via scikit-image +legacy-api-wrap==1.4 + # via scanpy +llvmlite==0.43.0 + # via numba + # via pynndescent +locket==1.0.0 + # via distributed + # via partd +lz4==4.3.3 + # via dask +markdown-it-py==3.0.0 + # via mdit-py-plugins + # via myst-parser + # via rich +markupsafe==2.1.5 + # via jinja2 + # via nbconvert +matplotlib==3.9.1 + # via scanpy + # via seaborn +matplotlib-inline==0.1.7 + # via ipykernel + # via ipython +mdit-py-plugins==0.4.1 + # via myst-parser +mdurl==0.1.2 + # via markdown-it-py +mistune==3.0.2 + # via nbconvert +more-itertools==10.3.0 + # via jaraco-classes + # via jaraco-functools +msgpack==1.0.8 + # via distributed +multidict==6.0.5 + # via aiohttp + # via yarl +mypy-extensions==1.0.0 + # via black +myst-nb==1.1.1 + # via tonic-vitessce +myst-parser==3.0.1 + # via myst-nb +natsort==8.4.0 + # via anndata + # via scanpy +nbclient==0.10.0 + # via jupyter-cache + # via myst-nb + # via nbconvert +nbconvert==7.16.4 + # via jupyter-server +nbformat==5.10.4 + # via jupyter-cache + # via jupyter-server + # via myst-nb + # via nbclient + # via nbconvert +negspy==0.2.24 + # via vitessce +nest-asyncio==1.6.0 + # via ipykernel +networkx==3.3 + # via scanpy + # via scikit-image +nh3==0.2.18 + # via readme-renderer +nodeenv==1.9.1 + # via pre-commit +numba==0.60.0 + # via pynndescent + # via scanpy + # via umap-learn +numcodecs==0.12.1 + # via vitessce + # via zarr +numpy==1.26.4 + # via anndata + # via bokeh + # via contourpy + # via dask + # via dask-image + # via h5py + # via imageio + # via matplotlib + # via numba + # via numcodecs + # via ome-zarr + # via pandas + # via patsy + # via pims + # via pyarrow + # via pywavelets + # via scanpy + # via scikit-image + # via scikit-learn + # via scipy + # via seaborn + # via statsmodels + # via tifffile + # via umap-learn + # via vitessce + # via zarr +ome-zarr==0.8.3 + # via vitessce +overrides==7.7.0 + # via jupyter-server +packaging==24.1 + # via anndata + # via black + # via bokeh + # via dask + # via distributed + # via ipykernel + # via jupyter-server + # via lazy-loader + # via matplotlib + # via nbconvert + # via pims + # via pydata-sphinx-theme + # via pytest + # via scanpy + # via scikit-image + # via sphinx + # via statsmodels +pandas==2.2.2 + # via anndata + # via bokeh + # via dask + # via dask-expr + # via dask-image + # via scanpy + # via seaborn + # via statsmodels + # via tonic-vitessce + # via vitessce +pandocfilters==1.5.1 + # via nbconvert +parso==0.8.4 + # via jedi +partd==1.4.2 + # via dask +pathspec==0.12.1 + # via black +patsy==0.5.6 + # via scanpy + # via statsmodels +pexpect==4.9.0 + # via ipython +pillow==10.4.0 + # via bokeh + # via imageio + # via matplotlib + # via scikit-image +pims==0.7 + # via dask-image +pkginfo==1.10.0 + # via twine +platformdirs==4.2.2 + # via black + # via jupyter-core + # via virtualenv +pluggy==1.5.0 + # via pytest +pre-commit==3.7.1 + # via tonic-vitessce +prometheus-client==0.20.0 + # via jupyter-server +prompt-toolkit==3.0.47 + # via ipython +psutil==6.0.0 + # via distributed + # via ipykernel +psygnal==0.11.1 + # via anywidget +ptyprocess==0.7.0 + # via pexpect + # via terminado +pure-eval==0.2.2 + # via stack-data +pyarrow==16.1.0 + # via dask + # via dask-expr +pyarrow-hotfix==0.6 + # via dask +pybtex==0.24.0 + # via pybtex-docutils + # via sphinxcontrib-bibtex +pybtex-docutils==1.0.3 + # via sphinxcontrib-bibtex +pycparser==2.22 + # via cffi +pydata-sphinx-theme==0.15.4 + # via sphinx-book-theme +pygments==2.18.0 + # via accessible-pygments + # via ipython + # via nbconvert + # via pydata-sphinx-theme + # via readme-renderer + # via rich + # via sphinx +pynndescent==0.5.13 + # via scanpy + # via umap-learn +pyparsing==3.1.2 + # via matplotlib +pytest==8.2.2 + # via tonic-vitessce +python-dateutil==2.9.0.post0 + # via arrow + # via botocore + # via jupyter-client + # via matplotlib + # via pandas +python-json-logger==2.0.7 + # via jupyter-events +pytz==2024.1 + # via pandas +pywavelets==1.6.0 + # via scikit-image +pyyaml==6.0.1 + # via bokeh + # via dask + # via distributed + # via jupyter-cache + # via jupyter-events + # via myst-nb + # via myst-parser + # via pre-commit + # via pybtex +pyzmq==26.0.3 + # via ipykernel + # via jupyter-client + # via jupyter-server +readme-renderer==44.0 + # via twine +referencing==0.35.1 + # via jsonschema + # via jsonschema-specifications + # via jupyter-events +requests==2.32.3 + # via ome-zarr + # via requests-toolbelt + # via sphinx + # via twine +requests-toolbelt==1.0.0 + # via twine +rfc3339-validator==0.1.4 + # via jsonschema + # via jupyter-events +rfc3986==2.0.0 + # via twine +rfc3986-validator==0.1.1 + # via jsonschema + # via jupyter-events +rich==13.7.1 + # via twine +rpds-py==0.19.0 + # via jsonschema + # via referencing +s3fs==2024.6.1 + # via fsspec +scanpy==1.10.2 + # via vitessce +scikit-image==0.20.0 + # via ome-zarr +scikit-learn==1.5.1 + # via pynndescent + # via scanpy + # via umap-learn +scipy==1.14.0 + # via anndata + # via dask-image + # via pynndescent + # via scanpy + # via scikit-image + # via scikit-learn + # via statsmodels + # via umap-learn + # via vitessce +seaborn==0.13.2 + # via scanpy +send2trash==1.8.3 + # via jupyter-server +session-info==1.0.0 + # via scanpy + # via tonic-vitessce +setuptools==70.3.0 + # via tonic-vitessce +simpervisor==1.0.0 + # via jupyter-server-proxy +six==1.16.0 + # via asttokens + # via bleach + # via patsy + # via pybtex + # via python-dateutil + # via rfc3339-validator +slicerator==1.1.0 + # via pims +sniffio==1.3.1 + # via anyio +snowballstemmer==2.2.0 + # via sphinx +sortedcontainers==2.4.0 + # via distributed +soupsieve==2.5 + # via beautifulsoup4 +sphinx==7.3.7 + # via myst-nb + # via myst-parser + # via pydata-sphinx-theme + # via sphinx-autodoc-typehints + # via sphinx-book-theme + # via sphinx-copybutton + # via sphinxcontrib-bibtex + # via sphinxext-opengraph + # via tonic-vitessce +sphinx-autodoc-typehints==2.2.2 + # via tonic-vitessce +sphinx-book-theme==1.1.3 + # via tonic-vitessce +sphinx-copybutton==0.5.2 + # via tonic-vitessce +sphinxcontrib-applehelp==1.0.8 + # via sphinx +sphinxcontrib-bibtex==2.6.2 + # via tonic-vitessce +sphinxcontrib-devhelp==1.0.6 + # via sphinx +sphinxcontrib-htmlhelp==2.0.5 + # via sphinx +sphinxcontrib-jsmath==1.0.1 + # via sphinx +sphinxcontrib-qthelp==1.0.7 + # via sphinx +sphinxcontrib-serializinghtml==1.1.10 + # via sphinx +sphinxext-opengraph==0.9.1 + # via tonic-vitessce +sqlalchemy==2.0.31 + # via jupyter-cache +stack-data==0.6.3 + # via ipython +starlette==0.14.0 + # via vitessce +statsmodels==0.14.2 + # via scanpy +stdlib-list==0.10.0 + # via session-info +tabulate==0.9.0 + # via jupyter-cache +tblib==3.0.0 + # via distributed +terminado==0.18.1 + # via jupyter-server + # via jupyter-server-terminals +threadpoolctl==3.5.0 + # via scikit-learn +tifffile==2020.10.1 + # via dask-image + # via generate-tiff-offsets + # via pims + # via scikit-image + # via vitessce +tinycss2==1.3.0 + # via nbconvert +toolz==0.12.1 + # via dask + # via distributed + # via ome-zarr + # via partd +tornado==6.4.1 + # via bokeh + # via distributed + # via ipykernel + # via jupyter-client + # via jupyter-server + # via jupyter-server-proxy + # via terminado +tqdm==4.66.4 + # via scanpy + # via umap-learn + # via vitessce +traitlets==5.14.3 + # via comm + # via ipykernel + # via ipython + # via ipywidgets + # via jupyter-client + # via jupyter-core + # via jupyter-events + # via jupyter-server + # via jupyter-server-proxy + # via matplotlib-inline + # via nbclient + # via nbconvert + # via nbformat +twine==5.1.1 + # via tonic-vitessce +types-python-dateutil==2.9.0.20240316 + # via arrow +typing-extensions==4.12.2 + # via anywidget + # via ipython + # via myst-nb + # via pydata-sphinx-theme + # via sqlalchemy +tzdata==2024.1 + # via pandas +ujson==5.10.0 + # via vitessce +umap-learn==0.5.6 + # via scanpy +uri-template==1.3.0 + # via jsonschema +urllib3==2.2.2 + # via botocore + # via distributed + # via requests + # via twine +uvicorn==0.30.1 + # via vitessce +virtualenv==20.26.3 + # via pre-commit +vitessce==3.2.7 + # via tonic-vitessce +wcwidth==0.2.13 + # via prompt-toolkit +webcolors==24.6.0 + # via jsonschema +webencodings==0.5.1 + # via bleach + # via tinycss2 +websocket-client==1.8.0 + # via jupyter-server +widgetsnbextension==4.0.11 + # via ipywidgets +wrapt==1.16.0 + # via aiobotocore +xyzservices==2024.6.0 + # via bokeh +yarl==1.9.4 + # via aiohttp +zarr==2.18.2 + # via ome-zarr + # via vitessce +zict==3.0.0 + # via distributed +zipp==3.19.2 + # via importlib-metadata diff --git a/scripts/ingest_data_for_vitessce.ipynb b/scripts/ingest_data_for_vitessce.ipynb new file mode 100644 index 0000000..c961aec --- /dev/null +++ b/scripts/ingest_data_for_vitessce.ipynb @@ -0,0 +1,563 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Data Ingestion, FOV Filtering, and ZARR File Generation" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "The autoreload extension is already loaded. To reload it, use:\n", + " %reload_ext autoreload\n" + ] + } + ], + "source": [ + "%load_ext autoreload\n", + "%autoreload 2" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "\n", + "import buckaroo # type: ignore # noqa: F401\n", + "import natsort as ns\n", + "import numpy as np\n", + "import pandas as pd\n", + "from tqdm.auto import tqdm\n", + "\n", + "import tonic_vitessce as tv" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## File / Data Setup" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [], + "source": [ + "cell_table_path = Path(\n", + " \"/Volumes/Shared/Noah Greenwald/TONIC_Cohort/analysis_files/combined_cell_table_normalized_cell_labels_updated.csv\"\n", + ")\n", + "cell_compartment_table_path = Path(\n", + " \"/Volumes/Shared/Noah Greenwald/TONIC_Cohort/intermediate_files/mask_dir/cell_annotation_mask.csv\"\n", + ")\n", + "harmonized_metadata_path = Path(\"/Volumes/Shared/Noah Greenwald/TONIC_Cohort/analysis_files/harmonized_metadata.csv\")\n", + "fov_dir = Path(\"/Volumes/Shared/Noah Greenwald/TONIC_Cohort/image_data/samples\")\n", + "cell_compartment_dir = Path(\n", + " \"/Volumes/Shared/Noah Greenwald/TONIC_Cohort/intermediate_files/mask_dir/individual_masks_no_tagg_tls\"\n", + ")\n", + "segmentation_dir = Path(\"/Volumes/Shared/Noah Greenwald/TONIC_Cohort/segmentation_data/deepcell_output\")\n", + "vitessce_ingestible_data_dir = Path(\"../data/vitessce_ingestable\")" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [], + "source": [ + "# Constants\n", + "rng = np.random.default_rng(12345)\n", + "N_FOVS = 10" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Select FOVs\n", + "\n", + "\n", + "Select FOVs by filtering to only include those with associated MIBI Data.\n", + "Subset those FOVs by only including the following time points:\n", + "- *baseline*\n", + "- *primary*\n", + "- *pre_nivo*\n", + "- *on_nivo*\n", + "\n", + "\n", + "Use the Harmonized Metadata file." + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "190e6891d57244b3b24d35e6b8e47873", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "BuckarooWidget(buckaroo_options={'sampled': ['random'], 'auto_clean': ['aggressive', 'conservative'], 'post_pr…" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "harmonized_metadata_df = pd.read_csv(harmonized_metadata_path)\n", + "harmonized_metadata_df" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [], + "source": [ + "timepoints = [\"baseline\", \"primary\", \"pre_nivo\", \"on_nivo\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [], + "source": [ + "mibi_data = (\n", + " harmonized_metadata_df.query(\"MIBI_data_generated == True\")\n", + " .sort_values(by=\"fov\", key=ns.natsort_keygen())\n", + " .reset_index(drop=True)\n", + " .drop(columns=[\"MIBI_data_generated\"])\n", + " .pipe(lambda df: df[df[\"Timepoint\"].isin(timepoints)])\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [], + "source": [ + "sample_fovs_df = mibi_data.sample(n=N_FOVS, random_state=rng)" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [], + "source": [ + "fovs_subset = sample_fovs_df[\"fov\"].tolist()" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [], + "source": [ + "fovs_subset = ns.natsorted(\n", + " [\n", + " \"TONIC_TMA7_R4C6\",\n", + " \"TONIC_TMA18_R2C3\",\n", + " \"TONIC_TMA9_R4C6\",\n", + " \"TONIC_TMA14_R7C6\",\n", + " \"TONIC_TMA15_R10C1\",\n", + " \"TONIC_TMA5_R5C1\",\n", + " \"TONIC_TMA15_R7C2\",\n", + " \"TONIC_TMA5_R1C2\",\n", + " \"TONIC_TMA17_R12C4\",\n", + " \"TONIC_TMA23_R10C1\",\n", + " ]\n", + ")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Channels" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "7ef7a004932640b8b4049d36be2dba3a", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "BuckarooWidget(buckaroo_options={'sampled': ['random'], 'auto_clean': ['aggressive', 'conservative'], 'post_pr…" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "harmonized_metadata_df[harmonized_metadata_df[\"fov\"].isin(fovs_subset)].sort_values(by=\"fov\", key=ns.natsort_keygen())[\n", + " [\"fov\", \"Timepoint\", \"Localization\"]\n", + "]" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "metadata": {}, + "outputs": [], + "source": [ + "channels = [\n", + " # \"Au\",\n", + " \"Calprotectin\",\n", + " \"CD11c\",\n", + " \"CD14\",\n", + " \"CD163\",\n", + " \"CD20\",\n", + " \"CD3\",\n", + " \"CD31\",\n", + " # \"CD38\",\n", + " \"CD4\",\n", + " \"CD45\",\n", + " # \"CD45RB\",\n", + " # \"CD45RO\",\n", + " \"CD56\",\n", + " # \"CD57\",\n", + " \"CD68\",\n", + " # \"CD69\",\n", + " \"CD8\",\n", + " # \"chan_115\",\n", + " # \"chan_141\",\n", + " # \"chan_39\",\n", + " # \"chan_45\",\n", + " # \"chan_48\",\n", + " \"ChyTr\",\n", + " \"CK17\",\n", + " \"Collagen1\",\n", + " \"ECAD\",\n", + " \"FAP\",\n", + " # \"Fe\",\n", + " \"Fibronectin\",\n", + " \"FOXP3\",\n", + " # \"GLUT1\",\n", + " \"H3K27me3\",\n", + " \"H3K9ac\",\n", + " # \"HLA1\",\n", + " \"HLADR\",\n", + " # \"IDO\",\n", + " # \"Ki67\",\n", + " # \"LAG3\",\n", + " # \"Noodle\",\n", + " # \"PD1\",\n", + " # \"PDL1\",\n", + " \"SMA\",\n", + " # \"TBET\",\n", + " # \"TCF1\",\n", + " # \"TIM3\",\n", + " \"Vim\",\n", + "]\n", + "used_channels = [\n", + " \"CD3\",\n", + " \"CD4\",\n", + " \"CD8\",\n", + " \"CD11c\",\n", + " \"CD14\",\n", + " \"CD20\",\n", + " \"CD31\",\n", + " \"CD45\",\n", + " \"CD56\",\n", + " \"CD68\",\n", + " \"CD163\",\n", + " \"CK17\",\n", + " \"Calprotectin\",\n", + " \"ChyTr\",\n", + " \"Collagen1\",\n", + " \"ECAD\",\n", + " \"FAP\",\n", + " \"FOXP3\",\n", + " \"Fibronectin\",\n", + " \"H3K9ac\",\n", + " \"H3K27me3\",\n", + " \"HLADR\",\n", + " \"SMA\",\n", + " \"Vim\",\n", + "]\n", + "channel_color_map = {\n", + " \"CD3\": \"cf6275\", # rose\n", + " \"CD4\": \"c65102\", # dark orange\n", + " \"CD8\": \"acbf69\", # light olive\n", + " \"CD11c\": \"c79fef\", # lavender\n", + " \"CD14\": \"ae7181\", # mauve\n", + " \"CD20\": \"c20078\", # magenta\n", + " \"CD31\": \"610023\", # burgundy\n", + " \"CD45\": \"d5b60a\", # dark yellow\n", + " \"CD56\": \"a83c09\", # rust\n", + " \"CD68\": \"ffffc2\", # cream\n", + " \"CD163\": \"650021\", # maroon\n", + " \"CK17\": \"05696b\", # dark aqua\n", + " \"Calprotectin\": \"f97306\", # orange\n", + " \"ChyTr\": \"ca6641\", # terracotta\n", + " \"Collagen1\": \"028f1e\", # emerald green\n", + " \"ECAD\": \"ffffd4\", # eggshell\n", + " \"FAP\": \"ffb16d\", # apricot\n", + " \"FOXP3\": \"bb3f3f\", # dull red\n", + " \"Fibronectin\": \"de0c62\", # cerise\n", + " \"H3K9ac\": \"0485d1\", # cerulean\n", + " \"H3K27me3\": \"047495\", # sea blue\n", + " \"HLADR\": \"feb308\", # amber\n", + " \"SMA\": \"a6814c\", # coffee\n", + " \"Vim\": \"c9ae74\", # sandstone\n", + "}" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Convert Cell Table to AnnData Tables" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [], + "source": [ + "# cell_table_df = pd.read_csv(cell_table_path, usecols=[*tv.WholeCellTableColumns])\n", + "cell_table_df = pd.read_csv(cell_table_path)" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "38b80b1b07e446e5a1bffba66c87213f", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "BuckarooWidget(buckaroo_options={'sampled': ['random'], 'auto_clean': ['aggressive', 'conservative'], 'post_pr…" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "cell_table_df" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [], + "source": [ + "cell_compartment_table_df = pd.read_csv(cell_compartment_table_path)" + ] + }, + { + "cell_type": "code", + "execution_count": 56, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "9ffd4dbe72224b86bd3bb54a1eab81c9", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + " 0%| | 0/10 [00:00 Iterator[str]: + return iter(self.var_columns + self.obs_columns + self.obsm_columns) + + +@dataclass +class NuclearTableConstants: + """Constants for the nuclear table""" + + var_columns: list[str] = field(default_factory=lambda: [f"{x}_nuclear" for x in VAR]) + obs_columns: list[str] = field(default_factory=lambda: [f"{x}_nuclear" for x in OBS]) + obsm_columns: list[str] = field(default_factory=lambda: [f"{x}_nuclear" for x in OBSM]) + + def __iter__(self) -> Iterator[str]: + return iter(self.var_columns + self.obs_columns + self.obsm_columns) + + +@dataclass +class SegmentationMasksConstants: + """Constants for the segmentation masks""" + + cell_segmentation: list[str] = field(default_factory=lambda: CELL_SEGMENTATION_MASKS) + compartments: list[str] = field(default_factory=lambda: COMPARTMENT_MASKS) + + def __iter__(self) -> Iterator[str]: + return iter(self.cell_segmentation + self.compartments) diff --git a/src/tonic_vitessce/pl/__init__.py b/src/tonic_vitessce/pl/__init__.py new file mode 100644 index 0000000..c2315dd --- /dev/null +++ b/src/tonic_vitessce/pl/__init__.py @@ -0,0 +1 @@ +from .basic import BasicClass, basic_plot diff --git a/src/tonic_vitessce/pl/basic.py b/src/tonic_vitessce/pl/basic.py new file mode 100644 index 0000000..ed390ef --- /dev/null +++ b/src/tonic_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/tonic_vitessce/pp/__init__.py b/src/tonic_vitessce/pp/__init__.py new file mode 100644 index 0000000..5e7e293 --- /dev/null +++ b/src/tonic_vitessce/pp/__init__.py @@ -0,0 +1 @@ +from .basic import basic_preproc diff --git a/src/tonic_vitessce/pp/basic.py b/src/tonic_vitessce/pp/basic.py new file mode 100644 index 0000000..5db1ec0 --- /dev/null +++ b/src/tonic_vitessce/pp/basic.py @@ -0,0 +1,17 @@ +from anndata import AnnData + + +def basic_preproc(adata: AnnData) -> int: + """Run a basic preprocessing on the AnnData object. + + Parameters + ---------- + adata + The AnnData object to preprocess. + + Returns + ------- + Some integer value. + """ + print("Implement a preprocessing function here.") + return 0 diff --git a/src/tonic_vitessce/tl/__init__.py b/src/tonic_vitessce/tl/__init__.py new file mode 100644 index 0000000..1f71fa7 --- /dev/null +++ b/src/tonic_vitessce/tl/__init__.py @@ -0,0 +1,3 @@ +from .basic import convert_fov_to_zarr, convert_segmentation_to_zarr, extract_fov_table, optimize_and_write_adata + +__all__ = ["extract_fov_table", "optimize_and_write_adata", "convert_fov_to_zarr", "convert_segmentation_to_zarr"] diff --git a/src/tonic_vitessce/tl/basic.py b/src/tonic_vitessce/tl/basic.py new file mode 100644 index 0000000..88b6cdf --- /dev/null +++ b/src/tonic_vitessce/tl/basic.py @@ -0,0 +1,197 @@ +from pathlib import Path +from typing import Literal + +import anndata as ad +import natsort as ns +import numpy as np +import pandas as pd +from tifffile import imread +from vitessce.data_utils import VAR_CHUNK_SIZE, multiplex_img_to_ome_zarr, optimize_adata, optimize_arr +from zarr import consolidate_metadata + +from tonic_vitessce.core import SegmentationMasks, WholeCellTableColumns + + +def extract_fov_table(cell_table_df: pd.DataFrame, cell_compartment_df: pd.DataFrame, fov: str) -> pd.DataFrame: + """Extracts a given FOV from the Cell Table. + + Parameters + ---------- + cell_table_df : pd.DataFrame + The Cell Table DataFrame. + cell_compartment_df : pd.DataFrame + The Cell Compartment DataFrame + fov : str + The field of view to extract. + + Returns + ------- + pd.DataFrame + The cell-wise data associated to a given `fov`. + """ + fov_ct: pd.DataFrame = ( + cell_table_df[cell_table_df["fov"] == fov] + .pipe( + lambda df: df.astype( + { + "label": "int", + } + ) + ) + .merge(right=cell_compartment_df, on=["fov", "label"], how="left") + .rename(columns={"mask_name": "compartment"}) + .pipe( + lambda df: df.astype( + { + **{ + c: "object" + for c in ["fov", "compartment", "cell_meta_cluster", "cell_cluster", "cell_cluster_broad"] + }, + "area": "int", + "convex_area": "int", + "num_concavities": "int", + **{c: "int" for c in WholeCellTableColumns.obsm_columns}, + }, + ) + ) + .sort_values(by="label") + .reset_index(drop=True) + .pipe(lambda df: df.set_index(pd.Index(list(range(1, len(df) + 1))))) + ) + return fov_ct + + +def optimize_and_write_adata( + fov_df: pd.DataFrame, + fov: str, + segmentation_dir: Path, + vitessce_fovs_path: Path, + var_cols: list[str], + obs_cols: list[str], +): + """Creates the `AnnData` object for a given FOV, optimizes it and writes it to disk. + + Parameters + ---------- + fov_df : pd.DataFrame + The cell-wise data associated to a given `fov`. + fov : str + The `fov` name. + var_type: Literal["whole_cell"] | Literal["nuclear"] + Either the whole_cell mask, or the nuclear mask + vitessce_fovs_path : Path + The output directory to place the FOVs. + """ + seg_mask = imread(segmentation_dir / f"{fov}_whole_cell.tiff").astype("int").squeeze() + n_unique_labels = len(np.unique(seg_mask)) + + whole_cell_df = fov_df[fov_df["label"].isin(range(1, n_unique_labels + 1))] + + fov_adata = ad.AnnData( + X=whole_cell_df[var_cols], + obs=whole_cell_df[obs_cols], + obsm={"spatial": whole_cell_df[WholeCellTableColumns.obsm_columns].to_numpy()}, + ) + + fov_optimized_adata = optimize_adata(adata=fov_adata, optimize_X=True) + + if not (vitessce_fov_path := vitessce_fovs_path / fov).exists(): + vitessce_fovs_path.mkdir(parents=True, exist_ok=True) + + fov_optimized_adata.strings_to_categoricals() + + fov_adata_zarr_store = vitessce_fov_path / "whole_cell_table.anndata.zarr" + + fov_optimized_adata.write_zarr(store=fov_adata_zarr_store, chunks=[fov_optimized_adata.shape[0], VAR_CHUNK_SIZE]) + consolidate_metadata(store=fov_adata_zarr_store) + + +def convert_fov_to_zarr( + fovs_dir: Path, + fov: str, + vitessce_fovs_path: Path, + channels: list[str] | None = None, + channel_colormap: dict | None = None, +) -> None: + """Converts the field of view (a folder of TIFFs) into a Zarr Store. + + Parameters + ---------- + fovs_dir : Path + The directory to all the FOVs. + fov : str + The fov to convert. + vitessce_fovs_path : Path + The output directory to place the fovs. + channels : list[str] | None, optional + The channels to convert, by default `None` which will use all channels + channel_colormap : dict | None, optional + A colormap per-channel, by default `None` which auto-assigns the colors. + """ + if channels is None: + channels = WholeCellTableColumns.var_columns + channel_paths = [fovs_dir / fov / f"{c}.tiff" for c in ns.natsorted(channels)] + + fov_img = optimize_arr(arr=imread(files=channel_paths)) + + if not (vitessce_fov_path := vitessce_fovs_path / fov).exists(): + vitessce_fovs_path.mkdir(parents=True, exist_ok=True) + + multiplex_img_to_ome_zarr( + img_arr=fov_img, + channel_names=channels, + img_name=fov, + axes="cyx", + chunks=(1, 256, 256), + channel_colors=channel_colormap, + output_path=vitessce_fov_path / "image.ome.zarr", + ) + + +def convert_segmentation_to_zarr( + fov: str, + segmentation_mask_type: Literal["cell_segmentation"] | Literal["compartment"], + segmentation_dir: Path, + vitessce_fovs_path: Path, +) -> None: + """Converts TIFF cell segmentation masks or compartment segmentation masks to OME-ZARR files. + + Parameters + ---------- + fov : str + The field of view. + segmentation_mask_type : Literal["cell_segmentation"] | Literal["compartment"] + The type of segmentation mask. + segmentation_dir : Path + The directory containing the specific segmentation masks. + vitessce_fovs_path : Path + The output directory to place the segmentation masks. + + """ + if segmentation_mask_type == "cell_segmentation": + segmentation_masks = ns.natsorted( + [(segmentation_dir / f"{fov}_{c}.tiff") for c in SegmentationMasks.cell_segmentation] + ) + elif segmentation_mask_type == "compartment": + segmentation_masks = ns.natsorted( + [(segmentation_dir / fov / f"{c}.tiff") for c in SegmentationMasks.compartments] + ) + + segmentation_array = optimize_arr(arr=imread(files=segmentation_masks).astype("int").squeeze()) + if not (vitessce_fov_path := vitessce_fovs_path / fov).exists(): + vitessce_fovs_path.mkdir(parents=True, exist_ok=True) + + channel_names = ( + SegmentationMasks.compartments + if segmentation_mask_type == "compartment" + else SegmentationMasks.cell_segmentation + ) + multiplex_img_to_ome_zarr( + img_arr=segmentation_array, + channel_names=channel_names, + img_name=f"{fov}_{segmentation_mask_type}", + axes="cyx", + chunks=(1, 256, 256), + channel_colors=None, + output_path=vitessce_fov_path / f"{segmentation_mask_type}.ome.zarr", + ) diff --git a/tests/test_basic.py b/tests/test_basic.py new file mode 100644 index 0000000..f081cd5 --- /dev/null +++ b/tests/test_basic.py @@ -0,0 +1,12 @@ +import pytest + +import tonic_vitessce + + +def test_package_has_version(): + assert tonic_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.