diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index af695c4..c256d00 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -42,8 +42,7 @@ repos: - id: nbstripout exclude: | (?x)( - docs/examples/| - docs/notes/ + docs/examples/ ) - repo: https://github.com/Lucas-C/pre-commit-hooks rev: v1.1.9 diff --git a/README.md b/README.md index 716fc3a..d093047 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ This package provides efficient and scalable handling of flow and mass cytometry - access to the entire [scanpy](https://scanpy.readthedocs.io/en/stable/) workflow functionality - GPU support through [rapids](https://github.com/clara-parabricks/rapids-single-cell-examples) -Follow [https://twitter.com/marenbuettner](https://twitter.com/marenbuettner) to learn about a first public release. +Follow [https://twitter.com/marenbuettner](https://twitter.com/marenbuettner) for updates. For the code enthusiasts: Find our code base on [Github](https://github.com/buettnerlab/pytometry). @@ -32,6 +32,10 @@ or from GitHub: pip install git+https://github.com/buettnerlab/pytometry.git ``` +## Updates + +- October 12th 2022: First public release announcement on [Twitter](https://twitter.com/marenbuettner/status/1580160765201244161?s=20&t=mTBLcUaqKs9eMzEpOWnG0g) + ## Citation Pytometry is currently a pre-print on [bioRxiv](https://www.biorxiv.org/content/10.1101/2022.10.10.511546v1). diff --git a/docs/guides/curate-data.ipynb b/docs/guides/curate-data.ipynb deleted file mode 100644 index 426819a..0000000 --- a/docs/guides/curate-data.ipynb +++ /dev/null @@ -1,60 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "0a9571ac-9c68-437f-ba51-95d06e283cac", - "metadata": {}, - "source": [ - "# How to curate data" - ] - }, - { - "cell_type": "markdown", - "id": "0abfc3c7", - "metadata": {}, - "source": [ - "```{note}\n", - "Any guide notebook is automatically run for testing! If a cell fails, the tests will fail! Try changing the assert statement below to observe.\n", - "\n", - "Note that task notebooks are neither tested, nor being built!\n", - "```" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "bcc0c374-0224-4935-b862-0b013c624375", - "metadata": {}, - "outputs": [], - "source": [ - "assert 1 == 1" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3.9.13 64-bit", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.13" - }, - "vscode": { - "interpreter": { - "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e" - } - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/guides/index.md b/docs/guides/index.md deleted file mode 100644 index 6b4baa7..0000000 --- a/docs/guides/index.md +++ /dev/null @@ -1,9 +0,0 @@ -# Guides - -These are guides on specific problems. The notebooks are executed in CI for testing. - -```{toctree} -:maxdepth: 1 - -curate-data -``` diff --git a/docs/index.md b/docs/index.md index 9d17635..bec4f2b 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,6 @@ ```{include} ../README.md :start-line: 0 -:end-line: 38 +:end-line: 42 ``` ```{toctree} @@ -10,7 +10,5 @@ tutorials/index api examples/index -guides/index -notes/index changelog ``` diff --git a/docs/notes/YYYY-MM-DD-my-design-choice.ipynb b/docs/notes/YYYY-MM-DD-my-design-choice.ipynb deleted file mode 100644 index ada86be..0000000 --- a/docs/notes/YYYY-MM-DD-my-design-choice.ipynb +++ /dev/null @@ -1,43 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "1d7b3b73-75f9-468d-8783-873ebadcab9b", - "metadata": {}, - "source": [ - "# My design choice" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "97ec6631-8473-4a2d-b488-def921bb83de", - "metadata": {}, - "outputs": [], - "source": [ - "import pytometry" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.7" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/notes/index.md b/docs/notes/index.md deleted file mode 100644 index fc82ca3..0000000 --- a/docs/notes/index.md +++ /dev/null @@ -1,11 +0,0 @@ -# Notes - -These are any notes on design decisions, prototypes, background that do not make it into the package. - -```{toctree} -:maxdepth: 1 -:glob: -:reversed: - -* -``` diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md index e3f4053..20023b0 100644 --- a/docs/tutorials/index.md +++ b/docs/tutorials/index.md @@ -1,10 +1,6 @@ # Tutorials -A step-wise pedagogic tutorial including a quickstart. The notebooks get executed in CI for testing. - -Ideally, each feature is explained in a separate clean notebook. - -This makes it both easy for the user to understand the documentation, and for the developer to increase test coverage. +These tutorials show how to use the pytometry functionality. ```{toctree} :maxdepth: 1 diff --git a/pyproject.toml b/pyproject.toml index a03ece7..80d7436 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,7 +41,6 @@ preview = true [tool.pytest.ini_options] testpaths = [ "tests", - "docs/guides", "docs/tutorials", ]