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fix: require current setuptools version in build-system, update docs (#…
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tedil authored Jan 24, 2025
1 parent 4ad4f0f commit 261944b
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41 changes: 26 additions & 15 deletions README.md
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@@ -9,33 +9,44 @@ Tooling for connecting GitLab, pipelines, and SODAR at CUBI.

## Getting Started

Clone CUBI-TK, create a conda environment and install using [`uv`](https://docs.astral.sh/uv/).
Clone CUBI-TK, create a conda environment and install using pip or [`uv`](https://docs.astral.sh/uv/).

Checkout the repository and create a conda environment:
```bash
$ git clone git@github.com:bihealth/cubi-tk.git
$ conda env create -n cubi-tk -f environment.yaml
$ conda activate cubi-tk
$ cd cubi-tk
$ uv python pin 3.12
$ uv sync
$ uv pip install -e .
# or, if you need snappy kickoff:
#$ GIT_LFS_SKIP_SMUDGE=1 uv pip install -e '.[snappy]'
git clone git@github.com:bihealth/cubi-tk.git
conda env create -n cubi-tk -f environment.yaml
conda activate cubi-tk
cd cubi-tk
```

Install the package using pip:
```bash
$ pip install -e .
```

Or using `uv`:
```bash
# if not using conda: `uv python install 3.12`
uv python pin 3.12
uv sync
uv pip install -e .
# alternatively, if you need snappy kickoff:
# GIT_LFS_SKIP_SMUDGE=1 uv pip install -e '.[snappy]'
```

## Building the Manual

```bash
$ uv sync --all-extras --group docs
$ cd docs_manual
$ uv run make clean html
$ xdg-open _build/html/index.html
uv sync --all-extras --group docs
cd docs_manual
uv run make clean html
xdg-open _build/html/index.html
```

## Argument Completion

```bash
$ cat >>~/.bashrc <<"EOF"
cat >>~/.bashrc <<"EOF"
eval "$(register-python-argcomplete cubi-tk)"
EOF
```
43 changes: 30 additions & 13 deletions docs_manual/installation.rst
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@@ -4,32 +4,49 @@
Installation
============

Clone CUBI-TK, create a conda environment and install using [`uv`](https://docs.astral.sh/uv/).
Clone CUBI-TK, create a conda environment and install using pip or `uv`_.

.. _uv: https://docs.astral.sh/uv/

Checkout the repository and create a conda environment:

.. code-block:: bash
git clone git@github.com:bihealth/cubi-tk.git
conda env create -n cubi-tk -f environment.yaml
conda activate cubi-tk
cd cubi-tk
Install the package using pip:

.. code-block:: bash
$ git clone git@github.com:bihealth/cubi-tk.git
$ conda env create -n cubi-tk -f environment.yaml
$ conda activate cubi-tk
$ cd cubi-tk
$ uv python pin 3.12
$ uv sync
$ uv pip install -e .
# or, if you need snappy kickoff:
#$ GIT_LFS_SKIP_SMUDGE=1 uv pip install -e '.[snappy]'
pip install -e .
Or using `uv`_:

.. code-block:: bash
# if not using conda: `uv python install 3.12`
uv python pin 3.12
uv sync
uv pip install -e .
# alternatively, if you need snappy kickoff:
# GIT_LFS_SKIP_SMUDGE=1 uv pip install -e '.[snappy]'
Run tests
---------

.. code-block:: bash
$ uv run make pytest
uv run make pytest
Build manual
------------

.. code-block:: bash
$ cd docs_manual
$ uv run make clean html
cd docs_manual
uv run make clean html
2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,5 +1,5 @@
[build-system]
requires = ["setuptools", "wheel"]
requires = ["setuptools>=75.8.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]

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