Metadata-Version: 2.4
Name: clinvar-build
Version: 0.1.1
Summary: Building a local copy of clinvar and querying these data
Author-email: A Floriaan Schmidt <floriaanschmidt@gmail.com>
License-Expression: GPL-3.0-or-later
Project-URL: Homepage, https://gitlab.com/SchmidtAF/clinvar-build
Project-URL: Documentation, https://schmidtaf.gitlab.io/clinvar-build/
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: <3.14,>=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: lxml>=5
Requires-Dist: pandas>=3.0.0
Provides-Extra: dev
Requires-Dist: python-build; extra == "dev"
Requires-Dist: twine; extra == "dev"
Requires-Dist: setuptools; extra == "dev"
Requires-Dist: wheel; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: pytest>=6; extra == "dev"
Requires-Dist: pytest-mock>=3; extra == "dev"
Requires-Dist: pytest-dependency>=0.5; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: bump2version>=1; extra == "dev"
Requires-Dist: codespell; extra == "dev"
Requires-Dist: jupyter; extra == "dev"
Requires-Dist: sphinx; extra == "dev"
Requires-Dist: sphinx-rtd-theme; extra == "dev"
Requires-Dist: sphinx-bootstrap-theme; extra == "dev"
Requires-Dist: furo; extra == "dev"
Requires-Dist: myst-parser; extra == "dev"
Requires-Dist: notebook; extra == "dev"
Requires-Dist: nbsphinx; extra == "dev"
Requires-Dist: nbsphinx-link; extra == "dev"
Requires-Dist: sphinx-argparse; extra == "dev"
Requires-Dist: numpydoc; extra == "dev"
Requires-Dist: docutils<0.21; extra == "dev"
Dynamic: license-file

# Building and querying clinvar
__version__: `0.1.1`

Clinvar-build is a python module to build a SQLite database using the 
publicly available XML data from Clinvar. 
The module is slipped with command line entry points for routine queries.

The documentation for clinvar-build can be found 
[here](https://SchmidtAF.gitlab.io/clinvar-build/). 

## Installation
The package is available on PyPI, and conda, with the latest source code
available on gitlab.

### Installation using PyPI

To install the package from PyPI, run:

```bash
pip install clinvar-build
```

This installs the latest stable release along with its dependencies.

### Installation using conda

A Conda package is maintained in my personal Conda channel.
To install from this channel, run:

```bash
conda install afschmidt::clinvar-build
```

### Installation using gitlab

If you require the latest updates, potentially not yet formally released,
you can install the package directly from GitLab.

First, clone the repository and move into its root directory:

```bash
git clone git@gitlab.com:SchmidtAF/plot-misc.git
cd plot-misc
```

Install the dependencies:

```bash
# From the root of the repository
conda env create --file ./resources/conda/envs/conda_create.yaml
```

To add to an existing environment use:

```bash
# From the root of the repository
conda env update --file ./resources/conda/envs/conda_update.yaml
```

Next the package can be installed:

```bash
make install
```

#### Development
For development work, install the package in editable mode with Git commit
hooks configured:

```bash
make install-dev
```
This command installs the package in editable mode and configures Git commit
hooks, allowing you to run `git pull` to update the repository or switch
branches without reinstalling.

#### Git Hooks Configuration

When setting up a development environment, the `setup-hooks` command 
configures Git hooks to enforce conventional commit message formatting and 
spell check using `codespell`.

To view the commit message format requirements, run:

```bash
./.githooks/commit-msg -help
```

For frequent use, add this function to your shell configuration (`~/.bashrc` 
or `~/.zshrc`):

```bash
commit-format-help() {
    local git_root
    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
    
    if [ -z "$git_root" ]; then
        echo "Error: Not inside a git repository"
        return 1
    fi
    
    local hook_path="$git_root/.githooks/commit-msg"
    
    if [ ! -f "$hook_path" ]; then
        echo "Error: commit-msg hook not found"
        return 1
    fi
    
    "$hook_path" --help
}
```

#### Validating the package

After installing the package from GitLab, you may wish to run the test
suite to confirm everything is working as expected:

```bash
# From the root of the repository
pytest tests
```

## Usage

Please have a look at the examples in 
[resources](https://gitlab.com/SchmidtAF/clinvar-build/-/tree/master/resources)
for some possible recipes. 
