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timsimaging

https://github.com/yinyuezhu/timsimaging

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: YinyueZhu
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 4.31 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

TIMSImaging

Tests PyPI PyPI - Python Version PyPI - License Documentation Status Codecov status Cookiecutter template from @cthoyt Code style: black Contributor Covenant

MALDI-TIMS-TOF raw data visualization and preprocessing

💪 Getting Started

TODO show in a very small amount of space the MOST useful thing your package can do. Make it as short as possible! You have an entire set of docs for later.

🚀 Installation

The most recent code and data can be installed directly from GitHub with:

shell pip install git+https://github.com/Vitek-Lab/https://github.com/YinyueZhu/TIMSImaging.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions The final section of the README is for if you want to get involved by making a code contribution. ### Development Installation To install in development mode, use the following: ```bash git clone git+https://github.com/Vitek-Lab/https://github.com/YinyueZhu/TIMSImaging.git cd https://github.com/YinyueZhu/TIMSImaging pip install -e . ``` ### Updating Package Boilerplate This project uses `cruft` to keep boilerplate (i.e., configuration, contribution guidelines, documentation configuration) up-to-date with the upstream cookiecutter package. Update with the following: ```shell pip install cruft cruft update ``` More info on Cruft's update command is available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project). ### 🥼 Testing After cloning the repository and installing `tox` and `tox-uv` with `pip install tox tox-uv`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/Vitek-Lab/https://github.com/YinyueZhu/TIMSImaging/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell git clone git+https://github.com/Vitek-Lab/https://github.com/YinyueZhu/TIMSImaging.git cd https://github.com/YinyueZhu/TIMSImaging tox -e docs open docs/build/html/index.html ``` The documentation automatically installs the package as well as the `docs` extra specified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins like `texext` can be added there. Additionally, they need to be added to the `extensions` list in [`docs/source/conf.py`](docs/source/conf.py). The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using [this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The [`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration you'll need. You can also set up continuous integration on GitHub to check not only that Sphinx can build the documentation in an isolated environment (i.e., with ``tox -e docs-test``) but also that [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html). #### Configuring ReadTheDocs 1. Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/ 2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository 3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters) 4. Click next, and you're good to go! ### 📦 Making a Release #### Configuring Zenodo [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI to each release of your package. 1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant" next to any organizations you want to enable the integration for, then click the big green "approve" button. This step only needs to be done once. 2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make a new repository, you'll have to come back to this After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate to https://zenodo.org/account/settings/github/repository/Vitek-Lab/https://github.com/YinyueZhu/TIMSImaging to see the DOI for the release and link to the Zenodo record for it. #### Registering with the Python Package Index (PyPI) You only have to do the following steps once. 1. Register for an account on the [Python Package Index (PyPI)](https://pypi.org/account/register) 2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to the "re-send verification email" button 3. 2-Factor authentication is required for PyPI since the end of 2023 (see this [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)). This means you have to first issue account recovery codes, then set up 2-factor authentication 4. Issue an API token from https://pypi.org/manage/account/token #### Configuring your machine's connection to PyPI You have to do the following steps once per machine. Create a file in your home directory called `.pypirc` and include the following: ```ini [distutils] index-servers = pypi testpypi [pypi] username = __token__ password = # This block is optional in case you want to be able to make test releases to the Test PyPI server [testpypi] repository = https://test.pypi.org/legacy/ username = __token__ password = ``` Note that since PyPI is requiring token-based authentication, we use `__token__` as the user, verbatim. If you already have a `.pypirc` file with a `[distutils]` section, just make sure that there is an `index-servers` key and that `pypi` is in its associated list. More information on configuring the `.pypirc` file can be found [here](https://packaging.python.org/en/latest/specifications/pypirc). #### Uploading to PyPI After installing the package in development mode and installing `tox` and `tox-uv` with `pip install tox tox-uv`, the commands for making a new release are contained within the `finish` environment in `tox.ini`. Run the following from the shell: ```shell tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `pyproject.toml`, `CITATION.cff`, `src/timsimaging/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). 4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. 5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use `tox -e bumpversion -- minor` after. #### Releasing on GitHub 1. Navigate to https://github.com/Vitek-Lab/https://github.com/YinyueZhu/TIMSImaging/releases/new to draft a new release 2. Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made 3. Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit 4. Click the big green "Publish Release" button This will trigger Zenodo to assign a DOI to your release as well.

Owner

  • Login: YinyueZhu
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.0.2
message: "If you use this software, please cite it as below."
title: "TIMSImaging"
authors:
  - name: "Yinyue Zhu"
version: 0.0.1-dev
doi:
url: "https://github.com/Vitek-Lab/https://github.com/YinyueZhu/TIMSImaging"

GitHub Events

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  • Push event: 8
Last Year
  • Push event: 8

Dependencies

pyproject.toml pypi
  • alphatims ==1.0.8
  • bokeh ==3.4.0
  • more_itertools *
  • numpy ==1.26.4
  • pandas ==2.2.1
  • scipy ==1.11.4
  • tqdm *
requirements.txt pypi
  • alphatims ==1.0.8
  • bokeh ==3.4.0
  • numpy ==1.26.4
  • pandas ==2.2.1
  • scipy ==1.11.4
src/timsimaging.egg-info/requires.txt pypi
  • alphatims ==1.0.8
  • bokeh ==3.4.0
  • coverage *
  • more_itertools *
  • numpy ==1.26.4
  • pandas ==2.2.1
  • pytest *
  • scipy ==1.11.4
  • sphinx *
  • sphinx-rtd-theme *
  • sphinx_automodapi *
  • tqdm *