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https://github.com/cthoyt/pubmed-downloader

Automate downloading and processing PubMed in bulk

https://github.com/cthoyt/pubmed-downloader

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 (13.6%) to scientific vocabulary

Keywords

pubmed pubmed-api
Last synced: 6 months ago · JSON representation ·

Repository

Automate downloading and processing PubMed in bulk

Basic Info
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 2
  • Releases: 10
Topics
pubmed pubmed-api
Created about 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Contributing Funding License Code of conduct Citation

README.md

PubMed Downloader

Tests PyPI PyPI - Python Version PyPI - License Documentation Status Codecov status Cookiecutter template from @cthoyt Ruff Contributor Covenant

Automate downloading and processing PubMed.

💪 Getting Started

The following will automatically download all 30M+ articles, organize them deterministically on the local filesystem using pystow, process them, cache them as JSON, and iterate over the articles in Pydantic models from newest to oldest:

```python import pubmed_downloader

for article in pubmeddownloader.iterateprocess_articles(): ... ```

The following will automatically download, organize, and structure 600K+ records in the NLM Catalog. A subset of these records correspond to journals.

```python import pubmed_downloader

for catalogrecord in pubmeddownloader.process_catalog(): ... ```

🚀 Installation

The most recent release can be installed from PyPI with uv:

console $ uv pip install pubmed_downloader

or with pip:

console $ python3 -m pip install pubmed_downloader

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

console $ uv pip install git+https://github.com/cthoyt/pubmed-downloader.git

or with pip:

console $ python3 -m pip install git+https://github.com/cthoyt/pubmed-downloader.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: ```console $ git clone git+https://github.com/cthoyt/pubmed-downloader.git $ cd pubmed-downloader $ uv pip install -e . ``` Alternatively, install using pip: ```console $ python3 -m pip install -e . ``` ### 🥼 Testing After cloning the repository and installing `tox` with `uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the unit tests in the `tests/` folder can be run reproducibly with: ```console $ tox -e py ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/cthoyt/pubmed-downloader/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```console $ git clone git+https://github.com/cthoyt/pubmed-downloader.git $ cd pubmed-downloader $ 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).

🧑‍💻 For Maintainers

See maintainer instructions ### Initial Configuration #### Configuring ReadTheDocs [ReadTheDocs](https://readthedocs.org) is an external documentation hosting service that integrates with GitHub's CI/CD. Do the following for each repository: 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! #### Configuring Archival on Zenodo [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI to each release of your package. Do the following for each repository: 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/cthoyt/pubmed-downloader to see the DOI for the release and link to the Zenodo record for it. #### Registering with the Python Package Index (PyPI) The [Python Package Index (PyPI)](https://pypi.org) hosts packages so they can be easily installed with `pip`, `uv`, and equivalent tools. 1. Register for an account [here](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 This only needs to be done once per developer. #### Configuring your machine's connection to PyPI This needs to be done once per machine. ```console $ uv tool install keyring $ keyring set https://upload.pypi.org/legacy/ __token__ $ keyring set https://test.pypi.org/legacy/ __token__ ``` Note that this deprecates previous workflows using `.pypirc`. ### 📦 Making a Release #### Uploading to PyPI After installing the package in development mode and installing `tox` with `uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run the following from the console: ```console $ tox -e finish ``` This script does the following: 1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to switch the version number in the `pyproject.toml`, `CITATION.cff`, `src/pubmed_downloader/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 [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package) 3. Uploads to PyPI using [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package). 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/cthoyt/pubmed-downloader/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. ### 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. Install cruft with either `uv tool install cruft` or `python3 -m pip install cruft` then run: ```console $ cruft update ``` More info on Cruft's update command is available [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).

Owner

  • Name: Charles Tapley Hoyt
  • Login: cthoyt
  • Kind: user
  • Location: Bonn, Germany
  • Company: RWTH Aachen University

Citation (CITATION.cff) 

cff-version: 1.0.2
message: "If you use this software, please cite it as below."
title: "PubMed Downloader"
authors:
  - name: "Charles Tapley Hoyt"
version: 0.0.13-dev
doi:
url: "https://github.com/cthoyt/pubmed-downloader"

GitHub Events

Total
  • Release event: 5
  • Delete event: 4
  • Issue comment event: 3
  • Push event: 39
  • Pull request event: 14
  • Create event: 11
Last Year
  • Release event: 5
  • Delete event: 4
  • Issue comment event: 3
  • Push event: 39
  • Pull request event: 14
  • Create event: 11

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 23 days
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.44
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 23 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.44
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • cthoyt (9)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 911 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 12
  • Total maintainers: 1
pypi.org: pubmed-downloader

Automate downloading and processing PubMed

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 911 Last month
Rankings
Dependent packages count: 9.6%
Average: 31.8%
Dependent repos count: 54.0%
Maintainers (1)
cthoyt
Funding
  • https://github.com/sponsors/cthoyt
Last synced: 6 months ago

Dependencies

.github/workflows/cruft.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • astral-sh/setup-uv v6 composite
  • peter-evans/create-pull-request v4 composite
.github/workflows/tests.yml actions
  • actions/checkout v4 composite
  • astral-sh/setup-uv v3 composite
  • codecov/codecov-action v4 composite
pyproject.toml pypi
  • beautifulsoup4 *
  • click *
  • curies >=0.10.6
  • lxml *
  • pydantic *
  • pydantic_extra_types *
  • pystow *
  • requests *
  • ssslm >=0.0.12
  • tqdm *