carrot-transform 0.3.3__tar.gz → 0.3.5__tar.gz

carrot_transform-0.3.5/PKG-INFO

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+Metadata-Version: 2.3
+Name: carrot_transform
+Version: 0.3.5
+Summary: 
+Author: anwarfg
+Author-email: 913028+anwarfg@users.noreply.github.com
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: click (>=8.1.7,<9.0.0)
+Requires-Dist: jinja2 (>=3.1.4,<4.0.0)
+Requires-Dist: numpy (<2)
+Requires-Dist: pandas (>=2.2.3,<3.0.0)
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <a href="https://carrot.ac.uk/" target="_blank">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="/images/logo-dark.png">
+    <img alt="Carrot Logo" src="/images/logo-primary.png" width="280"/>
+  </picture>
+  </a>
+</p>
+
+<p align="center">
+
+<a href="https://github.com/Health-Informatics-UoN/carrot-transform/releases">
+  <img src="https://img.shields.io/github/v/release/Health-Informatics-UoN/carrot-transform" alt="Release">
+</a>
+<a href="https://opensource.org/license/mit">
+  <img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License">
+</a>
+</p>
+
+
+<div align="center">
+  <strong>
+  <h2>Streamlined Data Transformation to OMOP</h2><br />
+<a href="https://carrot.ac.uk/">Carrot Transform</a> automates data transformation processes and facilitates the standardisation of datasets to the OMOP vocabulary, simplifying the integration of diverse data sources.
+  <br />
+  </strong>
+</div>
+
+<p align="center">
+  <br />
+  <a href="https://carrot.ac.uk/transform" rel="dofollow"><strong>Explore the docs »</strong></a>
+  <br />
+<br />  
+
+<a href="https://carrot.ac.uk/">Carrot Mapper</a> is a webapp which allows the user to use the metadata (as output by [WhiteRabbit](https://github.com/OHDSI/WhiteRabbit)) from a dataset to produce mapping rules to the OMOP standard, in the JSON format. These can be ingested by [Carrot Transform](https://carrot.ac.uk/transform/quickstart) to perform the mapping of the contents of the dataset to OMOP.
+
+Carrot Transform transforms input data into tab separated variable files of standard OMOP tables, with  concepts mapped according to the provided rules (generated from Carrot Mapper).
+
+## Quick Start for Developers
+
+To have the project up and running, please follow the [Quick Start Guide](https://carrot.ac.uk/transform/quickstart).
+
+## Release Procedure 
+To release a new version of `carrot-transform` follow these steps: 
+
+### 1. Prepare the repository
+  - First ensure that repository is clean and all required changes have been merged. 
+  - Pull the latest changes from `main` with `git pull origin main`. 
+
+### 2. Create a release branch 
+
+- Now create a new feature branch name `release/v<NEW-VERSION>` (e.g. `release/v0.2.0`). 
+
+### 3. Update the version number 
+- Use poetry to bump the version. For example, for a minor version update invoke: 
+```bash
+poetry version minor 
+```
+- Commit and push the changes (to the release feature branch):
+```bash 
+NEW_VERSION=$(poetry version -s)
+git add pyproject.toml
+git commit -m "Bump version to $NEW_VERSION"
+git push --set-upstream origin release/v$NEW_VERSION
+```
+
+### 4. Create pull request 
+- Open a pull request from `release/v$NEW_VERSION` to `main` and await approval.
+### 5. Merge and tag 
+- After approval merge the the feature branch to `main`. 
+- Checkout to `main`, pull updates, and create a tag corresponding to the new version number. 
+```bash 
+git checkout main
+git pull origin main
+git tag -a "$NEW_VERSION" -m "Release $NEW_VERSION"
+git push origin "$NEW_VERSION"
+```
+
+### 6. Create a release
+- We must now link the tag to a release in the GitHub repository. To do this from the command line first install GitHub command line tools `gh` and then invoke: 
+```bash 
+gh release create "$TAG" --title "$TAG" --notes "Release for $VERSION"
+```
+
+- Alternatively, follow the instructions in the [GitHub documentation](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository) to manually create a release. 
+## License
+
+This repository's source code is available under the [MIT license](LICENSE).

carrot_transform-0.3.5/README.md

@@ -0,0 +1,88 @@
+<p align="center">
+  <a href="https://carrot.ac.uk/" target="_blank">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="/images/logo-dark.png">
+    <img alt="Carrot Logo" src="/images/logo-primary.png" width="280"/>
+  </picture>
+  </a>
+</p>
+
+<p align="center">
+
+<a href="https://github.com/Health-Informatics-UoN/carrot-transform/releases">
+  <img src="https://img.shields.io/github/v/release/Health-Informatics-UoN/carrot-transform" alt="Release">
+</a>
+<a href="https://opensource.org/license/mit">
+  <img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License">
+</a>
+</p>
+
+
+<div align="center">
+  <strong>
+  <h2>Streamlined Data Transformation to OMOP</h2><br />
+<a href="https://carrot.ac.uk/">Carrot Transform</a> automates data transformation processes and facilitates the standardisation of datasets to the OMOP vocabulary, simplifying the integration of diverse data sources.
+  <br />
+  </strong>
+</div>
+
+<p align="center">
+  <br />
+  <a href="https://carrot.ac.uk/transform" rel="dofollow"><strong>Explore the docs »</strong></a>
+  <br />
+<br />  
+
+<a href="https://carrot.ac.uk/">Carrot Mapper</a> is a webapp which allows the user to use the metadata (as output by [WhiteRabbit](https://github.com/OHDSI/WhiteRabbit)) from a dataset to produce mapping rules to the OMOP standard, in the JSON format. These can be ingested by [Carrot Transform](https://carrot.ac.uk/transform/quickstart) to perform the mapping of the contents of the dataset to OMOP.
+
+Carrot Transform transforms input data into tab separated variable files of standard OMOP tables, with  concepts mapped according to the provided rules (generated from Carrot Mapper).
+
+## Quick Start for Developers
+
+To have the project up and running, please follow the [Quick Start Guide](https://carrot.ac.uk/transform/quickstart).
+
+## Release Procedure 
+To release a new version of `carrot-transform` follow these steps: 
+
+### 1. Prepare the repository
+  - First ensure that repository is clean and all required changes have been merged. 
+  - Pull the latest changes from `main` with `git pull origin main`. 
+
+### 2. Create a release branch 
+
+- Now create a new feature branch name `release/v<NEW-VERSION>` (e.g. `release/v0.2.0`). 
+
+### 3. Update the version number 
+- Use poetry to bump the version. For example, for a minor version update invoke: 
+```bash
+poetry version minor 
+```
+- Commit and push the changes (to the release feature branch):
+```bash 
+NEW_VERSION=$(poetry version -s)
+git add pyproject.toml
+git commit -m "Bump version to $NEW_VERSION"
+git push --set-upstream origin release/v$NEW_VERSION
+```
+
+### 4. Create pull request 
+- Open a pull request from `release/v$NEW_VERSION` to `main` and await approval.
+### 5. Merge and tag 
+- After approval merge the the feature branch to `main`. 
+- Checkout to `main`, pull updates, and create a tag corresponding to the new version number. 
+```bash 
+git checkout main
+git pull origin main
+git tag -a "$NEW_VERSION" -m "Release $NEW_VERSION"
+git push origin "$NEW_VERSION"
+```
+
+### 6. Create a release
+- We must now link the tag to a release in the GitHub repository. To do this from the command line first install GitHub command line tools `gh` and then invoke: 
+```bash 
+gh release create "$TAG" --title "$TAG" --notes "Release for $VERSION"
+```
+
+- Alternatively, follow the instructions in the [GitHub documentation](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository) to manually create a release. 
+## License
+
+This repository's source code is available under the [MIT license](LICENSE).

carrot_transform-0.3.5/carrottransform/_version.py

@@ -0,0 +1,6 @@
+from importlib.metadata import version
+
+try:
+    __version__ = version("carrot_transform")  # Defined in the pyproject.toml 
+except Exception:
+    __version__ = "unknown"