carrot-transform 0.3.3__py3-none-any.whl → 0.3.5__py3-none-any.whl

carrot_transform-0.3.5.dist-info/METADATA

@@ -0,0 +1,106 @@
+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.dist-info/RECORD

@@ -0,0 +1,25 @@
+carrottransform/__init__.py,sha256=cQJKTCpG2qmKxDl-VtSWQ3_WFjyzg4u_8nZacWAHFcU,73
+carrottransform/_version.py,sha256=bm7SM-_MN0gstlNsCDO6dAajKcjQD-NxI_xpvfRx0Ts,172
+carrottransform/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+carrottransform/cli/command.py,sha256=xYTaJsVZyRYv0CzUwrh7ZPK8hhGyC3MDfvVYxHcXYSM,508
+carrottransform/cli/subcommands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+carrottransform/cli/subcommands/run.py,sha256=GfRHG_aLoBxuXkpGTTrRmsEcNUjTUB6cl8f1B7lTBt8,28461
+carrottransform/config/OMOPCDM_postgresql_5.3_ddl.sql,sha256=fXrPfdL3IzU5ux55ogsQKjjd-c1KzdP_N2A_JjlY3gk,18084
+carrottransform/config/omop.json,sha256=OT3jvfPjKhjsDnQcQw1OAEOHhQLoHXNxTj_MDwNbYqo,1934
+carrottransform/examples/test/inputs/Covid19_test.csv,sha256=d5t7Lfhkwbfe3Uk2IBqB2ZT5o0h9QaeraC8E5-IMERo,67521
+carrottransform/examples/test/inputs/Demographics.csv,sha256=_ukUTpD4g751sL_mSL3f26T_Edd2kvH-evwm54VfXJI,85237
+carrottransform/examples/test/inputs/Symptoms.csv,sha256=5dvGv16PNJJO_lFc0reRmQbE3m7iWfWajl51JDsqg0M,78447
+carrottransform/examples/test/inputs/covid19_antibody.csv,sha256=SPCpyqpTbVq9987jXZ8AS4FEkrchRMAIYhTQJjfpwfY,98927
+carrottransform/examples/test/inputs/vaccine.csv,sha256=_gcM-SIymyt2Dkkr_zGmQI9keIdmDm-gDI_QvXXLFrY,44037
+carrottransform/examples/test/rules/rules_14June2021.json,sha256=n2OYNFhbx-NLhmqjAad6RsfXjQFknZIgQ7a5uyJF0Co,13226
+carrottransform/tools/__init__.py,sha256=b3JuCwgJVx0rqx5igB8hNNKO0ktlbQjHGHwy-vzpdo0,198
+carrottransform/tools/click.py,sha256=5fxl9zL6piwWMN4cSule0tG90E9g7eFNosoSu1ES1og,471
+carrottransform/tools/file_helpers.py,sha256=_NRswYjqpBBkp4efMBhFf9XIRaqYTw1-jA22usyrbqA,1204
+carrottransform/tools/mappingrules.py,sha256=jvWTLCQoLoCegmLWHPyRSRVOTLejp7LzmFMr-ENmuTU,7121
+carrottransform/tools/metrics.py,sha256=VrcePVGwgHCJqQ1i9Q_KqL6Cv8IbIce2pSRSBth9808,11011
+carrottransform/tools/omopcdm.py,sha256=fcqIub5ud57i-5J3iUvPi2dqfGgyjWnWJTH1djQzq9E,8603
+carrot_transform-0.3.5.dist-info/LICENSE,sha256=pqIiuuTs6Na-oFd10MMsZoZmdfhfUhHeOtQzgzSkcaw,1082
+carrot_transform-0.3.5.dist-info/METADATA,sha256=cW5wfZRrZoai-nnV5k9FVYY8-XGm24Qadu0hYV4P9R8,4206
+carrot_transform-0.3.5.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+carrot_transform-0.3.5.dist-info/entry_points.txt,sha256=z7qmjTl7C8shrYiPBy6yZo9RRZ31Jcvo6L8ntdqbs2E,74
+carrot_transform-0.3.5.dist-info/RECORD,,

{carrot_transform-0.3.3.dist-info → carrot_transform-0.3.5.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.0.1
+Generator: poetry-core 2.1.2
 Root-Is-Purelib: true
 Tag: py3-none-any

carrot_transform-0.3.5.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+carrot-transform=carrottransform.cli.command:transform
+

carrottransform/_version.py

@@ -1,2 +1,6 @@
-# TODO - pick this up automatically when building
-__version__ = '0.3.2'
+from importlib.metadata import version
+
+try:
+    __version__ = version("carrot_transform")  # Defined in the pyproject.toml 
+except Exception:
+    __version__ = "unknown"