carrot-transform 0.3.4__py3-none-any.whl → 0.4.0__py3-none-any.whl

{carrot_transform-0.3.4.dist-info → carrot_transform-0.4.0.dist-info}/METADATA

@@ -1,30 +1,25 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: carrot_transform
-Version: 0.3.4
-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: pandas (>=2.2.3,<3.0.0)
-Requires-Dist: pytest (>=8.3.4,<9.0.0)
+Version: 0.4.0
+Author-email: anwarfg <913028+anwarfg@users.noreply.github.com>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: click<9,>=8.1.7
+Requires-Dist: ruff>=0.12.0
 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"/>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/Health-Informatics-UoN/carrot-transform/refs/heads/main/images/logo-dark.png">
+    <img alt="Carrot Logo" src="https://raw.githubusercontent.com/Health-Informatics-UoN/carrot-transform/refs/heads/main/images/logo-primary.png" width="280"/>
   </picture>
   </a>
 </p>
 
+
 <p align="center">
 
 <a href="https://github.com/Health-Informatics-UoN/carrot-transform/releases">
@@ -54,11 +49,36 @@ Description-Content-Type: text/markdown
 
 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
+## Quick Start
 
 To have the project up and running, please follow the [Quick Start Guide](https://carrot.ac.uk/transform/quickstart).
 
+If you need to perform development, [there's a brief guide here](https://carrot.ac.uk/transform/development) to get the tool up and running.
+
+## Formatting and Linting
+
+This project is using [ruff](https://docs.astral.sh/ruff/) to check formatting and linting. 
+The only dependency is the [`uv` command line tool.](https://docs.astral.sh/uv/)
+The `.vscode/tasks.json` file contains a task to run this tool for the currently open file. 
+The commands can be run on thier own (in the root folder) like this ...
+
+```bash
+# reformat all the files in `./`
+λ uv run ruff format .
+
+# run linting checks all the files in `./` 
+λ uv run ruff check .
+
+# check and fix all the files in `./`
+λ uv run ruff check --fix .
+
+# check and fix all the files in `./` but do so so more eggrsively
+λ uv run ruff check --fix --unsafe-fixes .
+```
+
+
 ## Release Procedure 
+
 To release a new version of `carrot-transform` follow these steps: 
 
 ### 1. Prepare the repository
@@ -84,6 +104,7 @@ git push --set-upstream origin release/v$NEW_VERSION
 
 ### 4. Create pull request 
 - Open a pull request from `release/v$NEW_VERSION` to `main` and await approval.
+
 ### 5. Merge and tag 
 - After approval merge the the feature branch to `main`. 
 - Checkout to `main`, pull updates, and create a tag corresponding to the new version number. 
@@ -95,12 +116,14 @@ git push origin "$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-0.4.0.dist-info/RECORD

@@ -0,0 +1,41 @@
+carrottransform/__init__.py,sha256=w-DhwucYR1NusuB8OSVCGg-FSXD7uGM4-qRYYVRQuFw,76
+carrottransform/_version.py,sha256=1cid5p9fGAqLJCh8-kGfJREN50SBD2zlOIxb22wmTsw,170
+carrottransform/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+carrottransform/cli/command.py,sha256=cBokJsMNPclG3kwey1FP4hd42tj-_fLvO6N5TY8ZaWA,592
+carrottransform/cli/subcommands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+carrottransform/cli/subcommands/run.py,sha256=vhZx0GkH_oSwX02hvoVG9c2QBpG43jdCQiTh--fcfZc,14846
+carrottransform/cli/subcommands/run_v2.py,sha256=cjqmQQsnk0TT_d8uER5FoieE-n70Pio1_CQhc_NORUo,3788
+carrottransform/config/OMOPCDM_postgresql_5.3_ddl.sql,sha256=fXrPfdL3IzU5ux55ogsQKjjd-c1KzdP_N2A_JjlY3gk,18084
+carrottransform/config/OMOPCDM_postgresql_5.4_ddl.sql,sha256=qax7pJC0ydOlj6rdpKyf1rZ_NILFkryHZYpcFTmh8dY,19615
+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/examples/test/rules/v1.json,sha256=eE1fMWbLdivDsTvTOzIYOhB7z9sHx6D_t7ohqveJCS0,8622
+carrottransform/examples/test/rules/v2.json,sha256=PxMY7OTgd9zIJWTyHjcHEGATwjiCR1a528DKW0Q3AOk,3293
+carrottransform/tools/__init__.py,sha256=xOaP6dK0oDi58Ifa0bm-gNFU5RL6iXmKfk10jTUPH1k,168
+carrottransform/tools/args.py,sha256=DrB5PhvPs01EfNRMIC8Xt4bYmYHXJcpanshDmJqaDtc,4324
+carrottransform/tools/click.py,sha256=5fxl9zL6piwWMN4cSule0tG90E9g7eFNosoSu1ES1og,471
+carrottransform/tools/concept_helpers.py,sha256=ShZ9q4JEhiI9NvxoZCENhRewlf7LUzy59ozda97adR4,2049
+carrottransform/tools/core.py,sha256=9WCmkY5xlte7sRbJbhwi6Pg1vHNsJBf6iFn0_DoCMQw,7921
+carrottransform/tools/date_helpers.py,sha256=Tj7zmu5j5M1NR9PfCYmlbfWbUv_ga1QMwouOfxyVzSQ,2333
+carrottransform/tools/file_helpers.py,sha256=wxrQ09CtnJQKx9uofI89ljTdWj1INockc1J77mQIJsc,6894
+carrottransform/tools/logger.py,sha256=MTTqX6xgvQId44GOLT2Rtog2HDdvUwQFzHWUiA7W6YQ,506
+carrottransform/tools/mapping_types.py,sha256=1jP3LdGzt3r1pXRk7xvyIURARFI0iPA4AsAF65pDVp4,758
+carrottransform/tools/mappingrules.py,sha256=EP8Qn4RFCeraUrrg4OKhNQ9IkQUAyUiVCm1kyYZJf_A,18912
+carrottransform/tools/metrics.py,sha256=v4JE7P-rC3wYzgYKouRkt7uYB8rPa_5FVyO-3r5wLHg,11702
+carrottransform/tools/omopcdm.py,sha256=lG6YRw99jX1x74k2O5Q_36a7KKl9UckIJ2LkyrIWd-w,8731
+carrottransform/tools/orchestrator.py,sha256=1hRuGSv7BaYGoYCDqzfgSbIRr--pTap8gUfzd8aiiHI,14162
+carrottransform/tools/person_helpers.py,sha256=AVpyy-s3ijwSNth-fO0tBC1InKfVXrvernHb19mrCYU,4257
+carrottransform/tools/record_builder.py,sha256=X4KlDrg56LTRVN3rz8hQKRTBtGdGdWK3wYAVJxuDSPs,16298
+carrottransform/tools/stream_helpers.py,sha256=izx9OxekIApFXzmTfcmwVxbAngzqDsIzzBS5hp2S-lA,2772
+carrottransform/tools/types.py,sha256=J9En6GBA21wBG0LyIpyzAP94WYEHgXfGpUSyyby9Ffk,1919
+carrottransform/tools/validation.py,sha256=1SNfL9uhQ1jWSoOx1mUtd7YtgLOY6IPRRFZGC5aG3Y4,1432
+carrot_transform-0.4.0.dist-info/METADATA,sha256=YkU8Fqs9zSk4_CdZBDbjX5KG6IILMwLQt6O5B1jboGA,4893
+carrot_transform-0.4.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+carrot_transform-0.4.0.dist-info/entry_points.txt,sha256=WSJqmgB8PEK8iMl3IFEMBYuyXtzHX5PaKbG13R54AH4,75
+carrot_transform-0.4.0.dist-info/licenses/LICENSE,sha256=pqIiuuTs6Na-oFd10MMsZoZmdfhfUhHeOtQzgzSkcaw,1082
+carrot_transform-0.4.0.dist-info/RECORD,,

{carrot_transform-0.3.4.dist-info → carrot_transform-0.4.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.1
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any

carrot_transform-0.4.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+carrot-transform = carrottransform.cli.command:transform

carrottransform/__init__.py

@@ -1,5 +1,5 @@
 from ._version import __version__
 
 params = {
-  'version':__version__,
+    "version": __version__,
 }

carrottransform/_version.py

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

carrottransform/cli/command.py

@@ -1,21 +1,25 @@
 # Package entry point - sets up the "run" subcommand
 from .subcommands.run import run
+from .subcommands.run_v2 import run_v2
 
 import carrottransform as c
 import click
 
+
 @click.group(invoke_without_command=True)
-@click.option("--version","-v",is_flag=True)
+@click.option("--version", "-v", is_flag=True)
 @click.pass_context
-def transform(ctx,version):
-    if ctx.invoked_subcommand == None :
+def transform(ctx, version):
+    if ctx.invoked_subcommand is None:
         if version:
             click.echo(c.__version__)
         else:
-            click.echo(ctx.get_help()) 
+            click.echo(ctx.get_help())
         return
 
+
 transform.add_command(run, "run")
+transform.add_command(run_v2, "run_v2")
 
 if __name__ == "__main__":
-  transform()
+    transform()