initated repo according to

.github/workflows/pages.yml

@@ -50,7 +50,7 @@ jobs:
           printf "Building the %s documentation\n" ${DOCDIR}
 
           cd docs
-          sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/template_for_python_projects
+          sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/rarelink_phenopacket_mapper
           make clean html
           
           mv _build/html/* ../gh-pages/${DOCDIR}

README.md

@@ -47,24 +47,24 @@ Only pull from `develop` to `main` with fully functional, tested and documented
 5. Change all relevant fields in the `pyproject.toml` and `docs/conf.py` files. (Don't forget the intersphinx setup)
 
 If you want to run sphinx locally: 
-- `sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/template_for_python_projects`
+- `sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/rarelink_phenopacket_mapper`
 - `make.bat` html
 - Open `docs/_build/html/index.html` in your browser
 
 
 
 You can also add a badge like this one to your README.md file:
-[![Build status](https://github.com/frehburg/TemplateForPythonProjects/workflows/CI/badge.svg)](https://github.com/frehburg/TemplateForPythonProjects/actions/workflows/python_ci.yml)  
-[Stable Documentation](https://frehburg.github.io/TemplateForPythonProjects/stable/)  
-[Latest Documentation](https://frehburg.github.io/TemplateForPythonProjects/latest/)  
+[![Build status](https://github.com/frehburg/rarelink_phenopacket_mapper/workflows/CI/badge.svg)](https://github.com/frehburg/TemplateForPythonProjects/actions/workflows/python_ci.yml)  
+[Stable Documentation](https://frehburg.github.io/rarelink_phenopacket_mapper/stable/)  
+[Latest Documentation](https://frehburg.github.io/rarelink_phenopacket_mapper/latest/)  
 
 See here a template for your README
 
-# Project Name
+# RareLink Phenopacket Mapper
 ![UML_and_flowchart](https://github.com/user-attachments/assets/56f68945-6b3f-4ad8-9bc3-986b71b1a53d)
 
 
-Brief description of your project.
+A package to map data from the RareLink format in REDCap to the GA4GH Phenopacket schema (v2).
 
 ## Table of Contents
 

docs/conf.py

@@ -14,7 +14,7 @@
 src_path = os.path.abspath(os.path.join('..', 'src'))
 sys.path.insert(0, src_path)
 
-project = 'template_for_python_projects'
+project = 'rarelink_phenopacket_mapper'
 copyright = '2024, test'
 author = 'test'
 release = '0.0.1'

docs/index.rst

@@ -1,9 +1,9 @@
-.. template_for_python_projects documentation master file, created by
+.. rarelink_phenopacket_mapper documentation master file, created by
    sphinx-quickstart on Mon Jul 22 10:25:34 2024.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to template_for_python_projects's documentation!
+Welcome to rarelink_phenopacket_mapper's documentation!
 =================================
 
 .. toctree::

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "template_for_python_projects"
+name = "rarelink_phenopacket_mapper"
 authors = [
     {name = "Filip Rehburg", email="filip.rehburg@charite.de"},
      ]
@@ -37,16 +37,16 @@ test = ["pytest>=7.0.0,<8.0.0"]
 docs = ["sphinx>=7.0.0", "sphinx-rtd-theme>=1.3.0", "sphinx-copybutton>=0.5.0"]
 
 [project.urls]
-homepage = "https://github.com/frehburg/template_for_python_projects"
-repository = "https://github.com/frehburg/template_for_python_projects.git"
-documentation = "https://frehburg.github.io/template_for_python_projects/stable"
-bugtracker = "https://github.com/frehburg/template_for_python_projects/issues"
+homepage = "https://github.com/frehburg/rarelink_phenopacket_mapper"
+repository = "https://github.com/frehburg/rarelink_phenopacket_mapper.git"
+documentation = "https://frehburg.github.io/rarelink_phenopacket_mapper/stable"
+bugtracker = "https://github.com/frehburg/rarelink_phenopacket_mapper/issues"
 
 [tool.setuptools]
 package-dir = { "" = "src" }
 
 [tool.setuptools.dynamic]
-version = { attr = "template_for_python_projects.__version__" }
+version = { attr = "rarelink_phenopacket_mapper.__version__" }
 
 # The following would provide a command line executable called `sample`
 # which executes the function `main` from this package when invoked.

src/template_for_python_projects/__init__.py

@@ -1,4 +1,4 @@
-"""An example description for the template_for_python_projects package."""
+"""An example description for the rarelink_phenopacket_mapper package."""
 
 __version__ = "0.0.1"
 

src/template_for_python_projects/example/minus.py

@@ -2,7 +2,7 @@ def minus(a: int, b: int) -> int:
     """
     This function returns the difference of two numbers.
 
-    Very similar to :func:`template_for_python_projects.example.plus.plus` but returns the difference instead of the
+    Very similar to :func:`rarelink_phenopacket_mapper.example.plus.plus` but returns the difference instead of the
     sum.
 
     :param a: an integer number

src/template_for_python_projects/example/plus.py

@@ -2,7 +2,7 @@ def plus(a: int, b: int) -> int:
     """
     This function returns the sum of two numbers.
 
-    Very similar to :func:`template_for_python_projects.example.minus.minus` but returns the sum instead of the
+    Very similar to :func:`rarelink_phenopacket_mapper.example.minus.minus` but returns the sum instead of the
     difference.
 
     :param a: an integer number

tests/example/test_minus.py

@@ -1,5 +1,5 @@
 import pytest
-import template_for_python_projects
+import rarelink_phenopacket_mapper
 
 
 @pytest.mark.parametrize("a, b, expected", [
@@ -12,4 +12,4 @@
     (10, -1, 11),
 ])
 def test_minus(a, b, expected):
-    assert template_for_python_projects.example.minus.minus(a, b) == expected
+    assert rarelink_phenopacket_mapper.example.minus.minus(a, b) == expected

tests/example/test_plus.py

@@ -1,5 +1,5 @@
 import pytest
-import template_for_python_projects
+import rarelink_phenopacket_mapper
 
 
 @pytest.mark.parametrize("a, b, expected", [
@@ -17,4 +17,4 @@
     (-1, 0, -1),
 ])
 def test_minus(a, b, expected):
-    assert template_for_python_projects.example.plus.plus(a, b) == expected
+    assert rarelink_phenopacket_mapper.example.plus.plus(a, b) == expected

tests/numpy_example/sum_over_array.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-import template_for_python_projects
+import rarelink_phenopacket_mapper
 
 
 @pytest.mark.parametrize("arr, expected", [
@@ -13,4 +13,4 @@
     ([2, 1, -3], 0),
 ])
 def test_sum_over_array(arr, expected):
-    assert template_for_python_projects.numpy_example.sum_over_array.sum_over_array(arr) == expected
+    assert rarelink_phenopacket_mapper.numpy_example.sum_over_array.sum_over_array(arr) == expected