see

.gitattributes

@@ -0,0 +1 @@
+reproschema/_version.py export-subst

.github/workflows/pythonpackage.yml

@@ -15,13 +15,13 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-18.04]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        os: [macos-latest, ubuntu-latest]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/pythonpublish.yml

@@ -21,7 +21,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install setuptools wheel twine pyyaml
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

.pre-commit-config.yaml

@@ -2,13 +2,13 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 23.1.0
     hooks:
     -   id: black

README.md

@@ -2,15 +2,32 @@
 
 # Reproschema Python library and Command Line Interface (CLI)
 
-
-### Installation
+## Installation
 
 reproschema requires Python 3.7+.
 
 ```
 pip install reproschema
 ```
 
+### Developer installation
+
+Install repo in developer mode:
+
+```
+git clone https://github.com/ReproNim/reproschema-py.git
+cd reproschema-py
+pip install -e .[dev]
+```
+
+It is also useful to install pre-commit, which takes care of styling when
+committing code. When pre-commit is used you may have to run git commit twice,
+since pre-commit may make additional changes to your code for styling and will
+not commit these changes by default:
+
+```
+pre-commit install
+```
 ## CLI usage
 
 This package installs `reproschema` a CLI.
@@ -34,25 +51,91 @@ Options:
 Commands:
   convert
   create
+  redcap2reproschema  Convert REDCap CSV files to Reproschema format.
+  reproschema2redcap  Convert reproschema protocol to REDCap CSV format.
   serve
   validate
 ```
 
-## Developer installation
+## `reproschema2redcap` Usage
 
-Install repo in developer mode:
+### Command-Line Usage
+
+You can use this feature directly from the command line. To convert ReproSchema protocol to REDCap CSV format, use the following command
 
 ```
-git clone https://github.com/ReproNim/reproschema-py.git
-cd reproschema-py
-pip install -e .[dev]
+reproschema reproschema2redcap <input_dir_path> <output_csv_filename>
 ```
 
-It is also useful to install pre-commit, which takes care of styling when
-committing code. When pre-commit is used you may have to run git commit twice,
-since pre-commit may make additional changes to your code for styling and will
-not commit these changes by default:
+- `<input_dir_path>`: The path to the root folder of a protocol. For example, to convert the reproschema-demo-protocol provided by ReproNim, you can use the following commands:
+  ```bash
+  git clone https://github.com/ReproNim/reproschema-demo-protocol.git
+  cd reproschema-demo-protocol
+  pwd
+  ```
+  In this case,  the output from `pwd` (which shows your current directory path)should be your `<input_dir_path>`.
+- `<output_csv_filename>`: The name of the output CSV file where the converted data will be saved.
+
+### Python Function Usage
+
+You can also use the `reproschema2redcap` function from the `reproschema-py` package in your Python code.
+
+```python
+from reproschema import reproschema2redcap
+
+input_dir_path = "path-to/reproschema-demo-protocol"
+output_csv_filename = "output.csv"
 
+reproschema2redcap(input_dir_path, output_csv_filename)
 ```
-pre-commit install
+
+## `redcap2reproschema` Usage
+The `redcap2reproschema` function is designed to process a given REDCap CSV file and YAML configuration to generate the output in the reproschema format.
+
+### Prerequisites
+Before the conversion, ensure you have the following:
+
+**YAML Configuration File**:
+   - Download [templates/redcap2rs.yaml](templates/redcap2rs.yaml) and fill it out with your protocol details.
+
+### YAML File Configuration
+In the `templates/redcap2rs.yaml` file, provide the following information:
+
+- **protocol_name**: This is a unique identifier for your protocol. Use underscores for spaces and avoid special characters.
+- **protocol_display_name**: The name that will appear in the application.
+- **protocol_description**: A brief description of your protocol.
+
+Example:
+```yaml
+protocol_name: "My_Protocol"
+protocol_display_name: "Assessment Protocol"
+protocol_description: "This protocol is for assessing cognitive skills."
+```
+### Command-Line Usage
+
+The `redcap2reproschema`` function has been integrated into a CLI tool, use the following command:
+```bash
+reproschema redcap2reproschema path/to/your_redcap_data_dic.csv path/to/your_redcap2rs.yaml
+```
+
+### Python Function Usage
+
+You can also use the `redcap2reproschema` function from the `reproschema-py` package in your Python code.
+
+```python
+from reproschema import redcap2reproschema
+
+csv_path = "path-to/your_redcap_data_dic.csv"
+yaml_path = "path-to/your_redcap2rs.yaml"
+
+reproschema2redcap(input_dir_path, output_csv_filename)
 ```
+
+After configuring the YAML file:
+
+1. Run the Python script with the paths to your CSV file and the YAML file as arguments.
+2. Command Format: `python script_name.py path/to/your_redcap_data_dic.csv path/to/your_redcap2rs.yaml`
+
+### Notes
+1. The script requires an active internet connection to access the GitHub repository.
+2. Make sure you use `git add`, `git commit`, `git push` properly afterwards to maintain a good version control for your converted data.

reproschema/__init__.py

@@ -45,3 +45,7 @@ def set_logger_level(lgr, level):
     lgr.warning(
         "Failed to check for a more recent version available with etelemetry: %s", exc
     )
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]