Created a docs version of the ReadMe file.

Author: Veronika271

reproschema-py-tutorial/docs/cli_usage.md

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+## CLI usage
+
+This package installs `reproschema` Command Line Interface (CLI).
+
+```
+$ reproschema --help
+
+$  A client to support interactions with ReproSchema
+
+  To see help for a specific command, run
+
+  reproschema COMMAND --help     e.g. reproschema validate --help
+
+Options:
+  --version
+  -l, --log-level [DEBUG|INFO|WARNING|ERROR|CRITICAL]
+                                  Log level name  [default: INFO]
+  --help                          Show this message and exit.
+
+Commands:
+  convert             Converts a path to a different format, jsonld,...
+  create
+  migrate             Updates to a new reproschema version
+  redcap2reproschema  Converts REDCap CSV files to Reproschema format.
+  reproschema2redcap  Converts reproschema protocol to REDCap CSV format.
+  serve
+  validate            Validates if the path has a valid reproschema format
+  reproschema2fhir       Generates FHIR questionnaire resources from reproschema activities
+  output2redcap  Generates redcap csv given the audio and survey data from reproschema ui
+```

reproschema-py-tutorial/docs/index.md

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+# Welcome to Reproschema-py
+
+For full documentation visit [Reproschema-py](https://github.com/ReproNim/reproschema-py).
+reproschema requires Python 3.10+
+
+## Project layout
+    mkdocs.yml    # The configuration file.
+    docs/
+        index.md  # The documentation homepage.
+        installation.md #A tutorial for installation.
+        cli_usage.md #Notes on CLI usage
+        reproschema2redcap.md #How to convert from resproschema to redcap
+        redcap2reproschema.md #How to convert from redcap to reproscehma
+        output2redcap.md #How to convert the output into redcap
+        reproschema2fhir.md #How to convert the reproschema into an FHIR Questionaire Resource

reproschema-py-tutorial/docs/installation.md

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+## Installation
+
+Use the following command to install reproschema:
+
+```
+pip install reproschema
+```
+
+### Developer installation
+
+Fork this repo to your own GitHub account, then clone and install your forked repo in the developer mode:
+
+```
+git clone https://github.com/<your github>/reproschema-py.git
+cd reproschema-py
+pip install -e .
+```
+#### Style
+This repo uses pre-commit to check styling.
+- Install pre-commit with pip: `pip install pre-commit`
+- In order to use it with the repository, you have to run `run pre-commit install` in the root directory the first time you use it.
+
+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.

reproschema-py-tutorial/docs/output2redcap.md

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+## `output2redcap`
+The `output2redcap` function is designed to process the output from reproschema-ui into a REDCap CSV file as seen [here](reproschema/example/redcap).
+
+
+### CLI Usage
+
+The `output2redcap` function has been integrated into a CLI tool, use the following command:
+```bash
+reproschema output2redcap ./path/to/your_reproschema-ui_files ./path/to/directory_you_want_to_save_output
+```

reproschema-py-tutorial/docs/redcap2reproschema.md

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+## `redcap2reproschema`
+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**: A unique identifier for your protocol. Use underscores for spaces and avoid special characters.
+- **protocol_display_name**: Name that will appear in the application.
+- **protocol_description**: A brief description of your protocol.
+- **redcap_version**: Version of your redcap file (you can customize it).
+
+Example:
+```yaml
+protocol_name: "My_Protocol"
+protocol_display_name: "Assessment Protocol"
+protocol_description: "This protocol is for assessing cognitive skills."
+redcap_version: "X.XX.X"
+```
+### CLI 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
+```
+
+Optionally you can provide a path to the output directory (default is the current directory) by adding the option: `--output-path PATH`
+### 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"
+output_path = "path-to/directory_you_want_to_save_output"
+
+redcap2reproschema(csv_file, yaml_file, output_path)
+```

reproschema-py-tutorial/docs/reproschema2fhir.md

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+## `reproschema2fhir`
+The `reproschema2fhir` function is designed to convert reproschema activities and items into a FHIR Questionnaire resource as seen [here](reproschema/example/fhir).
+
+### CLI Usage
+
+The `reproschema2fhir` function has been integrated into a CLI tool, use the following command:
+```bash
+reproschema reproschema2fhir ./path/to/your_reproschema_activities ./path/to/directory_you_want_to_save_output
+```
+### Notes
+1. The script requires an active internet connection to access the GitHub repository.

reproschema-py-tutorial/docs/reproschema2redcap.md

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+## `reproschema2redcap`
+
+### CLI Usage
+
+You can use this feature directly from the command line. To convert ReproSchema protocol to REDCap CSV format, use the following command
+
+```
+reproschema reproschema2redcap <input_dir_path> <output_csv_filename>
+```
+
+- `<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)
+```

reproschema-py-tutorial/mkdocs.yml

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+site_name: My Docs
+nav:
+  - Home: index.md
+  - Installation: installation.md
+  - CLI Usage: cli_usage.md
+  - Converting from reproschema to redcap: reproschema2redcap.md
+  - Converting from redcap to reproschema: redcap2reproschema.md
+  - Converting the output into redcap: output2redcap.md
+  - Converting the reproschema into an FHIR Questionaire Resource: reproschema2fhir.md
+
+theme: readthedocs