Detailed Running
----------------

Code Structure
~~~~~~~~~~~~~~

The **Partial Pressures Module** is designed to calculate partial pressures from hadronic susceptibilities. 
The module is implemented within a Docker container to ensure portability and consistency. 
The workflow involves parsing input parameters, performing core computations, and generating output files for further analysis. 
Below is a detailed explanation of the code structure and its components.

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1. **Input Files**:
   - **`config.yaml`**: This file specifies the ranges for :math:`T`, :math:`\mu_B`, :math:`\mu_Q`, and :math:`\mu_S`, as well as user-defined options for:
     - **Thermodynamics**: Thermodynamic data to be stored in the output.
     - **File structure**: Input directory, file extensions, and output format.

2. **Configuration Validation**:
   - The `OpenAPI_Specifications_validator.py` script validates the `config.yaml` file against the OpenAPI specifications defined in `OpenAPI_Specifications-PartPress.yaml`. This ensures that all required parameters are provided and conform to the expected structure.

3. **Core Computation**:
   - The main script, `MUSES_Wrapper.py`, orchestrates the execution of the module. It validates inputs, processes susceptibility data, and calls the `PartialPressure` function from `src/Partial_Pressure_Equations.py` to compute the partial pressures.

4. **Output Files**:
   - The results of the computation are saved in the `output/` directory. The following files are generated:
     - **`Partial_Pressures.csv` or `Partial_Pressures.tsv`**: Contains the calculated partial pressures and their associated errors for each temperature point.
     - **`Partial_Pressures-metadata.yaml`**: Describes the structure and units of the output data.
     - **`status.yaml`**: Provides the status of the module's execution, including success or error messages.

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Core function (in `src/Partial_Pressure_Equations.py`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The `Partial_Pressure_Equations.py` script contains the core functions for reading susceptibility data, combining data from multiple files, and calculating partial pressures. Below is an overview of the key functions:

1. **`generate_formula(coefficients, variables)`**:
   - Computes a linear combination of variables using the provided coefficients.
   - Used to calculate partial pressures based on susceptibility data.

2. **`generate_error(coefficients, variables)`**:
   - Computes the error associated with a linear combination using the square root of the sum of squared terms.
   - Used to calculate the errors for the partial pressures.

3. **`ReadDataOfOneFileIntoArray(filename, allow_warnings=True)`**:
   - Reads susceptibility data from a single file and organizes it into arrays for temperatures and chi values.
   - Handles errors such as missing or malformed data.

4. **`combine_data_from_files(input_folder, file_extension=".hrg")`**:
   - Combines susceptibility data from multiple files in the specified input folder.
   - Handles issues such as missing files, mismatched data lengths, and files with no error data.
   - Returns averaged temperature values, combined chi values, and associated error points.

5. **`PartialPressure(input_dir, output_dir, output_format="csv", file_extension=".hrg")`**:
   - The main function for calculating partial pressures.
   - Reads susceptibility data from the input directory, either from a single file (`dat.txt`) or by combining multiple files.
   - Computes partial pressures and their errors for each temperature point using predefined equations and coefficients.
   - Writes the results to an output file in the specified format (`csv` or `tsv`).

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Workflow Overview
~~~~~~~~~~~~~~~~~~

The module's workflow can be summarized as follows:

1. **Input Validation**:
   - The `config.yaml` file is validated against the OpenAPI specifications.
   - Missing or invalid parameters are flagged, and execution is halted if necessary.

2. **Data Processing**:
   - Susceptibility data is read from the input directory.
   - If multiple files are provided, their data is combined and averaged.

3. **Partial Pressure Calculation**:
   - Partial pressures and their errors are calculated for each temperature point using the `PartialPressure` function.
   - The calculations are based on predefined equations and coefficients for each partial pressure.

4. **Output Generation**:
   - The results are written to an output file in the specified format.
   - Metadata describing the output structure is saved in a separate YAML file.
   - A status file is generated to indicate the success or failure of the module's execution.

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Code Organization
~~~~~~~~~~~~~~~~~~

The module's code is organized into the following directories:

- **`api/`**:
  - Contains the OpenAPI specifications and the input validation script.
  - Key file: `OpenAPI_Specifications_validator.py`.

- **`src/`**:
  - Contains the core computation script for calculating partial pressures.
  - Key file: `Partial_Pressure_Equations.py`.

- **`input/`**:
  - Contains the `config.yaml` file and susceptibility data files.

- **`output/`**:
  - Stores the generated output files, including results, metadata, and status.

- **`test/`**:
  - Contains reference files and test cases for validating the module's functionality.