mock rfluka executable resolves #637

[reviewpad[bot]]

Thank you @hendzeld for this first contribution!

[reviewpad[bot]]

Reviewpad Report

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• Please provide a description for the pull request

[reviewpad[bot]]

AI-Generated Summary: This pull request includes 2 commits, adding a Python script and a bash script. The first commit introduces a Python script (generate.py) to create a bash script that generates mock Fluka output files from existing files in a directory, encoding the file contents in base64. The second commit adds the created bash script (rfluka) that can decode base64-encoded contents of the files and generate the corresponding Fluka output files.

[reviewpad[bot]]

AI-Generated Summary: This pull request consists of 3 patches that add files and implement modifications related to generating a bash script for creating mock FLUKA output files.

1. The first patch adds a new Python script generate.py under the tests/res/fluka/mock directory. This script contains functions for generating a bash script that produces mock FLUKA output files from existing files in the selected directory.

2. The second patch introduces a new bash script, rfluka, that generates mock FLUKA output files. It is added under the tests/res/fluka/mock directory.

3. The third and final patch resolves style issues in the generate.py script. It has made changes to the comments, multiline string formatting, and added a missing import statement for the sys module.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces a new Python script (generate.py) and a rfluka mock script to generate mock FLUKA output files from existing files in a selected directory. The main changes include:

1. The addition of a generator script (generate.py) that creates a bash script with base64 encoded contents of FLUKA output files.
2. Resolution of style issues in the generate.py script.
3. An update of the description in the generate.py script to provide more details on what the script does.

The bash script generated by the Python script is named rfluka, and contains commands to decode the base64 content back to the original FLUKA output files when executed.

[reviewpad[bot]]

AI-Generated Summary: This pull request includes 5 patches:

1. Generator of rfluka mock: Generates a bash script that returns files saved as base64
2. Add rfluka mock script: Adds the rfluka bash script that generates mock FLUKA output files from files existing in the selected directory
3. Resolve style issues: Fixes some Python style issues in the generate.py script
4. Update description: Improves the description of the generate.py script's functionality
5. Use index instead of name for variables: Improves the way variables are named in the generate.py script by using index numbers instead of file names

[reviewpad[bot]]

AI-Generated Summary: This pull request consists of 6 patches that primarily focus on the generation of mock FLUKA output files using a Python script, which subsequently generates a bash script containing these files as base64 encoded strings. The key changes include:

1. Creation of generate.py, a script for generating a bash script that yields mock FLUKA output files from existing files in a selected directory.
2. Addition of a rfluka mock script containing base64 encoded FLUKA output files.
3. Style updates and improvements to the generate.py script, such as adding more detailed documentation and compliance with Python conventions.
4. Changing the variable names in the generate.py script to use indices instead of names.
5. Updating the description in generate.py to provide more context for its usage.
6. Updates to the rfluka mock script, modifiying the file naming structure to match the updated generate.py script.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces two new files, generate.py and rfluka. The generate.py script is designed to collect all fluka output files in the current directory and generate a bash script named rfluka. This script will contain all the fluka output files as base64 encoded strings, and running it will create all the fluka output files in the current directory. The new rfluka file is a sample bash script generated by the generate.py script.

[grzanka]

@hendzeld can you add an unit tests which uses this mock (via subprocess call), generates some Fluka output in temporary directory and reading it like in the script here: https://github.com/DataMedSci/pymchelper/blob/master/examples/comparison.py ?

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces several changes and new files related to handling mock scripts and code review tests for Fluka. It includes:

1. A new __init__.py file in the tests/res/mocks directory, containing the import for Pathlib.Path.
2. A new Python script generate_fluka.py, which collects all Fluka output files in the current directory and creates a bash script named rfluka containing base64 encoded strings of Fluka output files.
3. A new Python module bash_script.py in tests/res/mocks/libs, which provides helper functions for creating bash scripts with embedded encoded Fluka files.
4. A newly generated rfluka bash script in tests/res/mocks containing base64-encoded Fluka output files.
5. Updates to the detect_zone.dat file in tests/res/shieldhit/generated, modifying the order and formatting of some lines.
6. A new test module test_mocks.py, containing a test for the Fluka mock script and related helper functions.

Note: The test test_fluka_mock is marked to be skipped on Windows operating systems.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces a set of new files and modifies existing ones for testing and generating mock data. Specifically, it adds three new Python files: generate_fluka.py, bash_script.py, and test_mocks.py. It also adds a rfluka bash script and modifies the detect_zone.dat file. The new Python files assist in creating a bash script, generating Fluka output files, and testing mock scripts. The rfluka bash script is created by generate_fluka.py and recreates Fluka output files in the current directory. The detect_zone.dat file's contents have been updated with seemingly updated data.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces several new files primarily focused on testing mock scripts and Fluka file generation. These files include:

1. tests/res/mocks/__init__.py: Initializes the test module and sets the PATH.
2. tests/res/mocks/generate_fluka.py: A script that collects all Fluka output files and generates a bash script named rfluka, which contains the Fluka output files as base64 encoded strings.
3. tests/res/mocks/libs/bash_script.py: A library for creating bash scripts with given file names and contents.
4. tests/res/mocks/rfluka: A generated bash script containing base64 encoded Fluka output files.
5. tests/test_mocks.py: Test cases for mock scripts, including a test function test_fluka_mock that checks if the Fluka output files are generated correctly.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces new files and functionality for generating Fluka output files along with their corresponding tests. It includes the creation of new library files for handling bash script generation, as well as a new script for generating Fluka output files. The pull request also adds a test suite for these new features.

[reviewpad[bot]]

AI-Generated Summary: This pull request adds new files and updates existing ones related to generating mock Fluka output files and test scripts. It introduces a new script generate_fluka.py for collecting Fluka output files and generating a corresponding bash script named rfluka. The libs/bash_script.py file provides methods to create the bash script while encoding and decoding file contents in base64. Additionally, new rfluka bash script and test module test_mocks.py are included to help test output generation and retrieval. Overall, this PR aims to streamline the process of handling Fluka output files for testing purposes.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces several new files to the project, mainly in the tests/res/mocks and tests/res/mocks/libs directories. These files provide support for generating and testing mock Fluka output files. A new test module, test_mocks.py, is included that tests the functionality of the Fluka mocks by executing the rfluka script and checking the generated Fluka files. The changes also include the rfluka script, which runs the base64 encoded Fluka output files and creates them in the current directory.

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AI-Generated Summary: This pull request introduces new files and modifications related to the generation and testing of mock files for a simulator. The new files include .vscode/settings.json for VSCode settings, a README.md with instructions on generating rfluka mock, and several Python scripts for generating and testing the rfluka mock.

The diff also adds a minimal fluka input file, a minimal rfluka mock script, and a test_mocks.py script for testing the rfluka mock.

[reviewpad[bot]]

AI-Generated Summary: This pull request adds new code to generate mock files for the simulator and for testing purposes. The diff includes:

1. A new README.md file explaining the purpose of the simulator mocks and how to generate an rfluka mock.
2. A minimal example of a Fluka input file, minimal.inp, along with a mock rfluka script.
3. A Python script, generate_rfluka_mock.py, to generate mock rfluka output based on a given input file.
4. A new library, bash_script.py, to create bash scripts with given parameters.
5. A new test file, test_mocks.py, that tests the functionality of the Fluka mock script.

The new code is helpful for testing the simulator without requiring real Fluka binaries.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces a new functionality to create mock scripts for running rfluka simulations. It adds new directory tests/res/mocks with several new files such as README.md, generate_rfluka_mock.py, bash_script.py, and sets up a test suite in tests/test_mocks.py. The added files contain instructions for generating rfluka mock, Python scripts to generate bash scripts that mimic rfluka, and unit tests to ensure the generated scripts work as expected.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces a mock generator for the rfluka simulator. It adds a new directory tests/res/mocks containing the generator script generate_rfluka_mock.py as well as various helper scripts and mock data. Additionally, a test file tests/test_mocks.py is added to verify the functionality of the generated mocks. The generator reads an input file, runs rfluka with it, and creates a bash script that mimics rfluka for the selected input file. The simulation includes 20 particles, two results and uses 4x4 bins.

[reviewpad[bot]]

AI-Generated Summary: This pull request includes the addition of simulator mocks for testing purposes. The new files added are:

1. README.md in tests/res/mocks/ directory, which contains instructions on generating the rfluka mock for testing.
2. A minimal Fluka input file (minimal.inp) as a test input for the rfluka mock.
3. Mock rfluka script (rfluka) which simulates minimal Fluka output files when run.
4. generate_rfluka_mock.py, a Python script to generate the rfluka mock script based on the provided Fluka input file.
5. bash_script.py, a Python library to generate a bash script with specified files and standard output/error streams.
6. test_mocks.py, a pytest module to test the generated rfluka mock and verify its outputs.

The pull request also modifies the file permissions for some of the new files. It introduces new functionality to generate and test rfluka mocks and verify their output while keeping the original functionality intact.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces a mock script for testing FLUKA without having the real FLUKA binaries. It adds a Python script for generating rfluka mocks, a bash script for simulating rfluka outputs, and test files to verify the output generated by these mocks. The pull request also includes a README file explaining how to generate rfluka mocks. The new test file test_fluka_minimal.py tests the FLUKA mock script to ensure it generates the expected results.

[reviewpad[bot]]

AI-Generated Summary: This pull request adds test support for a mock FLUKA simulator by providing FLUKA input and output files, as well as a script to generate the rfluka mock for testing purposes. New tests are added in test_fluka_minimal.py to verify the FLUKA mock script output, with specific test cases for minimal001_fort.21 and minimal001_fort.22 output files. Additionally, a README.md file is included in the mocks directory to provide details on generating the rfluka mock script.

[reviewpad[bot]]

AI-Generated Summary: This pull request introduces a mock for the FLUKA radiation transport software. It adds a new test module test_fluka_minimal.py under the tests/mock directory, which verifies the correctness of the mock script by comparing the generated output files with the expected results. There is a new README under tests/res/mocks, explaining the process of generating the rfluka mock, and several new input and mock files are being added. Additionally, a new Python script generate_rfluka_mock.py is introduced to generate the rfluka mock based on the given input file.

Overall, this pull request is aimed at providing a framework for testing the FLUKA radiation transport software without requiring the actual binaries, which may require a license.

[reviewpad[bot]]

AI-Generated Summary: This pull request includes changes that primarily focus on adding support for a mock Fluka test suite. The changes can be summarized as follows:

1. Modification of the .deepsource.toml file to update the test_patterns to include tests in subdirectories.
2. Addition of the new test file test_fluka_minimal.py which includes a set of test cases for the mock Fluka test suite.
3. Addition of the README.md file under the tests/res/mocks directory which provides information about simulator mocks and how to generate the rfluka mock.
4. Addition of new files, including minimal.inp, rfluka, and generate_rfluka_mock.py, to support the mock Fluka test generation and execution.
5. Addition of the bash_script.py file that provides functions for encoding single files into bash scripts and generating a mock bash script with given name and files to save.

[reviewpad[bot]]

AI-Generated Summary: This pull request includes changes to support and test Fluka mock scripts. The changes can be broken down as:

1. Modification of .deepsource.toml to support multiple test patterns.
2. Addition of a test script test_fluka_minimal.py to test Fluka mock.
3. Addition of Fluka minimal input files and mock scripts.
4. Creation of a python script generate_rfluka_mock.py to generate rfluka mock and bash_script.py to support encoding single files.

These changes will enable the testing of Fluka mock scripts without access to the actual Fluka executables.

[reviewpad[bot]]

📈 Pull Request Metrics

💻 Coding Time: 46 minutes 🛻 Pickup Time: 2 days 👀 Review Time: 11 days