### Initial Development Setup

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/CLAUDE.md

Sets up a virtual environment and installs all packages in development mode. Use this for initial project setup.

```bash
python -m venv idmtools
idmtools\Scripts\activate  # Windows

python dev_scripts/bootstrap.py
```

--------------------------------

### Install Dependencies

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/singularity/covasim/README.md

Run this command after creating a virtual environment to install all necessary project dependencies.

```bash
pip install -r requirements.txt
```

--------------------------------

### Example IDMTools INI Configuration

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/idmtools_ini_alias/README.md

Illustrates platform configuration when an idmtools.ini file is present. No specific setup is required beyond having the file.

```python
example_idmtools_ini_config.py
```

--------------------------------

### Install and Serve MkDocs Locally

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/development/release-process.md

Install documentation dependencies and serve the documentation locally for development. Auto-reloads on changes.

```bash
pip install -r docs/requirements.txt

mkdocs build

mkdocs serve
```

--------------------------------

### Install Nano Text Editor

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/dev_scripts/linux-test-env/README.md

Install the nano text editor within the container. This is an example of installing additional packages needed for development or debugging.

```bash
sudo apt install nano
```

--------------------------------

### Install idmtools File and Process Platform Packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Installs packages for the File and Process platforms.

```bash
pip install idmtools-platform-general
```

--------------------------------

### Development Installation

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/DEVELOPMENT_README.md

Install the required packages for development. Use `make setup-dev` on Unix-like systems or `pymake setup-dev` on Windows. Alternatively, use the bootstrap script.

```bash
make setup-dev
```

```bash
python dev_scripts/bootstrap.py
```

```bash
pymake setup-dev
```

```bash
python dev_scripts\bootstrap.py
```

--------------------------------

### Install idmtools with specific platform support

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/faq/index.md

Use this command to install idmtools with support for only the platforms you need, reducing installation size.

```bash
pip install idmtools[platform]
```

--------------------------------

### Platform Configuration File

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/platforms.md

Example configuration file for setting up platforms.

```APIDOC
## Platform Configuration

### Configuration File

Example `~/.idmtools/idmtools.ini`:

```ini

[My_Container]
type = Container
max_workers = 4
job_dirrectory = /tmp/idmtools

```
```

--------------------------------

### Setup Development Environment

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/dev_scripts/linux-test-env/README.md

Run this command before building to create necessary worker containers.

```bash
make setup-dev
```

--------------------------------

### Container Platform Configuration File Example

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/platforms.md

An example INI configuration file for setting up a Container platform, specifying type, max workers, and job directory.

```ini
[My_Container]
type = Container
max_workers = 4
job_dirrectory = /tmp/idmtools

```

--------------------------------

### Install idmtools Platform Components from Development Branch

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/DEVELOPMENT_README.md

Use this command to install the idmtools_platform_comps package directly from the 'dev' branch of the GitHub repository. Ensure you have pip installed.

```bash
pip install git+https://github.com/InstituteforDiseaseModeling/idmtools.git@dev#egg="idmtools_platform_comps&subdirectory=idmtools_platform_comps"
```

--------------------------------

### Run Simple Sweep Example

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/parameter_sweeps/README.md

Navigate to the example directory and run the basic parameter sweep script. This will create and run simulations locally, saving results to the idmtools working directory.

```bash
cd examples/tutorials/parameter_sweeps
python simple_sweep.py
```

--------------------------------

### Initialize Container Platform

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_platform_container/README.md

This is the basic example for initializing the Container Platform. Specify the job directory to store experiment outputs.

```python
from idmtools.core.platform_factory import Platform
platform = Platform('CONTAINER', job_directory='<user job directory>')
```

--------------------------------

### Install idmtools Slurm Platform Packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Installs packages for the Slurm platform.

```bash
pip install idmtools-platform-slurm
```

--------------------------------

### Install idmtools Local Container Platform Packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Installs packages for the local Container platform.

```bash
pip install idmtools-platform-container
```

--------------------------------

### Install idmtools CLI Tools

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Installs the command-line interface tools for idmtools.

```bash
pip install idmtools-cli
```

--------------------------------

### Developer Installation from Source

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

Installs the development version of idmtools from source code using the provided bootstrap script.

```bash
python dev_scripts/bootstrap.py
```

--------------------------------

### Install IDMtools with Platform Support

Source: https://context7.com/institutefordiseasemodeling/idmtools/llms.txt

Install IDMtools using pip, specifying desired platform support. Use '[full]' for all platforms.

```bash
pip install idmtools[full]
```

```bash
pip install idmtools[idm]
```

```bash
pip install idmtools[slurm]
```

```bash
pip install idmtools[container]
```

--------------------------------

### Install MkDocs and Plugins

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/SKILL.md

Install MkDocs, the Material theme, and essential plugins for Python documentation, Markdown extensions, and diagram support. Use this command to set up the necessary tools for migrating your documentation.

```bash
pip install mkdocs mkdocs-material mkdocstrings[python] \
    mkdocs-gen-files mkdocs-literate-nav mkdocs-section-index \
    mkdocs-autorefs pymdown-extensions
```

```bash
pip install mkdocs-plantuml-local  # or handle via pre-rendered images
```

--------------------------------

### Example Override Configuration (Calculon)

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/idmtools_ini_alias/README.md

Demonstrates overriding platform configuration without an idmtools.ini file, specifically for the 'calculon' environment. This is useful for dynamic configuration.

```python
example_override_config_calculon.py
```

--------------------------------

### Example idmtools Version Output

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_cli/README.md

This is an example of the output you can expect when running the 'idmtools version' command, showing versions of the core tool and its plugins.

```bash
emodpy                               Version: 1.3.0                          
  Plugins:
    EMODTask                  
idmtools                             Version: 3.1.0                 
  Plugins:
    CommandTask               
idmtools-cli                         Version: 3.1.0                
idmtools-models                      Version: 3.1.0                 
  Plugins:
    JSONConfiguredPythonTask  
    JSONConfiguredRTask       
    JSONConfiguredTask        
    PythonTask                
    RTask                     
    ScriptWrapperTask         
    TemplatedScriptTask       
idmtools-platform-comps              Version: 3.1.0                
  Plugins:
    COMPSPlatform             
    SSMTPlatform                        
idmtools-platform-slurm              Version: 3.1.0                  
  Plugins:
    SlurmPlatform             
```

--------------------------------

### Example Folder Structure with Suite

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_platform_container/README.md

Illustrates the default directory structure when a suite and experiment are defined, showing name truncation and UUID inclusion.

```bash
job_directory/
└── s_my_very_long_suite_name_for_m_12345678-9abc-def0-1234-56789abcdef0/
    └── e_test_experiment_with_calibrati_abcd1234-5678-90ef-abcd-1234567890ef/
        └── 7c9e6679-7425-40de-944b-e07fc1f90ae7/
```

--------------------------------

### Specify Docker Image (General)

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/platforms/container.md

Example of how to specify a Docker image when creating a Platform instance. This is a general configuration option.

```python
platform = Platform('Container', job_directory='any_dir',
                    docker_image='my_docker_image:x.x.x')
```

--------------------------------

### Install Covasim (Optional)

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_platform_comps/prototypes/covasim_model/README.md

Install Covasim from PyPi if you need local development support. This is optional for running simulations on the cluster.

```bash
pip install covasim
```

--------------------------------

### Install idmtools packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/tutorials/python-models.md

Install the idmtools package with the necessary extras for your target platform (COMPS, container, Slurm, or all).

```bash
pip install idmtools[idm]        # COMPS platform
pip install idmtools[container]  # Container platform (local Docker)
pip install idmtools[slurm]      # Slurm platform
pip install idmtools[full]       # All platforms
```

--------------------------------

### Install Other Packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/DEVELOPMENT_README.md

Placeholder for installing additional idmtools-related packages. Adapt the pattern shown for core and platform components.

```bash
... pip install other packages
```

--------------------------------

### Install WSL2 on Windows

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/DEVELOPMENT_README.md

Commands to install and set WSL2 as the default version on Windows. This is often a prerequisite for containerized development.

```powershell
wsl --install
```

```powershell
wsl --set-default-version 2
```

```powershell
wsl --set-version <Distro> 2
```

--------------------------------

### mpirun Output Example

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/platform_container/perf_tests/perf_test_result_burnin.txt

Shows the mpirun output format when multiple tasks are contending for resources.

```text
[0] Rank 0 ...
[1] Rank 1 ...
[2] Rank 2 ...
[3] Rank 3 ...
```

--------------------------------

### Install idmtools for COMPS

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

Installs idmtools core, CLI, models, and COMPS platform packages for running simulations in COMPS.

```bash
pip install idmtools[idm]
```

--------------------------------

### Install and Configure mkdocs-redirects Plugin

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/SKILL.md

Install the mkdocs-redirects plugin and configure it in mkdocs.yml to handle page redirects. The redirect map is typically parsed from a redirects.txt file.

```bash
pip install mkdocs-redirects
```

```yaml
plugins:
  - redirects:
      redirect_maps:
        'old-page.md': 'new-page.md'
```

--------------------------------

### Example Output Files

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/platform_container/perf_tests/perf_test_result_burnin.txt

Illustrates the typical state file output generated during a burn-in run.

```text
state-03650.dtk   17 MB
state-07300.dtk   17 MB
```

--------------------------------

### Install Individual idmtools Packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

Install specific idmtools packages to create minimal environments. Available packages include core, CLI, platform support, models, and testing utilities.

```bash
pip install idmtools
```

```bash
pip install idmtools-cli
```

```bash
pip install idmtools-platform-comps
```

```bash
pip install idmtools-models
```

```bash
pip install idmtools-platform-general
```

```bash
pip install idmtools-platform-slurm
```

```bash
pip install idmtools-platform-container
```

```bash
pip install idmtools-test
```

--------------------------------

### Example Folder Structure without Suite

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_platform_container/README.md

Shows the directory structure when only an experiment is defined, omitting the suite-specific directory.

```bash
job_directory/
└── e_test_experiment_with_calibrati_abcd1234-5678-90ef-abcd-1234567890ef/
    └── 7c9e6679-7425-40de-944b-e07fc1f90ae7/
```

--------------------------------

### Full idmtools Installation

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

Installs all idmtools packages, excluding idmtools-test. Includes core, CLI, models, COMPS, General, Container, and Slurm platforms.

```bash
pip install idmtools[full]
```

--------------------------------

### Install idmtools for Docker

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

Installs idmtools core, CLI, models, General, and Container platform packages for running simulations in Docker containers locally.

```bash
pip install idmtools[container]
```

--------------------------------

### Build and Serve Documentation

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/DEVELOPMENT_README.md

Build the documentation and launch a local web server to preview changes. The server watches for file modifications and reloads automatically.

```bash
make build-docs
```

```bash
make build-docs-server
```

--------------------------------

### Troubleshoot Stuck Dev Install

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/DEVELOPMENT_README.md

If the development installation gets stuck, it might be due to changed company credentials. Try installing the problematic package directly using `pip install -e .` within its directory.

```bash
cd idmtools_platform_comps
pip install -e .
```

--------------------------------

### Install and Update Packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_platform_container/docker_image/rocky_meta_runtime.txt

Installs essential packages like rpm, dnf-plugins-core, python3, python3-devel, mpich, epel-release, wget, and nano, and updates existing packages.

```dockerfile
RUN /bin/sh -c yum -y install rpm dnf-plugins-core  && yum -y update  && dnf -y install     python3     python3-devel     mpich     epel-release     wget     nano # buildkit
```

--------------------------------

### Get idmtools-cli Version

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_cli/README.md

Use the 'version' command to check the version of idmtools and its installed plugins.

```bash
idmtools version
```

--------------------------------

### Basic Container Platform Usage Example

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/platforms/container.md

Demonstrates initializing the ContainerPlatform, defining a command task, creating an experiment, and running it. Ensure Docker is running and accessible.

```python
from idmtools.entities.command_task import CommandTask
from idmtools.entities.experiment import Experiment
from idmtools_platform_container.container_platform import ContainerPlatform

# Initialize the platform
from idmtools.core.platform_factory import Platform
platform = Platform('Container', job_directory="destination_directory")
# Or
# platform = ContainerPlatform(job_directory="destination_directory")

# Define task
command = "echo 'Hello, World!'"
task = CommandTask(command=command)

# Run an experiment
experiment = Experiment.from_task(task, name="example")
experiment.run(platform=platform)
```

--------------------------------

### Get Current Package Version

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/development/release-process.md

Execute this script to display the current version of all installed packages, as determined by setuptools-scm.

```bash
python dev_scripts/get_version.py
```

--------------------------------

### Instantiate PlatformAnalysis with Analyzers

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/data-analysis/platform-analysis.md

Example of instantiating PlatformAnalysis, passing analyzer classes and their arguments. Ensure analyzer classes are passed, not instances.

```python
from idmtools.analysis.download_analyzer import DownloadAnalyzer
from myanalyzers import MyCSVAnalyzer

analysis = PlatformAnalysis(
    platform=platform,
    experiment_ids=['exp-id'],
    analyzers=[DownloadAnalyzer, MyCSVAnalyzer],   # classes, not instances
    analyzers_args=[
        {'filenames': ['output/InsetChart.json']},
        {'filenames': ['output/data.csv'], 'output_path': 'results'},
    ]
)
```

--------------------------------

### Run Linux Test Environment

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/dev_scripts/linux-test-env/README.md

Start the Linux test environment container. This command should be run from the directory containing the docker-compose file.

```bash
docker-compose run linuxtst
```

--------------------------------

### Build Documentation Locally

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

Steps to build and serve the idmtools documentation locally. Requires creating a virtual environment, installing dependencies, and running build commands.

```bash
pip install -r docs/requirements.txt
python dev_scripts/bootstrap.py
mkdocs build
mkdocs serve
```

--------------------------------

### Install idmtools Core from Development Branch

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/DEVELOPMENT_README.md

Use this command to install the idmtools_core package directly from the 'dev' branch of the GitHub repository. Ensure you have pip installed.

```bash
pip install git+https://github.com/InstituteforDiseaseModeling/idmtools.git@dev#egg="idmtools&subdirectory=idmtools_core"
```

--------------------------------

### Install Package

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/platforms/container.md

Add this dependency to your Dockerfile to install a package.

```dockerfile
RUN pip install my-package
```

--------------------------------

### Install idmtools Core Package

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Installs only the core functionality of idmtools.

```bash
pip install idmtools
```

--------------------------------

### Resource Usage Over Time (Initialization Phase)

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/platform_container/perf_tests/perf_test_result_burnin.txt

Tracks memory and CPU usage during the script start and initialization phase, showing significant memory growth.

```text
Timestamp (approx)	    PID	    %CPU	%MEM	VSZ (virtual)	RSS (resident)	Comment / Interpretation
15:39 ( t + 0 min )	    2427662	101	    35.8	6.7 GB	        5.9 GB	Script start – allocating data structures / loading input with "python example_container.py"
15:39 ( t + ~1 min )	2427662	101	    36.9	6.9 GB	        6.0 GB	Memory continues to grow during initialization.
15:39 ( t + ~2 min )	2427662	101	    38.9	7.2 GB	        6.4 GB	Peak allocation phase – approaching 40 % of system RAM.
```

--------------------------------

### Install JFrog CLI on Windows

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/dev_scripts/jfrog_stage_to_prod.md

Installs the JFrog CLI using PowerShell. Ensure you have administrator privileges. After installation, you will be prompted to log in via your web browser and configure a new server.

```powershell
powershell "Start-Process -Wait -Verb RunAs powershell '-NoProfile iwr https://releases.jfrog.io/artifactory/jfrog-cli/v2-jf/[RELEASE]/jfrog-cli-windows-amd64/jf.exe -OutFile $env:SYSTEMROOT\system32\jf.exe'"
```

```powershell
jf login
```

```powershell
jf c add
```

```powershell
jf config show
```

--------------------------------

### Create and Run an Experiment

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/core.md

Demonstrates creating an Experiment from a SimulationBuilder and running it on a specified platform. Ensure the platform is correctly configured.

```python
experiment = Experiment.from_builder(builder, task, name="My Experiment")
experiment.run(platform=platform, wait_until_done=True)
```

--------------------------------

### Install idmtools-test package

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

Installs the idmtools-test package, which may be needed for running unittests.

```bash
pip install idmtools-test
```

--------------------------------

### Set up a virtual environment

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/platforms/container.md

Create and activate a Python virtual environment for idmtools. This isolates project dependencies.

```bash
python -m venv container_env

# Windows
container_env\Scripts\activate

# Linux/macOS
source container_env/bin/activate
```

--------------------------------

### Common Development Commands

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/DEVELOPMENT_README.md

Explore available development tasks by running `make help` or `pymake help` on Windows. These commands cover environment setup, cleaning, linting, and testing.

```bash
setup-dev   -   Setup dev environment(assumes you already have a virtualenv)
setup-dev-no-docker -   Setup dev environment(assumes you already have a virtualenv) exlcuding docker builds for the local platform
clean       -   Clean up temporary files
clean-all   -   Deep clean project
lint        -   Lint package and tests
test        -   Run Unit tests
test-all    -   Run Tests that require docker and external systems
coverage    -   Run tests and generate coverage report that is shown in browser
```

--------------------------------

### Development Installation of idmtools

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Clones the idmtools repository and installs it in editable mode for development purposes.

```bash
git clone https://github.com/institutefordiseasemodeling/idmtools.git
cd idmtools
python dev_scripts/bootstrap.py
```

--------------------------------

### Setuptools-scm Configuration

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/development/release-process.md

TOML configuration for setuptools-scm to manage dynamic versioning based on git tags.

```toml
[project]
dynamic = ["version"]

[tool.setuptools_scm]
root = ".."
version_scheme = "no-guess-dev"
local_scheme = "no-local-version"
fallback_version = "0.0.0.dev0"
```

--------------------------------

### Install idmtools COMPS Platform Packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Installs packages specifically for the IDM COMPS platform.

```bash
pip install idmtools-platform-comps
```

--------------------------------

### Create Platform Instance by Name

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/platforms.md

Instantiate a platform using its name. Configuration can be provided directly or loaded from a config file.

```python
from idmtools.core.platform_factory import Platform

# Create platform by name
platform = Platform("COMPS")

# With configuration
platform = Platform(
    "COMPS",
    endpoint="https://comps.idmod.org",
    environment="Bayesian"
)

# From config file
platform = Platform("COMPS", missing_ok=True)
```

--------------------------------

### Install idmtools Python/R Models

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Installs packages for developing Python and R models with idmtools.

```bash
pip install idmtools-models
```

--------------------------------

### Remove Singularity Setup

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/platforms/container.md

When migrating from COMPS to Container Platform, remove Singularity setup code.

```python
# Remove this when using Container Platform
emod_task.set_sif(sif_path)

```

--------------------------------

### Verify idmtools Installation using Python

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Checks the installed version of idmtools by importing it in a Python script.

```python
python -c "import idmtools; print(idmtools.__version__)"
```

--------------------------------

### Create and Run a Simulation Suite

Source: https://context7.com/institutefordiseasemodeling/idmtools/llms.txt

This snippet demonstrates how to create a Suite, add experiments to it, and run all experiments within the suite. It also shows how to retrieve the suite ID and the status of individual experiments.

```python
suite = Suite(name="Model Comparison Study")
suite.update_tags({"study": "baseline_comparison", "version": "1.0"})

# Create suite on platform first
platform.create_items([suite])

# Add experiments to suite
suite.add_experiment(exp1)
suite.add_experiment(exp2)

# Run all experiments in suite
suite.run(platform=platform, wait_until_done=True)

print(f"Suite ID: {suite.id}")
for exp in [exp1, exp2]:
    print(f"  Experiment '{exp.name}': {exp.status}")
```

--------------------------------

### Verify idmtools Installation using CLI

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/getting-started/installation.md

Checks the installed version of idmtools using the command-line interface.

```bash
idmtools --version
```

--------------------------------

### Initialize Container Platform (Default)

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/platform_container/perf_tests/perf_test_result_burnin.txt

Sets up the ContainerPlatform with default settings, suitable for balanced parallelization. The default max_job is 4.

```python
platform = Platform("Container", job_directory="DEST")   # default max_job = 4
```

--------------------------------

### Install Extra Python Packages at Runtime

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_platform_container/docker_image/debian/README.md

When creating a Platform object, you can specify additional Python packages to be installed within the container at runtime using the `extra_packages` argument. Alternatively, use the `idmtools container install` CLI command.

```python
from idmtools.core.platform_factory import Platform
platform = Platform('CONTAINER', docker_image='debian12-env', extra_packages=['emodpy~=2.0.0', 'pytest'])
```

--------------------------------

### Create and Run a Suite of Experiments

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/core.md

Illustrates creating a Suite to group multiple experiments and then running the entire suite on a platform. This is useful for managing complex studies.

```python
from idmtools.entities.suite import Suite

suite = Suite(name="Complete Study")
suite.add_experiment(exp1)
suite.add_experiment(exp2)
suite.run(platform=platform)
```

--------------------------------

### Install Python Requirements

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/idmtools_platform_container/docker_image/rocky_meta_runtime.txt

Installs Python dependencies from a requirements file. Ensure requirements.txt is present in the build context.

```dockerfile
RUN CONTAINER_VERSION=0.0.1 /bin/sh -c bash -c "pip3 install -r /tmp/requirements.txt" # buildkit
```

--------------------------------

### Instantiate a Platform Connection

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/core.md

Provides an example of creating a platform instance using the Platform factory. Specify the platform name and any necessary connection details like endpoint and environment.

```python
from idmtools.core.platform_factory import Platform

platform = Platform("COMPS", endpoint="...", environment="...")
```

--------------------------------

### Build Ubuntu Base Image

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/singularity/covasim/README.md

Execute this script to build the base Ubuntu image for the project.

```python
python3 build_ubuntu_base.py
```

--------------------------------

### Build and Serve MkDocs Site

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/SKILL.md

Commands to build the MkDocs static site, serve it locally with live reloading, and check for broken links using linkchecker.

```bash
mkdocs build --strict
```

```bash
mkdocs serve
```

```bash
mkdocs build && linkchecker site/
```

--------------------------------

### Show Container Platform CLI Help

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/cli/index.md

Use this command to display help information for the Container platform CLI, including available commands and options.

```bash
idmtools container --help
```

--------------------------------

### Example Override Configuration (Belegost)

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/examples/idmtools_ini_alias/README.md

Shows how to override platform configuration without an idmtools.ini file, tailored for the 'belegost' environment. This method allows for flexible configuration management.

```python
example_override_config_belegost.py
```

--------------------------------

### Install idmtools with COMPS support

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/platforms/comps.md

Install the necessary idmtools package for COMPS platform integration. This can be done using pip.

```bash
pip install idmtools[idm]
# or
pip install idmtools-platform-comps
```

--------------------------------

### Configure COMPS Platform

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/platforms.md

Set up a COMPS platform instance with specific parameters like endpoint, environment, priority, and number of cores.

```python
from idmtools.core.platform_factory import Platform

platform = Platform(
    "COMPS",
    endpoint="https://comps.idmod.org",
    environment="Nibbler",
    priority="Highest",
    num_cores=1
)
```

--------------------------------

### Run Experiment on COMPS Platform

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/platforms.md

Example of creating a COMPS platform instance and running an experiment, with options to wait for completion and filter simulations by tags.

```python
# Create platform
platform = Platform(
    "COMPS",
    endpoint="https://comps.idmod.org",
    environment="Calculon"
)

# Run experiment
experiment.run(platform=platform, wait_until_done=True)

# Filter simulations by tags
simulations = platform.filter_simulations_by_tags(
    suite_id, item_type=ItemType.SUITE,
    tags={"a": lambda v: 1 <= v <= 2, "sim_tag": "test_tag"}, entity_type=True)

# Get experiment details
exp = platform.get_item(exp_id, ItemType.EXPERIMENT)
print(f"Status: {exp.status}")
print(f"Simulations: {len(exp.simulations)}")
```

--------------------------------

### Install idmtools[full] on macOS

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

On macOS, square brackets in pip install commands may need to be escaped with a backslash.

```bash
pip install idmtools\[full\]
```

--------------------------------

### Load Templates from Files

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/models.md

This example shows how to define a template content that can be loaded from a file, demonstrating Jinja2 syntax for variable substitution in a JSON configuration.

```json
# config_template.json
"""
{
    "population": {{population}},
    "parameters": {
        "beta": {{beta}},
        "gamma": {{gamma}}
    },
    "output": {
        "format": "{{output_format}}",
        "directory": "{{output_dir}}"
    }
}
"""

```

--------------------------------

### Force Start Container

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/platforms/container.md

Forces the start of a new or previously stopped container. Use when a container needs to be explicitly restarted.

```python
with Platform("Container", job_directory="DEST", force_start=True) as platform:
    experiment.run(wait_until_done=True)
```

--------------------------------

### Create and Run a Basic Experiment

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/user-guide/creating-simulations.md

This snippet demonstrates the basic workflow for creating a Python task, wrapping it in an experiment, and running it on a specified platform. Ensure 'model.py' exists locally.

```python
from idmtools.core.platform_factory import Platform
from idmtools.entities.experiment import Experiment
from idmtools.entities.simulation import Simulation
from idmtools_models.python.json_python_task import JSONConfiguredPythonTask

# Create platform
platform = Platform('Container', job_directory='anywhere')

# Create a python task that runs a model.py. Make sure model.py exists in local dir
task = JSONConfiguredPythonTask(script_path="model.py")

# Add to experiment (required for commission)
experiment = Experiment.from_task(
    task,
    name="My First Experiment"
)

# Commission
experiment.run(wait_until_done=True, platform=platform)

# Check status
print(f"Status: {experiment.status}")
```

--------------------------------

### Install Package from TestPyPI

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/development/release-process.md

Installs a specific version of an idmtools package from TestPyPI, falling back to the main PyPI if the version is not found.

```bash
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ idmtools==3.x.x
```

--------------------------------

### Run Experiment on Local Slurm Platform

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/api/platforms.md

Example of configuring a local Slurm platform with additional parameters and running an experiment. Includes refreshing the experiment status.

```python
# Create platform
platform = Platform("SLURM_LOCAL", job_directory=".",  mail_user="test@test.com",
                            account="test_acct", mail_type="begin", mem_per_cpu=2048)
)

# Run
experiment.run(platform=platform, wait_until_done=True)

# Check job status
experiment.refresh_status(platform)
```

--------------------------------

### Install idmtools for Slurm

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/README.md

Installs idmtools core, CLI, models, and Slurm platform packages for running simulations in a Slurm cluster.

```bash
pip install idmtools[slurm]
```

--------------------------------

### Install Extra Packages in Container

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/docs/platforms/container.md

Installs specified Python packages into the container at runtime. Ensure packages are available on PyPI or a configured index.

```python
from idmtools.assets import Asset, AssetCollection
from idmtools.core.platform_factory import Platform
from idmtools.entities.command_task import CommandTask
from idmtools.entities.experiment import Experiment
import os

platform = Platform("Container", job_directory="DEST", new_container=True,
                    extra_packages=['astor', 'numpy', 'pytest'],
                    docker_image="ghcr.io/institutefordiseasemodeling/container-rocky-runtime:0.0.6")
command = "python Assets/model_file.py"
task = CommandTask(command=command)

model_asset = Asset(absolute_path=os.path.join("inputs", "extra_packages", "model_file.py"))
common_assets = AssetCollection()
common_assets.add_asset(model_asset)

experiment = Experiment.from_task(task, name="run_with_extra_packages", assets=common_assets)
experiment.run(wait_until_done=True, platform=platform)
```

--------------------------------

### Install idmtools Container Packages

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/MAC_README.md

Install only the idmtools container-specific packages if your focus is on running simulations using the local Docker container platform.

```bash
pip install idmtools[container] --full-reinstall --no-cache-dir --upgrade
```

--------------------------------

### Install Full idmtools Package

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/MAC_README.md

Install or update all idmtools related packages to the latest version. This command ensures you have the complete set of tools.

```bash
pip install idmtools[full] --full-reinstall --no-cache-dir --upgrade
```

--------------------------------

### Top-Level Development Commands

Source: https://github.com/institutefordiseasemodeling/idmtools/blob/main/CLAUDE.md

Common commands for setting up development environments, running tests, performing code quality checks, and building documentation from the repository root.

```bash
# Setup
make setup-dev              # Full dev setup with Docker builds
make setup-dev-no-docker    # Dev setup without Docker builds

# Testing
make test                   # Run tests excluding COMPS and Docker
make test-smoke             # Run smoke tests (fastest)
make test-all               # Run all tests (serial + parallel)
make test-failed            # Rerun only failed tests
make test-comps             # Run COMPS platform tests
make test-docker            # Run Docker platform tests

# Code Quality
make lint                   # Run flake8 on all packages
make clean                  # Clean temporary files
make clean-all              # Deep clean (requires re-running setup-dev)

# Coverage
make coverage               # Generate coverage report
make coverage-report        # View coverage in browser

# Documentation
make build-docs             # Build documentation
make build-docs-server      # Build docs with auto-reload at localhost:8000
```