microlens-submit 0.17.6

A tool for managing and submitting microlensing solutions

microlens-submit

A stateful submission toolkit for the RGES-PIT Microlensing Data Challenge.

microlens-submit provides a robust, version-controlled workflow for managing, validating, and packaging your challenge submission over a long period. It supports both a programmatic Python API and a full-featured Command Line Interface (CLI) for language-agnostic use.

Full documentation is hosted on Read the Docs. A comprehensive tutorial notebook is available at docs/Submission_Tool_Tutorial.ipynb. Challenge participants who prefer not to use this tool can consult the Submission Manual for the manual submission format.

Key Features

• Persistent Projects: Treat your submission as a local project that you can load, edit, and save over weeks or months.
• Python API & CLI: Use the tool directly in your Python analysis scripts or via the command line.
• Solution Management: Easily add, update, and deactivate degenerate solutions for any event without losing your work history.
• Active Solution Control: Quickly list just the active solutions or mark all solutions inactive in one call.
• Automatic Validation: Aggressive data validation powered by Pydantic ensures your submission is always compliant with the challenge rules.
• Parameter Validation: Centralized validation logic checks parameter completeness, types, and physical consistency based on model type and higher-order effects.
• Rich Documentation: Notes field supports Markdown formatting for creating detailed, structured documentation and submission dossiers.
• Environment Capture: Automatically records your Python dependencies for each specific model fit, ensuring reproducibility.
• Optional Posterior Storage: Record the path to posterior samples for any solution.
• Simple Export: Packages all your active solutions into a clean, standardized .zip archive for final submission.
• Bulk Import: Import multiple solutions at once from a CSV file using the import-solutions CLI command. Supports column mapping, alias handling, duplicate handling, notes, dry-run, and validation options.

Installation

The package is available on PyPI:

pip install microlens-submit

Quickstart Using the Command Line Interface (CLI)

The CLI is the recommended way to interact with your submission project.

You can pass --no-color to any command if your terminal does not support ANSI colors.

Windows note: If microlens-submit is not found after pip install, your Python Scripts folder is likely missing from PATH. Try py -m pip install microlens-submit and run py -m microlens_submit.cli --help, or add the Scripts path shown by py -m pip show -f microlens-submit to PATH.

1. Initialize your project:

   microlens-submit init --team-name "Planet Pounders" --tier "experienced" ./my_submission
   cd ./my_submission
   

   If you prefer to initialize inside an existing folder, run microlens-submit init without a path after cd into it.

   To pass validation, you need to have provided a repo_url and hardware_info to the project and have a git project initialized in your sumission-project directory. On Roman Nexus, you can use microlens-submit nexus-init to auto-populate hardware info.

   microlens-submit set-repo-url <url> ./
   microlens-submit set-hardware-info --cpu-details "intel i7 xxx" --ram-gb 32 ./
   # if your git repo lives elsewhere:
   microlens-submit set-git-dir /path/to/repo ./
   

2. Add a new solution to an event:

   microlens-submit add-solution ogle-2025-blg-0042 1S2L \
       --param t0=555.5 \
       --param u0=0.1 \
       --param tE=25.0 \
       --notes "This is a great fit!"
   

   Model types must be one of 1S1L, 1S2L, 2S1L, 2S2L, 1S3L, 2S3L, or other. This will create a new solution and print its unique solution_id.

   You can run the same command with --dry-run first to verify the parsed input without saving anything.

3. Bulk import multiple solutions from a CSV file:

   microlens-submit import-solutions tests/data/test_import.csv --dry-run
   

   See the file tests/data/test_import.csv for a comprehensive example covering all features and edge cases. You can use this file as a template for your own imports.

4. Deactivate a solution that didn't work out: microlens-submit deactivate <solution_id>

5. List all solutions for an event: microlens-submit list-solutions ogle-2025-blg-0042

6. Validate solutions and check for issues: microlens-submit validate-solution <solution_id>

7. Export your final submission: microlens-submit export final_submission.zip

Note: When you add a solution, it's automatically validated and any warnings are displayed. Use --dry-run to check validation without saving.

Using the Python API

For those who want to integrate the tool directly into their Python analysis pipeline.

import microlens_submit

# Load or create the project
sub = microlens_submit.load(project_path="./my_challenge_submission")
sub.team_name = "Planet Pounders"
sub.tier = "experienced"

# Get an event and add a solution
evt = sub.get_event("ogle-2025-blg-0042")
params = {"t0": 555.5, "u0": 0.1, "tE": 25.0}
sol = evt.add_solution(model_type="1S2L", parameters=params)

# Record compute info for this specific run
sol.set_compute_info(cpu_hours=15.5)
sol.notes = "This fit was generated from our Python script."

# Save progress to disk
sub.save()

# When ready, export the final package
sub.export("final_submission.zip")

Development

The full development plan can be found in agents.md. Contributions are welcome!

To build and test this project, install the development dependencies using either pip install -e .[dev] or pip install -r requirements-dev.txt. These packages are required to run the test suite and are listed in requirements-dev.txt. After installing the dependencies, run pre-commit install to set up the Git hooks for automatic formatting and linting. The development environment needs the following Python libraries.

Core Dependencies:

• typer[all]: For building the powerful command-line interface. The [all] extra ensures shell completion support is included.
• pydantic: For aggressive data validation and settings management.

Testing Dependencies:

• pytest: The standard framework for testing Python code.
• pytest-cov: To measure test coverage.

Packaging & Distribution Dependencies:

• build: For building the package from the pyproject.toml file.
• twine: For uploading the final package to PyPI.

Test Data

A comprehensive test CSV file is provided at tests/data/test_import.csv. This file is used in the test suite and can be copied or adapted for your own bulk imports or for development/testing purposes.

Citation

If you use microlens-submit in your research, please cite the project using the metadata provided in the CITATION.cff file. Most reference managers can import this file directly.

Bibtex:

@software{malpas_2025_18601472,
  author       = {Malpas, Amber},
  title        = {microlens-submit},
  month        = oct,
  year         = 2025,
  publisher    = {Zenodo},
  version      = {v0.16.3},
  doi          = {10.5281/zenodo.18601472},
  url          = {https://doi.org/10.5281/zenodo.18601472},
}

Cite without version: Malpas, A. (2025). microlens-submit. Zenodo. https://doi.org/10.5281/zenodo.17459752

Cite current version: Malpas, A. (2025). microlens-submit (v0.16.3). Zenodo. https://doi.org/10.5281/zenodo.17468488