OpenFreeEnergy/openfe
Dec 2024 – Jun 2026
9 Months active
Languages Used
PDBPythonSDFYAMLrstBashRSTpy
Technical Skills
CI/CDCode CleanupCode RefactoringComputational ChemistryData ManagementDocumentation
Josh Horton
PROFILE
Josh Horton
Over a 9-month period, contributed to OpenFreeEnergy/openfe by developing and refining advanced molecular simulation workflows. Focused on robust API integration, CLI development, and scientific computing, the work included implementing features such as hybrid topology support, adaptive protocol settings, and automated partial charge generation. Leveraged Python and YAML to enhance configuration management, improve test automation, and streamline data handling. Addressed reliability through deterministic testing, dependency management, and error handling improvements. Integrated external APIs like Cinnabar FEMap and optimized performance for molecular dynamics simulations. These efforts improved reproducibility, configurability, and scalability, supporting both research acceleration and maintainable, user-friendly software engineering.
Overall Statistics
Feature vs Bugs
69%Features
Repository Contributions
72Total
Bugs
11
Commits
72
Features
24
Lines of code
33,291
Activity Months9
Your Network
26 peopleWork History
June 2026
1 Commits • 1 Features
Jun 1, 2026June 2026 monthly summary for OpenFreeEnergy/openfe: Delivered an integration of the Cinnabar FEMap API into the FE calculation pipeline, migrating to the c-f package to improve data handling and calculation accuracy. Strengthened dependency management and test stability by addressing numpy compatibility changes, updating tests for sorted-output references, and rebaselining as needed. Enhanced CI and development workflow with pre-commit automation and environment tweaks (adjusttext), plus release-notes updates for stakeholder visibility. Overall, these efforts reduce manual maintenance, improve data fidelity, and set the project up for scalable feature work in the next sprint.
1 Commits • 1 Features
Jun 1, 2026June 2026 monthly summary for OpenFreeEnergy/openfe: Delivered an integration of the Cinnabar FEMap API into the FE calculation pipeline, migrating to the c-f package to improve data handling and calculation accuracy. Strengthened dependency management and test stability by addressing numpy compatibility changes, updating tests for sorted-output references, and rebaselining as needed. Enhanced CI and development workflow with pre-commit automation and environment tweaks (adjusttext), plus release-notes updates for stakeholder visibility. Overall, these efforts reduce manual maintenance, improve data fidelity, and set the project up for scalable feature work in the next sprint.
June 2026
April 2026
2 Commits • 2 Features
Apr 1, 2026Concise monthly summary for OpenFreeEnergy/openfe (April 2026).
April 2026
2 Commits • 2 Features
Apr 1, 2026Concise monthly summary for OpenFreeEnergy/openfe (April 2026).
December 2025
2 Commits • 1 Features
Dec 1, 2025December 2025 – OpenFreeEnergy/openfe: Delivered key feature to extend hybrid topology simulations with CMAP torsion support (Amber ff19SB), and strengthened reliability with charge consistency tests for the espaloma forcefield. These efforts broaden simulation capabilities, improve accuracy, and reduce drift, delivering tangible business value for users building Amber ff19SB-based workflows.
2 Commits • 1 Features
Dec 1, 2025December 2025 – OpenFreeEnergy/openfe: Delivered key feature to extend hybrid topology simulations with CMAP torsion support (Amber ff19SB), and strengthened reliability with charge consistency tests for the espaloma forcefield. These efforts broaden simulation capabilities, improve accuracy, and reduce drift, delivering tangible business value for users building Amber ff19SB-based workflows.
December 2025
October 2025
5 Commits • 3 Features
Oct 1, 2025In 2025-10, the OpenFreeEnergy/openfe team delivered major performance, configurability, and documentation improvements across the Hybrid Topology Factory (HTF) and adaptive OpenFE workflows. The work focused on accelerating research tempo, improving reliability, and reducing manual tuning through targeted optimizations, tests, and clear user guidance.
October 2025
5 Commits • 3 Features
Oct 1, 2025In 2025-10, the OpenFreeEnergy/openfe team delivered major performance, configurability, and documentation improvements across the Hybrid Topology Factory (HTF) and adaptive OpenFE workflows. The work focused on accelerating research tempo, improving reliability, and reducing manual tuning through targeted optimizations, tests, and clear user guidance.
September 2025
6 Commits • 1 Features
Sep 1, 2025September 2025 OpenFreeEnergy/openfe monthly summary: In September, the team delivered a major CLI mapping overhaul with KartografAtomMapper set as the default, updated defaults for distance, hydrogen mapping, and ring matching to enhance RBFE network planning. We hardened constraint atom mapping error handling with a Counter-based check to prevent multiple deletions and improved exception messages, complemented by tests and release notes updates. These changes improve reliability, debugging efficiency, and user-facing feedback, driving better planning accuracy and faster iteration.
6 Commits • 1 Features
Sep 1, 2025September 2025 OpenFreeEnergy/openfe monthly summary: In September, the team delivered a major CLI mapping overhaul with KartografAtomMapper set as the default, updated defaults for distance, hydrogen mapping, and ring matching to enhance RBFE network planning. We hardened constraint atom mapping error handling with a Counter-based check to prevent multiple deletions and improved exception messages, complemented by tests and release notes updates. These changes improve reliability, debugging efficiency, and user-facing feedback, driving better planning accuracy and faster iteration.
September 2025
April 2025
9 Commits • 4 Features
Apr 1, 2025April 2025 monthly summary for OpenFreeEnergy/openfe. Delivered major feature improvements across restraint geometry, distance geometry robustness, and validation logic; enhanced testing infrastructure for reproducibility and offline testing; strengthened OpenMM integration readiness. Highlights include extensive tests, naming and data-management improvements, and a clearer validation workflow.
April 2025
9 Commits • 4 Features
Apr 1, 2025April 2025 monthly summary for OpenFreeEnergy/openfe. Delivered major feature improvements across restraint geometry, distance geometry robustness, and validation logic; enhanced testing infrastructure for reproducibility and offline testing; strengthened OpenMM integration readiness. Highlights include extensive tests, naming and data-management improvements, and a clearer validation workflow.
February 2025
4 Commits • 1 Features
Feb 1, 2025February 2025 monthly summary for OpenFreeEnergy/openfe. Focused on delivering documentation and CLI guidance for automatic partial charge generation during network planning. No major bugs fixed this month. Impact: improved onboarding and reproducibility of charge-generation workflows, enabling users to configure partial charges via YAML and follow CLI tutorials, which accelerates network planning and reduces configuration errors. Technologies/skills demonstrated: documentation best practices, YAML configuration, CLI/tutorial authoring, and cross-repo collaboration across the OpenFreeEnergy project.
4 Commits • 1 Features
Feb 1, 2025February 2025 monthly summary for OpenFreeEnergy/openfe. Focused on delivering documentation and CLI guidance for automatic partial charge generation during network planning. No major bugs fixed this month. Impact: improved onboarding and reproducibility of charge-generation workflows, enabling users to configure partial charges via YAML and follow CLI tutorials, which accelerates network planning and reduces configuration errors. Technologies/skills demonstrated: documentation best practices, YAML configuration, CLI/tutorial authoring, and cross-repo collaboration across the OpenFreeEnergy project.
February 2025
January 2025
34 Commits • 9 Features
Jan 1, 2025January 2025 OpenFreeEnergy/openfe monthly summary focused on enabling modern dependency compatibility, more reliable CI, and faster network/charge workflows. Key outcomes include pymbar 4 compatibility and stability hardening, CLI and network planning alignment with new behavior, parallel processing for charge calculations, expanded test coverage and determinism, and updated documentation with pinned dependencies to maintain compatibility. These efforts increase reliability, speed up end-to-end simulations, and reduce integration risk for downstream users.
January 2025
34 Commits • 9 Features
Jan 1, 2025January 2025 OpenFreeEnergy/openfe monthly summary focused on enabling modern dependency compatibility, more reliable CI, and faster network/charge workflows. Key outcomes include pymbar 4 compatibility and stability hardening, CLI and network planning alignment with new behavior, parallel processing for charge calculations, expanded test coverage and determinism, and updated documentation with pinned dependencies to maintain compatibility. These efforts increase reliability, speed up end-to-end simulations, and reduce integration risk for downstream users.
December 2024
9 Commits • 2 Features
Dec 1, 2024December 2024 monthly summary for OpenFreeEnergy/openfe. Focused on delivering reliable RBFE tooling improvements, expanding charge-change support, and maintaining a clean, testable codebase. Key outcomes include more stable test results, enhanced network planning for charged transformations, and streamlined CLI workflows, all contributing to faster release cycles and higher confidence in results.
9 Commits • 2 Features
Dec 1, 2024December 2024 monthly summary for OpenFreeEnergy/openfe. Focused on delivering reliable RBFE tooling improvements, expanding charge-change support, and maintaining a clean, testable codebase. Key outcomes include more stable test results, enhanced network planning for charged transformations, and streamlined CLI workflows, all contributing to faster release cycles and higher confidence in results.
December 2024
Activity
Loading activity data...
Quality Metrics
Correctness92.0%
Maintainability91.6%
Architecture88.8%
Performance86.6%
AI Usage21.2%
Skills & Technologies
Programming Languages
BashPDBPythonRSTSDFYAMLpypythonreStructuredTextrst
Technical Skills
API DesignAPI DevelopmentAPI IntegrationAPI developmentAPI integrationBug FixCI/CDCI/CD OptimizationCLICLI DevelopmentCode CleanupCode RefactoringCommand-Line Interface (CLI) DevelopmentComputational ChemistryConfiguration
Repositories Contributed To
Overview of all repositories you've contributed to across your timeline