bioconda/bioconda-recipes
Nov 2024 – Jun 2026
6 Months active
Languages Used
ShellYAMLC++CMakeCbashyaml
Technical Skills
Build SystemC++Package ManagementBuild System ConfigurationBuild SystemsC++ Development
Milot Mirdita
PROFILE
Milot Mirdita
Over six months, contributed to the bioconda/bioconda-recipes repository by delivering seven features and resolving critical build issues across bioinformatics packages. Focused on packaging, build system configuration, and cross-platform compatibility, this work included integrating CUDA support for MMseqs2 and Foldseek, enabling GPU-accelerated workflows, and applying GCC13 compatibility patches to maintain reliable builds. Leveraged C, C++, and CMake to update build scripts, metadata, and dependency management, ensuring reproducible installations and streamlined release management. Improvements to Folddisco and FoldMason packaging enhanced performance and environment reproducibility, supporting researchers with faster onboarding and reduced maintenance overhead in complex software environments.
Overall Statistics
Feature vs Bugs
88%Features
Repository Contributions
11Total
Bugs
1
Commits
11
Features
7
Lines of code
913
Activity Months6
Your Network
639 peopleWork History
June 2026
1 Commits • 1 Features
Jun 1, 2026June 2026: Delivered Folddisco packaging and dependency improvements for bioconda/bioconda-recipes. Updated Folddisco to version 2.9375a2d, along with build script and metadata changes to improve functionality and dependency resolution. This work enhances install reliability, environment reproducibility, and downstream compatibility, supporting faster time-to-value for users. No major bugs reported this month.
1 Commits • 1 Features
Jun 1, 2026June 2026: Delivered Folddisco packaging and dependency improvements for bioconda/bioconda-recipes. Updated Folddisco to version 2.9375a2d, along with build script and metadata changes to improve functionality and dependency resolution. This work enhances install reliability, environment reproducibility, and downstream compatibility, supporting faster time-to-value for users. No major bugs reported this month.
June 2026
October 2025
1 Commits • 1 Features
Oct 1, 2025Monthly summary for 2025-10: Focused on delivering a high-value feature upgrade in bioconda-recipes and stabilizing the FoldMason integration. The work ensures compatibility with the latest FoldMason release and its publication, while delivering performance improvements on AVX2-capable CPUs.
October 2025
1 Commits • 1 Features
Oct 1, 2025Monthly summary for 2025-10: Focused on delivering a high-value feature upgrade in bioconda-recipes and stabilizing the FoldMason integration. The work ensures compatibility with the latest FoldMason release and its publication, while delivering performance improvements on AVX2-capable CPUs.
July 2025
3 Commits • 1 Features
Jul 1, 2025July 2025 (2025-07) monthly summary for bioconda/bioconda-recipes. Focused on stabilizing GCC13 compatibility and delivering an updated MMseqs2 release in the BiocondaRecipes workflow. Key features delivered: - GCC13 compatibility patches applied to two packaging recipes (spacepharer and plass) to fix build failures under GCC13, including patch adjustments to MMseqs2 build and header/CMake policy updates. - MMseqs2 Bioconda Recipe version bump to a new release (18-8cc5): updated version string and SHA256 checksum and reset build number to 0 for a fresh build. Major bugs fixed: - Patch for spacepharer to address GCC13-related build failure (#58053). - Plass compilation fix to align headers and CMake policy with GCC13 (#58052). Overall impact and accomplishments: - Restored reliable, GCC13-compatible builds across targeted architectures, reducing manual maintenance and customer-facing build failures. - Maintained currency of the Bioconda recipe for MMseqs2, enabling users to install the latest release with reproducible builds. - Streamlined repository hygiene by removing obsolete architecture failure logs where irrelevant to current GCC13 compatibility work. Technologies/skills demonstrated: - Packaging patching and patch application in a large bioinformatics ecosystem. - Version management, checksum validation (SHA256) and build-number handling. - Cross-architecture build maintenance and release readiness. Business value: - Improves stability and reproducibility of MMseqs2 deployments via Bioconda, accelerating user onboarding and reducing support overhead. - Enables timely delivery of compatibility fixes and new releases, supporting downstream workflows and pipelines.
3 Commits • 1 Features
Jul 1, 2025July 2025 (2025-07) monthly summary for bioconda/bioconda-recipes. Focused on stabilizing GCC13 compatibility and delivering an updated MMseqs2 release in the BiocondaRecipes workflow. Key features delivered: - GCC13 compatibility patches applied to two packaging recipes (spacepharer and plass) to fix build failures under GCC13, including patch adjustments to MMseqs2 build and header/CMake policy updates. - MMseqs2 Bioconda Recipe version bump to a new release (18-8cc5): updated version string and SHA256 checksum and reset build number to 0 for a fresh build. Major bugs fixed: - Patch for spacepharer to address GCC13-related build failure (#58053). - Plass compilation fix to align headers and CMake policy with GCC13 (#58052). Overall impact and accomplishments: - Restored reliable, GCC13-compatible builds across targeted architectures, reducing manual maintenance and customer-facing build failures. - Maintained currency of the Bioconda recipe for MMseqs2, enabling users to install the latest release with reproducible builds. - Streamlined repository hygiene by removing obsolete architecture failure logs where irrelevant to current GCC13 compatibility work. Technologies/skills demonstrated: - Packaging patching and patch application in a large bioinformatics ecosystem. - Version management, checksum validation (SHA256) and build-number handling. - Cross-architecture build maintenance and release readiness. Business value: - Improves stability and reproducibility of MMseqs2 deployments via Bioconda, accelerating user onboarding and reducing support overhead. - Enables timely delivery of compatibility fixes and new releases, supporting downstream workflows and pipelines.
July 2025
March 2025
1 Commits • 1 Features
Mar 1, 2025March 2025: Spacedust Bioconda Recipe Integration completed for bioconda-recipes. Delivered a full recipe with build scripts, configuration files, and compatibility patches to support modern compilers. Result: end-users can install and run Spacedust for de novo discovery of conserved gene clusters in microbial genomes directly from conda. This work improves reproducibility and lowers setup friction for researchers, aligning with packaging and distribution goals.
March 2025
1 Commits • 1 Features
Mar 1, 2025March 2025: Spacedust Bioconda Recipe Integration completed for bioconda-recipes. Delivered a full recipe with build scripts, configuration files, and compatibility patches to support modern compilers. Result: end-users can install and run Spacedust for de novo discovery of conserved gene clusters in microbial genomes directly from conda. This work improves reproducibility and lowers setup friction for researchers, aligning with packaging and distribution goals.
January 2025
4 Commits • 2 Features
Jan 1, 2025January 2025 monthly summary for bioconda/bioconda-recipes: Two high-impact feature deliveries with packaging improvements and cross-platform enhancements. MMseqs2 packaging stability and release; updated to 17.b804f and removed wget dependency to resolve zlib conflict. Foldseek 10 release: added CUDA support for Linux, updated macOS deployment target for Apple Silicon, and patched Metal compatibility. Impact: improved build reliability, broader platform support, enabling faster sequence analysis for users; reduces potential runtime conflicts and promotes smoother adoption. Technologies/skills demonstrated: dependency management, cross-platform build configuration, CUDA-enabled acceleration readiness, Apple Silicon macOS readiness, packaging hygiene (checksum updates).
4 Commits • 2 Features
Jan 1, 2025January 2025 monthly summary for bioconda/bioconda-recipes: Two high-impact feature deliveries with packaging improvements and cross-platform enhancements. MMseqs2 packaging stability and release; updated to 17.b804f and removed wget dependency to resolve zlib conflict. Foldseek 10 release: added CUDA support for Linux, updated macOS deployment target for Apple Silicon, and patched Metal compatibility. Impact: improved build reliability, broader platform support, enabling faster sequence analysis for users; reduces potential runtime conflicts and promotes smoother adoption. Technologies/skills demonstrated: dependency management, cross-platform build configuration, CUDA-enabled acceleration readiness, Apple Silicon macOS readiness, packaging hygiene (checksum updates).
January 2025
November 2024
1 Commits • 1 Features
Nov 1, 2024November 2024 performance summary for bioconda-recipes: Delivered CUDA-enabled Linux build and packaging upgrade for MMseqs2, enabling GPU-accelerated workflows. Updated to MMseqs2 16.747c6, implemented architecture-friendly build system changes, and refreshed packaging metadata (meta.yaml) with the new version, SHA256, license, and CUDA dependencies to ensure reproducible, GPU-ready distributions.
November 2024
1 Commits • 1 Features
Nov 1, 2024November 2024 performance summary for bioconda-recipes: Delivered CUDA-enabled Linux build and packaging upgrade for MMseqs2, enabling GPU-accelerated workflows. Updated to MMseqs2 16.747c6, implemented architecture-friendly build system changes, and refreshed packaging metadata (meta.yaml) with the new version, SHA256, license, and CUDA dependencies to ensure reproducible, GPU-ready distributions.
Activity
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Quality Metrics
Correctness89.0%
Maintainability87.2%
Architecture83.6%
Performance81.8%
AI Usage20.0%
Skills & Technologies
Programming Languages
CC++CMakeShellYAMLbashyaml
Technical Skills
Build SystemBuild System ConfigurationBuild SystemsCC DevelopmentC++C++ DevelopmentDevOpsPackage ManagementPerformance OptimizationRustSoftware CompilationSoftware Release Managementbuild automationmacOS Development
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