Introduce AssayCode and the DotMatch 0.2.0 assay platform - #54

Draft

dnncha wants to merge 93 commits into

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codex/industry-domination-implementation

Commits on Jul 13, 2026

Commits on Jul 14, 2026

Add AssayCode platform identity
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Add AssayCode platform identity
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fbff021
Add AssayCode compatibility tests
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Add AssayCode platform guide
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Install AssayCode command with DotMatch
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Add AssayCode to documentation
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c967444
Position AssayCode as the DotMatch platform
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f38cd06
Add AssayScript v2 compiler foundation
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Expose AssayScript compilation in AssayCode
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Test AssayScript compiler contracts
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Add calibrated and joint decoding foundation
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Test calibrated and joint decoding
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d215c39
Add streaming assay quality monitor
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6a836fb
Expose streaming AssayCode watch command
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ee39e57
Test streaming assay watch decisions
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6d3ef62
Test AssayCode in Bioconda recipe
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7cd3e5c
Rewrite paper around auditable assay compilation
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Add assay decoding references
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Document AssayCode compiler and monitoring
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Record AssayCode experimental evidence boundary
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Add AssayCode readiness gate
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Gate AssayCode release readiness
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Align AssayCode readiness claim check
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Align rewritten paper with JOSS structure
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3dfdfcd
Repair and extend Bioconda AssayCode smoke tests
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ed89820
Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Prepare AssayCode 0.2.0 release metadata
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Align AssayCode 0.2.0 version
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Align AssayCode 0.2.0 version
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Align AssayCode 0.2.0 version
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Prepare 0.2.0 distribution record
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Align site lockfile with 0.2.0
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1ab824e
Document AssayCode 0.2.0 changes
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Correct 0.2.0 packaging and Bioconda handoff
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Align preferred citation with rewritten paper
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Add calibrated decoding file interfaces
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Expose calibrated AssayCode decoding workflow
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Test calibrated decoding CLI workflow
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Gate calibrated AssayCode CLI workflow
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Document calibrated AssayCode evaluation CLI
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Add deterministic assay panel simulation
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Test deterministic assay simulation
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Expose assay panel simulation in AssayCode CLI
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Exercise AssayCode simulation CLI
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Enforce integer calibration counts
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Test strict abundance prior counts
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Document experimental assay simulation
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Record AssayCode digital twin
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Gate assay simulation assets
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Describe experimental assay digital twin
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Bound assay simulation scientific claims
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Rebrand public site around AssayCode
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Update AssayCode site metadata
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Gate AssayCode site positioning
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Register AssayCode and AssayScript branding
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Describe AssayCode distribution identity
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Lead README with AssayCode platform
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Keep compatibility wording machine-checkable
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Align posterior assertion with selective threshold
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Smoke test the 0.2.0 container version
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0b1c9c3
Distinguish current and future BioContainers tags
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857445c
Repair and extend AssayCode readiness gate
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0b798ee
Preserve package metadata contract
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Add AssayCode dual-package Bioconda handoff
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Add AssayCode dual-package Bioconda handoff
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Add AssayCode dual-package Bioconda handoff
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Add AssayCode dual-package Bioconda handoff
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Fix Bioconda handoff regex parsing
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Fix Bioconda handoff regex parsing
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Gate both Bioconda package coordinates
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Require AssayCode Bioconda handoff assets
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Document dual-package Bioconda rollout
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Record dual-package Bioconda strategy
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Track AssayCode Bioconda coordinate
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Verify both Bioconda package coordinates
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Test AssayCode distribution verification
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Explain dual-package install strategy
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Use portable Bioconda handoff example path
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Align 0.2 citation discovery metadata
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Commits on Jul 15, 2026

Harden quickstart and release version gates
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989365c
Repair source blobs in hosted PR branch
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