Pin DayOA 1.0.0 release

Author: iamh2o

config/daylily_available_repositories.yaml

@@ -7,7 +7,7 @@ repositories:
     description: "Primary whole genome and multiomics workflows."
     https_url: https://github.com/Daylily-Informatics/daylily-omics-analysis.git
     ssh_url: git@github.com:Daylily-Informatics/daylily-omics-analysis.git
-    default_ref: 0.7.763
+    default_ref: 1.0.0
     relative_path: daylily-omics-analysis
     analysis_commands:
       - command_id: illumina_snv_alignstats
@@ -329,7 +329,7 @@ repositories:
           - ILMN
         compatible_data_modes:
           - run_directory_mount
-        git_tag: 0.7.763
+        git_tag: 1.0.0
         no_containerized: false
       - command_id: illumina_bclconvert
         display_name: "Illumina BCL Convert"
@@ -356,7 +356,7 @@ repositories:
           - ILMN
         compatible_data_modes:
           - run_directory_mount
-        git_tag: 0.7.763
+        git_tag: 1.0.0
         no_containerized: false
       - command_id: ont_run_qc
         display_name: "ONT Run QC"
@@ -383,7 +383,7 @@ repositories:
           - ONT
         compatible_data_modes:
           - run_directory_mount
-        git_tag: 0.7.763
+        git_tag: 1.0.0
         no_containerized: false
       - command_id: ultima_run_qc
         display_name: "Ultima Run QC"
@@ -410,7 +410,7 @@ repositories:
           - ULTIMA
         compatible_data_modes:
           - run_directory_mount
-        git_tag: 0.7.763
+        git_tag: 1.0.0
         no_containerized: false
   rna-seq-star-deseq2:
     display_name: "RNA-seq STAR + DESeq2"

daylily_ec/resources/payload/config/daylily_available_repositories.yaml

@@ -7,7 +7,7 @@ repositories:
     description: "Primary whole genome and multiomics workflows."
     https_url: https://github.com/Daylily-Informatics/daylily-omics-analysis.git
     ssh_url: git@github.com:Daylily-Informatics/daylily-omics-analysis.git
-    default_ref: 0.7.763
+    default_ref: 1.0.0
     relative_path: daylily-omics-analysis
     analysis_commands:
       - command_id: illumina_snv_alignstats
@@ -329,7 +329,7 @@ repositories:
           - ILMN
         compatible_data_modes:
           - run_directory_mount
-        git_tag: 0.7.763
+        git_tag: 1.0.0
         no_containerized: false
       - command_id: illumina_bclconvert
         display_name: "Illumina BCL Convert"
@@ -356,7 +356,7 @@ repositories:
           - ILMN
         compatible_data_modes:
           - run_directory_mount
-        git_tag: 0.7.763
+        git_tag: 1.0.0
         no_containerized: false
       - command_id: ont_run_qc
         display_name: "ONT Run QC"
@@ -383,7 +383,7 @@ repositories:
           - ONT
         compatible_data_modes:
           - run_directory_mount
-        git_tag: 0.7.763
+        git_tag: 1.0.0
         no_containerized: false
       - command_id: ultima_run_qc
         display_name: "Ultima Run QC"
@@ -410,7 +410,7 @@ repositories:
           - ULTIMA
         compatible_data_modes:
           - run_directory_mount
-        git_tag: 0.7.763
+        git_tag: 1.0.0
         no_containerized: false
   rna-seq-star-deseq2:
     display_name: "RNA-seq STAR + DESeq2"

docs/plans/run_directory_mounting_ledger.md

@@ -54,7 +54,7 @@ Gate 0 status: `SUCCESS`
 | DOC-001 | Docs | Update DayEC/DayOA docs and examples for run mounts, run analysis, BCL Convert, and cleanup safety. | `SUCCESS` | `feature_implementation` | Gate 5 | orchestrator | `docs/cli_reference.md`; DayOA `docs/ops/multiqc_qc_targets.md`, `docs/ops/tests.md`, `docs/catalog_of_tools.md`; `git diff --check` passed in both repos. |  | Operator docs describe mount lifecycle commands, mounted staging fields, run-context QC, and BCL Convert run outputs. |
 | QA-001 | QA | Run focused and broad local tests across implemented DayEC, DayOA, and Ursa PR #3 surfaces. | `SUCCESS` | `contract_test` | Gate 5 | orchestrator | DayEC `python -m pytest -q` -> `844 passed, 7 skipped`; DayOA focused pytest -> `10 passed`; DayOA BCL shell suite -> `11 passed`; Ursa PR #3 `python -m pytest -q` -> `312 passed, 2 skipped`; Ursa PR #3 `python -m ruff check ...` and `git diff --check` passed. |  | Local validation is green except DayOA Snakemake dry-run could not run because Snakemake is unavailable in this shell. |
 | LIVE-001 | Live QA | Run live FSx DRA smoke on a designated non-production cluster. | `FAIL` | `integration_runtime_failure` | Gate 5 | orchestrator | User approved live mount attempt for profile `lsmc`, region `us-west-2`, cluster `may26-d`, run prefixes `20260512_LH01106_0006_A23K3H2LT4` and `20260512_LH01106_0007_B23K5JKLT4`. `daylily-ec --json mount rundir ... 20260512_LH01106_0006_A23K3H2LT4` failed with AWS `UnsupportedOperation`: `This file system does not support data repository associations.` `aws fsx describe-file-systems` resolved `fs-0c43ddf4b70dc87d8`, `FileSystemType=LUSTRE`, `DeploymentType=SCRATCH_2`; `describe-data-repository-associations` and `daylily-ec mounts list` both returned no associations/mounts. | `may26-d` uses FSx for Lustre `SCRATCH_2` with filesystem-level `DataRepositoryConfiguration`; AWS does not support creating additional DRAs for this filesystem. | No run directory mounts were created. Retry requires a cluster/filesystem deployment that supports FSx data repository associations. |
-| REL-001 | Release | Prepare major bare-semver release plan: DayEC `3.0.0`, DayOA next major from non-`v` tags, Ursa next major from resolved repo. | `SUCCESS` | `plan_amendment` | Gate 5 | orchestrator | Non-`v` semver tags inspected: DayEC latest `2.3.4`; DayOA latest `0.7.763`; Ursa implementation target is now PR #3 base `46b5b10` in `/Users/jmajor/.codex/worktrees/run-directory-mounts-ursa-pr3/daylily-ursa`. |  | Planned release targets are DayEC `3.0.0`, DayOA `1.0.0`, and Ursa `3.0.0` against the PR #3 worktree. |
+| REL-001 | Release | Prepare major bare-semver release plan: DayEC `3.0.0`, DayOA next major from non-`v` tags, Ursa next major from resolved repo. | `SUCCESS` | `plan_amendment` | Gate 5 | orchestrator | Non-`v` semver tags inspected: DayEC latest `2.3.4`; DayOA latest `0.7.763`; Ursa implementation target is now PR #3 base `46b5b10` in `/Users/jmajor/.codex/worktrees/run-directory-mounts-ursa-pr3/daylily-ursa`. Follow-up release execution: DayOA `1.0.0` is the release tag for the run-directory analysis contract, and DayEC catalog pins were updated to use `1.0.0`. |  | Release targets are DayEC `3.0.0`, DayOA `1.0.0`, and Ursa `3.0.0` against the PR #3 worktree; release is proceeding by explicit user direction even though `LIVE-001` remains `FAIL`. |
 
 ## Gate 4 Ursa Reopen
 
@@ -83,4 +83,4 @@ After the original terminal report, the user made `/Users/jmajor/projects/daylil
 - Cleanup: the nine approved `lsmc-dayoa-omics-analysis-us-west-2` staged prefixes were deleted after dry-run evidence and separate user confirmation; final object counts are zero.
 - Ursa status: the original checkout `/Users/jmajor/projects/daylily/daylily-ursa` remains dirty with user-owned changes; implementation is complete in the PR #3 worktree `/Users/jmajor/.codex/worktrees/run-directory-mounts-ursa-pr3/daylily-ursa` on `codex/run-directory-mounts-ursa-pr3`.
 - Live AWS result: the approved `may26-d` live DRA mount attempt failed before creating any association because FSx `fs-0c43ddf4b70dc87d8` is Lustre `SCRATCH_2` and AWS returned `UnsupportedOperation` for `CreateDataRepositoryAssociation`.
-- Publish status: implementation branches were committed and pushed: DayEC `codex/run-directory-mounts` at `360f6597`, DayOA `codex/dayoa-run-directory-mounts` at `47f2c66`, and Ursa PR #3 worktree branch `codex/run-directory-mounts-ursa-pr3` at `9d4f592`. Release tags were not created or pushed because the live DRA smoke row remains `BLOCKED`.
+- Publish status: implementation branches were committed and pushed: DayEC `codex/run-directory-mounts`, DayOA `codex/dayoa-run-directory-mounts`, and Ursa PR #3 worktree branch `codex/run-directory-mounts-ursa-pr3`. Follow-up release tags are DayOA `1.0.0`, DayEC `3.0.0`, and Ursa `3.0.0`; the release proceeds by explicit user direction while `LIVE-001` remains `FAIL`.