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Add Flex GEX support, release tooling, and docs updates #190

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Merged
rob-p merged 21 commits into from
Mar 19, 2026
Merged

Add Flex GEX support, release tooling, and docs updates #190

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0f23336
Merge pull request #188 from COMBINE-lab/main
rob-p Mar 17, 2026
5154110
Add Organism, ProtocolType enums and Flex chemistry schema fields
rob-p Mar 17, 2026
3b8f5dc
Add flex-quant subcommand for 10x Flex GEX pipeline
rob-p Mar 17, 2026
7938d09
Register 10x Flex GEX chemistries in chemistry registry
rob-p Mar 17, 2026
9bac37e
Fix flex-quant: correct piscem subcommand and serde field mapping
rob-p Mar 17, 2026
dc86498
Skip seq_geom_parser validation for piscem-extended geometries
rob-p Mar 18, 2026
7830233
Fix flex-quant: include all probes in t2g and use map-scrna subcommand
rob-p Mar 18, 2026
a81dc74
Remove --struct-constraints from flex-quant
rob-p Mar 18, 2026
09826ed
Revert "Remove --struct-constraints from flex-quant"
rob-p Mar 18, 2026
247b6d3
make clippy happy
rob-p Mar 19, 2026
e03e7f5
Merge pull request #189 from COMBINE-lab/multi-sample-rad
rob-p Mar 19, 2026
a5146f9
update docs
rob-p Mar 19, 2026
c987667
update .gitignore
rob-p Mar 19, 2026
16139c3
update cargo files
rob-p Mar 19, 2026
b73cae9
update url
rob-p Mar 19, 2026
135f412
update url
rob-p Mar 19, 2026
92e67c7
update env
rob-p Mar 19, 2026
5999b50
fix version
rob-p Mar 19, 2026
2070cdd
new cmdlib breaks stuff
rob-p Mar 19, 2026
849e6d6
lock necessary versions
rob-p Mar 19, 2026
5e95dad
fix paths again
rob-p Mar 19, 2026
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5 changes: 1 addition & 4 deletions .github/workflows/test_simpleaf.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ jobs:
if: "!contains(github.event.head_commit.message, 'skip ci')"
strategy:
matrix:
os: [ubuntu-latest, macos-13]
os: [ubuntu-latest, macos-15]
runs-on: ${{ matrix.os }}
steps:
- name: Checkout repository
Expand All @@ -27,9 +27,6 @@ jobs:
override: true
components: rustfmt

- name: Check format
run: cargo fmt -- --check

- name: Build
run: cargo build --verbose --release

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4 changes: 4 additions & 0 deletions .gitignore
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Expand Up @@ -22,6 +22,10 @@ TEST_REF
TEST_REF_CLAPV4
TEST_REF_ROERS
blarg
gencode_v49_simpleaf/
pbmc_1k_v3_test_quant/
pbmc_1k_v3_test_quant_new/
scripts/download_accessions_rush.sh

# macOS Finder metadata
**/.DS_Store
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