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Merge pull request #83 from metabarcoding/push-xssnppvunmlq

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Push xssnppvunmlq
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coissac
2026-02-09 09:58:06 +01:00
committed by GitHub
parent 43d6cbe56a d00ab6f83a
commit 09d437d10f
2 changed files with 18 additions and 11 deletions
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16
Makefile
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@@ -141,9 +141,19 @@ jjpush:
echo "$(BLUE)→ Documenting version bump commit...$(NC)"; \
jj auto-describe; \
echo "$(BLUE)→ Generating release notes from $$previous_tag to current commit...$(NC)"; \
if command -v orla >/dev/null 2>&1; then \
release_message=$$(ORLA_MAX_TOOL_CALLS=50 jj log -r "$$previous_tag::@" -T 'commit_id.short() ++ " " ++ description' | \
orla agent -m ollama:qwen3-coder-next:latest "synthétise en anglais l'ensemble des commits présentés en un message de nouvelle version pour ma page GitHub. Tu détailleras précisément les changements, sans exposer de code, et tu éviteras toute redondance dans le texte généré."); \
if command -v orla >/dev/null 2>&1 && command -v jq >/dev/null 2>&1; then \
release_json=$$(ORLA_MAX_TOOL_CALLS=50 jj log -r "$$previous_tag::@" -T 'commit_id.short() ++ " " ++ description' | \
orla agent -m ollama:qwen3-coder-next:latest \
"Summarize the following commits into a GitHub release note for version $$version. Ignore commits related to version bumps, .gitignore changes, or any internal housekeeping that is irrelevant to end users. Describe each user-facing change precisely without exposing code. Eliminate redundancy. Output strictly valid JSON with no surrounding text, using this exact schema: {\"title\": \"<short release title>\", \"body\": \"<detailed markdown release notes>\"}"); \
release_json=$$(echo "$$release_json" | sed -n '/^{/,/^}/p'); \
release_title=$$(echo "$$release_json" | jq -r '.title // empty') ; \
release_body=$$(echo "$$release_json" | jq -r '.body // empty') ; \
if [ -n "$$release_title" ] && [ -n "$$release_body" ]; then \
release_message="$$release_title"$$'\n\n'"$$release_body"; \
else \
echo "$(YELLOW)⚠ JSON parsing failed, falling back to raw output$(NC)"; \
release_message="Release $$version"$$'\n\n'"$$release_json"; \
fi; \
else \
release_message="Release $$version"; \
fi; \

13
obitests/obitools/obisuperkmer/test.sh
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@@ -230,19 +230,16 @@ else
((failed++))
fi
# Test 12: Verify super k-mers are shorter than or equal to parent sequences
# Test 12: Verify each super k-mer length is >= k (default k=31)
((ntest++))
# Count nucleotides in input sequences (excluding headers)
input_bases=$(grep -v "^>" "${TEST_DIR}/test_sequences.fasta" | tr -d '\n' | wc -c)
# Count nucleotides in output sequences (excluding headers)
output_bases=$(grep -v "^>" "${TMPDIR}/output_default.fasta" | tr -d '\n' | wc -c)
min_len=$(grep -v "^>" "${TMPDIR}/output_default.fasta" | awk '{print length}' | sort -n | head -1)
if [ "$output_bases" -le "$input_bases" ]
if [ "$min_len" -ge 31 ]
then
log "$MCMD: super k-mer total length <= input length OK"
log "$MCMD: all super k-mers have length >= k OK"
((success++))
else
log "$MCMD: super k-mer total length > input length - failed"
log "$MCMD: some super k-mers shorter than k ($min_len < 31) - failed"
((failed++))
fi