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Fix broken GitHub Actions CI: 429 rate limiting, empty workflow, stale PyPI version #259

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Fix broken GitHub Actions CI: 429 rate limiting, empty workflow, stale PyPI version #259

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9b10799
Initial plan
Copilot Apr 7, 2026
b8bfe50
Fix broken GitHub Actions CI: handle 429 rate limiting, remove empty …
Copilot Apr 7, 2026
8107437
Add diagnostic file-size and head printout at end of get_data.sh
Copilot Apr 7, 2026
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37 changes: 0 additions & 37 deletions .github/workflows/test-workflow.yml
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2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

setuptools.setup(
name="massql",
version="2026.03.14",
version="2026.04.07",
author="Mingxun Wang",
author_email="mwang87@gmail.com",
description="Mass spectrometry query language python implementation",
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25 changes: 21 additions & 4 deletions tests/get_data.sh
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Original file line number Diff line number Diff line change
@@ -1,14 +1,17 @@
mkdir -p data
cd data

# Rate limit: at most 10 files/minute => sleep 6s between downloads.
# massiveproxy.gnps2.org enforces per-IP rate limiting (~1 request per 70 seconds).
# Use --retry-on-http-error=429 with exponential backoff (--waitretry=120, --tries=10)
# so wget retries automatically after waiting long enough for the rate limit to reset.
download() {
wget --no-verbose --tries=3 --waitretry=5 --output-document="$1" "$2"
sleep 6
wget --no-verbose --tries=10 --waitretry=120 --retry-on-http-error=429 --output-document="$1" "$2"
sleep 5
}

download GNPS00002_A3_p.mzML "https://massiveproxy.gnps2.org/massiveproxy/MSV000084494/ccms_peak/raw/GNPS00002_A3_p.mzML"
download GNPS00002_A3_p.mzml "https://massiveproxy.gnps2.org/massiveproxy/MSV000084494/ccms_peak/raw/GNPS00002_A3_p.mzML"
# mzml (lowercase) is the same file as mzML - copy to avoid an extra rate-limited request
cp GNPS00002_A3_p.mzML GNPS00002_A3_p.mzml
download GNPS00002_A10_n.mzML "https://massiveproxy.gnps2.org/massiveproxy/MSV000084494/ccms_peak/raw/GNPS00002_A10_n.mzML"
download QC_0.mzML "https://massiveproxy.gnps2.org/massiveproxy/MSV000085852/ccms_peak/QC_raw/QC_0.mzML"
download bld_plt1_07_120_1.mzML "https://massiveproxy.gnps2.org/massiveproxy/MSV000085944/ccms_peak/raw_data/bld_plt1_07_120_1.mzML"
Expand All @@ -28,3 +31,17 @@ download MMSRG_027.mzML "https://massiveproxy.gnps2.org/massiveproxy/MSV00008826
download featurelist_pos.mgf "https://massiveproxy.gnps2.org/massiveproxy/MSV000086995/updates/2022-01-18_mwang87_e619431a/peak/bahbobeh/featurelist_pos.mgf"
download GT15A.mzML "https://massiveproxy.gnps2.org/massiveproxy/MSV000087048/ccms_peak/Green_Tea_manuscript_data/GT15A.mzML"
download PLT2_B1.mzML "https://massiveproxy.gnps2.org/massiveproxy/MSV000088800/ccms_peak/NRRL_PLT2_czapek_solid_raw/PLT2_B1.mzML"

# --- Diagnostic: print file sizes and first 5 lines of each downloaded file ---
echo ""
echo "=== Downloaded file sizes ==="
ls -lh .

echo ""
echo "=== File heads for debugging ==="
for f in *.mzML *.mzml *.mzXML *.mgf *.json; do
[ -f "$f" ] || continue
echo ""
echo "--- $f ($(wc -c < "$f") bytes) ---"
head -5 "$f"
done
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