add back scripts to installation

MANIFEST.in

@@ -1,4 +1,5 @@
 include *.md
+include scripts/*
 include hera_cal/VERSION
 include hera_cal/GIT_INFO
 recursive-include hera_cal/data *

pyproject.toml

@@ -62,6 +62,35 @@ dev = [
     "ruff",
 ]
 
+[tool.setuptools]
+script-files = [
+    "scripts/apply_cal.py",
+    "scripts/auto_reflection_run.py",
+    "scripts/baseline_chunker.py",
+    "scripts/chunk_files.py",
+    "scripts/delay_filter_run.py",
+    "scripts/extract_autos.py",
+    "scripts/extract_hh.py",
+    "scripts/flag_all.py",
+    "scripts/lstbin_run.py",
+    "scripts/lstbin_simple.py",
+    "scripts/model_calibration_run.py",
+    "scripts/multiply_gains.py",
+    "scripts/noise_from_autos.py",
+    "scripts/post_redcal_abscal_run.py",
+    "scripts/query_ex_ants.py",
+    "scripts/red_average.py",
+    "scripts/redcal_run.py",
+    "scripts/select_spw_ranges.py",
+    "scripts/smooth_cal_run.py",
+    "scripts/subselect.py",
+    "scripts/throw_away_flagged_antennas.py",
+    "scripts/time_average.py",
+    "scripts/time_chunk_from_baseline_chunks_run.py",
+    "scripts/tophat_frfilter_run.py",
+    "scripts/transfer_flags.py"
+]
+
 [tool.pytest]
 addopts = "--ignore=scripts --cov=hera_cal --cov-config=.coveragerc"