minor fixes for p3a run

src/sp_validation/catalog.py

@@ -235,8 +235,9 @@ def check_invalid(dd, key, val, stats_file, name=None, verbose=False):
     for i in range(len(key)):
         w = dd[key[i]] == val[i]
         n_inv_psf = len(np.where(w)[0])
-        msg = "Invalid {} found for {}/{} = {:.1g}% objects".format(
-            name[i], n_inv_psf, n_all, n_inv_psf / n_all
+        msg = (
+            f"Invalid {name[i]} found for {n_inv_psf}/{n_all}"
+            + f" = {n_inv_psf / n_all:.3%} objects"
         )
         io.print_stats(msg, stats_file, verbose=verbose)
 
@@ -523,6 +524,10 @@ def write_shape_catalog(
         fields = []
         for col, _ in col_info_arr:
             arr = np.asarray(col.array)
+            if str(col.format) == "L":
+                # astropy holds FITS logicals as the characters 'T'/'F'
+                # (84/70); write booleans, not those codes.
+                arr = arr == ord("T")
             if arr.ndim == 2:
                 for idx in range(arr.shape[1]):
                     fields.append((f"{col.name}_{idx}", arr[:, idx]))

src/sp_validation/catalog_builders.py

@@ -159,7 +159,7 @@ def write_hdf5_header(self, hd5file):
             input HDF5 file
 
         """
-        author = os.getenv("USER")
+        author = os.getenv("USER", "unknown")
         software_name = "sp_validation"
         software_version = version(software_name)
         date = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")

src/sp_validation/tests/test_catalog_flag_roundtrip.py

@@ -80,3 +80,44 @@ def test_reduce_mem_never_narrows_integers(reduce_mem):
         assert builder.dtype_out(name, np.dtype(">f8")) == np.dtype(">f8")
     expected = np.float32 if reduce_mem else np.dtype(">f8")
     assert builder.dtype_out("NGMIX_G1_NOSHEAR", np.dtype(">f8")) == expected
+
+
+@pytest.mark.parametrize("extension", [".fits", ".hdf5"])
+def test_mask_columns_roundtrip_as_booleans(tmp_path, extension):
+    """Logical (format "L") mask columns come back as booleans, True = masked.
+
+    astropy holds FITS logicals as the characters 'T'/'F'; the HDF5 writer
+    must not store those character codes (84/70), which every mask cut
+    (``kind: equal, value: False``) would read as masked.
+    """
+    with np.printoptions():
+        params = runpy.run_path(str(ROOT / "scripts/calibration/params.py"))
+    masked = np.array([0, 1, 1, 0], dtype=np.int8)
+    columns = {name: masked for name in params["mask_columns"]}
+    assert all(params["add_cols_pre_cal_format"][name] == "L" for name in columns)
+    # Columns of other formats alongside, as in the real comprehensive catalogue
+    others = {
+        "TILE_ID": np.array([b"200.300", b"200.300", b"201.300", b"201.300"]),
+        "NUMBER": np.arange(len(masked)),
+        "FLAGS": np.array([0, 2, 3, 0]),
+    }
+    path = tmp_path / f"comprehensive{extension}"
+    write_shape_catalog(
+        str(path),
+        np.zeros(len(masked)),
+        np.zeros(len(masked)),
+        np.ones(len(masked)),
+        add_cols=columns | others,
+        add_cols_format=params["add_cols_pre_cal_format"],
+    )
+    if extension == ".fits":
+        written = fits.getdata(path, 1)
+    else:
+        with h5py.File(path, "r") as catalog:
+            written = catalog["data"][:]
+
+    np.testing.assert_array_equal(written["NUMBER"], others["NUMBER"])
+    np.testing.assert_array_equal(written["FLAGS"], others["FLAGS"])
+    for name in columns:
+        assert written[name].dtype == np.bool_, name
+        np.testing.assert_array_equal(written[name], masked.astype(bool), err_msg=name)