Get rid of the - on flags in API

src/pint/models/jump.py

@@ -209,7 +209,7 @@ def add_jump_and_flags(self, toa_flags, flag="gui_jump", flag_value=None):
         """
         in_use = set()
         for pm in self.jumps:
-            if pm.flag == "-" + flag:
+            if pm.flag == flag:
                 in_use.add(pm.flag_value)
         if flag_value is None:
             i = 1
@@ -231,7 +231,7 @@ def add_jump_and_flags(self, toa_flags, flag="gui_jump", flag_value=None):
         param = maskParameter(
             name="JUMP",
             index=i,
-            flag="-" + flag,
+            flag=flag,
             flag_value=flag_value,
             value=0.0,
             units="second",

src/pint/models/parameter.py

@@ -42,6 +42,7 @@
     time_to_longdouble,
     time_to_mjd_string,
 )
+from pint.toa import FlagDict
 from pint.utils import split_prefixed_name
 
 log = logging.getLogger(__name__)
@@ -1529,14 +1530,7 @@ def validate(flag, flag_value):
         elif flag == "tel":
             return get_observatory(flag_value).name
         else:
-            if not isinstance(flag_value, str):
-                raise ValueError(
-                    f"When selecting by {flag} one must supply a "
-                    f"string not {flag_value}"
-                )
-            # FlagDict.validate() once #1074 is merged.
-            if len(flag_value.split()) != 1:
-                raise ValueError(f"Flag value {repr(flag_value)} cannot occur in TOAs.")
+            FlagDict.check_allowed_value(flag, flag_value)
             return flag_value
 
     @staticmethod
@@ -1568,11 +1562,7 @@ def flag(self, flag):
             )
         else:
             flag = flag.lower()
-            if flag not in self.allowed_non_flags and not flag.startswith("-"):
-                raise ValueError(
-                    f"Flags must be indicated with -, and the only "
-                    f"non-flags allowed are {maskParameter.allowed_non_flags}."
-                )
+            FlagDict.check_allowed_key(flag)
             self._flag = flag
 
     @property
@@ -1633,10 +1623,10 @@ def from_parfile_line(self, line):
         -----
         The accepted formats for most flags::
 
-            NAME flag flag_value parameter_value
-            NAME flag flag_value parameter_value fit_flag
-            NAME flag flag_value parameter_value fit_flag uncertainty
-            NAME flag flag_value parameter_value uncertainty
+            NAME -flag flag_value parameter_value
+            NAME -flag flag_value parameter_value fit_flag
+            NAME -flag flag_value parameter_value fit_flag uncertainty
+            NAME -flag flag_value parameter_value uncertainty
 
         If the flag is one of MJD or FREQ then::
 
@@ -1659,13 +1649,23 @@ def from_parfile_line(self, line):
             return False
 
         try:
-            self.flag = k[1]
+            flag = k[1].lower()
         except IndexError:
             raise ValueError(
                 "{}: No flag found on timfile line {!r}".format(self.name, line)
             )
+        if flag in self.allowed_non_flags:
+            self.flag = flag
+        elif not flag.startswith("-"):
+            raise ValueError(
+                f"Flags must be indicated with -, and the only "
+                f"non-flags allowed are {maskParameter.allowed_non_flags}."
+            )
+        else:
+            # Strip leading -
+            self.flag = flag[1:]
 
-        if self.flag in self.wants_two_values:
+        if flag in self.wants_two_values:
             flag_value_str = k[2], k[3]
             len_flag_v = 2
         else:
@@ -1703,7 +1703,11 @@ def as_parfile_line(self):
             name = self.origin_name
         else:
             name = self.use_alias
-        line = "%-15s %s " % (name, self.flag)
+        if self.flag in self.allowed_non_flags:
+            flag = self.flag
+        else:
+            flag = "-" + self.flag
+        line = "%-15s %s " % (name, flag)
         if isinstance(self.flag_value, str):
             line += self.flag_value
         else:

src/pint/models/timing_model.py

@@ -1289,9 +1289,9 @@ def jump_flags_to_params(self, toas, flag="jump"):
 
         new_jumps = []
         # check if any TOAs are jumped
-        jumped = set(
-            flag_dict[flag] for flag_dict in toas.table["flags"] if flag in flag_dict
-        )
+        jumped = set(toas[flag])
+        if "" in jumped:
+            jumped.remove("")
         if not jumped:
             log.info("No jump flags to process from .tim file")
             return new_jumps
@@ -1318,7 +1318,7 @@ def jump_flags_to_params(self, toas, flag="jump"):
             param = maskParameter(
                 name="JUMP",
                 index=next_free_index,
-                flag="-" + flag,
+                flag=flag,
                 flag_value=j,
                 value=0.0,
                 units="second",

tests/test_dmefac_dmequad.py

@@ -38,7 +38,7 @@ def test_no_efact_noequad(test_toas, test_model):
 
 
 def test_only_one_efact(test_toas, test_model):
-    test_model.DMEFAC1.flag = "-fe"
+    test_model.DMEFAC1.flag = "fe"
     test_model.DMEFAC1.flag_value = "Rcvr_800"
     test_model.DMEFAC1.value = 10
     test_model.setup()
@@ -50,7 +50,7 @@ def test_only_one_efact(test_toas, test_model):
 
 
 def test_only_one_equad(test_toas, test_model):
-    test_model.DMEQUAD1.flag = "-fe"
+    test_model.DMEQUAD1.flag = "fe"
     test_model.DMEQUAD1.flag_value = "YUPPI"
     test_model.DMEQUAD1.value = 10
     test_model.setup()
@@ -65,10 +65,10 @@ def test_only_one_equad(test_toas, test_model):
 
 
 def test_only_one_equad_one_efact_same_backend(test_toas, test_model):
-    test_model.DMEQUAD1.flag = "-fe"
+    test_model.DMEQUAD1.flag = "fe"
     test_model.DMEQUAD1.flag_value = "Rcvr_800"
     test_model.DMEQUAD1.value = 10
-    test_model.DMEFAC1.flag = "-fe"
+    test_model.DMEFAC1.flag = "fe"
     test_model.DMEFAC1.flag_value = "Rcvr_800"
     test_model.DMEFAC1.value = 10
     test_model.setup()
@@ -88,10 +88,10 @@ def test_only_one_equad_one_efact_same_backend(test_toas, test_model):
 
 
 def test_only_one_equad_one_efact_different_backend(test_toas, test_model):
-    test_model.DMEQUAD1.flag = "-fe"
+    test_model.DMEQUAD1.flag = "fe"
     test_model.DMEQUAD1.flag_value = "Rcvr_800"
     test_model.DMEQUAD1.value = 10
-    test_model.DMEFAC1.flag = "-fe"
+    test_model.DMEFAC1.flag = "fe"
     test_model.DMEFAC1.flag_value = "YUPPI"
     test_model.DMEFAC1.value = 20
     test_model.setup()

tests/test_flagging_clustering.py

@@ -55,14 +55,10 @@ def test_jump_by_cluster(setup_NGC6440E):
     m_copy.add_component(PhaseJump(), validate=False)
     cp_copy = m_copy.components["PhaseJump"]
     par_copy = p.maskParameter(
-        name="JUMP", flag="-toacluster", value=0.2, flag_value="41", units=u.s
+        name="JUMP", flag="toacluster", value=0.2, flag_value="41", units=u.s
     )
     # this should be identical to the cluster above
     cp_copy.add_param(par_copy, setup=True)
     assert set(cp.JUMP1.select_toa_mask(setup_NGC6440E.t)) == set(
         cp_copy.JUMP1.select_toa_mask(setup_NGC6440E.t)
     )
-
-
-if __name__ == "__main__":
-    pass

tests/test_jump.py

@@ -47,7 +47,7 @@ def test_add_jumps_and_flags(setup_NGC6440E):
     selected_toa_ind2 = [10, 11, 12]
     j2 = cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind2])
     jp2 = getattr(cp, j2)
-    assert jp2.flag == "-gui_jump"
+    assert jp2.flag == "gui_jump"
     assert jp2.flag_value == "2"
     # check previous jump flags unaltered
     for d in setup_NGC6440E.t.table["flags"][selected_toa_ind]:
@@ -274,7 +274,7 @@ def test_multiple_jumps_add():
     [
         pint.models.parameter.maskParameter(
             name="JUMP",
-            flag="-fish",
+            flag="fish",
             flag_value="carp",
             units=u.s,
             value=7,

tests/test_mask_parameter.py

@@ -106,12 +106,12 @@ def test_name_mask(toas):
 
 def test_flag_mask(toas):
     with pytest.raises(ValueError):
-        maskParameter("test2", flag="-fe", flag_value=430)
-    mp_flag2 = maskParameter("test2", flag="-fe", flag_value="430")
+        maskParameter("test2", flag="fe", flag_value=430)
+    mp_flag2 = maskParameter("test2", flag="fe", flag_value="430")
     assert mp_flag2.flag_value == "430"
     with pytest.raises(ValueError):
-        maskParameter("test2", flag="fe", flag_value="430")
-    mp_flag3 = maskParameter("test2", flag="-fe", flag_value="L-wide")
+        maskParameter("test2", flag="-fe", flag_value="430")
+    mp_flag3 = maskParameter("test2", flag="fe", flag_value="L-wide")
     assert mp_flag3.flag_value == "L-wide"
     select_toas = mp_flag3.select_toa_mask(toas)
     assert len(select_toas) > 0

tests/test_parameters.py

@@ -91,7 +91,7 @@ def test_read_par_line_expected_values():
     assert_allclose(test_m.JUMP7.uncertainty_value, 10.5)
     assert_allclose(test_m.JUMP6.value, 0.1)
     assert_allclose(test_m.JUMP6.uncertainty_value, 10.0)
-    assert test_m.JUMP12.flag == "-testflag"
+    assert test_m.JUMP12.flag == "testflag"
     assert not test_m.JUMP12.frozen
     assert test_m.JUMP12.flag_value == "flagvalue"
     assert_allclose(test_m.JUMP12.value, 0.1)
@@ -179,7 +179,7 @@ def test_read_par_line(self):
         self.assertTrue(np.isclose(test_m.JUMP7.uncertainty_value, 10.5))
         self.assertTrue(np.isclose(test_m.JUMP6.value, 0.1))
         self.assertTrue(np.isclose(test_m.JUMP6.uncertainty_value, 10.0))
-        self.assertEqual(test_m.JUMP12.flag, "-testflag")
+        self.assertEqual(test_m.JUMP12.flag, "testflag")
         self.assertEqual(test_m.JUMP12.frozen, False)
         self.assertEqual(test_m.JUMP12.flag_value, "flagvalue")
         self.assertTrue(np.isclose(test_m.JUMP12.value, 0.1))
@@ -600,16 +600,17 @@ def test_parameter_can_be_pickled(p):
     ("freq", (1000.0 * u.MHz, 2000.0 * u.MHz)),
     ("mjd", (57000.0, 58000.0)),
     ("mjd", [57000.0, 58000.0]),
-    ("-fish", "carp"),
+    ("fish", "carp"),
     ("freq", (2000.0 * u.MHz, np.inf * u.MHz)),
     ("freq", np.array([1000, 2000], dtype=np.longdouble) * u.MHz),
 ]
 invalid_settings = [
     ("tel", (10, 20)),
     ("freq", "ao"),
     ("mjd", ([], [])),
-    ("-fish", (1, 2)),
-    ("-fish", ["c", "a", "r", "p"]),
+    ("-fish", "carp"),
+    ("fish", (1, 2)),
+    ("fish", ["c", "a", "r", "p"]),
 ]
 
 

tests/test_timing_model.py

@@ -339,9 +339,9 @@ def test_jump_flags_to_params(timfile_jumps, timfile_nojumps, model_0437):
     m.jump_flags_to_params(t)
     assert "PhaseJump" in m.components
     assert len(m.components["PhaseJump"].jumps) == 2
-    assert ("-jump", "1") in [
+    assert ("jump", "1") in [
         (j.flag, j.flag_value) for j in m.components["PhaseJump"].jumps
     ]
-    assert ("-jump", "2") in [
+    assert ("jump", "2") in [
         (j.flag, j.flag_value) for j in m.components["PhaseJump"].jumps
     ]