sage.knots: Modularization fixes (imports), # needs

src/bin/sage-fixdoctests

@@ -38,6 +38,7 @@ import subprocess
 import sys
 
 from argparse import ArgumentParser
+from collections import defaultdict
 from pathlib import Path
 
 from sage.doctest.control import DocTestDefaults, DocTestController
@@ -459,6 +460,8 @@ def process_grouped_blocks(grouped_iterator, distribution=None, venv=None, envir
         src_in_lines = src_in.splitlines()
         shallow_copy_of_src_in_lines = list(src_in_lines)
         file_optional_tags = set(parse_file_optional_tags(enumerate(src_in_lines)))
+        persistent_tags_counts = defaultdict(int)
+        tags_counts = defaultdict(int)
 
         for block in blocks:
             try:
@@ -474,13 +477,15 @@ def process_grouped_blocks(grouped_iterator, distribution=None, venv=None, envir
 
         # Remove duplicate optional tags and rewrite all '# optional' that should be '# needs'
         persistent_optional_tags = {}
+        persistent_optional_tags_counted = False
         for i, line in enumerate(src_in_lines):
             if m := re.match(' *sage: *(.*)#', line):
                 tags, line_sans_tags, is_persistent = parse_optional_tags(line, return_string_sans_tags=True)
                 if is_persistent:
                     persistent_optional_tags = {tag: explanation
                                                 for tag, explanation in tags.items()
                                                 if explanation or tag not in file_optional_tags}
+                    persistent_optional_tags_counted = False
                     line = update_optional_tags(line, tags=persistent_optional_tags, force_rewrite='standard')
                     if re.fullmatch(' *sage: *', line):
                         # persistent (block-scoped or file-scoped) tag was removed, so remove the whole line
@@ -491,9 +496,19 @@ def process_grouped_blocks(grouped_iterator, distribution=None, venv=None, envir
                             if explanation or (tag not in file_optional_tags
                                                and tag not in persistent_optional_tags)}
                     line = update_optional_tags(line, tags=tags, force_rewrite='standard')
+                    if not persistent_optional_tags_counted:
+                        persistent_tags_counts[frozenset(persistent_optional_tags)] += 1
+                        persistent_optional_tags_counted = True
+                    tags_counts[frozenset(tags)] += 1
                 src_in_lines[i] = line
             elif line.strip() in ['', '"""', "'''"]:    # Blank line or end of docstring
                 persistent_optional_tags = {}
+                persistent_optional_tags_counted = False
+            elif re.match(' *sage: ', line):
+                if not persistent_optional_tags_counted:
+                    persistent_tags_counts[frozenset(persistent_optional_tags)] += 1
+                    persistent_optional_tags_counted = True
+                tags_counts[frozenset()] += 1
 
         if src_in_lines != shallow_copy_of_src_in_lines:
             if (output := output_filename(input)) is None:
@@ -523,6 +538,21 @@ def process_grouped_blocks(grouped_iterator, distribution=None, venv=None, envir
 
         unprocessed_files.discard(input)
 
+        if args.verbose:
+            if file_optional_tags:
+                print(f"File tags: ")
+                print(f"       {' '.join(sorted(file_optional_tags))}")
+            if persistent_tags_counts:
+                print(f"Doctest blocks by persistent tags: ")
+                for tags, count in sorted(persistent_tags_counts.items(),
+                                          key=lambda i: i[1], reverse=True):
+                    print(f"{count:6} {' '.join(sorted(tags)) or '(untagged)'}")
+            if tags_counts:
+                print(f"Doctest examples by tags: ")
+                for tags, count in sorted(tags_counts.items(),
+                                          key=lambda i: i[1], reverse=True):
+                    print(f"{count:6} {' '.join(sorted(tags)) or '(untagged)'}")
+
 
 def fix_with_distribution(file_set, distribution=None, verbose=False):
     if verbose:

src/sage/features/sagemath.py

@@ -538,6 +538,32 @@ def __init__(self):
                              spkg='sagemath_ntl', type='standard')
 
 
+class sage__libs__homfly(JoinFeature):
+    r"""
+    A :class:`sage.features.Feature` describing the presence of :mod:`sage.libs.homfly`.
+
+    In addition to the modularization purposes that this tag serves,
+    it also provides attribution to the upstream project.
+
+    TESTS::
+
+        sage: from sage.features.sagemath import sage__libs__homfly
+        sage: sage__libs__homfly().is_present()                                         # needs sage.libs.homfly
+        FeatureTestResult('sage.libs.homfly', True)
+    """
+    def __init__(self):
+        r"""
+        TESTS::
+
+            sage: from sage.features.sagemath import sage__libs__homfly
+            sage: isinstance(sage__libs__homfly(), sage__libs__homfly)
+            True
+        """
+        JoinFeature.__init__(self, 'sage.libs.homfly',
+                             [PythonModule('sage.libs.homfly')],
+                             spkg='sagemath_homfly', type='standard')
+
+
 class sage__libs__pari(JoinFeature):
     r"""
     A :class:`~sage.features.Feature` describing the presence of :mod:`sage.libs.pari`.
@@ -1130,6 +1156,7 @@ def all_features():
             sage__libs__ecl(),
             sage__libs__flint(),
             sage__libs__gap(),
+            sage__libs__homfly(),
             sage__libs__linbox(),
             sage__libs__m4ri(),
             sage__libs__ntl(),

src/sage/knots/gauss_code.py

@@ -1,3 +1,4 @@
+# sage.doctest: needs sage.graphs
 """
 Helper functions related to Gauss codes of knots
 

src/sage/knots/knot.py

@@ -1,3 +1,4 @@
+# sage.doctest: needs sage.graphs sage.groups
 r"""
 Knots
 
@@ -271,10 +272,12 @@ def dt_code(self):
             sage: K = Knot([[1,5,2,4],[5,3,6,2],[3,1,4,6]])
             sage: K.dt_code()
             [4, 6, 2]
+
             sage: B = BraidGroup(4)
             sage: K = Knot(B([1, 2, 1, 2]))
             sage: K.dt_code()
             [4, -6, 8, -2]
+
             sage: K = Knot([[[1, -2, 3, -4, 5, -1, 2, -3, 4, -5]],
             ....:          [1, 1, 1, 1, 1]])
             sage: K.dt_code()
@@ -678,9 +681,11 @@ def from_table(self, n, k):
         """
         if n > 10:
             raise ValueError('more than 10 crossings, not in the knot table')
-        from sage.groups.braid import BraidGroup
         if (n, k) in small_knots_table:
             m, word = small_knots_table[(n, k)]
+
+            from sage.groups.braid import BraidGroup
+
             G = BraidGroup(m)
             return Knot(G(word))
         else:

src/sage/knots/knotinfo.py

@@ -1,3 +1,4 @@
+# sage.doctest: needs sage.graphs sage.groups
 r"""
 Access to the KnotInfo database
 
@@ -156,7 +157,7 @@
     True
     sage: K.is_amphicheiral()
     True
-    sage: K.jones_polynomial()
+    sage: K.jones_polynomial()                                                          # needs sage.symbolic
     t^2 - t - 1/t + 1/t^2 + 1
     sage: K.kauffman_polynomial()
     a^2*z^2 + a*z^3 - a^2 - a*z + 2*z^2 + a^-1*z^3 - 1 - a^-1*z + a^-2*z^2 - a^-2
@@ -871,7 +872,7 @@ def three_genus(self):
 
         EXAMPLES::
 
-            sage: KnotInfo.K5_2.three_genus()     # optional - databsase_knotinfo
+            sage: KnotInfo.K5_2.three_genus()     # optional - database_knotinfo
             1
 
         Note that this differs from the corresponding result in Sage
@@ -899,7 +900,7 @@ def signature(self):
 
         EXAMPLES::
 
-            sage: KnotInfo.K5_2.signature()       # optional - databsase_knotinfo
+            sage: KnotInfo.K5_2.signature()       # optional - database_knotinfo
             1
         """
         return knotinfo_int(self[self.items.signature])
@@ -1361,14 +1362,16 @@ def kauffman_polynomial(self, var1='a', var2='z', original=False):
         EXAMPLES::
 
             sage: L = KnotInfo.L2a1_1
+            sage: K = KnotInfo.K4_1
+
             sage: L.kauffman_polynomial()
             a^-1*z - a^-1*z^-1 + a^-2 + a^-3*z - a^-3*z^-1
-            sage: K = KnotInfo.K4_1
             sage: K.kauffman_polynomial()
             a^2*z^2 + a*z^3 - a^2 - a*z + 2*z^2 + a^-1*z^3 - 1 - a^-1*z + a^-2*z^2 - a^-2
 
         Comparison with Jones polynomial::
 
+            sage: # needs sage.symbolic
             sage: k    = _
             sage: a, z = k.variables()
             sage: j    = K.jones_polynomial(skein_normalization=True)
@@ -1467,7 +1470,7 @@ def jones_polynomial(self, variab=None, skein_normalization=False, puiseux=False
         EXAMPLES::
 
             sage: K = KnotInfo.K4_1
-            sage: Kj = K.jones_polynomial(); Kj
+            sage: Kj = K.jones_polynomial(); Kj                                         # needs sage.symbolic
             t^2 - t - 1/t + 1/t^2 + 1
             sage: Kjs = K.jones_polynomial(skein_normalization=True); Kjs
             A^-8 - A^-4 + 1 - A^4 + A^8
@@ -1477,17 +1480,17 @@ def jones_polynomial(self, variab=None, skein_normalization=False, puiseux=False
         for proper links::
 
             sage: L = KnotInfo.L2a1_1
-            sage: Lj = L.jones_polynomial(); Lj
+            sage: Lj = L.jones_polynomial(); Lj                                         # needs sage.symbolic
             -x^5 - x
-            sage: Ljt = L.jones_polynomial(use_sqrt=True); Ljt
+            sage: Ljt = L.jones_polynomial(use_sqrt=True); Ljt                          # needs sage.symbolic
             -t^(5/2) - sqrt(t)
             sage: Ljp = L.jones_polynomial(puiseux=True); Ljp
             -t^(1/2) - t^(5/2)
             sage: Ljs = L.jones_polynomial(skein_normalization=True); Ljs
             -A^2 - A^10
-            sage: Lj.parent()
+            sage: Lj.parent()                                                           # needs sage.symbolic
             Symbolic Ring
-            sage: Ljt.parent()
+            sage: Ljt.parent()                                                          # needs sage.symbolic
             Symbolic Ring
             sage: Ljp.parent()
             Puiseux Series Ring in t over Integer Ring
@@ -1497,17 +1500,17 @@ def jones_polynomial(self, variab=None, skein_normalization=False, puiseux=False
         Comparison with Sage's results::
 
             sage: k = K.link()
-            sage: kj = k.jones_polynomial()
-            sage: bool(Kj == kj)
+            sage: kj = k.jones_polynomial()                                             # needs sage.symbolic
+            sage: bool(Kj == kj)                                                        # needs sage.symbolic
             True
             sage: kjs = k.jones_polynomial(skein_normalization=True)
             sage: Kjs == kjs
             True
             sage: l = L.link()
-            sage: lj = l.jones_polynomial()
-            sage: bool(Lj == lj)
+            sage: lj = l.jones_polynomial()                                             # needs sage.symbolic
+            sage: bool(Lj == lj)                                                        # needs sage.symbolic
             False
-            sage: bool(Ljt == lj)   # see note above
+            sage: bool(Ljt == lj)   # see note above                                    # needs sage.symbolic
             True
             sage: ljs = l.jones_polynomial(skein_normalization=True)
             sage: Ljs == ljs
@@ -1517,6 +1520,8 @@ def jones_polynomial(self, variab=None, skein_normalization=False, puiseux=False
         of the positive crossings of the right-handed trefoil)::
 
             sage: K3_1  = KnotInfo.K3_1
+
+            sage: # needs sage.symbolic
             sage: K3_1j = K3_1.jones_polynomial()
             sage: L2a1_1j = Ljt     # see note above
             sage: R = L2a1_1j.parent()
@@ -1725,7 +1730,7 @@ def conway_polynomial(self, var='t', original=False):
             sage: Lc = L.conway_polynomial(); Lc
             t^3
 
-        Comparision to Sage's results::
+        Comparison to Sage's results::
 
             sage: Kc == K.link().conway_polynomial()
             True
@@ -1734,7 +1739,7 @@ def conway_polynomial(self, var='t', original=False):
 
         Launch the KnotInfo description web-page::
 
-            sage: K.items.conway_polynomial.description_webpage() # not tested
+            sage: K.items.conway_polynomial.description_webpage()  # not tested
             True
         """
         conway_polynomial = self[self.items.conway_polynomial]
@@ -1831,7 +1836,7 @@ def khovanov_polynomial(self, var1='q', var2='t', base_ring=ZZ, original=False,
             False
 
 
-        Comparision to Sage's results::
+        Comparison to Sage's results::
 
             sage: Kk == K.link().khovanov_polynomial()
             True
@@ -2689,20 +2694,23 @@ def _test_recover(self, **options):
 
         EXAMPLES::
 
-            sage: TestSuite(KnotInfo.L5a1_0.series()).run(verbose=True)  # indirec doctest
+            sage: TestSuite(KnotInfo.L5a1_0.series()).run(verbose=True)  # indirect doctest
             running ._test_category() . . . pass
             running ._test_new() . . . pass
             running ._test_not_implemented_methods() . . . pass
             running ._test_pickling() . . . pass
             running ._test_recover() . . . pass
-            sage: TestSuite(KnotInfo.K6_1.series()).run(max_samples=infinity)  # indirec doctest
+            sage: TestSuite(KnotInfo.K6_1.series()).run(max_samples=infinity)  # indirect doctest
         """
         tester = options['tester']
         max_samples = tester._max_samples
-        if max_samples:
-            tester.assertTrue(self.is_recoverable(unique=False, max_samples=max_samples))
-        else:
-            tester.assertTrue(self.is_recoverable(unique=False))
+        try:
+            if max_samples:
+                tester.assertTrue(self.is_recoverable(unique=False, max_samples=max_samples))
+            else:
+                tester.assertTrue(self.is_recoverable(unique=False))
+        except ImportError:
+            pass
 
     def inject(self, verbose=True):
         r"""
@@ -2716,7 +2724,6 @@ def inject(self, verbose=True):
 
         EXAMPLES::
 
-            sage: from sage.knots.knotinfo import KnotInfoSeries
             sage: KnotInfoSeries(6, True, True).inject()
             Defining K6
             sage: K6(2)