Deprecate TreeIterator

doc/_toc.yml

@@ -72,7 +72,7 @@ parts:
   - file: pages/mvdes
   - file: pages/tsoverview
   - file: pages/tstypes
-  - file: pages/tablefs
+  # - file: pages/tablefs
   - file: pages/recorders
 - caption: Technical details
   chapters:

doc/misc/changelog.md

@@ -1494,7 +1494,7 @@ release candidates (see below) plus the following:
   {issue}`389`
   {issue}`390`
   {issue}`392`
-* {func}`fwdpy11.TableCollection.fs` added.  See {ref}`tablefs`.
+* {func}`fwdpy11.TableCollection.fs` added.  See `tablefs`.
   PR {pr}`387`
   PR {pr}`399`
 * Creating populations from `msprime` input improved.

fwdpy11/_types/table_collection.py

@@ -1,7 +1,7 @@
+from deprecated import deprecated
 from typing import Iterable
 
 import numpy as np
-import scipy.sparse  # type: ignore
 
 from .._fwdpy11 import Edge, MutationRecord, Node, Site, ll_TableCollection
 
@@ -181,6 +181,7 @@ def _ndfs(
         later.
         """
         from . import TreeIterator
+        import scipy.sparse  # type: ignore
 
         shapes = tuple(len(i) + 1 for i in samples)
         dok_JFS = [scipy.sparse.dok_matrix(shapes, dtype=np.int32) for i in windows]
@@ -240,6 +241,7 @@ def _fs_implementation(self, samples, windows, include_function, simplify):
             simplify,
         )
 
+    @deprecated(reason="dependency on scikit is a problem")
     def fs(
         self,
         samples,

pyproject.toml

@@ -26,7 +26,6 @@ dependencies = [
     "attrs >= 20.3.0",
     "black",
     "numpy < 2.0",
-    "scipy",
     "tskit >= 0.5.6",
     "demes ~= 0.2.2",
     "Deprecated",

requirements/minimal_install_requirements.txt

@@ -3,5 +3,4 @@ attrs >= 20.3.0
 demes == 0.2.2
 numpy < 2
 tskit >= 0.5.6
-scipy
 Deprecated