deprecate TableCollection.fs (#1292)

* remove scipy as a dependency Closes #1271
molpopgen · Apr 10, 2024 · 92aa92c · 92aa92c
1 parent 2c820bf
commit 92aa92c
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diff --git a/doc/_toc.yml b/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:

diff --git a/doc/misc/changelog.md b/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.

diff --git a/fwdpy11/_types/table_collection.py b/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,

diff --git a/pyproject.toml b/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",

diff --git a/requirements/minimal_install_requirements.txt b/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
diff --git a/tests/test_TableCollection_fs.py b/tests/test_TableCollection_fs.py