deprecate AutoMBAR (PR #285)

- fix #284
- Deprecate AutoMBAR (for removal in 2.0.0)
- test DeprecationWarning
- silence this warning otherwise
- update docs
- update CHANGES

CHANGES

@@ -27,6 +27,10 @@ Fixes
  there are no spaces around the equal sign (issue #272, PR #273). 
  - Pre-processing function slicing will not drop NaN rows (issue
  #274, PR #275).
+
+Deprecations
+ - deprecate AutoMBAR for removal in 2.0 because pymbar 4 already contains
+ equivalent functionality (issue #284, PR #285).
 
 Internal Enhancements (do not affect API)
  - Blackfy the codebase (PR #280).

src/alchemlyb/estimators/mbar_.py

@@ -1,4 +1,5 @@
 import logging
+from warnings import warn
 
 import pandas as pd
 import pymbar
@@ -200,6 +201,9 @@ class AutoMBAR(MBAR):
  .. versionadded:: 0.6.0
  .. versionchanged:: 1.0.0
  AutoMBAR accepts the `method` argument.
+ .. deprecated:: 1.0.1
+ Deprecate AutoMBAR in favour of MBAR for pymbar4. It will be removed
+ in alchemlyb 2.0.0.
  """
 
  def __init__(
@@ -210,6 +214,10 @@ def __init__(
  verbose=False,
  method=None,
  ):
+ warn(
+ "From version 2.0.0, this will be replaced by the default alchemlyb.estimators.MBAR.",
+ DeprecationWarning,
+ )
  super().__init__(
  maximum_iterations=maximum_iterations,
  relative_tolerance=relative_tolerance,

src/alchemlyb/tests/pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+filterwarnings =
+ ignore:From version 2.0.0, this will be replaced by the default alchemlyb.estimators.MBAR.:DeprecationWarning:

src/alchemlyb/tests/test_fep_estimators.py

@@ -55,6 +55,10 @@ def test_mbar(self, X_delta_f):
 class TestAutoMBAR(TestMBAR):
  cls = AutoMBAR
 
+ def test_autombar(self, X_delta_f):
+ with pytest.deprecated_call():
+ self.compare_delta_f(X_delta_f)
+
 
 class TestMBAR_fail:
  def test_failback_adaptive(self, gmx_ABFE_complex_n_uk):