add deprecation warnings for old backends (#3902)

* add deprecation warnings for old backends

* mention backend deprecation #3902

* fix typo

Co-authored-by: Colin <[email protected]>

Co-authored-by: Michael Osthege <[email protected]>
Co-authored-by: Colin <[email protected]>

Author: michaelosthege

RELEASE-NOTES.md

@@ -18,7 +18,8 @@
 ### Maintenance
 - Remove `sample_ppc` and `sample_ppc_w` that were deprecated in 3.6.
 - Tuning results no longer leak into sequentially sampled `Metropolis` chains (see #3733 and #3796).
-- Deprecated `sd` in version 3.7 has been replaced by `sigma` now raises `DepreciationWarning` on using `sd` in continuous, mixed and timeseries distributions. (see #3837 and #3688).
+- Deprecated `sd` in version 3.7 has been replaced by `sigma` now raises `DeprecationWarning` on using `sd` in continuous, mixed and timeseries distributions. (see #3837 and #3688).
+- We'll deprecate the `Text` and `SQLite` backends and the `save_trace`/`load_trace` functions, since this is now done with ArviZ. (see [#3902](https://github.com/pymc-devs/pymc3/pull/3902))
 - In named models, `pm.Data` objects now get model-relative names (see [#3843](https://github.com/pymc-devs/pymc3/pull/3843)).
 - `pm.sample` now takes 1000 draws and 1000 tuning samples by default, instead of 500 previously (see [#3855](https://github.com/pymc-devs/pymc3/pull/3855)).
 - Dropped some deprecated kwargs and functions (see [#3906](https://github.com/pymc-devs/pymc3/pull/3906))

pymc3/backends/ndarray.py

@@ -21,6 +21,7 @@
 import os
 import shutil
 from typing import Optional, Dict, Any, List
+import warnings
 
 import numpy as np
 from pymc3.backends import base
@@ -52,6 +53,12 @@ def save_trace(trace: MultiTrace, directory: Optional[str]=None, overwrite=False
     -------
     str, path to the directory where the trace was saved
     """
+    warnings.warn(
+        'The `save_trace` function will soon be removed.'
+        'Instead, use ArviZ to save/load traces.',
+        DeprecationWarning,
+    )
+
     if directory is None:
         directory = '.pymc_{}.trace'
         idx = 1
@@ -89,6 +96,11 @@ def load_trace(directory: str, model=None) -> MultiTrace:
     -------
     pm.Multitrace that was saved in the directory
     """
+    warnings.warn(
+        'The `load_trace` function will soon be removed.'
+        'Instead, use ArviZ to save/load traces.',
+        DeprecationWarning,
+    )
     straces = []
     for subdir in glob.glob(os.path.join(directory, '*')):
         if os.path.isdir(subdir):
@@ -106,6 +118,11 @@ class SerializeNDArray:
 
     def __init__(self, directory: str):
         """Helper to save and load NDArray objects"""
+        warnings.warn(
+            'The `SerializeNDArray` class will soon be removed. '
+            'Instead, use ArviZ to save/load traces.',
+            DeprecationWarning,
+        )
         self.directory = directory
         self.metadata_path = os.path.join(self.directory, self.metadata_file)
         self.samples_path = os.path.join(self.directory, self.samples_file)
@@ -367,6 +384,7 @@ def _slice_as_ndarray(strace, idx):
 
     return sliced
 
+
 def point_list_to_multitrace(point_list: List[Dict[str, np.ndarray]], model: Optional[Model]=None) -> MultiTrace:
     '''transform point list into MultiTrace'''
     _model = modelcontext(model)

pymc3/backends/sqlite.py

@@ -32,6 +32,7 @@
 """
 import numpy as np
 import sqlite3
+import warnings
 
 from ..backends import base, ndarray
 from . import tracetab as ttab
@@ -89,6 +90,12 @@ class SQLite(base.BaseTrace):
     """
 
     def __init__(self, name, model=None, vars=None, test_point=None):
+        warnings.warn(
+            'The `SQLite` backend will soon be removed. '
+            'Please switch to a different backend. '
+            'If you have good reasons for using the SQLite backend, file an issue and tell us about them.',
+            DeprecationWarning,
+        )
         super().__init__(name, model, vars, test_point)
         self._var_cols = {}
         self.var_inserts = {}  # varname -> insert statement
@@ -322,6 +329,12 @@ def load(name, model=None):
     -------
     A MultiTrace instance
     """
+    warnings.warn(
+        'The `sqlite.load` function will soon be removed. '
+        'Please use ArviZ to save traces. '
+        'If you have good reasons for using the `load` function, file an issue and tell us about them. ',
+        DeprecationWarning,
+    )
     db = _SQLiteDB(name)
     db.connect()
     varnames = _get_table_list(db.cursor)

pymc3/backends/text.py

@@ -33,6 +33,7 @@
 import os
 import re
 import pandas as pd
+import warnings
 
 from ..backends import base, ndarray
 from . import tracetab as ttab
@@ -57,6 +58,12 @@ class Text(base.BaseTrace):
     """
 
     def __init__(self, name, model=None, vars=None, test_point=None):
+        warnings.warn(
+            'The `Text` backend will soon be removed. '
+            'Please switch to a different backend. '
+            'If you have good reasons for using the Text backend, file an issue and tell us about them. ',
+            DeprecationWarning,
+        )
         if not os.path.exists(name):
             os.mkdir(name)
         super().__init__(name, model, vars, test_point)
@@ -185,6 +192,12 @@ def load(name, model=None):
     -------
     A MultiTrace instance
     """
+    warnings.warn(
+        'The `load` function will soon be removed. '
+        'Please use ArviZ to save traces. '
+        'If you have good reasons for using the `load` function, file an issue and tell us about them. ',
+        DeprecationWarning,
+    )
     files = glob(os.path.join(name, 'chain-*.csv'))
 
     if len(files) == 0:
@@ -224,6 +237,12 @@ def dump(name, trace, chains=None):
     chains: list
         Chains to dump. If None, all chains are dumped.
     """
+    warnings.warn(
+        'The `dump` function will soon be removed. '
+        'Please use ArviZ to save traces. '
+        'If you have good reasons for using the `dump` function, file an issue and tell us about them. ',
+        DeprecationWarning,
+    )
     if not os.path.exists(name):
         os.mkdir(name)
     if chains is None:

pymc3/backends/tracetab.py

@@ -17,6 +17,7 @@
 
 import numpy as np
 import pandas as pd
+import warnings
 
 from ..util import get_default_varnames
 
@@ -39,6 +40,12 @@ def trace_to_dataframe(trace, chains=None, varnames=None, include_transformed=Fa
         If true transformed variables will be included in the resulting
         DataFrame.
     """
+    warnings.warn(
+        'The `trace_to_dataframe` function will soon be removed. '
+        'Please use ArviZ to save traces. '
+        'If you have good reasons for using the `trace_to_dataframe` function, file an issue and tell us about them. ',
+        DeprecationWarning,
+    )
     var_shapes = trace._straces[0].var_shapes
 
     if varnames is None: