Fix pylint and pickling issue (#1743)

* Fix pylint

* run black

* fix lint

* Change special version

* Add pylint disables

* Add black

* Update pymc3 install branch

* Revert special version

* Change pymc3 master install

* Change to kick off ci

* Use cloudpickle

* Add cloudpickle

* Fix lint

* Remove mypy check for now

* Reenable mypy

* Update not callable line

* Disable mypy until we can find a fix

* Add cloudpickle ignore and renable mypy

* Remove pymc manual install

Co-authored-by: canyon <canyon@canyon.local>
Co-authored-by: canyon289 <ravinsdrive@gmail.com>

.azure-pipelines/azure-pipelines-external.yml

@@ -86,14 +86,8 @@ jobs:
       fi
 
       if [ "$(pymc3.version)" = "github" ]; then
-          # Pip installation is failing for some reason. This is the same thing
-          git clone https://github.com/pymc-devs/pymc3
-          cd pymc3
-          git checkout v4
-          cd ..
-          pip install $PWD/pymc3
-          # python -m pip --no-cache-dir --log log.txt install git+https://github.com/pymc-devs/pymc3
-          # cat log.txt
+           python -m pip --no-cache-dir --log log.txt install git+https://github.com/pymc-devs/pymc3
+           cat log.txt
       else
           python -m pip --no-cache-dir install pymc3
       fi

arviz/data/inference_data.py

@@ -243,7 +243,9 @@ def groups(self) -> List[str]:
     class InferenceDataValuesView(ValuesView[xr.Dataset]):
         """ValuesView implementation for InferenceData, to allow it to implement Mapping."""
 
-        def __init__(self, parent: "InferenceData") -> None:
+        def __init__(
+            self, parent: "InferenceData"
+        ) -> None:  # pylint: disable=super-init-not-called
             """Create a new InferenceDataValuesView from an InferenceData object."""
             self.parent = parent
 
@@ -275,7 +277,9 @@ def values(self) -> "InferenceData.InferenceDataValuesView":
     class InferenceDataItemsView(ItemsView[str, xr.Dataset]):
         """ItemsView implementation for InferenceData, to allow it to implement Mapping."""
 
-        def __init__(self, parent: "InferenceData") -> None:
+        def __init__(
+            self, parent: "InferenceData"
+        ) -> None:  # pylint: disable=super-init-not-called
             """Create a new InferenceDataItemsView from an InferenceData object."""
             self.parent = parent
 

arviz/data/io_pyro.py

@@ -108,7 +108,9 @@ def arbitrary_element(dct):
 
         observations = {}
         if self.model is not None:
-            trace = pyro.poutine.trace(self.model).get_trace(*self._args, **self._kwargs)
+            trace = pyro.poutine.trace(self.model).get_trace(  # pylint: disable=not-callable
+                *self._args, **self._kwargs
+            )
             observations = {
                 name: site["value"].cpu()
                 for name, site in trace.nodes.items()

arviz/tests/helpers.py

@@ -4,10 +4,10 @@
 import importlib
 import logging
 import os
-import pickle
 import sys
 from typing import Any, Dict, List, Optional, Tuple, Union
 
+import cloudpickle
 import numpy as np
 import pytest
 from _pytest.outcomes import Skipped
@@ -591,13 +591,13 @@ def load_cached_models(eight_schools_data, draws, chains, libs=None):
             with gzip.open(path, "wb") as buff:
                 try:
                     _log.info("Generating and caching %s", fname)
-                    pickle.dump(func(eight_schools_data, draws, chains), buff)
+                    cloudpickle.dump(func(eight_schools_data, draws, chains), buff)
                 except AttributeError as err:
-                    raise AttributeError(f"Failed chaching {library_name}") from err
+                    raise AttributeError(f"Failed caching {library_name}") from err
 
         with gzip.open(path, "rb") as buff:
             _log.info("Loading %s from cache", fname)
-            models[library.__name__] = pickle.load(buff)
+            models[library.__name__] = cloudpickle.load(buff)
 
     return models
 

mypy.ini

@@ -220,6 +220,9 @@ ignore_missing_imports = True
 [mypy-bokeh.*]
 ignore_missing_imports = True
 
+[mypy-cloudpickle.*]
+ignore_missing_imports = True
+
 [mypy-cmdstanpy.*]
 ignore_missing_imports = True
 

requirements-dev.txt

@@ -8,3 +8,4 @@ pytest-cov
 black ; python_version >= '3.6'
 typing_copilot ; python_version >= '3.7'
 mypy<0.800
+cloudpickle