Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 2] #26

CloudChaoszero · 2021-01-19T03:19:20Z

Description

The following is a large PR breakdown of PR #16.

Replace PyMC3 dependent plots with arviz plots in case studies & examples.

The issue is a 3-part step for the following:
- Initiative via Issue Remove Plots & Diagnostics from PyMC Code Base pymc#4371 (Leave open)

Replace parameter sd with sigma (e.g. some examples have pm.Normal(...sd=...)

Closes issue Use sigma instead of sd #2

…h sigma

review-notebook-app · 2021-01-19T03:19:25Z

Check out this pull request on

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review-notebook-app · 2021-01-29T11:58:35Z

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MarcoGorelli commented on 2021-01-29T11:58:34Z
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rather than ignoring warnings, can you do this such that it doesn't produce a warning at all (does specifying model=model work?)

OriolAbril commented on 2021-02-04T21:27:27Z
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It won't work because under the hood conversion in plotting/stats functions does not accept conversion kwargs. Here I would recommend using return_inferencedata, it looks like the trace is only used to call arviz functions. Otherwise, to avoid all warnings, all plots should be called from within a model context so arviz has access to the model instance

CloudChaoszero commented on 2021-02-05T08:03:12Z
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Thanks for the feedback @MarcoGorelli! I found that Oriol's return_inference param recommendation panned out.

OriolAbril · 2021-02-04T21:27:28Z

It won't work because under the hood conversion in plotting/stats functions does not accept conversion kwargs. Here I would recommend using return_inferencedata, it looks like the trace is only used to call arviz functions. Otherwise, to avoid all warnings, all plots should be called from within a model context so arviz has access to the model instance

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review-notebook-app · 2021-02-04T21:34:37Z

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OriolAbril commented on 2021-02-04T21:34:37Z
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var_names

…arnames to var_names

CloudChaoszero · 2021-02-05T08:03:13Z

Thanks for the feedback @MarcoGorelli! I found that Oriol's return_inference param recommendation panned out.

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MarcoGorelli · 2021-02-05T08:09:43Z

examples/case_studies/multilevel_modeling.ipynb

@@ -76,7 +76,9 @@
    "from theano import tensor as tt\n",


Did you save the notebooks after having re-run them? The watermarks still show old "last updated" dates

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If there's nothing to be updated in this notebook, then perhaps it could be unstaged?
git fetch upstream git checkout upstream/main -- examples/case_studies/multilevel_modeling.ipynb git add examples/case_studies/multilevel_modeling.ipynb git commit -m 'unstage multilevel_modeling' git push

Acknowledged. Thanks for the snippet!

review-notebook-app · 2021-02-07T20:27:27Z

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OriolAbril commented on 2021-02-07T20:27:27Z
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Is this still needed?

CloudChaoszero commented on 2021-02-08T05:49:03Z
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Not anymore. Thanks for the note!

review-notebook-app · 2021-02-07T20:27:28Z

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OriolAbril commented on 2021-02-07T20:27:28Z
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It looks like the plot output is missing here

CloudChaoszero · 2021-02-08T05:48:34Z

Note on examples/case_studies/LKJ.ipynb

For this line in
traceFit = pm.fit(n=35000, method="fullrank_advi", obj_n_mc=3)

we get the following

FullRank Advi & obj_n_mc Error


You can find the C code in this temporary file: /var/folders/gs/knb4q5ps7dz5y6v28xzt80f00000gn/T/theano_compilation_error_tszs_x7a
library imit=] is not found.
-----------------------------------------
ImportErrorTraceback (most recent call last)
~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/scan/scan_perform_ext.py in <module>
     46     if version != getattr(scan_perform, "_version", None):
---> 47         raise ImportError("Scan code version mismatch")
     48 except ImportError:

ImportError: Scan code version mismatch

During handling of the above exception, another exception occurred:

ImportErrorTraceback (most recent call last)
~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/scan/scan_perform_ext.py in <module>
     67             if version != getattr(scan_perform, "_version", None):
---> 68                 raise ImportError()
     69 

ImportError: 

During handling of the above exception, another exception occurred:

ExceptionTraceback (most recent call last)
<ipython-input-13-ebbf72273d20> in <module>
      8     W_plot = pm.Deterministic("W_plot", W[:3, 0])
      9 
---> 10     traceFit = pm.fit(n=35000, method="fullrank_advi", obj_n_mc=3)
     11     trace = traceFit.sample(N_SAMPLE * 4)
     12 

~/Documents/Projects-Dev/pymc3/pymc3/variational/inference.py in fit(n, local_rv, method, model, random_seed, start, inf_kwargs, **kwargs)
    830     else:
    831         raise TypeError(f"method should be one of {set(_select.keys())} or Inference instance")
--> 832     return inference.fit(n, **kwargs)

~/Documents/Projects-Dev/pymc3/pymc3/variational/inference.py in fit(self, n, score, callbacks, progressbar, **kwargs)
    142             callbacks = []
    143         score = self._maybe_score(score)
--> 144         step_func = self.objective.step_function(score=score, **kwargs)
    145         if progressbar:
    146             progress = progress_bar(range(n), display=progressbar)

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/configparser.py in res(*args, **kwargs)
     46         def res(*args, **kwargs):
     47             with self:
---> 48                 return f(*args, **kwargs)
     49 
     50         return res

~/Documents/Projects-Dev/pymc3/pymc3/variational/opvi.py in step_function(self, obj_n_mc, tf_n_mc, obj_optimizer, test_optimizer, more_obj_params, more_tf_params, more_updates, more_replacements, total_grad_norm_constraint, score, fn_kwargs)
    360         )
    361         if score:
--> 362             step_fn = theano.function([], updates.loss, updates=updates, **fn_kwargs)
    363         else:
    364             step_fn = theano.function([], None, updates=updates, **fn_kwargs)

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/compile/function/__init__.py in function(inputs, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input)
    335         # note: pfunc will also call orig_function -- orig_function is
    336         #      a choke point that all compilation must pass through
--> 337         fn = pfunc(
    338             params=inputs,
    339             outputs=outputs,

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/compile/function/pfunc.py in pfunc(params, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input, output_keys)
    522         inputs.append(si)
    523 
--> 524     return orig_function(
    525         inputs,
    526         cloned_outputs,

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/compile/function/types.py in orig_function(inputs, outputs, mode, accept_inplace, name, profile, on_unused_input, output_keys)
   1979         )
   1980         with config.change_flags(compute_test_value="off"):
-> 1981             fn = m.create(defaults)
   1982     finally:
   1983         t2 = time.time()

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/compile/function/types.py in create(self, input_storage, trustme, storage_map)
   1834 
   1835         with config.change_flags(traceback__limit=config.traceback__compile_limit):
-> 1836             _fn, _i, _o = self.linker.make_thunk(
   1837                 input_storage=input_storage_lists, storage_map=storage_map
   1838             )

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/link/basic.py in make_thunk(self, input_storage, output_storage, storage_map)
    264 
    265     def make_thunk(self, input_storage=None, output_storage=None, storage_map=None):
--> 266         return self.make_all(
    267             input_storage=input_storage,
    268             output_storage=output_storage,

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/link/vm.py in make_all(self, profiler, input_storage, output_storage, storage_map)
   1129                 # no_recycling here.
   1130                 thunks.append(
-> 1131                     node.op.make_thunk(node, storage_map, compute_map, [], impl=impl)
   1132                 )
   1133                 linker_make_thunk_time[node] = time.time() - thunk_start

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/scan/op.py in make_thunk(self, node, storage_map, compute_map, no_recycling, impl)
   1040                 cython_destroy_map = [0 for x in range(len(node.outputs))]
   1041             cython_destroy_map = np.asarray(cython_destroy_map, dtype="int32")
-> 1042             from . import scan_perform_ext
   1043 
   1044             def p(node, args, outs):

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/scan/scan_perform_ext.py in <module>
     85                 code = f.read()
     86 
---> 87             cmodule.GCC_compiler.compile_str(
     88                 dirname, code, location=loc, preargs=preargs, hide_symbols=False
     89             )

~/opt/anaconda3/envs/pymc3-dev-py38/lib/python3.8/site-packages/theano/link/c/cmodule.py in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)
   2544             # difficult to read.
   2545             compile_stderr = compile_stderr.replace("\n", ". ")
-> 2546             raise Exception(
   2547                 f"Compilation failed (return status={status}): {compile_stderr}"
   2548             )

Exception: ('The following error happened while compiling the node', forall_inplace,cpu,scan_fn}(TensorConstant{3}, Elemwise{Add}[(0, 0)].0, IncSubtensor{InplaceSet;:int64:}.0, TensorConstant{3}, TensorConstant{3}, <TensorType(float64, matrix)>, Elemwise{Composite{(i0 + Cast{float64}(i1))}}.0), '\n', 'Compilation failed (return status=1): In file included from /Users/CloudChaoszero/.theano/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.8.6-64/scan_perform/mod.cpp:4:. In file included from /Users/CloudChaoszero/opt/anaconda3/envs/pymc3-dev-py38/include/python3.8/Python.h:25:. In file included from /usr/local/include/stdio.h:64:. /usr/local/include/_stdio.h:93:16: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].         unsigned char   *_base;.                         ^. /usr/local/include/_stdio.h:93:16: note: insert \'_Nullable\' if the pointer may be null.         unsigned char   *_base;.                         ^.                           _Nullable . /usr/local/include/_stdio.h:93:16: note: insert \'_Nonnull\' if the pointer should never be null.         unsigned char   *_base;.                         ^.                           _Nonnull . /usr/local/include/_stdio.h:138:32: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].         int     (* _Nullable _read) (void *, char *, int);.                                           ^. /usr/local/include/_stdio.h:138:32: note: insert \'_Nullable\' if the pointer may be null.         int     (* _Nullable _read) (void *, char *, int);.                                           ^.                                            _Nullable. /usr/local/include/_stdio.h:138:32: note: insert \'_Nonnull\' if the pointer should never be null.         int     (* _Nullable _read) (void *, char *, int);.                                           ^.                                            _Nonnull. /usr/local/include/_stdio.h:138:40: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].         int     (* _Nullable _read) (void *, char *, int);.                                                   ^. /usr/local/include/_stdio.h:138:40: note: insert \'_Nullable\' if the pointer may be null.         int     (* _Nullable _read) (void *, char *, int);.                                                   ^.                                                    _Nullable. /usr/local/include/_stdio.h:138:40: note: insert \'_Nonnull\' if the pointer should never be null.         int     (* _Nullable _read) (void *, char *, int);.                                                   ^.                                                    _Nonnull. /usr/local/include/_stdio.h:139:35: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].         fpos_t  (* _Nullable _seek) (void *, fpos_t, int);.                                           ^. /usr/local/include/_stdio.h:139:35: note: insert \'_Nullable\' if the pointer may be null.         fpos_t  (* _Nullable _seek) (void *, fpos_t, int);.                                           ^.                                            _Nullable. /usr/local/include/_stdio.h:139:35: note: insert \'_Nonnull\' if the pointer should never be null.         fpos_t  (* _Nullable _seek) (void *, fpos_t, int);.                                           ^.                                            _Nonnull. /usr/local/include/_stdio.h:140:32: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].         int     (* _Nullable _write)(void *, const char *, int);.                                           ^. /usr/local/include/_stdio.h:140:32: note: insert \'_Nullable\' if the pointer may be null.         int     (* _Nullable _write)(void *, const char *, int);.                                           ^.                                            _Nullable. /usr/local/include/_stdio.h:140:32: note: insert \'_Nonnull\' if the pointer should never be null.         int     (* _Nullable _write)(void *, const char *, int);.                                           ^.                                            _Nonnull. /usr/local/include/_stdio.h:140:46: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].         int     (* _Nullable _write)(void *, const char *, int);.                                                         ^. /usr/local/include/_stdio.h:140:46: note: insert \'_Nullable\' if the pointer may be null.         int     (* _Nullable _write)(void *, const char *, int);.                                                         ^.                                                          _Nullable. /usr/local/include/_stdio.h:140:46: note: insert \'_Nonnull\' if the pointer should never be null.         int     (* _Nullable _write)(void *, const char *, int);.                                                         ^.                                                          _Nonnull. /usr/local/include/_stdio.h:144:18: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].         struct __sFILEX *_extra; /* additions to FILE to not break ABI */.                         ^. /usr/local/include/_stdio.h:144:18: note: insert \'_Nullable\' if the pointer may be null.         struct __sFILEX *_extra; /* additions to FILE to not break ABI */.                         ^.                           _Nullable . /usr/local/include/_stdio.h:144:18: note: insert \'_Nonnull\' if the pointer should never be null.         struct __sFILEX *_extra; /* additions to FILE to not break ABI */.                         ^.                           _Nonnull . In file included from /Users/CloudChaoszero/.theano/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.8.6-64/scan_perform/mod.cpp:4:. In file included from /Users/CloudChaoszero/opt/anaconda3/envs/pymc3-dev-py38/include/python3.8/Python.h:25:. /usr/local/include/stdio.h:67:13: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. extern FILE *__stdinp;.             ^. /usr/local/include/stdio.h:67:13: note: insert \'_Nullable\' if the pointer may be null. extern FILE *__stdinp;.             ^.               _Nullable . /usr/local/include/stdio.h:67:13: note: insert \'_Nonnull\' if the pointer should never be null. extern FILE *__stdinp;.             ^.               _Nonnull . /usr/local/include/stdio.h:386:41: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].                  int (* _Nullable)(void *, const char *, int),.                                         ^. /usr/local/include/stdio.h:386:41: note: insert \'_Nullable\' if the pointer may be null.                  int (* _Nullable)(void *, const char *, int),.                                         ^.                                          _Nullable. /usr/local/include/stdio.h:386:41: note: insert \'_Nonnull\' if the pointer should never be null.                  int (* _Nullable)(void *, const char *, int),.                                         ^.                                          _Nonnull. /usr/local/include/stdio.h:386:55: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].                  int (* _Nullable)(void *, const char *, int),.                                                       ^. /usr/local/include/stdio.h:386:55: note: insert \'_Nullable\' if the pointer may be null.                  int (* _Nullable)(void *, const char *, int),.                                                       ^.                                                        _Nullable. /usr/local/include/stdio.h:386:55: note: insert \'_Nonnull\' if the pointer should never be null.                  int (* _Nullable)(void *, const char *, int),.                                                       ^.                                                        _Nonnull. /usr/local/include/stdio.h:387:44: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].                  fpos_t (* _Nullable)(void *, fpos_t, int),.                                            ^. /usr/local/include/stdio.h:387:44: note: insert \'_Nullable\' if the pointer may be null.                  fpos_t (* _Nullable)(void *, fpos_t, int),.                                            ^.                                             _Nullable. /usr/local/include/stdio.h:387:44: note: insert \'_Nonnull\' if the pointer should never be null.                  fpos_t (* _Nullable)(void *, fpos_t, int),.                                            ^.                                             _Nonnull. /usr/local/include/stdio.h:388:41: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].                  int (* _Nullable)(void *));.                                         ^. /usr/local/include/stdio.h:388:41: note: insert \'_Nullable\' if the pointer may be null.                  int (* _Nullable)(void *));.                                         ^.                                          _Nullable. /usr/local/include/stdio.h:388:41: note: insert \'_Nonnull\' if the pointer should never be null.                  int (* _Nullable)(void *));.                                         ^.                                          _Nonnull. /usr/local/include/stdio.h:384:6: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. FILE    *funopen(const void *,.         ^. /usr/local/include/stdio.h:384:6: note: insert \'_Nullable\' if the pointer may be null. FILE    *funopen(const void *,.         ^.           _Nullable . /usr/local/include/stdio.h:384:6: note: insert \'_Nonnull\' if the pointer should never be null. FILE    *funopen(const void *,.         ^.           _Nonnull . In file included from /Users/CloudChaoszero/.theano/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.8.6-64/scan_perform/mod.cpp:4:. In file included from /Users/CloudChaoszero/opt/anaconda3/envs/pymc3-dev-py38/include/python3.8/Python.h:34:. /usr/local/include/stdlib.h:134:25: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. double   atof(const char *);.                          ^. /usr/local/include/stdlib.h:134:25: note: insert \'_Nullable\' if the pointer may be null. double   atof(const char *);.                          ^.                           _Nullable. /usr/local/include/stdlib.h:134:25: note: insert \'_Nonnull\' if the pointer should never be null. double   atof(const char *);.                          ^.                           _Nonnull. /usr/local/include/stdlib.h:135:22: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. int      atoi(const char *);.                          ^. /usr/local/include/stdlib.h:135:22: note: insert \'_Nullable\' if the pointer may be null. int      atoi(const char *);.                          ^.                           _Nullable. /usr/local/include/stdlib.h:135:22: note: insert \'_Nonnull\' if the pointer should never be null. int      atoi(const char *);.                          ^.                           _Nonnull. /usr/local/include/stdlib.h:136:23: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. long     atol(const char *);.                          ^. /usr/local/include/stdlib.h:136:23: note: insert \'_Nullable\' if the pointer may be null. long     atol(const char *);.                          ^.                           _Nullable. /usr/local/include/stdlib.h:136:23: note: insert \'_Nonnull\' if the pointer should never be null. long     atol(const char *);.                          ^.                           _Nonnull. /usr/local/include/stdlib.h:139:20: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].          atoll(const char *);.                           ^. /usr/local/include/stdlib.h:139:20: note: insert \'_Nullable\' if the pointer may be null.          atoll(const char *);.                           ^.                            _Nullable. /usr/local/include/stdlib.h:139:20: note: insert \'_Nonnull\' if the pointer should never be null.          atoll(const char *);.                           ^.                            _Nonnull. /usr/local/include/stdlib.h:141:26: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. void    *bsearch(const void *__key, const void *__base, size_t __nel,.                             ^. /usr/local/include/stdlib.h:141:26: note: insert \'_Nullable\' if the pointer may be null. void    *bsearch(const void *__key, const void *__base, size_t __nel,.                             ^.                               _Nullable . /usr/local/include/stdlib.h:141:26: note: insert \'_Nonnull\' if the pointer should never be null. void    *bsearch(const void *__key, const void *__base, size_t __nel,.                             ^.                               _Nonnull . /usr/local/include/stdlib.h:141:45: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. void    *bsearch(const void *__key, const void *__base, size_t __nel,.                                                ^. /usr/local/include/stdlib.h:141:45: note: insert \'_Nullable\' if the pointer may be null. void    *bsearch(const void *__key, const void *__base, size_t __nel,.                                                ^.                                                  _Nullable . /usr/local/include/stdlib.h:141:45: note: insert \'_Nonnull\' if the pointer should never be null. void    *bsearch(const void *__key, const void *__base, size_t __nel,.                                                ^.                                                  _Nonnull . /usr/local/include/stdlib.h:142:59: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].             size_t __width, int (* _Nonnull __compar)(const void *, const void *));.                                                                  ^. /usr/local/include/stdlib.h:142:59: note: insert \'_Nullable\' if the pointer may be null.             size_t __width, int (* _Nonnull __compar)(const void *, const void *));.                                                                  ^.                                                                   _Nullable. /usr/local/include/stdlib.h:142:59: note: insert \'_Nonnull\' if the pointer should never be null.             size_t __width, int (* _Nonnull __compar)(const void *, const void *));.                                                                  ^.                                                                   _Nonnull. /usr/local/include/stdlib.h:142:73: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness].             size_t __width, int (* _Nonnull __compar)(const void *, const void *));.                                                                                ^. /usr/local/include/stdlib.h:142:73: note: insert \'_Nullable\' if the pointer may be null.             size_t __width, int (* _Nonnull __compar)(const void *, const void *));.                                                                                ^.                                                                                 _Nullable. /usr/local/include/stdlib.h:142:73: note: insert \'_Nonnull\' if the pointer should never be null.             size_t __width, int (* _Nonnull __compar)(const void *, const void *));.                                                                                ^.                                                                                 _Nonnull. /usr/local/include/stdlib.h:141:6: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. void    *bsearch(const void *__key, const void *__base, size_t __nel,.         ^. /usr/local/include/stdlib.h:141:6: note: insert \'_Nullable\' if the pointer may be null. void    *bsearch(const void *__key, const void *__base, size_t __nel,.         ^.           _Nullable . /usr/local/include/stdlib.h:141:6: note: insert \'_Nonnull\' if the pointer should never be null. void    *bsearch(const void *__key, const void *__base, size_t __nel,.         ^.           _Nonnull . /usr/local/include/stdlib.h:147:25: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. char    *getenv(const char *);.                            ^. /usr/local/include/stdlib.h:147:25: note: insert \'_Nullable\' if the pointer may be null. char    *getenv(const char *);.                            ^.                             _Nullable. /usr/local/include/stdlib.h:147:25: note: insert \'_Nonnull\' if the pointer should never be null. char    *getenv(const char *);.                            ^.                             _Nonnull. /usr/local/include/stdlib.h:147:6: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. char    *getenv(const char *);.         ^. /usr/local/include/stdlib.h:147:6: note: insert \'_Nullable\' if the pointer may be null. char    *getenv(const char *);.         ^.           _Nullable . /usr/local/include/stdlib.h:147:6: note: insert \'_Nonnull\' if the pointer should never be null. char    *getenv(const char *);.         ^.           _Nonnull . /usr/local/include/stdlib.h:156:23: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. int      mblen(const char *__s, size_t __n);.                           ^. /usr/local/include/stdlib.h:156:23: note: insert \'_Nullable\' if the pointer may be null. int      mblen(const char *__s, size_t __n);.                           ^.                             _Nullable . /usr/local/include/stdlib.h:156:23: note: insert \'_Nonnull\' if the pointer should never be null. int      mblen(const char *__s, size_t __n);.                           ^.                             _Nonnull . /usr/local/include/stdlib.h:157:26: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. size_t   mbstowcs(wchar_t * __restrict , const char * __restrict, size_t);.                           ^. /usr/local/include/stdlib.h:157:26: note: insert \'_Nullable\' if the pointer may be null. size_t   mbstowcs(wchar_t * __restrict , const char * __restrict, size_t);.                           ^.                             _Nullable. /usr/local/include/stdlib.h:157:26: note: insert \'_Nonnull\' if the pointer should never be null. size_t   mbstowcs(wchar_t * __restrict , const char * __restrict, size_t);.                           ^.                             _Nonnull. /usr/local/include/stdlib.h:157:52: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. size_t   mbstowcs(wchar_t * __restrict , const char * __restrict, size_t);.                                                     ^. /usr/local/include/stdlib.h:157:52: note: insert \'_Nullable\' if the pointer may be null. size_t   mbstowcs(wchar_t * __restrict , const char * __restrict, size_t);.                                                     ^.                                                       _Nullable. /usr/local/include/stdlib.h:157:52: note: insert \'_Nonnull\' if the pointer should never be null. size_t   mbstowcs(wchar_t * __restrict , const char * __restrict, size_t);.                                                     ^.                                                       _Nonnull. /usr/local/include/stdlib.h:158:21: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. int      mbtowc(wchar_t * __restrict, const char * __restrict, size_t);.                         ^. /usr/local/include/stdlib.h:158:21: note: insert \'_Nullable\' if the pointer may be null. int      mbtowc(wchar_t * __restrict, const char * __restrict, size_t);.                         ^.                           _Nullable. /usr/local/include/stdlib.h:158:21: note: insert \'_Nonnull\' if the pointer should never be null. int      mbtowc(wchar_t * __restrict, const char * __restrict, size_t);.                         ^.                           _Nonnull. /usr/local/include/stdlib.h:158:46: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]. int      mbtowc(wchar_t * __restrict, const char * __restrict, size_t);.                                                  ^. /usr/local/include/stdlib.h:158:46: note: insert \'_Nullable\' if the pointer may be null. int      mbtowc(wchar_t * __restrict, const char * __restrict, size_t);.                                                  ^.                                                    _Nullable. /usr/local/include/stdlib.h:158:46: note: insert \'_Nonnull\' if the pointer should never be null. int      mbtowc(wchar_t * __restrict, const char * __restrict, size_t);.                                                  ^.                                                    _Nonnull. /usr/local/include/stdlib.h:160:18: warning: pointer is missing

What I did here was change the param obj_n_mc=3 to obj_n_mc=1. I suspect this is an issue with my device and Theano compiler within scan_perform_ext 🤷 . Just a thought, based on this past discourse inquiry

CloudChaoszero · 2021-02-08T05:49:03Z

Not anymore. Thanks for the note!

View entire conversation on ReviewNB

twiecki · 2021-03-08T10:39:37Z

Thanks @CloudChaoszero!

🎨 Update plots from pymc to arviz dependencies & replace param sd wit…

6f1a2a2

…h sigma

Use return_inference to get proper Notebook output and change param v…

fd1e946

…arnames to var_names

MarcoGorelli reviewed Feb 5, 2021

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unstage multilevel_modeling

e666460

CloudChaoszero requested a review from MarcoGorelli February 6, 2021 16:43

CloudChaoszero added 2 commits February 7, 2021 21:46

🎨 Remove Warning Ignores and re-run files

810dd7a

🎨 Remove Warning Ignores and re-run files

05ab6b3

OriolAbril approved these changes Feb 8, 2021

View reviewed changes

twiecki merged commit da07736 into pymc-devs:main Mar 8, 2021

CloudChaoszero deleted the replace-pymc3-arviz-plots_part2 branch April 5, 2021 01:52

twiecki pushed a commit that referenced this pull request Jan 17, 2023

fix missing file (#26)

676e769

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Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 2] #26

Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 2] #26

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Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 2] #26

Replacing PyMC3 plots w/ Arviz plots & sigma Param change [Part 2] #26

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CloudChaoszero commented Jan 19, 2021

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Note on examples/case_studies/LKJ.ipynb

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