Merge pull request #76 from pymc-devs/main

Sync Fork from Upstream Repo

Author: sthagen

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
     - id: isort
       name: isort
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.21.2
+  rev: v2.23.0
   hooks:
     - id: pyupgrade
       args: [--py37-plus]
@@ -28,11 +28,16 @@ repos:
   hooks:
     - id: black
 - repo: https://github.com/PyCQA/pylint
-  rev: v2.9.3
+  rev: v2.9.5
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]
       files: ^pymc3/
+- repo: https://github.com/MarcoGorelli/madforhooks
+  rev: 0.2.1
+  hooks:
+    - id: no-print-statements
+      files: ^pymc3/
 - repo: local
   hooks:
     - id: check-no-tests-are-ignored

pymc3/distributions/logprob.py

@@ -277,7 +277,7 @@ def convert_indices(indices, entry):
 
 
 def indices_from_subtensor(idx_list, indices):
-    """Compute a useable index tuple from the inputs of a ``*Subtensor**`` ``Op``."""
+    """Compute a usable index tuple from the inputs of a ``*Subtensor**`` ``Op``."""
     return tuple(
         tuple(convert_indices(list(indices), idx) for idx in idx_list) if idx_list else indices
     )

pymc3/math.py

@@ -294,7 +294,7 @@ def perform(self, node, inputs, outputs, params=None):
             log_det = np.sum(np.log(np.abs(s)))
             z[0] = np.asarray(log_det, dtype=x.dtype)
         except Exception:
-            print(f"Failed to compute logdet of {x}.")
+            print(f"Failed to compute logdet of {x}.", file=sys.stdout)
             raise
 
     def grad(self, inputs, g_outputs):

pymc3/sampling_jax.py

@@ -1,6 +1,7 @@
 # pylint: skip-file
 import os
 import re
+import sys
 import warnings
 
 xla_flags = os.getenv("XLA_FLAGS", "").lstrip("--")
@@ -206,7 +207,7 @@ def sample_numpyro_nuts(
             rv_samples.name = rv.name
             sample_outputs.append(rv_samples)
 
-    print("Compiling...")
+    print("Compiling...", file=sys.stdout)
 
     tic1 = pd.Timestamp.now()
     _sample = compile_rv_inplace(
@@ -219,14 +220,14 @@ def sample_numpyro_nuts(
     )
     tic2 = pd.Timestamp.now()
 
-    print("Compilation time = ", tic2 - tic1)
+    print("Compilation time = ", tic2 - tic1, file=sys.stdout)
 
-    print("Sampling...")
+    print("Sampling...", file=sys.stdout)
 
     *mcmc_samples, leapfrogs_taken = _sample()
     tic3 = pd.Timestamp.now()
 
-    print("Sampling time = ", tic3 - tic2)
+    print("Sampling time = ", tic3 - tic2, file=sys.stdout)
 
     posterior = {k.name: v for k, v in zip(sample_outputs, mcmc_samples)}
 

pymc3/tuning/starting.py

@@ -18,6 +18,7 @@
 @author: johnsalvatier
 """
 import copy
+import sys
 
 import aesara.gradient as tg
 import numpy as np
@@ -153,7 +154,7 @@ def dlogp_func(x):
             assert isinstance(cost_func.progress, ProgressBar)
             cost_func.progress.total = last_v
             cost_func.progress.update(last_v)
-            print()
+            print(file=sys.stdout)
 
     mx0 = RaveledVars(mx0, x0.point_map_info)