no print statements

pymc-devs · Jul 25, 2021 · b69d99e · b69d99e
1 parent bc2c24a
commit b69d99e
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Showing 5 changed files with 12 additions and 7 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -33,6 +33,11 @@ repos:
     - id: pylint
       args: [--rcfile=.pylintrc]
       files: ^pymc3/
+- repo: https://github.com/MarcoGorelli/madforhooks
+  rev: 0.2.0
+  hooks:
+    - id: no-print-statements
+      files: ^pymc3/
 - repo: local
   hooks:
     - id: check-no-tests-are-ignored

diff --git a/docs/source/pymc-examples b/docs/source/pymc-examples
diff --git a/pymc3/math.py b/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}.")
+            sys.stdout.write(f"Failed to compute logdet of {x}.\n")
             raise
 
     def grad(self, inputs, g_outputs):

diff --git a/pymc3/sampling_jax.py b/pymc3/sampling_jax.py
@@ -206,7 +206,7 @@ def sample_numpyro_nuts(
             rv_samples.name = rv.name
             sample_outputs.append(rv_samples)
 
-    print("Compiling...")
+    sys.stdout.write("Compiling...\n")
 
     tic1 = pd.Timestamp.now()
     _sample = compile_rv_inplace(
@@ -219,14 +219,14 @@ def sample_numpyro_nuts(
     )
     tic2 = pd.Timestamp.now()
 
-    print("Compilation time = ", tic2 - tic1)
+    sys.stdout.write(f"Compilation time = {tic2-tic1}")
 
-    print("Sampling...")
+    sys.stdout.write("Sampling...\n")
 
     *mcmc_samples, leapfrogs_taken = _sample()
     tic3 = pd.Timestamp.now()
 
-    print("Sampling time = ", tic3 - tic2)
+    sys.stdout.write(f"Sampling time = {tic3-tic2}")
 
     posterior = {k.name: v for k, v in zip(sample_outputs, mcmc_samples)}
 

diff --git a/pymc3/tuning/starting.py b/pymc3/tuning/starting.py
@@ -153,7 +153,7 @@ def dlogp_func(x):
             assert isinstance(cost_func.progress, ProgressBar)
             cost_func.progress.total = last_v
             cost_func.progress.update(last_v)
-            print()
+            sys.stdout.write("\n")
 
     mx0 = RaveledVars(mx0, x0.point_map_info)
+22 −0		.github/ISSUE_TEMPLATE/bug-report.md
+8 −0		.github/ISSUE_TEMPLATE/config.yml
+20 −0		.github/ISSUE_TEMPLATE/notebook-proposal.md
+39 −0		.github/ISSUE_TEMPLATE/tracker.md
+16 −0		.github/PULL_REQUEST_TEMPLATE.md
+1 −1		.github/workflows/pre-commit.yml
+1 −0		.gitignore
+11 −1		.pre-commit-config.yaml
+78 −0		CODE_OF_CONDUCT.md
+108 −0		CONTRIBUTING.md
+0 −2		README.md
+133 −0		README.rst
+92 −141		examples/case_studies/BEST.ipynb
+139 −96		examples/case_studies/LKJ.ipynb
+1,968 −0		examples/case_studies/bayesian_ab_testing.ipynb
+5 −5		examples/case_studies/blackbox_external_likelihood.ipynb
+5 −5		examples/case_studies/conditional-autoregressive-model.ipynb
+3 −3		examples/case_studies/disaster_model.py
+3 −3		examples/case_studies/disaster_model_theano_op.py
+333 −447		examples/case_studies/factor_analysis.ipynb
+2 −1		examples/case_studies/garch_example.py
+2 −1		examples/case_studies/gelman_schools.py
+25 −18		examples/case_studies/hierarchical_partial_pooling.ipynb
+1,145 −0		examples/case_studies/item_response_nba.ipynb
+2 −2		examples/case_studies/lightspeed_example.py
+124 −130		examples/case_studies/log-gaussian-cox-process.ipynb
+ −		examples/case_studies/mediation.png
+871 −0		examples/case_studies/mediation_analysis.ipynb
+920 −0		examples/case_studies/moderation_analysis.ipynb
+ −		examples/case_studies/moderation_figure.png
+263 −54		examples/case_studies/probabilistic_matrix_factorization.ipynb
+403 −520		examples/case_studies/putting_workflow.ipynb
+1,449 −524		examples/case_studies/rugby_analytics.ipynb
+116 −113		examples/case_studies/stochastic_volatility.ipynb
+145 −0		examples/data/AirPassengers.csv
+46,862 −0		examples/data/item_response_nba.csv
+1 −1		examples/data/mastectomy.csv
+244 −0		examples/data/muscle-percent-males-interaction.csv
+41 −34		examples/diagnostics_and_criticism/Bayes_factor.ipynb
+598 −566		examples/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.ipynb
+132 −171		examples/diagnostics_and_criticism/model_averaging.ipynb
+77 −77		examples/diagnostics_and_criticism/model_comparison.ipynb
+66 −61		examples/diagnostics_and_criticism/posterior_predictive.ipynb
+1,346 −182		examples/diagnostics_and_criticism/sampler-stats.ipynb
+1,775 −0		examples/gaussian_processes/GP-Heteroskedastic.ipynb
+85 −102		examples/gaussian_processes/GP-Kron.ipynb
+5 −5		examples/gaussian_processes/GP-Latent.ipynb
+4 −4		examples/gaussian_processes/GP-Marginal.ipynb
+1,082 −310		examples/gaussian_processes/GP-MeansAndCovs.ipynb
+647 −0		examples/generalized_linear_models/GLM-binomial-regression.ipynb
+448 −58		examples/generalized_linear_models/GLM-hierarchical-binominal-model.ipynb
+1,110 −110		examples/generalized_linear_models/GLM-hierarchical.ipynb
+59 −56		examples/generalized_linear_models/GLM-linear.ipynb
+81 −64		examples/generalized_linear_models/GLM-logistic.ipynb
+561 −642		examples/generalized_linear_models/GLM-model-selection.ipynb
+655 −0		examples/generalized_linear_models/GLM-out-of-sample-predictions.ipynb
+797 −268		examples/generalized_linear_models/GLM-poisson-regression.ipynb
+400 −340		examples/generalized_linear_models/GLM-robust-with-outlier-detection.ipynb
+1,766 −0		examples/generalized_linear_models/GLM-simpsons-paradox.ipynb
+912 −0		examples/generalized_linear_models/GLM-truncated-censored-regression.ipynb
+2,686 −395		examples/generalized_linear_models/GLM.ipynb
+426 −384		examples/getting_started.ipynb
+101 −506		examples/mixture_models/dependent_density_regression.ipynb
+1,930 −0		examples/mixture_models/dirichlet_mixture_of_multinomials.ipynb
+0 −4		examples/mixture_models/dp_mix.ipynb
+5 −5		examples/mixture_models/gaussian_mixture_model.ipynb
+7 −7		examples/ode_models/ODE_API_shapes_and_benchmarking.ipynb
+492 −176		examples/ode_models/ODE_with_manual_gradients.ipynb
+3 −3		examples/pymc3_howto/LKJ_correlation.py
+148 −159		examples/pymc3_howto/data_container.ipynb
+36 −24		examples/pymc3_howto/lasso_block_update.ipynb
+3 −2		examples/pymc3_howto/rankdata_ordered.py
+351 −58		examples/pymc3_howto/sampling_compound_step.ipynb
+27 −22		examples/pymc3_howto/sampling_conjugate_step.ipynb
+91 −83		examples/pymc3_howto/updating_priors.ipynb
+3 −7		examples/samplers/DEMetropolisZ_EfficiencyComparison.ipynb
+2 −11		examples/samplers/DEMetropolisZ_tune_drop_fraction.ipynb
+56 −56		examples/samplers/GLM-hierarchical-jax.ipynb
+711 −540		examples/samplers/MLDA_gravity_surveying.ipynb
+1 −1		examples/samplers/MLDA_introduction.ipynb
+62 −101		examples/samplers/MLDA_simple_linear_regression.ipynb
+212 −164		examples/samplers/MLDA_variance_reduction_linear_regression.ipynb
+5 −5		examples/samplers/SMC-ABC_Lotka-Volterra_example.ipynb
+1 −1		examples/samplers/SMC2_gaussians.ipynb
+6 −5		examples/samplers/samplers_mvnormal.py
+153 −207		examples/survival_analysis/bayes_param_survival_pymc3.ipynb
+290 −157		examples/survival_analysis/censored_data.ipynb
+58 −53		examples/survival_analysis/cox_model.ipynb
+684 −208		examples/survival_analysis/survival_analysis.ipynb
+11 −0		examples/table_of_contents_examples.js
+1,165 −0		examples/time_series/Air_passengers-Prophet_with_Bayesian_workflow.ipynb
+3 −2		examples/time_series/arma_example.py
+3 −2		examples/variational_inference/bayesian_neural_network_advi.ipynb
+84 −79		examples/variational_inference/empirical-approx-overview.ipynb
+1 −1		examples/variational_inference/normalizing_flows_overview.ipynb
+7 −6		examples/variational_inference/variational_api_quickstart.ipynb