test: unify using @pytest.mark.flaky(...) & bump pytest plugins (aw…

…slabs#3132)

*Issue #, if available:*

*Description of changes:*
seem that there is mix of few packages and maybe better to use just
`pytest` extension


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copy, and redistribute this contribution, under the terms of your
choice.


**Please tag this pr with at least one of these labels to make our
release process faster:** BREAKING, new feature, bug fix, other change,
dev setup

cc: @lostella

---------

Co-authored-by: Lorenzo Stella <lorenzostella@gmail.com>

.github/workflows/mxnet_nightly.yml

@@ -36,4 +36,4 @@ jobs:
  -r requirements/requirements-extras-autogluon.txt
  - name: Test with pytest
  run: |
- pytest -m 'not (gpu or serial)' --cov src/gluonts --cov-report=term --cov-report xml test
+ pytest -m 'not (gpu or serial)' --cov=gluonts --cov-report=term --cov-report xml test

.github/workflows/test_release_unix_nightly.yml

@@ -36,4 +36,4 @@ jobs:
  - name: Test with pytest
  run: |
  cd gluon-ts
- pytest -m 'not (gpu or serial)' --cov src/gluonts --cov-report=term --cov-report xml test
+ pytest -m 'not (gpu or serial)' --cov=gluonts --cov-report=term --cov-report xml test

.github/workflows/test_release_win32_nightly.yml

@@ -37,4 +37,4 @@ jobs:
  - name: Test with pytest
  run: |
  cd gluon-ts
- pytest -m 'not (gpu or serial)' --cov src/gluonts --cov-report=term --cov-report xml test
+ pytest -m 'not (gpu or serial)' --cov=gluonts --cov-report=term --cov-report xml test

pyproject.toml

@@ -5,6 +5,7 @@ line-length = 79
 minversion = "6.0"
 timeout = 60
 addopts = """
+ --color=yes
  --doctest-modules
  --ignore src/gluonts/block.py
  --ignore src/gluonts/distribution.py

requirements/requirements-test.txt

@@ -1,9 +1,9 @@
-pandas>=1.1
-flaky~=3.6
-pytest-cov==2.6.*
-pytest-timeout~=1.3
-pytest-xdist~=1.27
-pytest>=6.0
+pandas >=1.1
+pytest >7.0
+pytest-cov >4.0,<5.0
+pytest-timeout >2.0, <3.0
+pytest-xdist >3.0, <4.0
+pytest-rerunfailures >=13.0, <14.0
 ujson
 orjson
 requests

test/ext/naive_2/test_predictors.py

@@ -17,7 +17,6 @@
 import numpy as np
 import pandas as pd
 import pytest
-from flaky import flaky
 
 from gluonts.dataset.artificial import constant_dataset
 from gluonts.dataset.common import Dataset
@@ -106,7 +105,7 @@ def test_predictor(make_predictor, freq: str):
 CONSTANT_DATASET_PREDICTION_LENGTH = dataset_info.prediction_length
 
 
-@flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize(
  "predictor, accuracy",
  [

test/mx/distribution/test_distribution_sampling.py

@@ -14,7 +14,6 @@
 import mxnet as mx
 import numpy as np
 import pytest
-from flaky import flaky
 
 from gluonts.core.serde import dump_json, load_json
 from gluonts.mx.model.tpp.distribution import Loglogistic, Weibull
@@ -149,7 +148,7 @@
 
 @pytest.mark.parametrize("distr_class, params", test_cases)
 @pytest.mark.parametrize("serialize_fn", serialize_fn_list)
-@flaky
+@pytest.mark.flaky(retries=3)
 def test_sampling(distr_class, params, serialize_fn) -> None:
  distr = distr_class(**params)
  distr = serialize_fn(distr)
@@ -205,7 +204,7 @@ def test_sampling(distr_class, params, serialize_fn) -> None:
 ]
 
 
-@flaky(min_passes=1, max_runs=3)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("distr, params, dim", test_cases_multivariate)
 @pytest.mark.parametrize("serialize_fn", serialize_fn_list)
 def test_multivariate_sampling(distr, params, dim, serialize_fn) -> None:
@@ -261,7 +260,7 @@ def test_piecewise_linear_sampling(distr, params, serialize_fn):
  assert samples.shape == (num_samples, 2)
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("alpha, beta", [(0.3, 0.9), (1.5, 1.7)])
 @pytest.mark.parametrize("zero_probability, one_probability", [(0.1, 0.2)])
 def test_inflated_beta_sampling(

test/mx/distribution/test_mixture.py

@@ -114,6 +114,8 @@ def diff(x: np.ndarray, y: np.ndarray) -> np.ndarray:
 def test_mixture(
  distr1: Distribution, distr2: Distribution, p: Tensor, serialize_fn
 ) -> None:
+ np.random.seed(0)
+ mx.random.seed(0)
  # sample from component distributions, and select samples
  samples1 = distr1.sample(num_samples=NUM_SAMPLES_LARGE)
  samples2 = distr2.sample(num_samples=NUM_SAMPLES_LARGE)

test/mx/distribution/test_mx_distribution_inference.py

@@ -15,6 +15,7 @@
 Test that maximizing likelihood allows to correctly recover distribution parameters for all
 distributions exposed to the user.
 """
+import random
 from functools import reduce
 
 from typing import List, Tuple
@@ -536,7 +537,7 @@ def test_dirichlet_multinomial(hybridize: bool) -> None:
  ), f"Covariance did not match: cov = {cov}, cov_hat = {cov_hat}"
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("hybridize", [True, False])
 @pytest.mark.parametrize("rank", [0, 1])
 def test_lowrank_multivariate_gaussian(hybridize: bool, rank: int) -> None:
@@ -604,7 +605,7 @@ def test_lowrank_multivariate_gaussian(hybridize: bool, rank: int) -> None:
  ), f"sigma did not match: sigma = {Sigma}, sigma_hat = {Sigma_hat}"
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("hybridize", [True, False])
 def test_empirical_distribution(hybridize: bool) -> None:
  r"""
@@ -757,6 +758,9 @@ def test_neg_binomial(mu_alpha: Tuple[float, float], hybridize: bool) -> None:
  """
  Test to check that maximizing the likelihood recovers the parameters
  """
+ random.seed(0)
+ np.random.seed(0)
+ mx.random.seed(0)
  # test instance
  mu, alpha = mu_alpha
 
@@ -1243,7 +1247,7 @@ def test_genpareto_likelihood(xi: float, beta: float, hybridize: bool) -> None:
 
 
 @pytest.mark.timeout(120)
-@pytest.mark.flaky(max_runs=6, min_passes=1)
+@pytest.mark.flaky(retries=6)
 @pytest.mark.parametrize("rate", [50.0])
 @pytest.mark.parametrize("zero_probability", [0.8, 0.2, 0.01])
 @pytest.mark.parametrize("hybridize", [False, True])
@@ -1255,8 +1259,11 @@ def test_inflated_poisson_likelihood(
  """
  Test to check that maximizing the likelihood recovers the parameters
  """
+ random.seed(0)
+ np.random.seed(0)
+ mx.random.seed(0)
  # generate samples
- num_samples = 1000 # Required for convergence
+ num_samples = 2000 # Required for convergence
 
  distr = ZeroInflatedPoissonOutput().distribution(
  distr_args=[
@@ -1291,7 +1298,7 @@ def test_inflated_poisson_likelihood(
 
 
 @pytest.mark.timeout(150)
-@pytest.mark.flaky(max_runs=6, min_passes=1)
+@pytest.mark.flaky(retries=6)
 @pytest.mark.parametrize("mu", [5.0])
 @pytest.mark.parametrize("alpha", [0.05])
 @pytest.mark.parametrize("zero_probability", [0.3])

test/mx/model/gpvar/test_gpvar.py

@@ -14,7 +14,6 @@
 import mxnet as mx
 
 import pytest
-from flaky import flaky
 
 from gluonts.dataset.artificial import constant_dataset
 from gluonts.dataset.common import TrainDatasets
@@ -93,7 +92,7 @@ def test_gpvar_proj():
  assert distr.mean.shape == (batch, dim)
 
 
-@flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("hybridize", [True, False])
 @pytest.mark.parametrize("target_dim_sample", [None, 2])
 @pytest.mark.parametrize("use_marginal_transformation", [True, False])

test/mx/model/simple_feedforward/test_model.py

@@ -31,7 +31,7 @@ def hyperparameters():
  )
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("hybridize", [True, False])
 @pytest.mark.parametrize("sampling", [True, False])
 def test_accuracy(accuracy_test, hyperparameters, hybridize, sampling):

test/mx/model/transformer/test_model.py

@@ -32,7 +32,7 @@ def hyperparameters():
  )
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("hybridize", [True, False])
 def test_accuracy(accuracy_test, hyperparameters, hybridize):
  hyperparameters.update(num_batches_per_epoch=80, hybridize=hybridize)

test/torch/model/test_estimators.py

@@ -19,6 +19,7 @@
 import pytest
 import pandas as pd
 import numpy as np
+from lightning import seed_everything
 
 from gluonts.dataset.repository import get_dataset
 from gluonts.model.predictor import Predictor
@@ -309,6 +310,7 @@ def test_estimator_constant_dataset(
  ],
 )
 def test_estimator_with_features(estimator_constructor):
+ seed_everything(42)
  freq = "1h"
  prediction_length = 12
 

test/torch/modules/test_torch_distribution_inference.py

@@ -19,6 +19,8 @@
 
 import numpy as np
 import pytest
+from lightning import seed_everything
+
 import torch
 import torch.nn as nn
 from scipy.special import softmax
@@ -119,7 +121,7 @@ def compare_logits(
  ).all(), f"logits did not match: logits_true = {param_true}, logits_hat = {param_hat}"
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("concentration1, concentration0", [(3.75, 1.25)])
 def test_beta_likelihood(concentration1: float, concentration0: float) -> None:
  """
@@ -158,7 +160,7 @@ def test_beta_likelihood(concentration1: float, concentration0: float) -> None:
  ), f"concentration0 did not match: concentration0 = {concentration0}, concentration0_hat = {concentration0_hat}"
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("concentration, rate", [(3.75, 1.25)])
 def test_gamma_likelihood(concentration: float, rate: float) -> None:
  """
@@ -193,7 +195,7 @@ def test_gamma_likelihood(concentration: float, rate: float) -> None:
  ), f"rate did not match: rate = {rate}, rate_hat = {rate_hat}"
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("loc, scale,", [(1.0, 0.1)])
 def test_normal_likelihood(loc: float, scale: float):
  locs = torch.zeros((NUM_SAMPLES,)) + loc
@@ -223,7 +225,7 @@ def test_normal_likelihood(loc: float, scale: float):
  ), f"scale did not match: scale = {scale}, scale_hat = {scale_hat}"
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("df, loc, scale,", [(6.0, 2.3, 0.7)])
 def test_studentT_likelihood(df: float, loc: float, scale: float):
  dfs = torch.zeros((NUM_SAMPLES,)) + df
@@ -258,7 +260,7 @@ def test_studentT_likelihood(df: float, loc: float, scale: float):
  ), f"scale did not match: scale = {scale}, scale_hat = {scale_hat}"
 
 
-@pytest.mark.flaky(max_runs=3, min_passes=1)
+@pytest.mark.flaky(retries=3)
 @pytest.mark.parametrize("rate", [1.0])
 def test_poisson(rate: float) -> None:
  """
@@ -297,6 +299,7 @@ def test_neg_binomial(total_count: float, logit: float) -> None:
  """
  Test to check that maximizing the likelihood recovers the parameters
  """
+ seed_everything(42)
  # generate samples
  total_counts = torch.zeros((NUM_SAMPLES,)) + total_count
  logits = torch.zeros((NUM_SAMPLES,)) + logit