Move tests outside of code directory

Author: Armavica

.github/workflows/tests.yml

@@ -38,65 +38,65 @@ jobs:
         python-version: ["3.10"]
         test-subset:
           - |
-            pymc/tests/test_util.py
-            pymc/tests/test_pytensorf.py
-            pymc/tests/test_math.py
-            pymc/tests/backends/test_base.py
-            pymc/tests/backends/test_ndarray.py
-            pymc/tests/step_methods/hmc/test_hmc.py
-            pymc/tests/test_func_utils.py
-            pymc/tests/distributions/test_shape_utils.py
-            pymc/tests/distributions/test_mixture.py
+            tests/test_util.py
+            tests/test_pytensorf.py
+            tests/test_math.py
+            tests/backends/test_base.py
+            tests/backends/test_ndarray.py
+            tests/step_methods/hmc/test_hmc.py
+            tests/test_func_utils.py
+            tests/distributions/test_shape_utils.py
+            tests/distributions/test_mixture.py
 
           - |
-            pymc/tests/distributions/test_continuous.py
-            pymc/tests/distributions/test_multivariate.py
+            tests/distributions/test_continuous.py
+            tests/distributions/test_multivariate.py
 
           - |
-            pymc/tests/distributions/test_bound.py
-            pymc/tests/distributions/test_censored.py
-            pymc/tests/distributions/test_simulator.py
-            pymc/tests/sampling/test_forward.py
-            pymc/tests/sampling/test_population.py
-            pymc/tests/stats/test_convergence.py
-            pymc/tests/stats/test_log_likelihood.py
-            pymc/tests/distributions/test_distribution.py
-            pymc/tests/distributions/test_discrete.py
+            tests/distributions/test_bound.py
+            tests/distributions/test_censored.py
+            tests/distributions/test_simulator.py
+            tests/sampling/test_forward.py
+            tests/sampling/test_population.py
+            tests/stats/test_convergence.py
+            tests/stats/test_log_likelihood.py
+            tests/distributions/test_distribution.py
+            tests/distributions/test_discrete.py
 
           - |
-            pymc/tests/tuning/test_scaling.py
-            pymc/tests/tuning/test_starting.py
-            pymc/tests/distributions/test_dist_math.py
-            pymc/tests/distributions/test_transform.py
-            pymc/tests/sampling/test_mcmc.py
-            pymc/tests/sampling/test_parallel.py
-            pymc/tests/test_printing.py
+            tests/tuning/test_scaling.py
+            tests/tuning/test_starting.py
+            tests/distributions/test_dist_math.py
+            tests/distributions/test_transform.py
+            tests/sampling/test_mcmc.py
+            tests/sampling/test_parallel.py
+            tests/test_printing.py
 
           - |
-            pymc/tests/distributions/test_timeseries.py
-            pymc/tests/gp/test_cov.py
-            pymc/tests/gp/test_gp.py
-            pymc/tests/gp/test_mean.py
-            pymc/tests/gp/test_util.py
-            pymc/tests/test_model.py
-            pymc/tests/test_model_graph.py
-            pymc/tests/ode/test_ode.py
-            pymc/tests/ode/test_utils.py
-            pymc/tests/step_methods/hmc/test_quadpotential.py
+            tests/distributions/test_timeseries.py
+            tests/gp/test_cov.py
+            tests/gp/test_gp.py
+            tests/gp/test_mean.py
+            tests/gp/test_util.py
+            tests/test_model.py
+            tests/test_model_graph.py
+            tests/ode/test_ode.py
+            tests/ode/test_utils.py
+            tests/step_methods/hmc/test_quadpotential.py
 
           - |
-            pymc/tests/distributions/test_truncated.py
-            pymc/tests/logprob/test_abstract.py
-            pymc/tests/logprob/test_censoring.py
-            pymc/tests/logprob/test_composite_logprob.py
-            pymc/tests/logprob/test_cumsum.py
-            pymc/tests/logprob/test_joint_logprob.py
-            pymc/tests/logprob/test_mixture.py
-            pymc/tests/logprob/test_rewriting.py
-            pymc/tests/logprob/test_scan.py
-            pymc/tests/logprob/test_tensor.py
-            pymc/tests/logprob/test_transforms.py
-            pymc/tests/logprob/test_utils.py
+            tests/distributions/test_truncated.py
+            tests/logprob/test_abstract.py
+            tests/logprob/test_censoring.py
+            tests/logprob/test_composite_logprob.py
+            tests/logprob/test_cumsum.py
+            tests/logprob/test_joint_logprob.py
+            tests/logprob/test_mixture.py
+            tests/logprob/test_rewriting.py
+            tests/logprob/test_scan.py
+            tests/logprob/test_tensor.py
+            tests/logprob/test_transforms.py
+            tests/logprob/test_utils.py
 
       fail-fast: false
     runs-on: ${{ matrix.os }}
@@ -164,10 +164,10 @@ jobs:
         floatx: [float64]
         python-version: ["3.8"]
         test-subset:
-          - pymc/tests/variational/test_approximations.py pymc/tests/variational/test_callbacks.py pymc/tests/variational/test_inference.py pymc/tests/variational/test_opvi.py pymc/tests/test_initial_point.py
-          - pymc/tests/test_model.py pymc/tests/sampling/test_mcmc.py
-          - pymc/tests/gp/test_cov.py pymc/tests/gp/test_gp.py pymc/tests/gp/test_mean.py pymc/tests/gp/test_util.py pymc/tests/ode/test_ode.py pymc/tests/ode/test_utils.py pymc/tests/smc/test_smc.py pymc/tests/sampling/test_parallel.py
-          - pymc/tests/step_methods/test_metropolis.py pymc/tests/step_methods/test_slicer.py pymc/tests/step_methods/hmc/test_nuts.py pymc/tests/step_methods/test_compound.py pymc/tests/step_methods/hmc/test_hmc.py
+          - tests/variational/test_approximations.py tests/variational/test_callbacks.py tests/variational/test_inference.py tests/variational/test_opvi.py tests/test_initial_point.py
+          - tests/test_model.py tests/sampling/test_mcmc.py
+          - tests/gp/test_cov.py tests/gp/test_gp.py tests/gp/test_mean.py tests/gp/test_util.py tests/ode/test_ode.py tests/ode/test_utils.py tests/smc/test_smc.py tests/sampling/test_parallel.py
+          - tests/step_methods/test_metropolis.py tests/step_methods/test_slicer.py tests/step_methods/hmc/test_nuts.py tests/step_methods/test_compound.py tests/step_methods/hmc/test_hmc.py
 
       fail-fast: false
     runs-on: ${{ matrix.os }}
@@ -238,16 +238,16 @@ jobs:
         python-version: ["3.9"]
         test-subset:
           - |
-            pymc/tests/sampling/test_parallel.py
-            pymc/tests/test_data.py
-            pymc/tests/test_model.py
+            tests/sampling/test_parallel.py
+            tests/test_data.py
+            tests/test_model.py
 
           - |
-            pymc/tests/sampling/test_mcmc.py
+            tests/sampling/test_mcmc.py
 
           - |
-            pymc/tests/backends/test_arviz.py
-            pymc/tests/variational/test_updates.py
+            tests/backends/test_arviz.py
+            tests/variational/test_updates.py
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -312,7 +312,7 @@ jobs:
         floatx: [float64]
         python-version: ["3.9"]
         test-subset:
-          - pymc/tests/sampling/test_jax.py pymc/tests/sampling/test_mcmc_external.py
+          - tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -383,7 +383,7 @@ jobs:
         floatx: [float32]
         python-version: ["3.10"]
         test-subset:
-        - pymc/tests/sampling/test_mcmc.py pymc/tests/ode/test_ode.py pymc/tests/ode/test_utils.py
+        - tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:

MANIFEST.in

@@ -1,4 +1,4 @@
-recursive-include pymc/tests/data *
+recursive-include tests/data *
 recursive-include source *
 # because of an upload-size limit by PyPI, we're temporarily removing docs from the tarball:
 recursive-exclude docs *

codecov.yml

@@ -20,7 +20,7 @@ coverage:
         base: auto
 
 ignore:
-  - "pymc/tests/*"
+  - "tests/*"
   - "pymc/_version.py"
 
 comment:

docs/source/contributing/implementing_distribution.md

@@ -233,14 +233,14 @@ pm.logcdf(blah, [-0.5, 1.5]).eval()
 
 ## 3. Adding tests for the new `RandomVariable`
 
-Tests for new `RandomVariables` are mostly located in `pymc/tests/distributions/test_*.py`.
+Tests for new `RandomVariables` are mostly located in `tests/distributions/test_*.py`.
 Most tests can be accommodated by the default `BaseTestDistributionRandom` class, which provides default tests for checking:
 1. Expected inputs are passed to the `rv_op` by the `dist` `classmethod`, via `check_pymc_params_match_rv_op`
 1. Expected (exact) draws are being returned, via `check_pymc_draws_match_reference`
 1. Shape variable inference is correct, via `check_rv_size`
 
 ```python
-from pymc.tests.distributions.util import BaseTestDistributionRandom, seeded_scipy_distribution_builder
+from tests.distributions.util import BaseTestDistributionRandom, seeded_scipy_distribution_builder
 
 class TestBlah(BaseTestDistributionRandom):
 
@@ -279,7 +279,7 @@ class TestBlahAltParam2(BaseTestDistributionRandom):
 
 ```
 
-Custom tests can also be added to the class as is done for the {class}`~pymc.tests.distributions.test_continuous.TestFlat`.
+Custom tests can also be added to the class as is done for the {class}`~tests.distributions.test_continuous.TestFlat`.
 
 ### Note on `check_rv_size` test:
 
@@ -292,7 +292,7 @@ tests_to_run = ["check_rv_size"]
 ```
 
 This is usually needed for Multivariate distributions.
-You can see an example in {class}`~pymc.tests.distributions.test_multivariate.TestDirichlet`.
+You can see an example in {class}`~tests.distributions.test_multivariate.TestDirichlet`.
 
 ### Notes on `check_pymcs_draws_match_reference` test
 
@@ -302,17 +302,17 @@ The latter kind of test (if warranted) can be performed with the aid of `pymc_ra
 This kind of test only makes sense if there is a good independent generator reference (i.e., not just the same composition of NumPy / SciPy calls that is done inside `rng_fn`).
 
 Finally, when your `rng_fn` is doing something more than just calling a NumPy or SciPy method, you will need to set up an equivalent seeded function with which to compare for the exact draws (instead of relying on `seeded_[scipy|numpy]_distribution_builder`).
-You can find an example in {class}`~pymc.tests.distributions.test_continuous.TestWeibull`, whose `rng_fn` returns `beta * np.random.weibull(alpha, size=size)`.
+You can find an example in {class}`~tests.distributions.test_continuous.TestWeibull`, whose `rng_fn` returns `beta * np.random.weibull(alpha, size=size)`.
 
 
 ## 4. Adding tests for the `logp` / `logcdf` methods
 
 Tests for the `logp` and `logcdf` mostly make use of the helpers `check_logp`, `check_logcdf`, and
-`check_selfconsistency_discrete_logcdf` implemented in `~pymc.tests.distributions.util`
+`check_selfconsistency_discrete_logcdf` implemented in `~tests.distributions.util`
 
 ```python
-from pymc.tests.distributions.util import check_logp, check_logcdf, Domain
-from pymc.tests.helpers import select_by_precision
+from tests.helpers import select_by_precision
+from tests.distributions.util import check_logp, check_logcdf, Domain
 
 R = Domain([-np.inf, -2.1, -1, -0.01, 0.0, 0.01, 1, 2.1, np.inf])
 Rplus = Domain([0, 0.01, 0.1, 0.9, 0.99, 1, 1.5, 2, 100, np.inf])
@@ -382,7 +382,7 @@ which checks if:
 
 import pytest
 from pymc.distributions import Blah
-from pymc.tests.distributions.util import assert_moment_is_expected
+from tests.distributions.util import assert_moment_is_expected
 
 @pytest.mark.parametrize(
     "param1, param2, size, expected",

docs/source/contributing/running_the_test_suite.md

@@ -19,7 +19,7 @@ Therefore, we recommend to run just specific tests that target the parts of the
 
 To run all tests from a single file:
 ```bash
-pytest -v pymc/tests/test_model.py
+pytest -v tests/test_model.py
 ```
 
 ```{tip}
@@ -31,7 +31,7 @@ By using the `-k` flag, you can filter for test cases that match a certain patte
 For example, the following command runs all test cases from `test_model.py` that have "coord" in their name:
 
 ```bash
-pytest -v pymc/tests/test_model.py -k coord
+pytest -v tests/test_model.py -k coord
 ```
 
 
@@ -40,7 +40,7 @@ Note that because you are not running the entire test suite, the coverage will b
 But you can still watch for specific line numbers of the code that you're working on.
 
 ```bash
-pytest -v --cov=pymc --cov-report term-missing pymc/tests/<name of test>.py
+pytest -v --cov=pymc --cov-report term-missing tests/<name of test>.py
 ```
 
 When you are reasonably confident about the changes you made, you can push the changes and open a pull request.

pymc/data.py

@@ -63,7 +63,7 @@ def get_data(filename):
     -------
     BytesIO of the data
     """
-    data_pkg = "pymc.tests"
+    data_pkg = "tests"
     try:
         content = pkgutil.get_data(data_pkg, os.path.join("data", filename))
     except FileNotFoundError:

scripts/check_all_tests_are_covered.py

@@ -23,7 +23,7 @@ def find_testfiles():
     dp_repo = Path(__file__).parent.parent
     all_tests = {
         str(fp.relative_to(dp_repo)).replace(os.sep, "/")
-        for fp in (dp_repo / "pymc" / "tests").glob("**/test_*.py")
+        for fp in (dp_repo / "tests").glob("**/test_*.py")
     }
     _log.info("Found %i tests in total.", len(all_tests))
     return all_tests

scripts/run_mypy.py

@@ -159,7 +159,7 @@ def check_no_unexpected_results(mypy_lines: Iterator[str]):
     args, _ = parser.parse_known_args()
 
     cp = subprocess.run(
-        ["mypy", "--show-error-codes", "--exclude", "pymc/tests", "pymc"],
+        ["mypy", "--show-error-codes", "--exclude", "tests", "pymc"],
         capture_output=True,
     )
     output = cp.stdout.decode()

setup.cfg

@@ -1,5 +1,5 @@
 [tool:pytest]
-testpaths = pymc/tests
+testpaths = tests
 
 [coverage:run]
 omit =  *examples*

pymc/tests/variational/__init__.py renamed to tests/__init__.py

@@ -11,3 +11,7 @@
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
+
+import pymc as pm
+
+_log = pm._log

pymc/tests/__init__.py renamed to tests/backends/__init__.py

@@ -22,7 +22,7 @@
 import pytest
 
 from pymc.backends import base
-from pymc.tests import models
+from tests import models
 
 
 class ModelBackendSetupTestCase:

pymc/tests/backends/fixtures.py renamed to tests/backends/fixtures.py

@@ -326,7 +326,7 @@ def test_overwrite_model_coords_dims(self):
         assert np.all(idata2.constant_data.x.dim2.values == np.array(["c1", "c2"]))
 
     def test_missing_data_model(self):
-        # source pymc/pymc/tests/test_missing.py
+        # source tests/test_missing.py
         data = ma.masked_values([1, 2, -1, 4, -1], value=-1)
         model = pm.Model()
         with model:

pymc/tests/backends/test_arviz.py renamed to tests/backends/test_arviz.py

@@ -17,7 +17,7 @@
 import pytest
 
 from pymc.backends import base, ndarray
-from pymc.tests.backends import fixtures as bf
+from tests.backends import fixtures as bf
 
 STATS1 = [{"a": np.float64, "b": bool}]
 

pymc/tests/backends/test_base.py renamed to tests/backends/test_base.py

@@ -32,7 +32,7 @@
 from pymc.logprob.joint_logprob import logp
 from pymc.logprob.utils import ParameterValueError
 from pymc.pytensorf import floatX
-from pymc.tests.distributions.util import (
+from tests.distributions.util import (
     BaseTestDistributionRandom,
     Circ,
     Domain,
@@ -49,8 +49,8 @@
     seeded_numpy_distribution_builder,
     seeded_scipy_distribution_builder,
 )
-from pymc.tests.helpers import select_by_precision
-from pymc.tests.logprob.utils import create_pytensor_params, scipy_logprob_tester
+from tests.helpers import select_by_precision
+from tests.logprob.utils import create_pytensor_params, scipy_logprob_tester
 
 try:
     from polyagamma import polyagamma_cdf, polyagamma_pdf, random_polyagamma

pymc/tests/backends/test_ndarray.py renamed to tests/backends/test_ndarray.py

@@ -33,7 +33,8 @@
 from pymc.logprob.joint_logprob import logp
 from pymc.logprob.utils import ParameterValueError
 from pymc.pytensorf import floatX
-from pymc.tests.distributions.util import (
+from pymc.vartypes import discrete_types
+from tests.distributions.util import (
     BaseTestDistributionRandom,
     Bool,
     Domain,
@@ -57,8 +58,7 @@
     seeded_numpy_distribution_builder,
     seeded_scipy_distribution_builder,
 )
-from pymc.tests.logprob.utils import create_pytensor_params, scipy_logprob_tester
-from pymc.vartypes import discrete_types
+from tests.logprob.utils import create_pytensor_params, scipy_logprob_tester
 
 
 def discrete_weibull_logpmf(value, q, beta):

pymc/tests/checks.py renamed to tests/checks.py

@@ -37,8 +37,8 @@
 )
 from pymc.logprob.utils import ParameterValueError
 from pymc.pytensorf import floatX
-from pymc.tests.checks import close_to
-from pymc.tests.helpers import verify_grad
+from tests.checks import close_to
+from tests.helpers import verify_grad
 
 
 @pytest.mark.parametrize(