Merge branch 'main' of https://github.com/pymc-devs/pymc3 into add-ze…

…rosumnormal

.github/workflows/pre-commit.yml

@@ -14,3 +14,53 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
     - uses: pre-commit/action@v2.0.0
+  mypy:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache conda
+        uses: actions/cache@v3
+        env:
+          # Increase this value to reset cache if environment-test.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-py39-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('conda-envs/environment-test.yml') }}
+      - name: Cache multiple paths
+        uses: actions/cache@v3
+        env:
+          # Increase this value to reset cache if requirements.txt has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/.cache/pip
+            $RUNNER_TOOL_CACHE/Python/*
+            ~\AppData\Local\pip\Cache
+          key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('requirements.txt') }}
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          mamba-version: "*"
+          activate-environment: pymc-test
+          channel-priority: strict
+          environment-file: conda-envs/environment-test.yml
+          python-version: 3.9
+          use-mamba: true
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - name: Install-pymc and mypy dependencies
+        run: |
+          conda activate pymc-test
+          pip install -e .
+          pip install --pre -U polyagamma
+          pip install mypy types-cachetools
+          python --version
+      - name: Run mypy
+        run: |
+          conda activate pymc-test
+          python ./scripts/run_mypy.py --verbose

.github/workflows/tests.yml

@@ -43,7 +43,7 @@ jobs:
             pymc/tests/test_aesaraf.py
             pymc/tests/test_math.py
             pymc/tests/backends/test_ndarray.py
-            pymc/tests/test_hmc.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
@@ -63,8 +63,7 @@ jobs:
           - |
             pymc/tests/tuning/test_scaling.py
             pymc/tests/tuning/test_starting.py
-            pymc/tests/test_shared.py
-            pymc/tests/test_types.py
+            pymc/tests/test_sampling.py
             pymc/tests/distributions/test_dist_math.py
             pymc/tests/distributions/test_transform.py
             pymc/tests/test_parallel_sampling.py
@@ -147,10 +146,10 @@ jobs:
         floatx: [float64]
         python-version: ["3.8"]
         test-subset:
-          - pymc/tests/test_variational_inference.py pymc/tests/test_initial_point.py
-          - pymc/tests/test_model.py pymc/tests/test_step.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/test_smc.py pymc/tests/test_parallel_sampling.py
-          - pymc/tests/test_sampling.py pymc/tests/test_posteriors.py
+          - 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/step_methods/test_compound.py pymc/tests/step_methods/hmc/test_hmc.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/test_parallel_sampling.py
+          - pymc/tests/test_sampling.py pymc/tests/step_methods/test_metropolis.py pymc/tests/step_methods/test_slicer.py pymc/tests/step_methods/hmc/test_nuts.py
 
       fail-fast: false
     runs-on: ${{ matrix.os }}
@@ -222,7 +221,7 @@ jobs:
           - |
             pymc/tests/test_parallel_sampling.py
             pymc/tests/test_data.py
-            pymc/tests/test_missing.py
+            pymc/tests/test_model.py
 
           - |
             pymc/tests/test_sampling.py

.pre-commit-config.yaml

@@ -13,24 +13,6 @@ repos:
     -   id: requirements-txt-fixer
         exclude: ^requirements-dev\.txt$
     -   id: trailing-whitespace
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.981
-  hooks:
-    - id: mypy
-      name: Run static type checks
-      language: python
-      entry: python ./scripts/run_mypy.py --verbose
-      additional_dependencies:
-      - pandas
-      - types-cachetools
-      - types-filelock
-      - types-setuptools
-      - arviz
-      - aeppl==0.0.36
-      - aesara==2.8.6
-      always_run: true
-      require_serial: true
-      pass_filenames: false
 - repo: https://github.com/PyCQA/isort
   rev: 5.10.1
   hooks:

conda-envs/environment-dev.yml

@@ -5,8 +5,8 @@ channels:
 - defaults
 dependencies:
 # Base dependencies
-- aeppl=0.0.36
-- aesara=2.8.6
+- aeppl=0.0.38
+- aesara=2.8.7
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/environment-test.yml

@@ -5,8 +5,8 @@ channels:
 - defaults
 dependencies:
 # Base dependencies
-- aeppl=0.0.36
-- aesara=2.8.6
+- aeppl=0.0.38
+- aesara=2.8.7
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/windows-environment-dev.yml

@@ -5,8 +5,8 @@ channels:
 - defaults
 dependencies:
 # Base dependencies (see install guide for Windows)
-- aeppl=0.0.36
-- aesara=2.8.6
+- aeppl=0.0.38
+- aesara=2.8.7
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/windows-environment-test.yml

@@ -5,8 +5,8 @@ channels:
 - defaults
 dependencies:
 # Base dependencies (see install guide for Windows)
-- aeppl=0.0.36
-- aesara=2.8.6
+- aeppl=0.0.38
+- aesara=2.8.7
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

docs/source/contributing/developer_guide_implementing_distribution.md → docs/source/contributing/implementing_distribution.md

@@ -1,12 +1,12 @@
 (implementing-a-distribution)=
-# Implementing a Distribution
+# Implementing a RandomVariable Distribution
 
 This guide provides an overview on how to implement a distribution for PyMC version `>=4.0.0`.
 It is designed for developers who wish to add a new distribution to the library.
 Users will not be aware of all this complexity and should instead make use of helper methods such as `~pymc.DensityDist`.
 
 PyMC {class}`~pymc.Distribution` builds on top of Aesara's {class}`~aesara.tensor.random.op.RandomVariable`, and implements `logp`, `logcdf` and `moment` methods as well as other initialization and validation helpers.
-Most notably `shape/dims` kwargs, alternative parametrizations, and default `transforms`.
+Most notably `shape/dims/observed` kwargs, alternative parametrizations, and default `transform`.
 
 Here is a summary check-list of the steps needed to implement a new distribution.
 Each section will be expanded below:
@@ -88,11 +88,11 @@ blah = BlahRV()
 Some important things to keep in mind:
 
 1. Everything inside the `rng_fn` method is pure Python code (as are the inputs) and should not make use of other `Aesara` symbolic ops. The random method should make use of the `rng` which is a NumPy {class}`~numpy.random.RandomState`, so that samples are reproducible.
-1. Non-default `RandomVariable` dimensions will end up in the `rng_fn` via the `size` kwarg. The `rng_fn` will have to take this into consideration for correct output. `size` is the specification used by NumPy and SciPy and works like PyMC `shape` for univariate distributions, but is different for multivariate distributions. For multivariate distributions the __`size` excludes the `ndim_supp` support dimensions__, whereas the __`shape` of the resulting `TensorVariabe` or `ndarray` includes the support dimensions__. This [discussion](https://github.com/numpy/numpy/issues/17669) may be helpful to get more context.
+1. Non-default `RandomVariable` dimensions will end up in the `rng_fn` via the `size` kwarg. The `rng_fn` will have to take this into consideration for correct output. `size` is the specification used by NumPy and SciPy and works like PyMC `shape` for univariate distributions, but is different for multivariate distributions. For multivariate distributions the __`size` excludes the `ndim_supp` support dimensions__, whereas the __`shape` of the resulting `TensorVariabe` or `ndarray` includes the support dimensions__. For more context check {doc}`The dimensionality notebook <pymc:dimensionality=>`.
 1. `Aesara` tries to infer the output shape of the `RandomVariable` (given a user-specified size) by introspection of the `ndim_supp` and `ndim_params` attributes. However, the default method may not work for more complex distributions. In that case, custom `_supp_shape_from_params` (and less probably, `_infer_shape`) should also be implemented in the new `RandomVariable` class. One simple example is seen in the {class}`~pymc.DirichletMultinomialRV` where it was necessary to specify the `rep_param_idx` so that the `default_supp_shape_from_params` helper method can do its job. In more complex cases, it may not suffice to use this default helper. This could happen for instance if the argument values determined the support shape of the distribution, as happens in the `~pymc.distributions.multivarite._LKJCholeskyCovRV`.
 1. It's okay to use the `rng_fn` `classmethods` of other Aesara and PyMC `RandomVariables` inside the new `rng_fn`. For example if you are implementing a negative HalfNormal `RandomVariable`, your `rng_fn` can simply return `- halfnormal.rng_fn(rng, scale, size)`.
 
-*Note: In addition to `size`, the PyMC API also provides `shape` and `dims` as alternatives to define a distribution dimensionality, but this is taken care of by {class}`~pymc.Distribution`, and should not require any extra changes.*
+*Note: In addition to `size`, the PyMC API also provides `shape`, `dims` and `observed` as alternatives to define a distribution dimensionality, but this is taken care of by {class}`~pymc.Distribution`, and should not require any extra changes.*
 
 For a quick test that your new `RandomVariable` `Op` is working, you can call the `Op` with the necessary parameters and then call `eval()` on the returned object:
 
@@ -129,9 +129,11 @@ Here is how the example continues:
 
 ```python
 
+import aesara.tensor as at
 from pymc.aesaraf import floatX, intX
 from pymc.distributions.continuous import PositiveContinuous
 from pymc.distributions.dist_math import check_parameters
+from pymc.distributions.shape_utils import rv_size_is_none
 
 
 # Subclassing `PositiveContinuous` will dispatch a default `log` transformation
@@ -231,15 +233,16 @@ 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/test_distributions_random.py`.
-Most tests can be accommodated by the default `BaseTestDistribution` class, which provides default tests for checking:
+Tests for new `RandomVariables` are mostly located in `pymc/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
 
-class TestBlah(BaseTestDistribution):
+class TestBlah(BaseTestDistributionRandom):
 
     pymc_dist = pm.Blah
     # Parameters with which to test the blah pymc Distribution
@@ -266,7 +269,7 @@ For instance, if it's just the inverse, testing with `1.0` is not very informati
 
 ```python
 
-class TestBlahAltParam2(BaseTestDistribution):
+class TestBlahAltParam2(BaseTestDistributionRandom):
 
     pymc_dist = pm.Blah
     # param2 is equivalent to 1 / alt_param2
@@ -276,7 +279,7 @@ class TestBlahAltParam2(BaseTestDistribution):
 
 ```
 
-Custom tests can also be added to the class as is done for the {class}`~pymc.tests.test_random.TestFlat`.
+Custom tests can also be added to the class as is done for the {class}`~pymc.tests.distributions.test_continuous.TestFlat`.
 
 ### Note on `check_rv_size` test:
 
@@ -289,37 +292,36 @@ tests_to_run = ["check_rv_size"]
 ```
 
 This is usually needed for Multivariate distributions.
-You can see an example in {class}`~pymc.test.test_random.TestDirichlet`.
+You can see an example in {class}`~pymc.tests.distributions.test_multivariate.TestDirichlet`.
 
 ### Notes on `check_pymcs_draws_match_reference` test
 
 The `check_pymcs_draws_match_reference` is a very simple test for the equality of draws from the `RandomVariable` and the exact same python function, given the same inputs and random seed.
 A small number (`size=15`) is checked. This is not supposed to be a test for the correctness of the random number generator.
-The latter kind of test (if warranted) can be performed with the aid of `pymc_random` and `pymc_random_discrete` methods in the same test file, which will perform an expensive statistical comparison between the `RandomVariable.rng_fn` and a reference Python function.
+The latter kind of test (if warranted) can be performed with the aid of `pymc_random` and `pymc_random_discrete` methods, which will perform an expensive statistical comparison between the `RandomVariable.rng_fn` and a reference Python function.
 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.test_distributions_random.TestWeibull`, whose `rng_fn` returns `beta * np.random.weibull(alpha, size=size)`.
+You can find an example in {class}`~pymc.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` methods are contained in `pymc/tests/test_distributions.py`, and most make use of the `TestMatchesScipy` class, which provides `check_logp`, `check_logcdf`, and
-`check_selfconsistency_discrete_logcdf` standard methods.
-These will suffice for most distributions.
+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`
 
 ```python
-
+from pymc.tests.distributions.util import check_logp, check_logcdf, Domain
 from pymc.tests.helpers import select_by_precision
 
 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])
 
-...
 
-def test_blah(self):
 
-  self.check_logp(
+def test_blah():
+
+  check_logp(
       pymc_dist=pm.Blah,
       # Domain of the distribution values
       domain=R,
@@ -333,7 +335,7 @@ def test_blah(self):
       n_samples=100,
   )
 
-  self.check_logcdf(
+  check_logcdf(
       pymc_dist=pm.Blah,
       domain=R,
       paramdomains={"mu": R, "sigma": Rplus},
@@ -370,15 +372,17 @@ def test_blah_logcdf(self):
 
 ## 5. Adding tests for the `moment` method
 
-Tests for the `moment` method are contained in `pymc/tests/test_distributions_moments.py`, and make use of the function `assert_moment_is_expected`
+Tests for the `moment` make use of the function `assert_moment_is_expected`
 which checks if:
 1. Moments return the `expected` values
 1. Moments have the expected size and shape
+1. Moments have a finite logp
 
 ```python
 
 import pytest
 from pymc.distributions import Blah
+from pymc.tests.distributions.util import assert_moment_is_expected
 
 @pytest.mark.parametrize(
     "param1, param2, size, expected",