Merge branch 'v3' into v3

.github/workflows/pytest.yml

@@ -13,6 +13,7 @@ jobs:
         floatx: [float32, float64]
         test-subset:
           - |
+            --ignore=pymc3/tests/test_backports.py
             --ignore=pymc3/tests/test_dist_math.py
             --ignore=pymc3/tests/test_distribution_defaults.py
             --ignore=pymc3/tests/test_distributions.py
@@ -42,6 +43,7 @@ jobs:
             pymc3/tests/test_shared.py
             pymc3/tests/test_smc.py
           - |
+            pymc3/tests/test_backports.py
             pymc3/tests/test_examples.py
             pymc3/tests/test_mixture.py
             pymc3/tests/test_ode.py

.github/workflows/release.yml

@@ -9,7 +9,7 @@ jobs:
   release-job:
     runs-on: ubuntu-latest
     env:
-      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN_PYMC3 }}
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ^(docs/logos|pymc3/tests/data)/
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v4.0.1
   hooks:
     -   id: check-merge-conflict
     -   id: check-toml
@@ -14,44 +14,43 @@ repos:
         exclude: ^requirements-dev\.txt$
     -   id: trailing-whitespace
 - repo: https://github.com/PyCQA/isort
-  rev: 5.7.0
+  rev: 5.10.1
   hooks:
     - id: isort
       name: isort
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.10.0
+  rev: v2.29.1
   hooks:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 20.8b1
+  rev: 21.12b0
   hooks:
     - id: black
 - repo: https://github.com/PyCQA/pylint
-  rev: pylint-2.6.0
+  rev: v2.12.2
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]
-      files: ^pymc3/
+      files: ^pymc/
+- repo: https://github.com/MarcoGorelli/madforhooks
+  rev: 0.2.1
+  hooks:
+    - id: conda-env-sorter
+      files: ^conda-envs/environment-dev-py.+\.yml$
 - repo: local
   hooks:
     - id: check-no-tests-are-ignored
+      additional_dependencies: [pandas,pyyaml]
       entry: python scripts/check_all_tests_are_covered.py
       files: ^\.github/workflows/pytest\.yml$
       language: python
       name: Check no tests are ignored
       pass_filenames: false
-    - id: conda-env-sort
-      additional_dependencies: [pyyaml]
-      entry: python scripts/sort_conda_envs.py
-      files: ^conda-envs/environment-dev-py37\.yml$
-      language: python
-      name: Sort dependencies in conda envs
-      types: [yaml]
     - id: pip-from-conda
       additional_dependencies: [pyyaml]
       entry: python scripts/generate_pip_deps_from_conda.py
-      files: ^conda-envs/
+      files: ^conda-envs/environment-dev-py.+.yml$
       language: python
       name: Generate pip dependency from conda
     - id: no-relative-imports

README.rst

@@ -1,4 +1,4 @@
-.. image:: https://cdn.rawgit.com/pymc-devs/pymc3/master/docs/logos/svg/PyMC3_banner.svg
+.. image:: https://cdn.rawgit.com/pymc-devs/pymc/v3/docs/logos/svg/PyMC3_banner.svg
     :height: 100px
     :alt: PyMC3 logo
     :align: center

RELEASE-NOTES.md

@@ -1,19 +1,42 @@
 # Release Notes
 
-## PyMC3 3.11.3 (TBD)
+## PyMC 3.11.5 (14 March 2022)
+### Backports
++ The `pm.logp(rv, x)` syntax is now available and recommended to make your model code `v4`-ready. Note that this backport is just an alias and much less capable than what's available with `pymc >=4` (see [#5083](https://github.com/pymc-devs/pymc/pulls/5083)).
++ The `pm.Distribution(testval=...)` kwarg was deprecated and will be replaced by `pm.Distribution(initval=...)`in `pymc >=4` (see [#5226](https://github.com/pymc-devs/pymc/pulls/5226)).
++ The `pm.sample(start=...)` kwarg was deprecated and will be replaced by `pm.sample(initvals=...)`in `pymc >=4` (see [#5226](https://github.com/pymc-devs/pymc/pulls/5226)).
++ `pm.Lognormal` is now available as an alias for `pm.Lognormal` (see [#5389](https://github.com/pymc-devs/pymc/pull/5389)).
+
+### Bugfixes
++ The upper limit for the SciPy version is `<1.8.0` and will most probably remain for all future `3.x.x` releases. For compatibility with newer SciPy versions please update to `pymc>=4.0.0`. Also see [#5448](https://github.com/pymc-devs/pymc/pull/5448).
++ A hotfix is applied on import to remain compatible with NumPy 1.22 (see [#5316](https://github.com/pymc-devs/pymc/pull/5316)).
+
+## PyMC3 3.11.4 (20 August 2021)
+
+### New Features
++ Generalized BART, bounded distributions like Binomial and Poisson can now be used as likelihoods (see [#4675](https://github.com/pymc-devs/pymc3/pull/4675), [#4709](https://github.com/pymc-devs/pymc3/pull/4709) and
+[#4720](https://github.com/pymc-devs/pymc3/pull/4720)).
++ `plot_gp_dist` is now available at the package level: `pm.plot_gp_dist` ([see #4835](https://github.com/pymc-devs/pymc3/pull/4835)).
++ The experimental JAX sampling was removed. It will be included in the upcoming `v4` release ([see #4866](https://github.com/pymc-devs/pymc3/pull/4866)).
++ `pm.intX` no longer downcasts integers unnecessarily (see [#4569](https://github.com/pymc-devs/pymc3/pull/4569))
+
 ### Maintenance
 + A deprecation warning from the `semver` package we use for checking backend compatibility was dealt with (see [#4547](https://github.com/pymc-devs/pymc3/pull/4547)).
 + `theano.printing.pydotprint` is now hotfixed upon import (see [#4594](https://github.com/pymc-devs/pymc3/pull/4594)).
 + Fix bug in the computation of the log pseudolikelihood values (SMC-ABC). (see [#4672](https://github.com/pymc-devs/pymc3/pull/4672)).
 + Fix `LKJCorr.random` method to work with `pm.sample_prior_predictive`. (see [#4780](https://github.com/pymc-devs/pymc3/pull/4780)).
 + Enable documentation generation via ReadTheDocs for upcoming v3 releases. (see [#4805](https://github.com/pymc-devs/pymc3/pull/4805)).
 + Remove `float128` dtype support (see [#4834](https://github.com/pymc-devs/pymc3/pull/4834)).
++ Use `to_tuple` function in `pm.fast_sample_posterior_predictive` to pass shape assertions (see [#4927](https://github.com/pymc-devs/pymc3/pull/4927)).
 
-### New Features
-+ Generalized BART, bounded distributions like Binomial and Poisson can now be used as likelihoods (see [#4675](https://github.com/pymc-devs/pymc3/pull/4675), [#4709](https://github.com/pymc-devs/pymc3/pull/4709) and
-[#4720](https://github.com/pymc-devs/pymc3/pull/4720)).
-+ `plot_gp_dist` is now available at the package level: `pm.plot_gp_dist` ([see #4835](https://github.com/pymc-devs/pymc3/pull/4835)).
-+ The experimental JAX sampling was removed. It will be included in the upcoming `v4` release ([see #4866](https://github.com/pymc-devs/pymc3/pull/4866)).
+**Release manager** for 3.11.4: Ravin Kumar ([@canyon289](https://github.com/canyon289))
+
+## PyMC3 3.11.3 (19 August 2021)
+
+### Maintenance
+* Broken release. Refer to 3.11.4
+
+**Release manager** for 3.11.3: Ravin Kumar ([@canyon289](https://github.com/canyon289))
 
 ## PyMC3 3.11.2 (14 March 2021)
 
@@ -34,7 +57,6 @@
 - `pm.make_shared_replacements` now retains broadcasting information which fixes issues with Metropolis samplers (see [#4492](https://github.com/pymc-devs/pymc3/pull/4492)).
 
 **Release manager** for 3.11.2: Michael Osthege ([@michaelosthege](https://github.com/michaelosthege))
-- `pm.intX` no longer downcasts integers unnecessarily (see [#4569](https://github.com/pymc-devs/pymc3/pull/4569))
 
 ## PyMC3 3.11.1 (12 February 2021)
 

conda-envs/environment-dev-py37.yml

@@ -8,16 +8,18 @@ dependencies:
 - libblas=*=*mkl
 - mkl-service
 - nbsphinx>=0.4
-- numpy=1.15
-- numpydoc>=0.9
-- pandas=0.24
+- numpy>=1.15,<1.22.2
+- numpydoc<1.2
+- pip
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.7
 - recommonmark>=0.4
-- scipy=1.2
+- scipy>=1.4.1,<1.8.0
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark
+- pip:
+  - deprecat

conda-envs/environment-dev-py38.yml

@@ -8,13 +8,18 @@ dependencies:
 - libblas=*=*mkl
 - mkl-service
 - nbsphinx>=0.4
-- numpydoc>=0.9
+- numpy>=1.15,<1.22.2
+- numpydoc<1.2
+- pip
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.8
 - recommonmark>=0.4
+- scipy>=1.4.1,<1.8.0
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark
+- pip:
+  - deprecat

conda-envs/environment-dev-py39.yml

@@ -8,13 +8,18 @@ dependencies:
 - libblas=*=*mkl
 - mkl-service
 - nbsphinx>=0.4
-- numpydoc>=0.9
+- numpy>=1.15,<1.22.2
+- numpydoc<1.2
+- pip
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.9
 - recommonmark>=0.4
+- scipy>=1.4.1,<1.8.0
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark
+- pip:
+  - deprecat

conda-envs/windows-environment-dev-py38.yml

@@ -16,11 +16,15 @@ dependencies:
 # Extra stuff for dev, testing and docs build
 - ipython>=7.16
 - nbsphinx>=0.4
-- numpydoc>=0.9
+- numpy>=1.15,<1.22.2
+- numpydoc<1.2
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
 - recommonmark>=0.4
+- scipy>=1.4.1,<1.8.0
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark
+- pip:
+  - deprecat

docs/source/PyMC3_and_Theano.rst

@@ -37,6 +37,8 @@ arbitrarily chosen) function
 First, we need to define symbolic variables for our inputs (this
 is similar to eg SymPy's `Symbol`)::
 
+    import pymc as pm
+    import numpy
     import theano
     import theano.tensor as tt
     # We don't specify the dtype of our input variables, so it
@@ -75,7 +77,7 @@ We can call this function with actual arrays as many times as we want::
 
     a_val = 1.2
     x_vals = np.random.randn(10)
-    y_vals = np.random.randn(10)
+    y_vals = np.int32(np.random.randn(10))
 
     out = func(a_val, x_vals, y_vals)
 
@@ -167,8 +169,8 @@ we generate a Theano variable. And for each variable (observed or otherwise)
 we add a term to the global logp. In the background something similar to
 this is happening::
 
-    # For illustration only, those functions don't actually exist
-    # in exactly this way!
+    # For illustration only, these functions don't exactly
+    # work this way!
     model = pm.Model()
 
     mu = tt.scalar('mu')

docs/source/_static/main.css

@@ -3,3 +3,130 @@
     margin: 0.5em;
     content: ":";
 }
+
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+  --pst-color-primary: 19, 6, 84;
+  --pst-color-success: 40, 167, 69;
+  --pst-color-info: 0, 123, 255; /*23, 162, 184;*/
+  --pst-color-warning: 255, 193, 7;
+  --pst-color-danger: 220, 53, 69;
+  --pst-color-text-base: 51, 51, 51;
+
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+  --pst-color-admonition-danger: var(--pst-color-danger);
+  --pst-color-admonition-error: var(--pst-color-danger);
+  --pst-color-admonition-hint: var(--pst-color-success);
+  --pst-color-admonition-tip: var(--pst-color-success);
+  --pst-color-admonition-important: var(--pst-color-success);
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+
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