Merge branch 'main' into add-zerosumnormal

Author: AlexAndorra

.gitattributes

@@ -0,0 +1 @@
+pymc/_version.py export-subst

.github/workflows/tests.yml

@@ -8,6 +8,7 @@ on:
       - "*.py"
       - "conda-envs/**"
       - "codecov.yml"
+      - "requirements*.txt"
       - "scripts/*.sh"
   push:
     branches: [main]
@@ -41,45 +42,45 @@ jobs:
             pymc/tests/distributions/test_logprob.py
             pymc/tests/test_aesaraf.py
             pymc/tests/test_math.py
-            pymc/tests/test_posdef_sym.py
-            pymc/tests/test_ndarray_backend.py
+            pymc/tests/backends/test_ndarray.py
             pymc/tests/test_hmc.py
             pymc/tests/test_func_utils.py
             pymc/tests/distributions/test_shape_utils.py
-            pymc/tests/test_starting.py
             pymc/tests/distributions/test_mixture.py
 
           - |
             pymc/tests/distributions/test_distribution.py
-            pymc/tests/distributions/test_bound.py
-            pymc/tests/distributions/test_censored.py
             pymc/tests/distributions/test_discrete.py
             pymc/tests/distributions/test_continuous.py
             pymc/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/distributions/test_truncated.py
 
           - |
-            pymc/tests/test_tuning.py
+            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_modelcontext.py
             pymc/tests/distributions/test_dist_math.py
-            pymc/tests/test_minibatches.py
-            pymc/tests/test_pickling.py
             pymc/tests/distributions/test_transform.py
             pymc/tests/test_parallel_sampling.py
             pymc/tests/test_printing.py
 
           - |
             pymc/tests/distributions/test_timeseries.py
-            pymc/tests/test_gp.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/test_ode.py
-            pymc/tests/test_profile.py
-            pymc/tests/test_quadpotential.py
+            pymc/tests/ode/test_ode.py
+            pymc/tests/ode/test_utils.py
+            pymc/tests/step_methods/hmc/test_quadpotential.py
 
       fail-fast: false
     runs-on: ${{ matrix.os }}
@@ -147,8 +148,8 @@ jobs:
         python-version: ["3.8"]
         test-subset:
           - pymc/tests/test_variational_inference.py pymc/tests/test_initial_point.py
-          - pymc/tests/test_pickling.py pymc/tests/test_profile.py pymc/tests/test_step.py
-          - pymc/tests/test_gp.py pymc/tests/test_ode.py pymc/tests/test_smc.py pymc/tests/test_parallel_sampling.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
 
       fail-fast: false
@@ -220,15 +221,15 @@ jobs:
         test-subset:
           - |
             pymc/tests/test_parallel_sampling.py
-            pymc/tests/test_data_container.py
+            pymc/tests/test_data.py
             pymc/tests/test_missing.py
 
           - |
             pymc/tests/test_sampling.py
 
           - |
-            pymc/tests/test_idata_conversion.py
-            pymc/tests/test_updates.py
+            pymc/tests/backends/test_arviz.py
+            pymc/tests/variational/test_updates.py
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:
@@ -361,7 +362,7 @@ jobs:
         floatx: [float32]
         python-version: ["3.10"]
         test-subset:
-        - pymc/tests/test_sampling.py pymc/tests/test_ode.py
+        - pymc/tests/test_sampling.py pymc/tests/ode/test_ode.py pymc/tests/ode/test_utils.py
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
         exclude: ^requirements-dev\.txt$
     -   id: trailing-whitespace
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.971
+  rev: v0.981
   hooks:
     - id: mypy
       name: Run static type checks
@@ -26,8 +26,8 @@ repos:
       - types-filelock
       - types-setuptools
       - arviz
-      - aesara==2.8.2
-      - aeppl==0.0.35
+      - aeppl==0.0.36
+      - aesara==2.8.6
       always_run: true
       require_serial: true
       pass_filenames: false
@@ -37,26 +37,28 @@ repos:
     - id: isort
       name: isort
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.37.3
+  rev: v2.38.2
   hooks:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 22.6.0
+  rev: 22.8.0
   hooks:
     - id: black
     - id: black-jupyter
 - repo: https://github.com/PyCQA/pylint
-  rev: v2.15.0
+  rev: v2.15.3
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]
       files: ^pymc/
+      exclude: (?x)(pymc/_version.py)
 - repo: https://github.com/MarcoGorelli/madforhooks
   rev: 0.3.0
   hooks:
     - id: no-print-statements
       files: ^pymc/
+      exclude: (?x)(pymc/_version.py)
 - repo: local
   hooks:
     - id: check-no-tests-are-ignored
@@ -77,6 +79,7 @@ repos:
       entry: from \.[\.\w]* import
       types: [python]
       language: pygrep
+      exclude: (?x)(pymc/_version.py|versioneer.py)
     - id: no-internal-links
       name: Check no links that should be cross-references are in the docs
       description: >-

GOVERNANCE.md

@@ -656,10 +656,10 @@ In addition, Council members are given administrative rights to all repositories
 the [pymc-devs](https://github.com/pymc-devs) organization.
 
 ##### Communication Focused Repositories
-Some repositories on Github may be used primarily for internal knowledge store and communication, rather than content tha tis curated, published, or released _by the project_ for external users.
+Some repositories on Github may be used primarily for internal knowledge store and communication, rather than content that is curated, published, or released _by the project_ for external users.
 
 The permissions of such repositories will be set in order to allow the same participation and access levels we use on private project communication channels like Slack.
-Therefore, similarly to slack, these repositories will be private and write permissions will be given to all recurrent contributors (that is, anyone with access to slack).
+Therefore, similarly to Slack, these repositories will be private and write permissions will be given to all recurrent contributors (that is, anyone with access to Slack).
 
 #### Discourse
 Similar to the above section, Discourse permissions are also mapped to the community team
@@ -718,7 +718,7 @@ provide examples on how to assign permissions:
   * Added to the PyMC_core Discourse group
   * Added to all private communication channels
   * Triage permissions on all repositories
-  * Access to PyMC gmail, drive and grant application platforms (i.e. CZI slack) as they are the main grant writing coordinator
+  * Access to PyMC Gmail, Drive and grant application platforms (i.e. CZI Slack) as they are the main grant writing coordinator
 
 </details>
 

MANIFEST.in

@@ -6,3 +6,4 @@ include requirements.txt
 include *.md *.rst
 include scripts/*.sh
 include LICENSE
+include versioneer.py

Makefile

@@ -52,16 +52,18 @@ help:
 
 clean:
 	rm -rf $(BUILDDIR)/*
+	rm -rf $(SOURCEDIR)/api/generated
 	rm -rf $(SOURCEDIR)/api/**/generated
 	rm -rf $(SOURCEDIR)/api/**/classmethods
+	rm -rf $(SOURCEDIR)/contributing/private_api/generated
 	rm -rf $(SOURCEDIR)/contributing/private_api/**/generated
 	rm -rf $(SOURCEDIR)/contributing/private_api/**/classmethods
 	rm -rf docs/jupyter_execute
 
 html:
 	$(SPHINXBUILD) $(SOURCEDIR) $(BUILDDIR) -b html
 	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)."
 
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@@ -199,4 +201,4 @@ pseudoxml:
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
 
 serve: html
-	cd $(BUILDDIR)/html && python -m http.server
+	python -m http.server --directory $(BUILDDIR)

README.rst

@@ -39,7 +39,7 @@ Getting started
 If you already know about Bayesian statistics:
 ----------------------------------------------
 
--  `API quickstart guide <https://docs.pymc.io/en/stable/pymc-examples/examples/pymc3_howto/api_quickstart.html>`__
+-  `API quickstart guide <https://www.pymc.io/projects/examples/en/latest/howto/api_quickstart.html>`__
 -  The `PyMC tutorial <https://docs.pymc.io/en/latest/learn/core_notebooks/pymc_overview.html>`__
 -  `PyMC examples <https://www.pymc.io/projects/examples/en/latest/gallery.html>`__ and the `API reference <https://docs.pymc.io/en/stable/api.html>`__
 

codecov.yml

@@ -23,6 +23,7 @@ coverage:
 
 ignore:
   - "pymc/tests/*"
+  - "pymc/_version.py"
 
 comment:
   layout: "reach, diff, flags, files"

conda-envs/environment-dev.yml

@@ -5,8 +5,8 @@ channels:
 - defaults
 dependencies:
 # Base dependencies
-- aeppl=0.0.35
-- aesara=2.8.2
+- aeppl=0.0.36
+- aesara=2.8.6
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1

conda-envs/environment-test.yml

@@ -5,8 +5,8 @@ channels:
 - defaults
 dependencies:
 # Base dependencies
-- aeppl=0.0.35
-- aesara=2.8.2
+- aeppl=0.0.36
+- aesara=2.8.6
 - arviz>=0.12.0
 - blas
 - cachetools>=4.2.1