Remove joint logprob test 6619

.github/config.yml

@@ -0,0 +1,26 @@
+# Comment to be posted to on first time issues
+newIssueWelcomeComment: >
+  [![Welcome Banner](https://zenodo.org/api/iiif/v2/0c0188d3-d03c-4830-a6e3-00405f5c22fa:8ff47a85-7250-4d86-8e48-2f346b48b2c1:BannerWelcome.jpg/full/750,/0/default.jpg)](https://zenodo.org/record/3695300)
+
+  :tada: Welcome to _PyMC_! :tada:
+  We're really excited to have your input into the project! :sparkling_heart:
+
+  <br>If you haven't done so already, please make sure you check out our [Contributing Guidelines](https://www.pymc.io/projects/docs/en/latest/contributing/index.html) and [Code of Conduct](https://github.com/pymc-devs/pymc/blob/main/CODE_OF_CONDUCT.md).
+
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  [![Thank You Banner](https://zenodo.org/api/iiif/v2/0c0188d3-d03c-4830-a6e3-00405f5c22fa:7fbd97cf-283b-480c-b8e1-11866e26245c:BannerThanks.jpg/full/750,/0/default.jpg)](https://zenodo.org/record/3695300)
+
+  :sparkling_heart: Thanks for opening this pull request! :sparkling_heart:
+  The _PyMC_ community really appreciates your time and effort to contribute to the project.
+  Please make sure you have read our [Contributing Guidelines](https://www.pymc.io/projects/docs/en/latest/contributing/index.html) and filled in our pull request template to the best of your ability.
+
+
+# Comment to be posted to on pull requests merged by a first time user
+firstPRMergeComment: >
+  [![Congratulations Banner](https://zenodo.org/api/iiif/v2/0c0188d3-d03c-4830-a6e3-00405f5c22fa:32fbdb89-ae1b-434e-830c-88ade86724cc:BannerCongratulations.jpg/full/750,/0/default.jpg)](https://zenodo.org/record/3695300)
+
+  Congrats on merging your first pull request! :tada:
+  We here at _PyMC_ are proud of you! :sparkling_heart:
+  Thank you so much for your contribution :gift:

.github/release.yml

@@ -17,6 +17,7 @@ changelog:
       labels:
         - bug
     - title: Documentation 📖
+      labels:
         - docs
     - title: Maintenance 🔧
       labels:

.github/workflows/rtd-link-preview.yml

@@ -0,0 +1,16 @@
+name: Read the Docs Pull Request Preview
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "pymc"

.github/workflows/tests.yml

@@ -2,23 +2,10 @@ name: tests
 
 on:
   pull_request:
-    paths:
-      - ".github/workflows/tests.yml"
-      - "pymc/**.py"
-      - "*.py"
-      - "conda-envs/**"
-      - "codecov.yml"
-      - "requirements*.txt"
-      - "scripts/*.sh"
   push:
-    branches: [main]
-    paths:
-      - ".github/workflows/tests.yml"
-      - "pymc/**.py"
-      - "*.py"
-      - "conda-envs/**"
-      - "codecov.yml"
-      - "scripts/*.sh"
+    branches:
+      - main
+
 
 # Tests are split into multiple jobs to accelerate the CI.
 # Different jobs should be organized to take approximately the same
@@ -30,12 +17,38 @@ on:
 # enforces that test run just once per OS / floatX setting.
 
 jobs:
+
+  changes:
+    name: "Check for changes"
+    runs-on: ubuntu-latest
+    outputs:
+      changes: ${{ steps.changes.outputs.src }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: dorny/paths-filter@v2
+        id: changes
+        with:
+          filters: |
+            src:
+              - ".github/workflows/tests.yml"
+              - "pymc/**/*.py"
+              - "tests/**/*.py"
+              - "*.py"
+              - "conda-envs/*"
+              - "requirements*.txt"
+              - "codecov.yml"
+              - "scripts/*.sh"
+
   ubuntu:
+    needs: changes
+    if: ${{ needs.changes.outputs.changes == 'true' }}
     strategy:
       matrix:
         os: [ubuntu-20.04]
         floatx: [float64]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         test-subset:
           - |
             tests/test_util.py
@@ -47,6 +60,7 @@ jobs:
             tests/test_func_utils.py
             tests/distributions/test_shape_utils.py
             tests/distributions/test_mixture.py
+            tests/test_testing.py
 
           - |
             tests/distributions/test_continuous.py
@@ -75,6 +89,7 @@ jobs:
           - |
             tests/distributions/test_timeseries.py
             tests/gp/test_cov.py
+            tests/gp/test_hsgp_approx.py
             tests/gp/test_gp.py
             tests/gp/test_mean.py
             tests/gp/test_util.py
@@ -88,10 +103,10 @@ jobs:
             tests/backends/test_mcbackend.py
             tests/distributions/test_truncated.py
             tests/logprob/test_abstract.py
+            tests/logprob/test_basic.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
@@ -158,7 +173,10 @@ jobs:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
+
   windows:
+    needs: changes
+    if: ${{ needs.changes.outputs.changes == 'true' }}
     strategy:
       matrix:
         os: [windows-latest]
@@ -231,7 +249,10 @@ jobs:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
+
   macos:
+    needs: changes
+    if: ${{ needs.changes.outputs.changes == 'true' }}
     strategy:
       matrix:
         os: [macos-latest]
@@ -307,12 +328,15 @@ jobs:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
+
   external_samplers:
+    needs: changes
+    if: ${{ needs.changes.outputs.changes == 'true' }}
     strategy:
       matrix:
         os: [ubuntu-20.04]
         floatx: [float64]
-        python-version: ["3.9"]
+        python-version: ["3.10"]
         test-subset:
           - tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
       fail-fast: false
@@ -377,12 +401,15 @@ jobs:
           env_vars: TEST_SUBSET
           name: JAX tests - ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
+
   float32:
+    needs: changes
+    if: ${{ needs.changes.outputs.changes == 'true' }}
     strategy:
       matrix:
         os: [windows-latest]
         floatx: [float32]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         test-subset:
         - tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py
       fail-fast: false
@@ -446,3 +473,17 @@ jobs:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }} ${{ matrix.floatx }}
           fail_ci_if_error: false
+
+  all_tests:
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    needs: [ changes, ubuntu, windows, macos, external_samplers, float32 ]
+    steps:
+      - name: Check build matrix status
+        if: ${{ needs.changes.outputs.changes == 'true' &&
+                ( needs.ubuntu.result != 'success' ||
+                  needs.windows.result != 'success' ||
+                  needs.macos.result != 'success' ||
+                  needs.external_samplers.result != 'success' ||
+                  needs.float32.result != 'success' ) }}
+        run: exit 1

.gitpod.yml

@@ -22,17 +22,14 @@ tasks:
 
       # Install dependencies
       sudo chown "$(id -u):$(id -g)" /opt/conda/conda-meta/history
-      micromamba install --yes --name base --file conda-envs/environment-dev.yml
-
-      # Install PyMC
-      pip install -e .
+      (micromamba install --yes --name base --file conda-envs/environment-dev.yml; pip install -e .) &> /tmp/install-init.log &
 
     command: |
       # Reinitialize devcontainer for good measure
       _dev-init.sh
 
       # Install the pre-commit hooks in the background if not already installed
-      pre-commit install --install-hooks
+      pre-commit install --install-hooks &> /tmp/pre-commit-init-output.log &
 
 vscode:
   extensions:

.pre-commit-config.yaml

@@ -34,12 +34,12 @@ repos:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 23.1.0
+  rev: 23.3.0
   hooks:
     - id: black
     - id: black-jupyter
 - repo: https://github.com/PyCQA/pylint
-  rev: v2.16.2
+  rev: v3.0.0a6
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]

MANIFEST.in

@@ -1,7 +1,3 @@
-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 *
 include requirements.txt
 include *.md *.rst
 include scripts/*.sh

README.rst

@@ -151,6 +151,8 @@ Sponsors
 
 |PyMCLabs|
 
+|Mistplay|
+
 .. |Binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/pymc-devs/pymc/main?filepath=%2Fdocs%2Fsource%2Fnotebooks
 .. |Build Status| image:: https://github.com/pymc-devs/pymc/workflows/pytest/badge.svg
@@ -159,9 +161,11 @@ Sponsors
    :target: https://codecov.io/gh/pymc-devs/pymc
 .. |Dockerhub| image:: https://img.shields.io/docker/automated/pymc/pymc.svg
    :target: https://hub.docker.com/r/pymc/pymc
-.. |NumFOCUS| image:: https://www.numfocus.org/wp-content/uploads/2017/03/1457562110.png
-   :target: http://www.numfocus.org/
 .. |NumFOCUS_badge| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
    :target: http://www.numfocus.org/
-.. |PyMCLabs| image:: https://raw.githubusercontent.com/pymc-devs/pymc/main/docs/logos/sponsors/pymc-labs.png
+.. |NumFOCUS| image:: https://github.com/pymc-devs/brand/blob/main/sponsors/sponsor_logos/sponsor_numfocus.png?raw=true
+   :target: http://www.numfocus.org/
+.. |PyMCLabs| image:: https://github.com/pymc-devs/brand/blob/main/sponsors/sponsor_logos/sponsor_pymc_labs.png?raw=true
    :target: https://pymc-labs.io
+.. |Mistplay| image:: https://github.com/pymc-devs/brand/blob/main/sponsors/sponsor_logos/sponsor_mistplay.png?raw=true
+   :target: https://www.mistplay.com/

benchmarks/benchmarks/benchmarks.py

@@ -18,7 +18,7 @@
 import numpy as np
 import pandas as pd
 import pytensor
-import pytensor.tensor as at
+import pytensor.tensor as pt
 
 import pymc as pm
 
@@ -61,8 +61,8 @@ def mixture_model(random_seed=1234):
         mu = pm.Normal("mu", mu=0.0, sigma=10.0, shape=w_true.shape)
         enforce_order = pm.Potential(
             "enforce_order",
-            at.switch(mu[0] - mu[1] <= 0, 0.0, -np.inf)
-            + at.switch(mu[1] - mu[2] <= 0, 0.0, -np.inf),
+            pt.switch(mu[0] - mu[1] <= 0, 0.0, -np.inf)
+            + pt.switch(mu[1] - mu[2] <= 0, 0.0, -np.inf),
         )
         tau = pm.Gamma("tau", alpha=1.0, beta=1.0, shape=w_true.shape)
         pm.NormalMixture("x_obs", w=w, mu=mu, tau=tau, observed=x)

conda-envs/environment-dev.yml

@@ -14,7 +14,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor=2.10.1
+- pytensor>=2.11.0,<2.12
 - python-graphviz
 - networkx
 - scipy>=1.4.1

conda-envs/environment-docs.yml

@@ -12,7 +12,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor=2.9.1
+- pytensor>=2.11.0,<2.12
 - python-graphviz
 - scipy>=1.4.1
 - typing-extensions>=3.7.4
@@ -23,13 +23,13 @@ dependencies:
 - myst-nb
 - numpydoc
 - pre-commit>=2.8.0
+- pymc-sphinx-theme==0.13
 - sphinx-copybutton
 - sphinx-design
 - sphinx-notfound-page
-- sphinx>=1.5
+- sphinx>=5
 - sphinxext-rediraffe
 - watermark
 - sphinx-remove-toctrees
 - pip:
-  - git+https://github.com/pymc-devs/pymc-sphinx-theme
   - numdifftools>=0.9.40

conda-envs/environment-test.yml

@@ -17,7 +17,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor=2.10.1
+- pytensor>=2.11.0,<2.12
 - python-graphviz
 - networkx
 - scipy>=1.4.1

conda-envs/windows-environment-dev.yml

@@ -14,7 +14,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor=2.10.1
+- pytensor>=2.11.0,<2.12
 - python-graphviz
 - networkx
 - scipy>=1.4.1

conda-envs/windows-environment-test.yml

@@ -17,7 +17,7 @@ dependencies:
 - numpy>=1.15.0
 - pandas>=0.24.0
 - pip
-- pytensor=2.10.1
+- pytensor>=2.11.0,<2.12
 - python-graphviz
 - networkx
 - scipy>=1.4.1