Merge Aeppl as logprob submodule

Author: pymc-devs

.github/workflows/tests.yml

@@ -85,6 +85,18 @@ jobs:
             pymc/tests/ode/test_utils.py
             pymc/tests/step_methods/hmc/test_quadpotential.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_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
+
       fail-fast: false
     runs-on: ${{ matrix.os }}
     env:

.pre-commit-config.yaml

@@ -85,7 +85,6 @@ repos:
           (?x)(arviz-devs.github.io|
                python.arviz.org|
                aesara.readthedocs.io|
-               aeppl.readthedocs.io|
                pymc-experimental.readthedocs.io|
                docs.pymc.io|
                www.pymc.io|

conda-envs/environment-dev.yml

@@ -5,7 +5,6 @@ channels:
 - defaults
 dependencies:
 # Base dependencies
-- aeppl=0.0.38
 - aesara=2.8.7
 - arviz>=0.13.0
 - blas
@@ -41,3 +40,4 @@ dependencies:
 - types-cachetools
 - pip:
   - git+https://github.com/pymc-devs/pymc-sphinx-theme
+  - numdifftools>=0.9.40

conda-envs/environment-test.yml

@@ -5,7 +5,6 @@ channels:
 - defaults
 dependencies:
 # Base dependencies
-- aeppl=0.0.38
 - aesara=2.8.7
 - arviz>=0.13.0
 - blas
@@ -29,3 +28,5 @@ dependencies:
 - pytest>=3.0
 - mypy=0.990
 - types-cachetools
+- pip:
+  - numdifftools>=0.9.40

conda-envs/windows-environment-dev.yml

@@ -5,7 +5,6 @@ channels:
 - defaults
 dependencies:
 # Base dependencies (see install guide for Windows)
-- aeppl=0.0.38
 - aesara=2.8.7
 - arviz>=0.13.0
 - blas
@@ -38,3 +37,4 @@ dependencies:
 - types-cachetools
 - pip:
   - git+https://github.com/pymc-devs/pymc-sphinx-theme
+  - numdifftools>=0.9.40

conda-envs/windows-environment-test.yml

@@ -5,7 +5,6 @@ channels:
 - defaults
 dependencies:
 # Base dependencies (see install guide for Windows)
-- aeppl=0.0.38
 - aesara=2.8.7
 - arviz>=0.13.0
 - blas
@@ -30,3 +29,5 @@ dependencies:
 - pytest>=3.0
 - mypy=0.990
 - types-cachetools
+- pip:
+  - numdifftools>=0.9.40

docs/source/conf.py

@@ -188,7 +188,6 @@
 intersphinx_mapping = {
     "arviz": ("https://python.arviz.org/en/latest/", None),
     "aesara": ("https://aesara.readthedocs.io/en/latest/", None),
-    "aeppl": ("https://aeppl.readthedocs.io/en/latest/", None),
     "home": ("https://www.pymc.io", None),
     "pmx": ("https://www.pymc.io/projects/experimental/en/latest", None),
     "numpy": ("https://numpy.org/doc/stable/", None),

docs/source/learn/core_notebooks/GLM_linear.ipynb

@@ -522,14 +522,15 @@
    "source": [
     "%load_ext watermark\n",
     "\n",
-    "%watermark -n -u -v -iv -w -p aesara,aeppl"
+    "%watermark -n -u -v -iv -w -p aesara"
    ]
   }
  ],
  "metadata": {
   "anaconda-cloud": {},
+  "hide_input": false,
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -543,14 +544,27 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.8.10"
   },
   "latex_envs": {
    "bibliofile": "biblio.bib",
    "cite_by": "apalike",
    "current_citInitial": 1,
    "eqLabelWithNumbers": true,
    "eqNumInitial": 0
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": false,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": false
   }
  },
  "nbformat": 4,

docs/source/learn/core_notebooks/model_comparison.ipynb

@@ -536,16 +536,17 @@
     }
    ],
    "source": [
-    "%watermark -n -u -v -iv -w -p xarray,aesara,aeppl"
+    "%watermark -n -u -v -iv -w -p xarray,aesara"
    ]
   }
  ],
  "metadata": {
+  "hide_input": false,
   "interpreter": {
    "hash": "baf205d70af30bf8b721a304f5a44beb31bf8af014f6b7340f1a7ae004926653"
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -559,7 +560,20 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.8.10"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": false,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": false
   }
  },
  "nbformat": 4,

docs/source/learn/core_notebooks/posterior_predictive.ipynb

@@ -4649,14 +4649,15 @@
    ],
    "source": [
     "%load_ext watermark\n",
-    "%watermark -n -u -v -iv -w -p aesara,aeppl"
+    "%watermark -n -u -v -iv -w -p aesara"
    ]
   }
  ],
  "metadata": {
   "anaconda-cloud": {},
+  "hide_input": false,
   "kernelspec": {
-   "display_name": "Python 3.9.13 ('pymc-dev-py39')",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -4670,7 +4671,20 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.8.10"
+  },
+  "toc": {
+   "base_numbering": 1,
+   "nav_menu": {},
+   "number_sections": true,
+   "sideBar": true,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
+   "toc_cell": false,
+   "toc_position": {},
+   "toc_section_display": true,
+   "toc_window_display": false
   },
   "vscode": {
    "interpreter": {