Graduate fgraph functionality from pymc-experimental

pymc-devs · Sep 4, 2023 · 5c833fd · 5c833fd
1 parent dfb05b6
commit 5c833fd
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Showing 22 changed files with 1,700 additions and 15 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -93,7 +93,10 @@ jobs:
             tests/gp/test_gp.py
             tests/gp/test_mean.py
             tests/gp/test_util.py
-            tests/test_model.py
+            tests/model/test_core.py
+            tests/model/test_fgraph.py
+            tests/model/transform/test_basic.py
+            tests/model/transform/test_conditioning.py
             tests/test_model_graph.py
             tests/ode/test_ode.py
             tests/ode/test_utils.py
@@ -187,7 +190,7 @@ jobs:
         python-version: ["3.9"]
         test-subset:
           - tests/variational/test_approximations.py tests/variational/test_callbacks.py tests/variational/test_inference.py tests/variational/test_opvi.py tests/test_initial_point.py
-          - tests/test_model.py tests/sampling/test_mcmc.py
+          - tests/model/test_core.py tests/sampling/test_mcmc.py
           - tests/gp/test_cov.py tests/gp/test_gp.py tests/gp/test_mean.py tests/gp/test_util.py tests/ode/test_ode.py tests/ode/test_utils.py tests/smc/test_smc.py tests/sampling/test_parallel.py
           - tests/step_methods/test_metropolis.py tests/step_methods/test_slicer.py tests/step_methods/hmc/test_nuts.py tests/step_methods/test_compound.py tests/step_methods/hmc/test_hmc.py
 
@@ -266,7 +269,7 @@ jobs:
             tests/sampling/test_parallel.py
             tests/test_data.py
             tests/variational/test_minibatch_rv.py
-            tests/test_model.py
+            tests/model/test_core.py
 
           - |
             tests/sampling/test_mcmc.py

diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -9,7 +9,9 @@ API
 
    api/distributions
    api/gp
-   api/model
+   api/model/core
+   api/model/fgraph
+   api/model/transform/conditioning
    api/samplers
    api/vi
    api/smc

diff --git a/docs/source/api/model.rst → docs/source/api/model/core.rst b/docs/source/api/model.rst → docs/source/api/model/core.rst
@@ -4,7 +4,7 @@ Model
 Model creation and inspection
 -----------------------------
 
-.. currentmodule:: pymc
+.. currentmodule:: pymc.model.core
 .. autosummary::
    :toctree: generated/
 

diff --git a/docs/source/api/model/fgraph.rst b/docs/source/api/model/fgraph.rst
@@ -0,0 +1,10 @@
+FunctionGraph
+-------------
+
+.. currentmodule:: pymc.model.fgraph
+.. autosummary::
+   :toctree: generated/
+
+   clone_model
+   fgraph_from_model
+   model_from_fgraph
diff --git a/docs/source/api/model/transform/conditioning.rst b/docs/source/api/model/transform/conditioning.rst
@@ -0,0 +1,18 @@
+Model Conditioning
+------------------
+
+.. currentmodule:: pymc.model.transform.conditioning
+.. autosummary::
+   :toctree: generated/
+
+   do
+   observe
+
+Others
+------
+
+.. autosummary::
+   :toctree: generated/
+
+   change_value_transforms
+   remove_value_transforms
diff --git a/docs/source/contributing/running_the_test_suite.md b/docs/source/contributing/running_the_test_suite.md
@@ -19,7 +19,7 @@ Therefore, we recommend to run just specific tests that target the parts of the
 
 To run all tests from a single file:
 ```bash
-pytest -v tests/test_model.py
+pytest -v tests/model/test_core.py
 ```
 
 ```{tip}
@@ -28,10 +28,10 @@ The `-v` flag is short-hand for `--verbose` and prints the names of the test cas
 
 Often, you'll want to focus on just a few test cases first.
 By using the `-k` flag, you can filter for test cases that match a certain pattern.
-For example, the following command runs all test cases from `test_model.py` that have "coord" in their name:
+For example, the following command runs all test cases from `test_core.py` that have "coord" in their name:
 
 ```bash
-pytest -v tests/test_model.py -k coord
+pytest -v tests/model/test_core.py -k coord
 ```
 
 

diff --git a/pymc/__init__.py b/pymc/__init__.py
@@ -63,7 +63,8 @@ def __set_compiler_flags():
     logsumexp,
     probit,
 )
-from pymc.model import *
+from pymc.model.core import *
+from pymc.model.transform.conditioning import do, observe
 from pymc.model_graph import model_to_graphviz, model_to_networkx
 from pymc.plots import *
 from pymc.printing import *

diff --git a/pymc/distributions/distribution.py b/pymc/distributions/distribution.py
@@ -53,7 +53,7 @@
 from pymc.logprob.abstract import MeasurableVariable, _icdf, _logcdf, _logprob
 from pymc.logprob.basic import logp
 from pymc.logprob.rewriting import logprob_rewrites_db
-from pymc.model import new_or_existing_block_model_access
+from pymc.model.core import new_or_existing_block_model_access
 from pymc.printing import str_for_dist
 from pymc.pytensorf import (
     collect_default_updates,

diff --git a/pymc/model/__init__.py b/pymc/model/__init__.py
@@ -0,0 +1,15 @@
+#   Copyright 2023 The PyMC Developers
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+from pymc.model.core import *
+from pymc.model.core import ValueGradFunction
diff --git a/pymc/model.py → pymc/model/core.py b/pymc/model.py → pymc/model/core.py