Prepare for 0.10 release

CHANGELOG.md

@@ -2,17 +2,130 @@
 
 All notable changes to this project will be documented in this file.
 
-## [0.8.0] - 2023-08-06
+## [0.10.0] - 2024-03-20
+
+### Documentation
+
+- Mention non-blocking sampling in readme  (Adrian Seyboldt)
+
+
+### Features
+
+- Allow sampling in the backgound (Adrian Seyboldt)
+
+- Implement check if background sampling is complete (Adrian Seyboldt)
+
+- Implement pausing and unpausing of samplers (Adrian Seyboldt)
+
+- Filter warnings and compile through pymc (Adrian Seyboldt)
+
+
+### Miscellaneous Tasks
+
+- Bump actions/setup-python from 4 to 5 (dependabot[bot])
+
+- Bump uraimo/run-on-arch-action from 2.5.0 to 2.7.1 (dependabot[bot])
+
+- Bump actions/checkout from 3 to 4 (dependabot[bot])
+
+- Bump actions/upload-artifact from 3 to 4 (dependabot[bot])
+
+- Bump the cargo group across 1 directory with 2 updates (dependabot[bot])
+
+- Some major version bumps in rust deps  (Adrian Seyboldt)
+
+- Bump dependency versions (Adrian Seyboldt)
+
+- Update changelog (Adrian Seyboldt)
+
+- Bump version (Adrian Seyboldt)
+
+
+### Performance
+
+- Set the number of parallel chains dynamically (Adrian Seyboldt)
+
+
+## [0.9.2] - 2024-02-19
+
+### Bug Fixes
+
+- Allow dims with only length specified (Adrian Seyboldt)
+
+
+### Documentation
+
+- Update suggested mamba commands in README (#70) (Ben Mares)
+
+- Fix README typo bridgestan→nutpie (#69) (Ben Mares)
+
+
+### Features
+
+- Handle missing libraries more robustly (#72) (Ben Mares)
+
+
+### Miscellaneous Tasks
+
+- Bump actions/download-artifact from 3 to 4 (dependabot[bot])
+
+
+### Ci
+
+- Make sure the local nutpie is installed (Adrian Seyboldt)
+
+- Install local nutpie package in all jobs (Adrian Seyboldt)
+
+
+## [0.9.0] - 2023-09-12
+
+### Bug Fixes
+
+- Better error context for init point errors (Adrian Seyboldt)
+
+
+### Features
+
+- Improve error message by providing context (Adrian Seyboldt)
+
+- Use standard normal to initialize chains (Adrian Seyboldt)
+
+
+### Miscellaneous Tasks
+
+- Update deps (Adrian Seyboldt)
+
+- Rename stan model transpose function (Adrian Seyboldt)
+
+- Update nutpie (Adrian Seyboldt)
+
+
+### Styling
+
+- Fix formatting (Adrian Seyboldt)
+
+
+## [0.8.0] - 2023-08-18
 
 ### Bug Fixes
 
 - Initialize points in uniform(-2, 2) (Adrian Seyboldt)
 
+- Multidimensional stan variables were stored in incorrect order (Adrian Seyboldt)
+
+- Fix with_coords for stan models (Adrian Seyboldt)
+
 
 ### Miscellaneous Tasks
 
 - Update deps (Adrian Seyboldt)
 
+- Update deps (Adrian Seyboldt)
+
+- Bump version (Adrian Seyboldt)
+
+- Update deps (Adrian Seyboldt)
+
 
 ## [0.7.0] - 2023-07-21
 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "nutpie"
-version = "0.9.2"
+version = "0.10.0"
 authors = [
     "Adrian Seyboldt <[email protected]>",
     "PyMC Developers <[email protected]>"
@@ -21,7 +21,7 @@ name = "_lib"
 crate-type = ["cdylib"]
 
 [dependencies]
-nuts-rs = "0.7.0"
+nuts-rs = "0.8.0"
 numpy = "0.20.0"
 ndarray = "0.15.6"
 rand = "0.8.5"

python/nutpie/compile_pymc.py

@@ -1,5 +1,6 @@
 import dataclasses
 import itertools
+import warnings
 from dataclasses import dataclass
 from importlib.util import find_spec
 from math import prod
@@ -200,12 +201,26 @@ def compile_pymc_model(model: "pm.Model", **kwargs) -> CompiledPyMCModel:
     logp_numba_raw, c_sig = _make_c_logp_func(
         n_dim, logp_fn, user_data, shared_logp, shared_data
     )
-    logp_numba = numba.cfunc(c_sig, **kwargs)(logp_numba_raw)
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            message="Cannot cache compiled function .* as it uses dynamic globals",
+            category=numba.NumbaWarning,
+        )
+
+        logp_numba = numba.cfunc(c_sig, **kwargs)(logp_numba_raw)
 
     expand_numba_raw, c_sig_expand = _make_c_expand_func(
         n_dim, n_expanded, expand_fn, user_data, shared_expand, shared_data
     )
-    expand_numba = numba.cfunc(c_sig_expand, **kwargs)(expand_numba_raw)
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            message="Cannot cache compiled function .* as it uses dynamic globals",
+            category=numba.NumbaWarning,
+        )
+
+        expand_numba = numba.cfunc(c_sig_expand, **kwargs)(expand_numba_raw)
 
     coords = {}
     for name, vals in model.coords.items():
@@ -276,6 +291,7 @@ def _make_functions(model):
     import pytensor
     import pytensor.link.numba.dispatch
     import pytensor.tensor as pt
+    from pymc.pytensorf import compile_pymc
 
     shapes = _compute_shapes(model)
 
@@ -340,9 +356,8 @@ def _make_functions(model):
     (logp, grad) = pytensor.graph_replace([logp, grad], replacements)
 
     # We should avoid compiling the function, and optimize only
-    logp_fn_pt = pytensor.compile.function.function(
-        (joined,), (logp, grad), mode=pytensor.compile.NUMBA
-    )
+    with model:
+        logp_fn_pt = compile_pymc((joined,), (logp, grad), mode=pytensor.compile.NUMBA)
 
     logp_fn = logp_fn_pt.vm.jit_fn
 
@@ -368,12 +383,13 @@ def _make_functions(model):
     num_expanded = count
 
     allvars = pt.concatenate([joined, *[var.ravel() for var in remaining_rvs]])
-    expand_fn_pt = pytensor.compile.function.function(
-        (joined,),
-        (allvars,),
-        givens=list(replacements.items()),
-        mode=pytensor.compile.NUMBA,
-    )
+    with model:
+        expand_fn_pt = compile_pymc(
+            (joined,),
+            (allvars,),
+            givens=list(replacements.items()),
+            mode=pytensor.compile.NUMBA,
+        )
     expand_fn = expand_fn_pt.vm.jit_fn
 
     return (