Merge pull request #40 from JakobRobnik/module

mclmc/...
JakobRobnik · Nov 11, 2023 · 92c8a13 · 92c8a13
2 parents 945cc58 + de8874a
commit 92c8a13
Show file tree

Hide file tree

Showing 22 changed files with 24 additions and 39 deletions.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -38,4 +38,4 @@ work and might even find some help from other people.
 
 **Docs**:
 
-For API docs, we use `pdoc`, which you can install with `pip`. Then do e.g. `pdoc sampling/sampler.py -o ./apidocs`. `pdoc` supports markdown, so markdown styled code comments inside triple quotes will be rendered automatically as documentation.
+For API docs, we use `pdoc`, which you can install with `pip`. Then do e.g. `pdoc mclmc/sampling/sampler.py -o ./apidocs`. `pdoc` supports markdown, so markdown styled code comments inside triple quotes will be rendered automatically as documentation.
diff --git a/Makefile b/Makefile
@@ -2,7 +2,7 @@ PKG_VERSION = $(shell python setup.py --version)
 
 test:
 	JAX_PLATFORM_NAME=cpu pytest --benchmark-disable
-	mypy sampling/sampler.py
+	mypy mclmc/sampling/sampler.py
 
 set-bench:
 	pytest --benchmark-autosave  

diff --git a/sampling/__init__.py → mclmc/__init__.py b/sampling/__init__.py → mclmc/__init__.py
diff --git a/mclmc/sampling/__init__.py b/mclmc/sampling/__init__.py
diff --git a/sampling/annealing.py → mclmc/sampling/annealing.py b/sampling/annealing.py → mclmc/sampling/annealing.py
@@ -1,9 +1,9 @@
 import matplotlib.pyplot as plt
 import jax
 import jax.numpy as jnp
-from sampling import dynamics
+from mclmc.sampling import dynamics
 
-from sampling.dynamics import update_momentum
+from mclmc.sampling.dynamics import update_momentum
 
 
 class vmap_target:

diff --git a/sampling/correlation_length.py → mclmc/sampling/correlation_length.py b/sampling/correlation_length.py → mclmc/sampling/correlation_length.py
diff --git a/sampling/dynamics.py → mclmc/sampling/dynamics.py b/sampling/dynamics.py → mclmc/sampling/dynamics.py
diff --git a/sampling/old_annealing.py → mclmc/sampling/old_annealing.py b/sampling/old_annealing.py → mclmc/sampling/old_annealing.py
diff --git a/sampling/sampler.cpp → mclmc/sampling/sampler.cpp b/sampling/sampler.cpp → mclmc/sampling/sampler.cpp
diff --git a/sampling/sampler.py → mclmc/sampling/sampler.py b/sampling/sampler.py → mclmc/sampling/sampler.py
@@ -6,9 +6,9 @@
 import jax
 import jax.numpy as jnp
 import numpy as np
-from sampling import dynamics
+from mclmc.sampling import dynamics
 
-from sampling.dynamics import MCLMCInfo, MCLMCState, build_kernel, run_kernel
+from mclmc.sampling.dynamics import MCLMCInfo, MCLMCState, build_kernel, run_kernel
 from .correlation_length import ess_corr
 
 class Target():

diff --git a/sampling/smc.py → mclmc/sampling/smc.py b/sampling/smc.py → mclmc/sampling/smc.py
diff --git a/notebooks/tutorials/intro_tutorial.ipynb b/notebooks/tutorials/intro_tutorial.ipynb
@@ -63,7 +63,7 @@
         "import numpy as np\n",
         "import matplotlib.pyplot as plt\n",
         "\n",
-        "from sampling.sampler import Sampler"
+        "from mclmc.sampling.sampler import Sampler"
       ]
     },
     {

diff --git a/notebooks/tutorials/smc.ipynb b/notebooks/tutorials/smc.ipynb
@@ -56,7 +56,7 @@
     "import sys  \n",
     "sys.path.insert(0, '../../')\n",
     "\n",
-    "from sampling.smc import Sampler\n",
+    "from mclmc.sampling.smc import Sampler\n",
     "import jax\n",
     "import jax.numpy as jnp\n",
     "\n",

diff --git a/sampling/__pycache__/correlation_length.cpython-38.pyc b/sampling/__pycache__/correlation_length.cpython-38.pyc
diff --git a/sampling/__pycache__/sampler.cpython-38.pyc b/sampling/__pycache__/sampler.cpython-38.pyc
diff --git a/speed-bench/plots.py b/speed-bench/plots.py
@@ -6,10 +6,10 @@
 
 sys.path.insert(0, './')
 
-import sampling
+import mclmc.sampling
 
-from sampling.sampler import Sampler, Target  
-from sampling.dynamics import update_momentum
+from mclmc.sampling.sampler import Sampler, Target  
+from mclmc.sampling.dynamics import update_momentum
 import jax 
 
 import jax.numpy as jnp

diff --git a/speed-bench/single.py b/speed-bench/single.py
@@ -6,10 +6,10 @@
 
 sys.path.insert(0, './')
 
-import sampling
+import mclmc.sampling
 
-from sampling.sampler import Sampler, Target  
-from sampling.dynamics import update_momentum
+from mclmc.sampling.sampler import Sampler, Target  
+from mclmc.sampling.dynamics import update_momentum
 import jax 
 
 import jax.numpy as jnp

diff --git a/tests/benchmarks.py b/tests/benchmarks.py
@@ -1,5 +1,5 @@
 from benchmarks.benchmarks_mchmc import *
-from sampling.sampler import Sampler
+from mclmc.sampling.sampler import Sampler
 #from benchmarks import german_credit
 import os
 import jax

diff --git a/tests/test_annealing.py b/tests/test_annealing.py
@@ -1,14 +1,8 @@
-import sys
-
-sys.path.insert(0, '../../')
-sys.path.insert(0, './')
-
-# from sampling.annealing import Sampler
 import jax
 import jax.numpy as jnp
-from sampling.annealing import Annealing
-from sampling.sampler import Sampler, Target
-import sampling.old_annealing as A
+from mclmc.sampling.annealing import Annealing
+from mclmc.sampling.sampler import Sampler, Target
+import mclmc.sampling.old_annealing as A
 
 temp_schedule = jnp.array([3.0, 2.0, 1.0])
 

diff --git a/tests/test_mclmc.py b/tests/test_mclmc.py
@@ -1,19 +1,14 @@
-import sys
-import time
 
 from pytest import raises
-import pytest
 
-sys.path.insert(0, '../../')
-sys.path.insert(0, './')
-from sampling.dynamics import leapfrog  
+from mclmc.sampling.dynamics import leapfrog  
+from mclmc.sampling.sampler import OutputType, Sampler, Target
 
 import jax
 import jax.numpy as jnp
 import numpy as np
 import matplotlib.pyplot as plt
 
-from sampling.sampler import OutputType, Sampler, Target
 
 nlogp = lambda x: 0.5*jnp.sum(jnp.square(x))
 

diff --git a/tests/test_momentum_update.py b/tests/test_momentum_update.py
@@ -1,10 +1,6 @@
 
-import sys  
-sys.path.insert(0, './')
-
-from sampling.dynamics import update_momentum
+from mclmc.sampling.dynamics import update_momentum
 import jax 
-
 import jax.numpy as jnp
 
 def update_momentum_unstable(d):

diff --git a/tests/tst_diagonal_precond.py b/tests/tst_diagonal_precond.py
@@ -6,9 +6,9 @@
 import jax.numpy as jnp
 import pandas as pd
 
-from sampling.sampler import Sampler
-from sampling.benchmark_targets import *
-from sampling.grid_search import search_wrapper
+from mclmc.sampling.sampler import Sampler
+from mclmc.sampling.benchmark_targets import *
+from mclmc.sampling.grid_search import search_wrapper