Nesterov line search

README.md

@@ -1,7 +1 @@
-# tensorpack
-A collection of tensor methods from the Meyer lab.
-
-To add it to your Python package, add the following line to `requirements.txt` and remake `venv`:
-```
-git+https://github.com/meyer-lab/tensorpack.git@main
-```
+# tensor-impute

makefile

@@ -6,7 +6,7 @@ test:
 	poetry run pytest -s -v -x
 
 coverage.xml:
-	poetry run pytest --junitxml=junit.xml --cov=tensorpack --cov-report xml:coverage.xml
+	poetry run pytest --junitxml=junit.xml --cov=timpute --cov-report xml:coverage.xml
 
 clean:
 	rm -rf coverage.xml

pyproject.toml

@@ -7,22 +7,20 @@ license = "MIT"
 
 [tool.poetry.dependencies]
 python = ">=3.11,<3.13"
-numpy = "^1.26"
-tensorly = "^0.8.1"
-matplotlib = "^3.5.0"
-tqdm = "^4.65"
+numpy = "^2.1"
+tensorly = "^0.8"
+matplotlib = "^3.9"
+tqdm = "^4.67"
 seaborn = "^0.13"
-xarray = "^2023"
-tensorpack = "^0.11"
+xarray = "^2024"
 scikit-learn = "^1.1.3"
-openpyxl = "^3.1.2"
-setuptools = "^69.5.1"
-pyright = "^1.1.389"
 
 [tool.poetry.dev-dependencies]
 pytest = "^8.3"
-pytest-cov = "^3.0.0"
-tensordata = {git = "https://github.com/meyer-lab/tensordata.git", branch = "main"}
+pytest-cov = "^6.0"
+tensordata = {git = "https://github.com/meyer-lab/tensordata.git", rev = "6afaec35c552c3ee91990db74c740728ddf37a55"}
+pyright = "^1.1.389"
+isort = "^5.13"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

timpute/__init__.py

@@ -1,2 +1,3 @@
+import tensorly as tl
+
 from .decomposition import Decomposition
-import tensorly as tl

timpute/data/import_hmsData.py

@@ -1,6 +1,7 @@
+import os
+
 import numpy as np
 import pandas as pd
-import os
 import xarray as xa
 
 

timpute/decomposition.py

@@ -1,15 +1,14 @@
 import pickle
+from typing import Optional
+
 import numpy as np
 import tensorly as tl
+from tqdm import tqdm
 
-from .tracker import Tracker
+from .impute_helper import calcR2X, chord_drop, entry_drop
 from .initialization import initialize_fac
-from .impute_helper import entry_drop, chord_drop
-from .impute_helper import calcR2X
 from .method_CLS import perform_CLS
-
-from copy import deepcopy
-from tqdm import tqdm
+from .tracker import Tracker
 
 
 class Decomposition:
@@ -43,7 +42,7 @@ def imputation(
         init="random",
         maxiter: int = 50,
         seed=1,
-        callback: Tracker = None,
+        callback: Optional[Tracker] = None,
         printRuntime=False,
     ):
         """
@@ -135,7 +134,7 @@ def imputation(
                     np.random.seed(int(x * seed))
                     CPinit = initialize_fac(missingCube.copy(), rr, init)
                 elif isinstance(init, tl.cp_tensor.CPTensor):
-                    CPinit = deepcopy(init)
+                    CPinit = init.cp_copy()
                 else:
                     raise ValueError(f'Initialization method "{init}" not recognized')
 
@@ -155,7 +154,6 @@ def imputation(
                     missingCube.copy(),
                     rank=rr,
                     n_iter_max=maxiter,
-                    mask=mask,
                     init=CPinit,
                     callback=callback,
                     tol=tol,

timpute/figures/common.py

@@ -1,11 +1,13 @@
 """
 This file contains functions that are used in multiple figures.
 """
-import seaborn as sns
 from string import ascii_lowercase
-import matplotlib
-from matplotlib import gridspec, pyplot as plt
 
+import matplotlib
+import seaborn as sns
+from matplotlib import gridspec
+from matplotlib import pyplot as plt
+from matplotlib.lines import Line2D
 
 matplotlib.rcParams["legend.labelspacing"] = 0.2
 matplotlib.rcParams["legend.fontsize"] = 8
@@ -68,4 +70,4 @@ def rgbs(color = 0, transparency = None):
     if transparency is not None:
         return tuple(list(color_rgbs[color]) + [transparency])
     else:
-        return color_rgbs[color]
+        return color_rgbs[color]

timpute/figures/figure2.py

@@ -1,8 +1,10 @@
 import math
+
 import numpy as np
+from figures import DATANAMES, METHODNAMES, METHODS, SAVENAMES
+
+from .common import getSetup, rgbs, subplotLabel
 from .figure_helper import loadImputation
-from .common import getSetup, subplotLabel, rgbs
-from figures import METHODS, METHODNAMES, SAVENAMES, DATANAMES
 
 # poetry run python -m timpute.figures.figure2
 

timpute/figures/figure3.py

@@ -1,9 +1,11 @@
 import math
+
 import numpy as np
+from figures import DATANAMES, DROPS, METHODNAMES, METHODS, SAVENAMES
 from matplotlib.lines import Line2D
+
+from .common import getSetup, rgbs, set_boxplot_color, subplotLabel
 from .figure_helper import loadImputation
-from .common import getSetup, subplotLabel, rgbs, set_boxplot_color
-from figures import METHODS, METHODNAMES, SAVENAMES, DATANAMES, DROPS
 
 # poetry run python -m timpute.figures.figure3
 

timpute/figures/figure4.py

@@ -1,7 +1,8 @@
 import numpy as np
+from figures import DATANAMES, METHODNAMES, METHODS, SAVENAMES
+
+from .common import getSetup, rgbs, subplotLabel
 from .figure_helper import loadImputation
-from .common import getSetup, subplotLabel, rgbs
-from figures import METHODS, METHODNAMES, SAVENAMES, DATANAMES
 
 # poetry run python -m timpute.figures.figure4
 

timpute/figures/figure5.py

@@ -1,8 +1,10 @@
 import numpy as np
+from figures import DATANAMES, METHODNAMES, METHODS, SAVENAMES
+
+from .common import getSetup, rgbs, subplotLabel
 from .figure_data import bestComps
 from .figure_helper import loadImputation
-from .common import getSetup, subplotLabel, rgbs
-from figures import METHODS, METHODNAMES, SAVENAMES, DATANAMES
+
 # from matplotlib.legend_handler import HandlerErrorbar
 
 # poetry run python -m timpute.figures.figure5

timpute/figures/figure_data.py

@@ -1,8 +1,10 @@
 import os
+
 import numpy as np
-from .figure_helper import runImputation, loadImputation
+from figures import DROPS, METHODNAMES, METHODS, SAVENAMES
+
 from ..generateTensor import generateTensor
-from figures import METHODS, METHODNAMES, SAVENAMES, DROPS
+from .figure_helper import loadImputation, runImputation
 
 # poetry run python -m timpute.figures.figure_data  
 

timpute/figures/figure_helper.py

@@ -1,5 +1,7 @@
 import os
+
 import numpy as np
+
 from ..decomposition import Decomposition
 from ..tracker import Tracker
 

timpute/figures/memUsage.py

@@ -1,11 +1,12 @@
 # import psutil
-import pickle
+import argparse
 import os
-import numpy as np
+import pickle
 import resource
-import argparse
 
-from figures import METHODS, METHODNAMES, SAVENAMES
+import numpy as np
+from figures import METHODNAMES, METHODS, SAVENAMES
+
 from ..decomposition import Decomposition
 from ..generateTensor import generateTensor
 

timpute/figures/supplements.py

@@ -1,9 +1,11 @@
 import pickle
-from figures import METHODNAMES, SAVENAMES, DATANAMES, DROPS
+
 import numpy as np
 import pandas as pd
-from .common import getSetup, rgbs
+from figures import DATANAMES, DROPS, METHODNAMES, SAVENAMES
+
 from ..decomposition import Decomposition
+from .common import getSetup, rgbs
 
 # poetry run python -m timpute.figures.supplements