Merge branch 'release/v0.1.9'

MANIFEST.in

@@ -3,9 +3,15 @@ include CONTRIBUTING.rst
 include HISTORY.rst
 include LICENSE
 include README.rst
+include Makefile
 
-recursive-include tests *
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
+recursive-include tests *.py
 
-recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+global-exclude *.py[co]
+prune */*.egg-info
+prune */*mypy_cache
+prune */*ipynb_checkpoints
+prune */__pycache__
+
+prune docs
+prune notebooks

docs/conf.py

@@ -165,9 +165,18 @@
 # the built documents.
 #
 # The short X.Y version.
-version = thermoextrap.__version__
-# The full version, including alpha/beta/rc tags.
-release = thermoextrap.__version__
+# versioning with scm with editable install has issues.
+# instead, try to use scm if available.
+try:
+    from setuptools_scm import get_version
+
+    version = get_version(root="..", relative_to=__file__)
+    release = version
+except ImportError:
+    version = thermoextrap.__version__
+    # The full version, including alpha/beta/rc tags.
+    release = thermoextrap.__version__
+
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

environment-tools.yaml

@@ -1,5 +1,6 @@
 # packages for development
 dependencies:
+  - matplotlib
   # linting
   # - black
   # - blackdoc

environment.yaml

@@ -5,12 +5,11 @@ channels:
 dependencies:
   - python>=3.8
   - sympy
-  - matplotlib
   - numpy
   - scipy
   - xarray
 #  - openmm
-  - cmomy
+  - cmomy>=0.1.9
   - custom-inherit
   - attrs
   - pymbar<4.0

setup.cfg

@@ -23,7 +23,9 @@ classifiers =
     Programming Language :: Python :: 3.10
     Topic :: Scientific/Engineering
 
-
+# TODO: fix optional dependcies.
+# For now, matplotlib is a strong dependency.
+# Also not sure about dask and bottleneck.
 [options]
 package_dir=
     =src
@@ -32,11 +34,11 @@ zip_safe = True # if using mypy, must be False
 include_package_data = True
 python_requires = >=3.8
 install_requires =
-    numpy >= 1.19
+    numpy >= 1.20
     xarray >= 0.16
     sympy
     scipy
-    cmomy >= 0.1.7
+    cmomy >= 0.1.9
     custom-inherit
     attrs
 

src/thermoextrap/gpr_active/active_utils.py

@@ -4,7 +4,6 @@
 import time
 
 import gpflow
-import matplotlib.pyplot as plt
 import numpy as np
 import sympy as sp
 
@@ -1046,6 +1045,9 @@ def do_plotting(self, x, y, err, alpha_list):
         Plots output used to select new update point.
         err is expected to be length 2 list with upper and lower confidence intervals
         """
+
+        import matplotlib.pyplot as plt
+
         fig, ax = plt.subplots()
         if self.compare_func is not None:
             compare_y = self.compare_func(x[:, None])

src/thermoextrap/recursive_interp.py

@@ -17,11 +17,21 @@
 
 try:
     import matplotlib.pyplot as plt
+
+    _HAS_PLT = True
 except ImportError:
-    print(
-        "Could not find matplotlib - plotting will fail, so ensure that all"
-        " doPlot options are set to False, which is the default."
-    )
+    _HAS_PLT = False
+    # print(
+    #     "Could not find matplotlib - plotting will fail, so ensure that all"
+    #     " doPlot options are set to False, which is the default."
+    # )
+
+
+def _has_plt():
+    if _HAS_PLT:
+        pass
+    else:
+        raise ImportError("install matplotlib for this functionality")
 
 
 class RecursiveInterp:
@@ -160,6 +170,7 @@ def recursiveTrain(
 
         # Do some plotting just as a visual for how things are going, if desired
         if doPlot:
+            _has_plt()
             if "val" in predictVals.dims:
                 toplot = predictVals.isel(val=0)
             else:
@@ -388,6 +399,7 @@ def checkPolynomialConsistency(self, doPlot=False):
 
         # Before loop, set up plot if wanted
         if doPlot:
+            _has_plt()
             pColors = plt.cm.cividis(np.linspace(0.0, 1.0, len(edgeSets)))
             pFig, pAx = plt.subplots()
             plotYmin = 1e10
@@ -450,6 +462,7 @@ def checkPolynomialConsistency(self, doPlot=False):
                     plotYmax = np.max(allPlotY)
 
         if doPlot:
+            _has_plt()
             for edge in self.edgeB:
                 pAx.plot([edge] * 2, [plotYmin, plotYmax], "k-")
             pAx.set_xlabel(r"$\beta$")

tox.ini

@@ -175,16 +175,23 @@ conda_deps =
     {[base]conda_deps_test}
     conda-remote: {[base]package_name}
     conda-local: {posargs}
+    conda: pymbar<4.0
+
 
 deps =
-    pypi-remote: {[base]package_name}
-    pypi-local: {posargs}
+    pypi-remote: {[base]package_name}[mbar,gpr]
+    pypi-local: {posargs}[mbar,gpr]
+    conda: tensorflow
+    conda: tensorflow-probability
+    conda: gpflow
+
 
 allowlist_externals =
     {[base]allowlist_externals}
 commands =
     {[base]commands_test_check}
-    pytest {toxinidir}
+    local: pytest {toxinidir}
+    remote: pytest {posargs} {toxinidir}
 
 # [testenv]
 # usedevelop =