Merge branch 'release/v0.2.1'

CONTRIBUTING.md

@@ -9,7 +9,7 @@ You can contribute in many ways:
 
 ### Report Bugs
 
-Report bugs at <https://github.com/usnistgov/thermoextrap/issues>.
+Report bugs at <https://github.com/usnistgov/thermo-extrap/issues>.
 
 If you are reporting a bug, please include:
 
@@ -35,7 +35,7 @@ articles, and such.
 
 ### Submit Feedback
 
-The best way to send feedback is to file an issue at <https://github.com/usnistgov/thermoextrap/issues>.
+The best way to send feedback is to file an issue at <https://github.com/usnistgov/thermo-extrap/issues>.
 
 If you are proposing a feature:
 

README.md

@@ -26,29 +26,33 @@
 [Numba]: https://numba.pydata.org/
 [xarray]: https://docs.xarray.dev/en/stable/
 [cmomy]: https://github.com/usnistgov/cmomy
+[gpr-link]: https://github.com/usnistgov/thermo-extrap/tree/master/docs/notebooks/gpr
+[notebook-link]: https://github.com/usnistgov/thermo-extrap/tree/master/docs/notebooks
+
 
 
 # `thermoextrap`: Thermodynamic Extrapolation/Interpolation Library
-This repository contains code used and described in:
 
-Monroe, J. I.; Hatch, H. W.; Mahynski, N. A.; Shell, M. S.; Shen, V. K. Extrapolation and Interpolation Strategies for Efficiently Estimating Structural Observables as a Function of Temperature and Density. J. Chem. Phys. 2020, 153 (14), 144101. https://doi.org/10.1063/5.0014282.
+This repository contains code used and described in references [^fn1] [^fn2].
+
+[^fn1]: [Extrapolation and Interpolation Strategies for Efficiently Estimating Structural Observables as a Function of Temperature and Density](https://doi.org/10.1063/5.0014282)
 
-Monroe, J. I.; Krekelberg, W. P.; McDannald, A.; Shen, V. K. Leveraging Uncertainty Estimates and Derivative Information in Gaussian Process Regression for Expedited Data Collection in Molecular Simulations. In preparation.
+[^fn2]: Leveraging Uncertainty Estimates and Derivative Information in Gaussian Process Regression for Expedited Data Collection in Molecular Simulations. In preparation.
 
 
 ## Overview
 
 If you find this code useful in producing published works, please provide an appropriate citation.
 Note that the second citation is focused on adding features that make use of GPR models based on derivative information produced by the core code base.
-For now, the GPR code, along with more information, may be found under docs/notebooks/gpr.
+For now, the GPR code, along with more information, may be found under [here][gpr-link].
 In a future release, we expect this to be fully integrated into the code base rather than a standalone module.
 
 Code included here can be used to perform thermodynamic extrapolation and
 interpolation of observables calculated from molecular simulations. This allows
 for more efficient use of simulation data for calculating how observables change
 with simulation conditions, including temperature, density, pressure, chemical
 potential, or force field parameters. Users are highly encourage to work through
-the Jupyter Notebook tutorial (Ideal_Gas_Example.ipynb) presenting examples for
+the [Jupyter Notebooks][notebook-link] presenting examples for
 a variety of different observable functional forms. We only guarantee that this
 code is functional for the test cases we present here or for which it has
 previously been applied Additionally, the code may be in continuous development

docs/Makefile

@@ -1,20 +1,46 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = thermoextrap
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SPHINXAUTOBUILD = sphinx-autobuild
 SOURCEDIR     = .
 BUILDDIR      = _build
 
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(SPHINXOPTS)
+
+ALLSPHINXAUTOOPTS = $(ALLSPHINXOPTS) \
+	--ignore "*/$(BUILDDIR)/*" \
+	--ignore "*/generated/*" \
+	--ignore "*/jupyter_execute/*" \
+	--ignore "*/.ipynb_checkpoints/*"
+
+
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(ALLSPHINXOPTS) $(O)
+
+
+allclean: clean
+	rm -rf $(BUILDDIR)/*
+	rm -rf generated/*
+	rm -rf reference/generated/*
 
-.PHONY: help Makefile
+.PHONY: help Makefile allclean
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(ALLSPHINXOPTS) $(O)
+
+
+.PHONY: livehtml
+livehtml:
+	$(SPHINXAUTOBUILD) "$(SOURCEDIR)" "$(BUILDDIR)/html" $(ALLSPHINXAUTOOPTS) $(O)
+
+
+.PHONY: showlinks
+showlinks:
+	python -m sphinx.ext.intersphinx $(BUILDDIR)/html/objects.inv

docs/conf.py

@@ -39,6 +39,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "sphinx.ext.autosectionlabel",
     "IPython.sphinxext.ipython_directive",
     "IPython.sphinxext.ipython_console_highlighting",
     # "nbsphinx",
@@ -59,6 +60,7 @@
 ]
 
 nitpicky = True
+autosectionlabel_prefix_document = True
 
 # -- myst stuff ---------------------------------------------------------
 myst_enable_extensions = [
@@ -259,7 +261,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/examples/beta-extrap.md

@@ -1,13 +1,14 @@
-# Thermodynamic extrapolation/interpolation
+# Extrapolation/interpolation in inverse temperature
 
 ```{toctree}
-:maxdepth: 1
+:maxdepth: 2
 
 ../notebooks/Temperature_Extrap_Case1
 ../notebooks/Temperature_Extrap_Case2
 ../notebooks/Temperature_Extrap_Case3
 ../notebooks/Temperature_Extrap_Case4
 ../notebooks/Temperature_Interp
 ../notebooks/Macrostate_Dist_Extrap
-../notebooks/Test_System_Ideal_Gas
+../notebooks/Customized_Derivatives
+
 ```

docs/examples/index.md

@@ -1,12 +1,13 @@
-# Notebook examples
-
-
+# User Guide
 
 
 :::{toctree}
 :maxdepth: 2
 
-thermoextrap
+../notebooks/Data_Organization
+../notebooks/Test_System_Ideal_Gas
 beta-extrap
+../notebooks/Customized_Derivatives
+
 gpr
 :::

docs/installation.md

@@ -44,20 +44,13 @@ The sources for thermodynamic-extrapolation can be downloaded from the [Github r
 You can either clone the public repository:
 
 ```console
-$ git clone git://github.com/wpk-nist-gov/thermoextrap
-```
-
-Or download the [tarball]:
-
-```console
-$ curl -OJL https://github.com/wpk-nist-gov/thermoextrap/tarball/master
+$ git clone git://github.com/usnistgov/thermo-extrap.git
 ```
 
 Once you have a copy of the source, you can install it with:
 
 ```console
-$ python setup.py install
+$ pip install .
 ```
 
-[github repo]: https://github.com/wpk-nist-gov/thermoextrap
-[tarball]: https://github.com/wpk-nist-gov/thermoextrap/tarball/master
+[github repo]: https://github.com/usnistgov/thermo-extrap