Merge branch 'release/v0.2.3'

.cruft.json

@@ -1,44 +1,52 @@
 {
-  "template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git",
-  "commit": "c209d4c07a6142de87d6b1600f7319ebc69729cd",
-  "checkout": "feature/markdown",
-  "skip": [
-    "src/thermoextrap/__init__.py",
-    "environment.yaml",
-    "HISTORY.md",
-    "AUTHORS.md",
-    "MANIFEST.in",
-      "README.md",
-    "docs/spelling_wordlist.txt",
-    "environment/"
-  ],
-  "context": {
-    "cookiecutter": {
-      "full_name": "William P. Krekelberg",
-      "email": "[email protected]",
-      "github_username": "usnistgov",
-      "pypi_username": "wpk-nist",
-      "conda_channel": "wpk-nist",
-      "project_name": "thermo-extrap",
-      "project_slug": "thermoextrap",
-      "_copy_without_render": [
-        "*.html",
-        "docs/_templates/*.rst",
-        "docs/_templates/autosummary/*.rst",
-        "docs/_templates/autodocsumm/*.rst"
-      ],
-      "project_short_description": "Thermodynamic extrapolation",
-      "version": "0.0.1",
-      "use_pytest": "y",
-      "use_pypi_deployment_with_travis": "n",
-      "command_line_interface": "No command-line interface",
-      "create_author_file": "y",
-      "open_source_license": "NIST license",
-      "sphinx_auto": "autosummary",
-      "sphinx_use_autodocsumm": "y",
-      "sphinx_theme": "sphinx_book_theme",
-      "_template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git"
-    }
-  },
-  "directory": null
+    "template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git",
+    "commit": "be1b9cec709f862f8de5132e517a42db90758f04",
+    "checkout": "feature/markdown",
+    "skip": [
+        "src/thermoextrap/__init__.py",
+        "environment.yaml",
+        "HISTORY.md",
+        "AUTHORS.md",
+        "MANIFEST.in",
+        "README.md",
+        "docs/spelling_wordlist.txt",
+        "environment/dev-extras.yaml",
+        "environment/docs-extras.yaml",
+        "environment/test-extras.yaml",
+        "docs/index.md",
+        "docs/installation.md",
+        ".gitignore"
+    ],
+    "context": {
+        "cookiecutter": {
+            "full_name": "William P. Krekelberg",
+            "email": "[email protected]",
+            "github_username": "usnistgov",
+            "pypi_username": "wpk-nist",
+            "conda_channel": "wpk-nist",
+            "project_name": "thermoextrap",
+            "project_slug": "thermoextrap",
+            "_copy_without_render": [
+                "*.html",
+                "docs/_templates/*.rst",
+                "docs/_templates/autosummary/*.rst",
+                "docs/_templates/autodocsumm/*.rst",
+                "docs/_static/*",
+                "docs/_static/css/*",
+                "docs/_static/js/*"
+            ],
+            "project_short_description": "Thermodynamic extrapolation",
+            "version": "0.0.1",
+            "use_pytest": "y",
+            "use_pypi_deployment_with_travis": "n",
+            "command_line_interface": "No command-line interface",
+            "create_author_file": "y",
+            "open_source_license": "NIST license",
+            "sphinx_auto": "autosummary",
+            "sphinx_use_autodocsumm": "y",
+            "sphinx_theme": "sphinx_book_theme",
+            "_template": "https://github.com/wpk-nist-gov/cookiecutter-pypackage.git"
+        }
+    },
+    "directory": null
 }

.gitignore

@@ -112,3 +112,4 @@ pyrightconfig.json
 /dist-conda/
 /cruft.patch
 /docs/jupyter_execute/
+/docs/reference/generated/

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "examples/data"]
+	path = examples/data
+	url = [email protected]:usnistgov/thermoextrap-data.git

.pre-commit-config.yaml

@@ -65,7 +65,7 @@ repos:
       - id: flake8
         stages: [manual]
         additional_dependencies: [flake8-docstrings]
-        exclude: ^tests/|docs/notebooks/gpr/|src/thermoextrap/legacy/|^docs/conf.py|^setup.py
+        exclude: ^tests/|examples/gpr_active_learning/|src/thermoextrap/legacy/|^docs/conf.py|^setup.py
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.1.1
     hooks:

CONTRIBUTING.md

@@ -9,7 +9,7 @@ You can contribute in many ways:
 
 ### Report Bugs
 
-Report bugs at <https://github.com/usnistgov/thermo-extrap/issues>.
+Report bugs at <https://github.com/usnistgov/thermoextrap/issues>.
 
 If you are reporting a bug, please include:
 
@@ -29,13 +29,13 @@ and "help wanted" is open to whoever wants to implement it.
 
 ### Write Documentation
 
-`thermo-extrap` could always use more documentation, whether as part of the
-official `thermo-extrap` docs, in docstrings, or even on the web in blog posts,
+`thermoextrap` could always use more documentation, whether as part of the
+official `thermoextrap` docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
 ### Submit Feedback
 
-The best way to send feedback is to file an issue at <https://github.com/usnistgov/thermo-extrap/issues>.
+The best way to send feedback is to file an issue at <https://github.com/usnistgov/thermoextrap/issues>.
 
 If you are proposing a feature:
 
@@ -94,7 +94,13 @@ Ready to contribute? Here's how to set up `thermoextrap` for local development.
     git clone [email protected]:your_name_here/thermoextrap.git
     ```
 
-3. Create development environment.  Using the makefile will install a development version using mamba.
+    The example notebooks require the `examples/data` submodule to be loaded.
+
+    ```bash
+    git submodule update --init --recursive
+    ```
+
+3. Create development environment.  Using the `make` will install a development version using mamba.
 
     ```bash
     make mamba-dev
@@ -151,7 +157,7 @@ Ready to contribute? Here's how to set up `thermoextrap` for local development.
     tox
     ```
 
-    or using the makefile:
+    or using the `make`:
 
     ```bash
     make test-all

README.md

@@ -9,25 +9,25 @@
 [black-badge]: https://img.shields.io/badge/code%20style-black-000000.svg
 [black-link]: https://github.com/ambv/black
 [pypi-badge]: https://img.shields.io/pypi/v/thermoextrap
-<!-- [pypi-badge]: https://badge.fury.io/py/thermo-extrap -->
+<!-- [pypi-badge]: https://badge.fury.io/py/thermoextrap -->
 [pypi-link]: https://pypi.org/project/thermoextrap
 [docs-badge]: https://img.shields.io/badge/docs-sphinx-informational
-[docs-link]: https://pages.nist.gov/thermo-extrap/
+[docs-link]: https://pages.nist.gov/thermoextrap/
 [repo-badge]: https://img.shields.io/badge/--181717?logo=github&logoColor=ffffff
-[repo-link]: https://github.com/usnistgov/thermo-extrap
+[repo-link]: https://github.com/usnistgov/thermoextrap
 [conda-badge]: https://img.shields.io/conda/v/wpk-nist/thermoextrap
 [conda-link]: https://anaconda.org/wpk-nist/thermoextrap
 <!-- Use total link so works from anywhere -->
 [license-badge]: https://img.shields.io/pypi/l/cmomy?color=informational
-[license-link]: https://github.com/usnistgov/thermo-extrap/blob/master/LICENSE
+[license-link]: https://github.com/usnistgov/thermoextrap/blob/master/LICENSE
 <!-- For more badges, see https://shields.io/category/other and https://naereen.github.io/badges/ -->
 
 [numpy]: https://numpy.org
 [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
+[gpr-link]: https://github.com/usnistgov/thermoextrap/tree/master/examples/gpr_active_learning
+[notebook-link]: https://github.com/usnistgov/thermoextrap/tree/master/examples/usage
 
 
 
@@ -92,6 +92,19 @@ If you install `thermoextrap` with conda, there are additional optional dependen
 pip install tensorflow tensorflow-probability gpflow
 ```
 
+To install from source do the following:
+```bash
+git clone [email protected]:usnistgov/thermoextrap.git
+cd thermoextrap
+pip install . [-e]
+```
+
+To (optionally) include the example data do the following:
+```bash
+git submodule update --init  --recursive
+```
+
+
 ## Example usage
 
 ```python
@@ -103,16 +116,14 @@ import thermoextrap
 
 ## Documentation
 
-See the [documentation][docs-link] for a look at `thermo-extrap` in action.
+See the [documentation][docs-link] for a look at `thermoextrap` in action.
 
-To have a look at using `thermo-extrap` with Gaussian process regression, look in the [gpr][docs/notebooks/gpr] directory.
+To have a look at using `thermoextrap` with Gaussian process regression, look in the [gpr][docs/notebooks/gpr] directory.
 
 ## License
 
 This is free software.  See [LICENSE][license-link].
 
-## Related wor
-
 ## Related work
 
 This package extensively uses the [cmomy] package to handle central comoments.

docs/conf.py

@@ -123,7 +123,7 @@
 
 html_context = {
     "github_user": "usnistgov",
-    "github_repo": "thermo-extrap",
+    "github_repo": "thermoextrap",
     "github_version": "master",
     "doc_path": "docs",
 }
@@ -231,7 +231,7 @@
 master_doc = "index"
 
 # General information about the project.
-project = "thermo-extrap"
+project = "thermoextrap"
 copyright = "2021, William P. Krekelberg"
 author = "William P. Krekelberg"
 
@@ -292,7 +292,7 @@
 html_theme_options = dict(
     # analytics_id=''  this is configured in rtfd.io
     # canonical_url="",
-    repository_url="https://github.com/usnistgov/thermo-extrap",
+    repository_url=f"https://github.com/{github_username}/thermoextrap",
     repository_branch=html_context["github_version"],
     path_to_docs=html_context["doc_path"],
     # use_edit_page_button=True,
@@ -374,7 +374,7 @@
     (
         master_doc,
         "thermoextrap.tex",
-        "thermo-extrap Documentation",
+        "thermoextrap Documentation",
         "William P. Krekelberg",
         "manual",
     ),
@@ -389,7 +389,7 @@
     (
         master_doc,
         "thermoextrap",
-        "thermo-extrap Documentation",
+        "thermoextrap Documentation",
         [author],
         1,
     ),
@@ -405,7 +405,7 @@
     (
         master_doc,
         "thermoextrap",
-        "thermo-extrap Documentation",
+        "thermoextrap Documentation",
         author,
         "thermoextrap",
         "One line description of project.",
@@ -482,7 +482,7 @@ def linkcode_resolve(domain, info):
 
     fn = os.path.relpath(fn, start=os.path.dirname(thermoextrap.__file__))
 
-    return f"https://github.com/{github_username}/thermo-extrap/blob/{html_context['github_version']}/src/thermoextrap/{fn}{linespec}"
+    return f"https://github.com/{github_username}/thermoextrap/blob/{html_context['github_version']}/src/thermoextrap/{fn}{linespec}"
 
 
 # only set spelling stuff if installed:

docs/examples/create-symlinks.sh

@@ -0,0 +1,46 @@
+# this creates symlinks to files in thermoextrap/examples directory.
+
+exts=(ipynb md)
+
+
+rm -rf usage
+for path in $(cat *.md | grep '^usage/'); do
+
+    target="../../examples/"${path}
+    name=$(basename $target)
+
+    if [ -f $target ]; then
+        # has extension
+
+        base=${name%.*}
+        ext=${name##*.}
+
+    else
+        # no extension.  Try to add one
+        for ext in ${exts[@]}; do
+            tmp=${target}.${ext}
+            if [ -f "${tmp}" ] ; then
+                base=$name
+                target=$tmp
+                break
+            fi
+        done
+    fi
+
+
+    new_dir=$(dirname $path)
+    mkdir -p $new_dir
+
+    total_target=$(realpath --relative-to=${new_dir} $target)
+
+    # echo "target $target"
+    # echo "base  $base"
+    # echo "ext  $ext"
+    echo "target $total_target"
+    echo "new_dir $new_dir"
+    echo ""
+
+
+    ln -s $total_target $new_dir
+
+done

docs/examples/gpr.md

@@ -1,20 +1,16 @@
-<!-- :::{include} ../notebooks/gpr/README.md -->
-<!-- ::: -->
+# GP Models Utilizing Derivative Information and Active Learning
 
-# Gaussian process regression
-
-The notebooks associated with this section can be found [here](https://github.com/usnistgov/thermo-extrap/tree/master/docs/notebooks/gpr)
+The notebooks contained here provide a set of tutorials for using the Gaussian Process Regression (GPR) modeling capabilities found in the {mod}`thermoextrap.gpr_active` module.
+For all of the code an analysis necessary to reproduce the paper associated with the development of this module, please see the [example_projects](https://github.com/usnistgov/thermoextrap/tree/master/examples/gpr_active_learning) directory.
 
+:::{include} ../../examples/gpr_active_learning/README.md
+:start-after: <!-- start-docs-readme -->
+:::
 
 ```{toctree}
 :maxdepth: 1
 
-../notebooks/gpr/README.md
-
-../notebooks/gpr/IdealGas
-../notebooks/gpr/analysis_LJ_GEMC
-../notebooks/gpr/analysis_LJ_NPT
-../notebooks/gpr/analysis_LJ_lnPi
-../notebooks/gpr/analysis_adsorption
-../notebooks/gpr/analysis_polymer
+usage/gpr/Ideal_Gas
+usage/gpr/LJ_lnPi
+usage/gpr/SWF_Adsorption
 ```