Merge pull request #191 from openforcefield/missed_files

Migrate Missed Files

Author: SimonBoothroyd

.github/CONTRIBUTING.md

@@ -1,7 +1,7 @@
 # How to contribute
 
 We welcome contributions from external contributors, and this document
-describes how to merge code changes into this propertyestimator. 
+describes how to merge code changes into this openff-evaluator. 
 
 ## Getting Started
 
@@ -19,7 +19,7 @@ describes how to merge code changes into this propertyestimator.
   [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/)
   with the branch name relating to the feature you are going to add.
 * When you are ready for others to examine and comment on your new feature,
-  navigate to your fork of propertyestimator on GitHub and open a [pull
+  navigate to your fork of openff-evaluator on GitHub and open a [pull
   request](https://help.github.com/articles/using-pull-requests/) (PR). Note that
   after you launch a PR from one of your fork's branches, all
   subsequent commits to that branch will be added to the open pull request
@@ -29,7 +29,7 @@ describes how to merge code changes into this propertyestimator.
 * If you're providing a new feature, you must add test cases and documentation.
 * When the code is ready to go, make sure you run the test suite using pytest.
 * When you're ready to be considered for merging, check the "Ready to go"
-  box on the PR page to let the propertyestimator devs know that the changes are complete.
+  box on the PR page to let the openff-evaluator devs know that the changes are complete.
   The code will not be merged until this box is checked, the continuous
   integration returns checkmarks,
   and multiple core developers give "Approved" reviews.

.gitignore

@@ -112,9 +112,9 @@ ENV/
 examples/property_estimator/stored_data/
 examples/property_estimator/working_directory/
 
-propertyestimator/data/properties/JCT/
+evaluator/data/properties/JCT/
 *dask-worker-space/
 
 integration_tests/thermoml/checked_thermoml_files
 
-propertyestimator/tests/**/*dat
+evaluator/tests/**/*dat

MANIFEST.in

@@ -2,5 +2,5 @@ include LICENSE
 include MANIFEST.in
 include versioneer.py
 
-graft propertyestimator
+graft evaluator
 global-exclude *.py[cod] __pycache__ *.so

README.md

@@ -3,13 +3,13 @@ OpenFF Evaluator
 [//]: # (Badges)
 
 [![Test Status](https://github.com/openforcefield/openff-evaluator/workflows/tests/badge.svg)](https://github.com/openforcefield/openff-evaluator/actions)
-[![Documentation Status](https://readthedocs.org/projects/property-estimator/badge/?version=latest)](https://property-estimator.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/openff-evaluator/badge/?version=latest)](https://openff-evaluator.readthedocs.io/en/latest/?badge=latest)
 [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/openforcefield/openff-evaluator.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/openforcefield/openff-evaluator/context:python)
 [![codecov](https://codecov.io/gh/openforcefield/openff-evaluator/branch/master/graph/badge.svg)](https://codecov.io/gh/openforcefield/openff-evaluator/branch/master)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 A distributed, automated property estimation toolkit from the Open Force Field Consortium. See the 
-[documentation](https://property-estimator.readthedocs.io) for more information.
+[documentation](https://openff-evaluator.readthedocs.io) for more information.
 
 #### Acknowledgements
 

devtools/README.md

@@ -67,5 +67,5 @@ is installed by looking at the `git` tags and how many commits ahead this versio
 \d+.\d+.\d+(?\+\d+-[a-z0-9]+)
 ```
 If the version of this commit is the same as a `git` tag, the installed version is the same as the tag, 
-e.g. `propertyestimator-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
+e.g. `evaluator-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
 ahead from the last tag, and then `-YYYYYY` where the `Y`'s are replaced with the `git` commit hash.

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = propertyestimator
+SPHINXPROJ    = evaluator
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/make.bat

@@ -9,7 +9,7 @@ if "%SPHINXBUILD%" == "" (
 )
 set SOURCEDIR=.
 set BUILDDIR=_build
-set SPHINXPROJ=propertyestimator
+set SPHINXPROJ=evaluator
 
 if "%1" == "" goto help
 

docs/tutorials/tutorial01.ipynb

@@ -69,7 +69,7 @@
    "execution_count": 2,
    "outputs": [],
    "source": [
-    "from propertyestimator.datasets.thermoml import ThermoMLDataSet"
+    "from evaluator.datasets.thermoml import ThermoMLDataSet"
    ],
    "metadata": {
     "collapsed": false,
@@ -294,7 +294,7 @@
     }
    ],
    "source": [
-    "from propertyestimator import unit\n",
+    "from evaluator import unit\n",
     "\n",
     "print(f\"There were {len(data_set)} properties before filtering\")\n",
     "\n",
@@ -319,7 +319,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    ".. note:: Here we have made use of the `propertyestimator.unit` module to attach units to the temperatures and pressures \n",
+    ".. note:: Here we have made use of the `evaluator.unit` module to attach units to the temperatures and pressures \n",
     "   we are filtering by. This module simply exposes a `UnitRegistry` from the fantastic [pint](https://pint.readthedocs.io/en/stable/) \n",
     "   library. Pint provides full support for attaching to units to values and is used extensively throughout this \n",
     "   framework.\n",
@@ -431,7 +431,7 @@
    "execution_count": 11,
    "outputs": [],
    "source": [
-    "from propertyestimator.thermodynamics import ThermodynamicState\n",
+    "from evaluator.thermodynamics import ThermodynamicState\n",
     "\n",
     "thermodynamic_state = ThermodynamicState(\n",
     "    temperature=298.15 * unit.kelvin, pressure=1.0 * unit.atmosphere\n",
@@ -459,7 +459,7 @@
    "execution_count": 12,
    "outputs": [],
    "source": [
-    "from propertyestimator.substances import Substance\n",
+    "from evaluator.substances import Substance\n",
     "\n",
     "ethanol = Substance.from_components(\"CCO\")\n",
     "isopropanol = Substance.from_components(\"CC(C)O\")"
@@ -486,7 +486,7 @@
    "execution_count": 13,
    "outputs": [],
    "source": [
-    "from propertyestimator.datasets import MeasurementSource\n",
+    "from evaluator.datasets import MeasurementSource\n",
     "\n",
     "source = MeasurementSource(doi=\"10.1016/S0021-9614(71)80108-8\")"
    ],
@@ -516,8 +516,8 @@
    "execution_count": 14,
    "outputs": [],
    "source": [
-    "from propertyestimator.datasets import PropertyPhase\n",
-    "from propertyestimator.properties import EnthalpyOfVaporization\n",
+    "from evaluator.datasets import PropertyPhase\n",
+    "from evaluator.properties import EnthalpyOfVaporization\n",
     "\n",
     "ethanol_hvap = EnthalpyOfVaporization(\n",
     "    thermodynamic_state=thermodynamic_state,\n",

evaluator/data/properties/README.md

@@ -1,6 +1,6 @@
-# Property Estimator Data
+# OpenFF Evaluator Data
 
-This directory contains data for running the PropertyEstimator class. 
+This directory contains data for the OpenFF Evaluator module. 
 
 ## Manifest
 

integration_tests/properties/submit_hydration_free_energy.sh

@@ -15,7 +15,7 @@
 . ~/.bashrc
 
 # Use the right conda environment
-conda activate propertyestimator
+conda activate evaluator
 module load cuda/10.1
 
 rm -rf solvation_free_energies && mkdir solvation_free_energies && cd solvation_free_energies