OpenFreeEnergy · IAlibay · Aug 21, 2022 · Aug 20, 2022
diff --git a/.github/CONTRIBUTING.md b/.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 arsenic. 
+describes how to merge code changes into this cinnabar. 
 
 ## Getting Started
 
@@ -19,7 +19,7 @@ describes how to merge code changes into this arsenic.
   [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 arsenic on GitHub and open a [pull
+  navigate to your fork of cinnabar 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 arsenic.
 * 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 arsenic devs know that the changes are complete.
+  box on the PR page to let the cinnabar 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.

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -70,7 +70,7 @@ jobs:
       - name: Run tests
         shell: bash -l {0}
         run: |
-          pytest -v --cov=arsenic --cov-report=xml --cov-report=term --color=yes arsenic/tests/
+          pytest -v --cov=cinnabar --cov-report=xml --cov-report=term --color=yes cinnabar/tests/
       - uses: codecov/codecov-action@v2
         with:
           files: ./coverage.xml
@@ -116,9 +116,9 @@ jobs:
       - name: Run pylint
         shell: bash -l {0}
         run: |
-          pylint arsenic/ --fail-under 6
+          pylint cinnabar/ --fail-under 6
       - name: Run black check
         shell: bash -l {0}
         if: always()
         run: |
-          black --check -l 99 arsenic/ --exclude arsenic/_version.py
+          black --check -l 99 cinnabar/ --exclude cinnabar/_version.py
diff --git a/.lgtm.yml b/.lgtm.yml
@@ -9,4 +9,4 @@ path_classifiers:
     - versioneer.py  # Set Versioneer.py to an external "library" (3rd party code)
     - devtools/*
   generated:
-    - arsenic/_version.py
+    - cinnabar/_version.py
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -2,5 +2,5 @@ include LICENSE
 include MANIFEST.in
 include versioneer.py
 
-graft arsenic
+graft cinnabar
 global-exclude *.py[cod] __pycache__ *.so
diff --git a/README.md b/README.md
@@ -1,10 +1,10 @@
-arsenic
+cinnabar (formerly Arsenic)
 ==============================
 [//]: # (Badges)
 
-[![CI](https://github.com/OpenFreeEnergy/arsenic/actions/workflows/ci.yml/badge.svg)](https://github.com/OpenFreeEnergy/arsenic/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/OpenFreeEnergy/arsenic/branch/main/graph/badge.svg)](https://codecov.io/gh/OpenFreeEnergy/arsenic)
-[![Documentation Status](https://readthedocs.org/projects/openff-arsenic/badge/?version=latest)](https://openff-arsenic.readthedocs.io/en/latest/?badge=latest)
+[![CI](https://github.com/OpenFreeEnergy/cinnabar/actions/workflows/ci.yml/badge.svg)](https://github.com/OpenFreeEnergy/cinnabar/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/OpenFreeEnergy/cinnabar/branch/main/graph/badge.svg)](https://codecov.io/gh/OpenFreeEnergy/cinnabar)
+[![Documentation Status](https://readthedocs.org/projects/openff-cinnabar/badge/?version=latest)](https://openff-cinnabar.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6210305.svg)](https://doi.org/10.5281/zenodo.6210305)
 
 # Reporting relative free energy results
@@ -15,11 +15,11 @@ Solution: package that accepts relative free energy results reliably, which is u
 
 ### USAGE
 
-`python arsenic.py example.csv `
+`python cinnabar.py example.csv `
 
 ### OPTIONS
 
-`python arsenic.py --help`
+`python cinnabar.py --help`
 
 ### Terminology
 D is difference (i.e. relative) while d is variance (i.e. error bar)

diff --git a/arsenic/__init__.py → cinnabar/__init__.py b/arsenic/__init__.py → cinnabar/__init__.py
@@ -1,5 +1,5 @@
 """
-arsenic
+cinnabar
 Report results for free energy simualtions
 """
 

diff --git a/arsenic/_version.py → cinnabar/_version.py b/arsenic/_version.py → cinnabar/_version.py
@@ -43,7 +43,7 @@ def get_config():
     cfg.style = "pep440"
     cfg.tag_prefix = ""
     cfg.parentdir_prefix = "None"
-    cfg.versionfile_source = "arsenic/_version.py"
+    cfg.versionfile_source = "cinnabar/_version.py"
     cfg.verbose = False
     return cfg
 

diff --git a/arsenic/arsenic.py → cinnabar/arsenic.py b/arsenic/arsenic.py → cinnabar/arsenic.py
diff --git a/arsenic/data/README.md → cinnabar/data/README.md b/arsenic/data/README.md → cinnabar/data/README.md
diff --git a/arsenic/data/__init__.py → cinnabar/data/__init__.py b/arsenic/data/__init__.py → cinnabar/data/__init__.py
diff --git a/arsenic/data/example.csv → cinnabar/data/example.csv b/arsenic/data/example.csv → cinnabar/data/example.csv
diff --git a/arsenic/plotlying.py → cinnabar/plotlying.py b/arsenic/plotlying.py → cinnabar/plotlying.py
diff --git a/arsenic/plotting.py → cinnabar/plotting.py b/arsenic/plotting.py → cinnabar/plotting.py
diff --git a/arsenic/stats.py → cinnabar/stats.py b/arsenic/stats.py → cinnabar/stats.py
diff --git a/arsenic/tests/__init__.py → cinnabar/tests/__init__.py b/arsenic/tests/__init__.py → cinnabar/tests/__init__.py
diff --git a/arsenic/tests/conftest.py → cinnabar/tests/conftest.py b/arsenic/tests/conftest.py → cinnabar/tests/conftest.py
@@ -1,14 +1,14 @@
 import pytest
 from importlib import resources
 
-from arsenic.wrangle import FEMap
+from cinnabar.wrangle import FEMap
 
 
 @pytest.fixture(scope="session")
 def fe_map():
     """FEMap using test csv data"""
 
-    with resources.path("arsenic.data", "example.csv") as fn:
+    with resources.path("cinnabar.data", "example.csv") as fn:
         femap = FEMap(fn)
 
     return femap
diff --git a/arsenic/tests/test_import.py → cinnabar/tests/test_import.py b/arsenic/tests/test_import.py → cinnabar/tests/test_import.py
@@ -2,11 +2,11 @@
 Import tests
 """
 
-import arsenic
+import cinnabar
 import pytest
 import sys
 
 
-def test_arsenic_imported():
+def test_cinnabar_imported():
     """Sample test, will always pass so long as import statement worked"""
-    assert "arsenic" in sys.modules
+    assert "cinnabar" in sys.modules
diff --git a/arsenic/tests/test_stats.py → cinnabar/tests/test_stats.py b/arsenic/tests/test_stats.py → cinnabar/tests/test_stats.py
@@ -2,8 +2,8 @@
 
 import networkx as nx
 import numpy as np
-from arsenic import stats
-from arsenic.stats import bootstrap_statistic
+from cinnabar import stats
+from cinnabar.stats import bootstrap_statistic
 
 
 def test_mle_easy():
@@ -126,7 +126,7 @@ def test_correlation_positive(fe_map):
     """
     Test that the absolute DG plots have the correct signs,
     and statistics within reasonable agreement to the example data
-    in `arsenic/data/example.csv`
+    in `cinnabar/data/example.csv`
     """
 
     nodes = fe_map.graph.nodes

diff --git a/arsenic/wrangle.py → cinnabar/wrangle.py b/arsenic/wrangle.py → cinnabar/wrangle.py
diff --git a/devtools/README.md b/devtools/README.md
@@ -54,5 +54,5 @@ 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. `arsenic-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
+e.g. `cinnabar-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.
diff --git a/devtools/conda-envs/env.yaml b/devtools/conda-envs/env.yaml
@@ -1,4 +1,4 @@
-name: arsenic
+name: cinnabar
 channels:
   - conda-forge
 dependencies:

diff --git a/docs/Makefile b/docs/Makefile
@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = arsenic
+SPHINXPROJ    = cinnabar
 SOURCEDIR     = .
 BUILDDIR      = _build
 

diff --git a/docs/README.md b/docs/README.md
@@ -1,4 +1,4 @@
-# Compiling arsenic's Documentation
+# Compiling cinnabar's Documentation
 
 The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/).
 To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed.

diff --git a/docs/api.rst b/docs/api.rst
@@ -4,7 +4,7 @@ API Documentation
 .. autosummary::
    :toctree: autosummary
 
-   arsenic.plotting
-   arsenic.plotlying
-   arsenic.stats
-   arsenic.wrangle
+   cinnabar.plotting
+   cinnabar.plotlying
+   cinnabar.stats
+   cinnabar.wrangle
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -6,11 +6,11 @@ Release history
 
 This section lists features and improvements of note in each release.
 
-The full release history can be viewed `at the GitHub arsenic releases page <https://github.com/OpenFreeEnergy/arsenic/releases>`_.
+The full release history can be viewed `at the GitHub cinnabar releases page <https://github.com/OpenFreeEnergy/cinnabar/releases>`_.
 
 0.2.1 - Release
 ---------------
 
 Bugfixes
 ^^^^^^^^
-Fix erroneous MLE estimate when self-edges are included (PR `#38 <https://github.com/openforcefield/openff-arsenic/pull/38>`_).
+Fix erroneous MLE estimate when self-edges are included (PR `#38 <https://github.com/OpenFreeEnergy/cinnabar/pull/38>`_).
diff --git a/docs/conf.py b/docs/conf.py
@@ -20,7 +20,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "arsenic"
+project = "cinnabar"
 copyright = (
     "2020, Hannah Bruce Macdonald. Project structure based on the "
     "Computational Molecular Science Python Cookiecutter version 1.1"
@@ -117,7 +117,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "arsenicdoc"
+htmlhelp_basename = "cinnabardoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -141,15 +141,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "arsenic.tex", "arsenic Documentation", "arsenic", "manual"),
+    (master_doc, "cinnabar.tex", "cinnabar Documentation", "cinnabar", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "arsenic", "arsenic Documentation", [author], 1)]
+man_pages = [(master_doc, "cinnabar", "cinnabar Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -160,10 +160,10 @@
 texinfo_documents = [
     (
         master_doc,
-        "arsenic",
-        "arsenic Documentation",
+        "cinnabar",
+        "cinnabar Documentation",
         author,
-        "arsenic",
+        "cinnabar",
         "Report results for free energy simualtions",
         "Miscellaneous",
     ),

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
@@ -1,4 +1,4 @@
 Getting Started
 ===============
 
-`arsenic` is a package to aid with the consistent and reliable plotting of results from free energy calculations. Fair assessment and comparison of computational methods relies on robust and reproduceable metrics, which `freeenergy framework` aims to provide.
+`cinnabar` is a package to aid with the consistent and reliable plotting of results from free energy calculations. Fair assessment and comparison of computational methods relies on robust and reproduceable metrics, which `freeenergy framework` aims to provide.
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,9 +1,9 @@
-.. arsenic documentation master file, created by
+.. cinnabar documentation master file, created by
    sphinx-quickstart on Thu Mar 15 13:55:56 2018.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to arsenic's documentation!
+Welcome to cinnabar's documentation!
 =========================================================
 
 .. toctree::

diff --git a/docs/make.bat b/docs/make.bat
@@ -9,7 +9,7 @@ if "%SPHINXBUILD%" == "" (
 )
 set SOURCEDIR=.
 set BUILDDIR=_build
-set SPHINXPROJ=arsenic
+set SPHINXPROJ=cinnabar
 
 if "%1" == "" goto help
 

diff --git a/examples/Untitled.ipynb b/examples/Untitled.ipynb
@@ -11,7 +11,7 @@
     "%matplotlib inline\n",
     "import matplotlib.pylab as plt\n",
     "\n",
-    "from arsenic import plotting, stats"
+    "from cinnabar import plotting, stats"
    ]
   },
   {
@@ -112,7 +112,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -126,7 +126,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.10.5"
   }
  },
  "nbformat": 4,

diff --git a/examples/first-example.ipynb b/examples/first-example.ipynb
@@ -19,7 +19,7 @@
     "%matplotlib inline\n",
     "import matplotlib.pylab as plt\n",
     "\n",
-    "from arsenic import plotting, stats, wrangle, absolute"
+    "from cinnabar import plotting, stats, wrangle, absolute"
    ]
   },
   {
@@ -579,7 +579,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -593,7 +593,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.10.5"
   }
  },
  "nbformat": 4,

diff --git a/setup.cfg b/setup.cfg
@@ -4,7 +4,7 @@
 # .coveragerc to control coverage.py and pytest-cov
 omit =
     # Omit generated versioneer
-    arsenic/_version.py
+    cinnabar/_version.py
 branch = True
 
 [yapf]
@@ -21,15 +21,15 @@ max-line-length = 119
 # Automatic version numbering scheme
 VCS = git
 style = pep440
-versionfile_source = arsenic/_version.py
-versionfile_build = arsenic/_version.py
+versionfile_source = cinnabar/_version.py
+versionfile_build = cinnabar/_version.py
 tag_prefix = ''
-parentdir_prefix = arsenic-
+parentdir_prefix = cinnabar-
 
 [aliases]
 test = pytest
 
 include_package_data = True
 
 [options.package_data]
-arsenic = "./arsenic/data/example.csv"
+cinnabar = "./cinnabar/data/example.csv"
diff --git a/setup.py b/setup.py
@@ -1,5 +1,5 @@
 """
-arsenic
+cinnabar
 
 Report results for free energy simulations.
 """
@@ -21,7 +21,7 @@
 
 setup(
     # Self-descriptive entries which should always be present
-    name='arsenic',
+    name='cinnabar',
     author='Open Free Energy',
     author_email='hannah.brucemacdonald@choderalab.org',
     description=short_description[0],