diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 6683664..95d2bf4 100644 --- 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 index 7280e52..84dd343 100644 --- 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 index a62f728..2e0998b 100644 --- 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 index c0916e5..acfff4a 100644 --- 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 \ No newline at end of file diff --git a/README.md b/README.md index c6fc07f..9c0f62d 100644 --- 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 b/cinnabar/__init__.py similarity index 96% rename from arsenic/__init__.py rename to cinnabar/__init__.py index 48adba1..0d8dafb 100644 --- a/arsenic/__init__.py +++ b/cinnabar/__init__.py @@ -1,5 +1,5 @@ """ -arsenic +cinnabar Report results for free energy simualtions """ diff --git a/arsenic/_version.py b/cinnabar/_version.py similarity index 99% rename from arsenic/_version.py rename to cinnabar/_version.py index 4a7610e..7868bce 100644 --- a/arsenic/_version.py +++ b/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 b/cinnabar/arsenic.py similarity index 100% rename from arsenic/arsenic.py rename to cinnabar/arsenic.py diff --git a/arsenic/data/README.md b/cinnabar/data/README.md similarity index 100% rename from arsenic/data/README.md rename to cinnabar/data/README.md diff --git a/arsenic/data/__init__.py b/cinnabar/data/__init__.py similarity index 100% rename from arsenic/data/__init__.py rename to cinnabar/data/__init__.py diff --git a/arsenic/data/example.csv b/cinnabar/data/example.csv similarity index 100% rename from arsenic/data/example.csv rename to cinnabar/data/example.csv diff --git a/arsenic/plotlying.py b/cinnabar/plotlying.py similarity index 100% rename from arsenic/plotlying.py rename to cinnabar/plotlying.py diff --git a/arsenic/plotting.py b/cinnabar/plotting.py similarity index 100% rename from arsenic/plotting.py rename to cinnabar/plotting.py diff --git a/arsenic/stats.py b/cinnabar/stats.py similarity index 100% rename from arsenic/stats.py rename to cinnabar/stats.py diff --git a/arsenic/tests/__init__.py b/cinnabar/tests/__init__.py similarity index 100% rename from arsenic/tests/__init__.py rename to cinnabar/tests/__init__.py diff --git a/arsenic/tests/conftest.py b/cinnabar/tests/conftest.py similarity index 64% rename from arsenic/tests/conftest.py rename to cinnabar/tests/conftest.py index 056f68c..ea73ee6 100644 --- a/arsenic/tests/conftest.py +++ b/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 b/cinnabar/tests/test_import.py similarity index 59% rename from arsenic/tests/test_import.py rename to cinnabar/tests/test_import.py index d38b840..42895df 100644 --- a/arsenic/tests/test_import.py +++ b/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 b/cinnabar/tests/test_stats.py similarity index 97% rename from arsenic/tests/test_stats.py rename to cinnabar/tests/test_stats.py index 1cf27fc..f03d870 100644 --- a/arsenic/tests/test_stats.py +++ b/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 b/cinnabar/wrangle.py similarity index 100% rename from arsenic/wrangle.py rename to cinnabar/wrangle.py diff --git a/devtools/README.md b/devtools/README.md index 275f4e6..22a2193 100644 --- 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 index 624f88b..77f112b 100644 --- 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 index 60f3281..e81b1ba 100644 --- 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 index 4c4cd97..1bb6784 100644 --- 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 index bfc045c..7dcb240 100644 --- 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 index a5c7409..abaacb1 100644 --- 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 `_. +The full release history can be viewed `at the GitHub cinnabar releases page `_. 0.2.1 - Release --------------- Bugfixes ^^^^^^^^ -Fix erroneous MLE estimate when self-edges are included (PR `#38 `_). +Fix erroneous MLE estimate when self-edges are included (PR `#38 `_). diff --git a/docs/conf.py b/docs/conf.py index d1d3533..7cc9050 100644 --- 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 ------------------------------------------------ @@ -141,7 +141,7 @@ # (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"), ] @@ -149,7 +149,7 @@ # 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 index d01d64c..355b082 100644 --- 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 index 3b32462..c53ca77 100644 --- 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 index 24d6f48..640c212 100644 --- 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 index 72a4f77..e0df99b 100644 --- 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 index d70170e..f7bb4a5 100644 --- 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 index e27328e..55f0242 100644 --- 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] @@ -21,10 +21,10 @@ 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 @@ -32,4 +32,4 @@ test = pytest include_package_data = True [options.package_data] -arsenic = "./arsenic/data/example.csv" \ No newline at end of file +cinnabar = "./cinnabar/data/example.csv" \ No newline at end of file diff --git a/setup.py b/setup.py index 5b94020..de06e4b 100644 --- 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],