diff --git a/README.md b/README.md index 58d7715..b3342b4 100644 --- a/README.md +++ b/README.md @@ -60,13 +60,12 @@ jupyter lab ├── CITATION.cff # This file describes how to cite the work contained in this repository. ├── LICENSE # Outlines what legal rights you have to use this software. ├── README.md # You are here! -├── code -│   ├── README.md # Human readable information about the little python package in here -│   ├── pyproject.toml # Machine readable information about that same package -│   ├── setup.cfg # Tells Pip how to install this package -│   ├── src -│   │   └── MCFF # The actual code lives in here! -│   └── tests # automated tests for the code +├── README.md # Human readable information about the little python package in here +├── pyproject.toml # Machine readable information about that same package +├── setup.cfg # Tells Pip how to install this package +├── src +|   └── MCFF # The actual code lives in here! +└─ tests # automated tests for the code └── learning # Supporting documentation ``` diff --git a/code/README.md b/code/README.md deleted file mode 100644 index e69de29..0000000 diff --git a/code/docs/Makefile b/docs/Makefile similarity index 100% rename from code/docs/Makefile rename to docs/Makefile diff --git a/code/docs/_static/custom.css b/docs/_static/custom.css similarity index 100% rename from code/docs/_static/custom.css rename to docs/_static/custom.css diff --git a/code/docs/_static/states.png b/docs/_static/states.png similarity index 100% rename from code/docs/_static/states.png rename to docs/_static/states.png diff --git a/code/docs/api_docs.rst b/docs/api_docs.rst similarity index 100% rename from code/docs/api_docs.rst rename to docs/api_docs.rst diff --git a/code/docs/conf.py b/docs/conf.py similarity index 100% rename from code/docs/conf.py rename to docs/conf.py diff --git a/code/docs/index.rst b/docs/index.rst similarity index 100% rename from code/docs/index.rst rename to docs/index.rst diff --git a/code/docs/learning/01 Introduction.ipynb b/docs/learning/01 Introduction.ipynb similarity index 100% rename from code/docs/learning/01 Introduction.ipynb rename to docs/learning/01 Introduction.ipynb diff --git a/code/docs/learning/02 Packaging It Up.ipynb b/docs/learning/02 Packaging It Up.ipynb similarity index 100% rename from code/docs/learning/02 Packaging It Up.ipynb rename to docs/learning/02 Packaging It Up.ipynb diff --git a/code/docs/learning/03 Writing a Markov Chain Monte Carlo Sampler.ipynb b/docs/learning/03 Writing a Markov Chain Monte Carlo Sampler.ipynb similarity index 100% rename from code/docs/learning/03 Writing a Markov Chain Monte Carlo Sampler.ipynb rename to docs/learning/03 Writing a Markov Chain Monte Carlo Sampler.ipynb diff --git a/code/docs/learning/04 Testing.ipynb b/docs/learning/04 Testing.ipynb similarity index 100% rename from code/docs/learning/04 Testing.ipynb rename to docs/learning/04 Testing.ipynb diff --git a/code/docs/learning/05 Adding Functionality.ipynb b/docs/learning/05 Adding Functionality.ipynb similarity index 100% rename from code/docs/learning/05 Adding Functionality.ipynb rename to docs/learning/05 Adding Functionality.ipynb diff --git a/code/docs/learning/06 Speeding It Up.ipynb b/docs/learning/06 Speeding It Up.ipynb similarity index 100% rename from code/docs/learning/06 Speeding It Up.ipynb rename to docs/learning/06 Speeding It Up.ipynb diff --git a/code/docs/learning/07 Producing Research Outputs.ipynb b/docs/learning/07 Producing Research Outputs.ipynb similarity index 100% rename from code/docs/learning/07 Producing Research Outputs.ipynb rename to docs/learning/07 Producing Research Outputs.ipynb diff --git a/code/docs/learning/08 Doing Reproducible Science.ipynb b/docs/learning/08 Doing Reproducible Science.ipynb similarity index 100% rename from code/docs/learning/08 Doing Reproducible Science.ipynb rename to docs/learning/08 Doing Reproducible Science.ipynb diff --git a/code/docs/learning/09 Adding Documentation.ipynb b/docs/learning/09 Adding Documentation.ipynb similarity index 100% rename from code/docs/learning/09 Adding Documentation.ipynb rename to docs/learning/09 Adding Documentation.ipynb diff --git a/code/docs/learning/assets/energy_diagram.png b/docs/learning/assets/energy_diagram.png similarity index 100% rename from code/docs/learning/assets/energy_diagram.png rename to docs/learning/assets/energy_diagram.png diff --git a/code/docs/learning/assets/matplotlibrc.json b/docs/learning/assets/matplotlibrc.json similarity index 100% rename from code/docs/learning/assets/matplotlibrc.json rename to docs/learning/assets/matplotlibrc.json diff --git a/code/docs/learning/data/test_state.png b/docs/learning/data/test_state.png similarity index 100% rename from code/docs/learning/data/test_state.png rename to docs/learning/data/test_state.png diff --git a/code/docs/make.bat b/docs/make.bat similarity index 100% rename from code/docs/make.bat rename to docs/make.bat diff --git a/code/docs/quickstart.rst b/docs/quickstart.rst similarity index 100% rename from code/docs/quickstart.rst rename to docs/quickstart.rst diff --git a/code/docs/requirements.txt b/docs/requirements.txt similarity index 100% rename from code/docs/requirements.txt rename to docs/requirements.txt diff --git a/code/pyproject.toml b/pyproject.toml similarity index 100% rename from code/pyproject.toml rename to pyproject.toml diff --git a/readthedocs.yaml b/readthedocs.yaml index 7b8fbeb..ab6c623 100644 --- a/readthedocs.yaml +++ b/readthedocs.yaml @@ -13,7 +13,7 @@ build: # Build documentation in the docs/ directory with Sphinx sphinx: - configuration: code/docs/conf.py + configuration: docs/conf.py # If using Sphinx, optionally build your docs in additional formats such as PDF # formats: @@ -23,6 +23,6 @@ sphinx: python: install: - requirements: requirements.txt - - requirements: code/docs/requirements.txt + - requirements: docs/requirements.txt - method: pip - path: code/ + path: . diff --git a/code/setup.cfg b/setup.cfg similarity index 100% rename from code/setup.cfg rename to setup.cfg diff --git a/code/src/MCFF/__init__.py b/src/MCFF/__init__.py similarity index 100% rename from code/src/MCFF/__init__.py rename to src/MCFF/__init__.py diff --git a/code/src/MCFF/ising_model.py b/src/MCFF/ising_model.py similarity index 100% rename from code/src/MCFF/ising_model.py rename to src/MCFF/ising_model.py diff --git a/code/src/MCFF/mcmc.py b/src/MCFF/mcmc.py similarity index 100% rename from code/src/MCFF/mcmc.py rename to src/MCFF/mcmc.py diff --git a/code/tests/test_energy.py b/tests/test_energy.py similarity index 89% rename from code/tests/test_energy.py rename to tests/test_energy.py index 87405bc..65f6de1 100644 --- a/code/tests/test_energy.py +++ b/tests/test_energy.py @@ -10,7 +10,9 @@ all_up = np.ones([100, 100]) all_down = -np.ones([100, 100]) random = np.random.choice([-1, 1], size=(100, 100)) custom = ( - 1 - 2 * imread(Path(__file__).parents[2] / "learning/data/test_state.png")[:, :, 0] + 1 + - 2 + * imread(Path(__file__).parents[1] / "docs/learning/data/test_state.png")[:, :, 0] ) # load a 100x100 png, take the red channel, remap 0,1 to -1,1 states = [all_up, all_down, random, custom] diff --git a/code/tests/test_energy_using_hypothesis.py b/tests/test_energy_using_hypothesis.py similarity index 100% rename from code/tests/test_energy_using_hypothesis.py rename to tests/test_energy_using_hypothesis.py