diff --git a/README.md b/README.md index f7832868..0aed1ae8 100644 --- a/README.md +++ b/README.md @@ -46,8 +46,7 @@ pitched at undergraduate level and above. The workspace includes the following main directories: - `notebooks`: **PyAutoFit** examples written as Jupyter notebooks. -- `scipts`: **PyAutoFit** examples written as Python scripts. -- `projects`: Example projects which use **PyAutoFit**, which serve as a illustration of model-fitting problems and the **PyAutoFit** API. +- `scripts`: **PyAutoFit** examples written as Python scripts. - `config`: Configuration files which customize **PyAutoFit**'s behaviour. - `dataset`: Where data is stored, including example datasets distributed with **PyAutoFit**. - `output`: Where the **PyAutoFit** analysis and visualization are output. diff --git a/config/README.md b/config/README.md index 115a631f..c27f43fd 100644 --- a/config/README.md +++ b/config/README.md @@ -1,13 +1,15 @@ -The `config` folder contains configuration files which customize default **PyAutoLens**. +The `config` folder contains configuration files which customize default **PyAutoFit**. # Folders +- `non_linear`: Configs for default non-linear search (e.g. MCMC, nested sampling) settings. - `priors`: Configs defining default priors assumed on every model component and set of parameters. +- `visualize`: Configs defining what images are output by a model fit. +- `build`: Configs used by the automated build and test system (not relevant to normal use). # Files -- `general.yaml`: Customizes general **PyAutoLens** settings. -- `non-linear.yaml`: Configs for default non-linear search (e.g. MCMC, nested sampling) settings. -- `logging.yaml`: Customizes the logging behaviour of **PyAutoLens**. -- `visualize.yaml`: Configs defining what images are output by a lens model fit. -- `notation.yaml`: Configs defining labels and formatting of model parameters when used for visualization. +- `general.yaml`: Customizes general **PyAutoFit** settings. +- `logging.yaml`: Customizes the logging behaviour of **PyAutoFit**. +- `notation.yaml`: Defines labels and formatting of model parameters when used for visualization. +- `output.yaml`: Customizes what a model-fit writes to the output folder. diff --git a/config/non_linear/README.md b/config/non_linear/README.md index f69c3b33..e1075f33 100644 --- a/config/non_linear/README.md +++ b/config/non_linear/README.md @@ -1,8 +1,9 @@ -The `non_linear` folder contains configuration files which customize the default behaviour of non-linear searches in -**PyAutoLens**. +The `non_linear` folder contains configuration files which customize the default behaviour of non-linear +searches in **PyAutoFit**. + +Defaults for individual searches (e.g. Nautilus, Emcee, LBFGS) ship with **PyAutoFit** itself; this folder +holds only the workspace-level overrides. # Files -- `mcmc.yaml`: Settings default behaviour of MCMC non-linear searches (e.g. Emcee). -- `nest.yaml`: Settings default behaviour of nested sampler non-linear searches (e.g. Dynesty). -- `mle.yaml`: Settings default behaviour of maximum likelihood estimator (mle) searches (e.g. LBFGS). +- `GridSearch.yaml`: Settings for the non-linear search grid search. diff --git a/config/visualize/README.md b/config/visualize/README.md index f5c61464..d7c7ef23 100644 --- a/config/visualize/README.md +++ b/config/visualize/README.md @@ -1,4 +1,4 @@ -The `config` folder contains configuration files which customize default **PyAutoLens**. +The `visualize` folder contains configuration files which customize what a model-fit outputs. # Files diff --git a/notebooks/cookbooks/README.md b/notebooks/cookbooks/README.md index c78b475b..6fa4ca58 100644 --- a/notebooks/cookbooks/README.md +++ b/notebooks/cookbooks/README.md @@ -7,7 +7,6 @@ The `cookbooks` folder contains cookbooks concisely explaining how to use differ - `search.py`: Custom settings of non-linear searches and a list of all searches available (e.g. MCM, nested sampling). - `result.py`: Using results from a non-linear search. - `samples.py`: Analysing the samples of a non linear search (e.g. maximum likelihood model, parameter errors). -- `config.py`: Defining configuration files associated with your user define model (e.g. automatic prior setup and parameter labels). +- `configs.py`: Defining configuration files associated with your user define model (e.g. automatic prior setup and parameter labels). - `multiple_datasets.py`: Fitting multiple datasets simultaneously via `Analysis` class summing. -- `database.py`: Using an sqlite3 database to store results of non-linear searches for fits to large datasets. - `multi_level_model.py`: Composing multi-level models from hierarchicies of Python classes. diff --git a/scripts/cookbooks/README.md b/scripts/cookbooks/README.md index c78b475b..6fa4ca58 100644 --- a/scripts/cookbooks/README.md +++ b/scripts/cookbooks/README.md @@ -7,7 +7,6 @@ The `cookbooks` folder contains cookbooks concisely explaining how to use differ - `search.py`: Custom settings of non-linear searches and a list of all searches available (e.g. MCM, nested sampling). - `result.py`: Using results from a non-linear search. - `samples.py`: Analysing the samples of a non linear search (e.g. maximum likelihood model, parameter errors). -- `config.py`: Defining configuration files associated with your user define model (e.g. automatic prior setup and parameter labels). +- `configs.py`: Defining configuration files associated with your user define model (e.g. automatic prior setup and parameter labels). - `multiple_datasets.py`: Fitting multiple datasets simultaneously via `Analysis` class summing. -- `database.py`: Using an sqlite3 database to store results of non-linear searches for fits to large datasets. - `multi_level_model.py`: Composing multi-level models from hierarchicies of Python classes.