[MNT] - Name update for new version

.github/workflows/build.yml

@@ -16,7 +16,7 @@ jobs:
     #   When ready to drop 3.6, can revert from 'ubuntu-20.04' -> 'ubuntu-latest'
     runs-on: ubuntu-20.04
     env:
-      MODULE_NAME: fooof
+      MODULE_NAME: specparam
     strategy:
       matrix:
         python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]

.gitignore

@@ -1,6 +1,6 @@
 # Ignore source release files
 /dist/*
-/fooof.egg-info/*
+/specparam.egg-info/*
 /build/*
 
 # Ignore notebook checkpoints

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contributing Guidelines
 
-Thank you for your interest in contributing to `fooof`!
+Thank you for your interest in contributing to `specparam`!
 
 We welcome all contributions to the project that extend or improve code and/or documentation!
 
@@ -55,7 +55,7 @@ and see if there is anything you would be interested in helping with. If so, joi
 
 All contributions must be within the scope of the module.
 
-`fooof` is a module for parameterizing neural power spectra. This includes model fitting, management and analysis of resulting parameters, and utilities to visualize power spectra and model results. This module also includes functionality to simulate power spectra based on the model.
+`specparam` is a module for parameterizing neural power spectra. This includes model fitting, management and analysis of resulting parameters, and utilities to visualize power spectra and model results. This module also includes functionality to simulate power spectra based on the model.
 
 Procedures and utilities that do not deal with operating upon power spectra or on model outputs will most likely be considered out of scope. Notably, this model does not include doing spectral estimation or time-domain analysis. For approaches such as these, the [neurodsp](https://github.com/neurodsp-tools/neurodsp/) module may be a more appropriate target.
 
@@ -120,8 +120,8 @@ All code contributed to the module should follow these conventions:
         * If a new approach is added, a new tutorial or example may be appropriate
     * To build and check the documentation locally:
         * Install the requirements for the docsite (`pip install -r requirements-doc.txt`)
-        * Move to the `fooof/doc` directory (`cd doc`)
+        * Move to the `specparam/doc` directory (`cd doc`)
         * Run `make html` to create a local copy of the documentation website
-        * The documentation can then be opened in a web browser by opening the file `fooof/doc/_build/html/index.html`
+        * The documentation can then be opened in a web browser by opening the file `specparam/doc/_build/html/index.html`
 
 For more guidelines on how to write well formated and organized code, check out the [Python API Checklist](http://python.apichecklist.com).

Makefile

@@ -18,7 +18,7 @@
 ##########################################################################
 ## VARIABLES
 
-MODULE      = fooof
+MODULE      = specparam
 LINT_FILE   = _lint.txt
 
 ##########################################################################

README.rst

@@ -1,6 +1,6 @@
-=========================================
-FOOOF - fitting oscillations & one over f
-=========================================
+=========================
+Spectral Parameterization
+=========================
 
 |ProjectStatus|_ |Version|_ |BuildStatus|_ |Coverage|_ |License|_ |PythonVersions|_ |Paper|_
 
@@ -26,7 +26,7 @@ FOOOF - fitting oscillations & one over f
 .. _Paper: https://doi.org/10.1038/s41593-020-00744-x
 
 
-FOOOF is a fast, efficient, and physiologically-informed tool to parameterize neural power spectra.
+Spectral parameterization is a fast, efficient, and physiologically-informed tool to parameterize neural power spectra.
 
 Overview
 --------
@@ -71,7 +71,7 @@ This documentation includes:
 Dependencies
 ------------
 
-FOOOF is written in Python, and requires Python >= 3.6 to run.
+SpecParam is written in Python, and requires Python >= 3.6 to run.
 
 It has the following required dependencies:
 
@@ -133,10 +133,10 @@ To install an editable version, download the development version as above, and r
 Matlab Support
 --------------
 
-FOOOF is implemented in Python, but there is also Matlab wrapper that allows you to use FOOOF from Matlab.
+`specparam` is implemented in Python, but there is also Matlab wrapper that allows you to use it from Matlab.
 The wrapper is available in the `fooof_mat <http://github.com/fooof-tools/fooof_mat>`_ repository.
 
-If you would like to use FOOOF, from Python, within a pipeline that is mostly in Matlab, the
+If you would like to use `specparam`, from Python, within a pipeline that is mostly in Matlab, the
 `mat_py_mat <https://github.com/fooof-tools/mat_py_mat>`_
 repository also has some examples and utilities for doing so.
 
@@ -186,27 +186,27 @@ The algorithm works on frequency representations, that is power spectra in linea
 **Fitting a Single Power Spectrum**
 
 With a power spectrum loaded (with 'freqs' storing frequency values, and 'spectrum' storing
-the power spectrum, both as 1D arrays in linear space) FOOOF can be used as follows:
+the power spectrum, both as 1D arrays in linear space) parameterization can be done as follows:
 
 .. code-block:: python
 
-    # Import the FOOOF object
-    from fooof import FOOOF
+    # Import the model object
+    from specparam import SpectralModel
 
-    # Initialize FOOOF object
-    fm = FOOOF()
+    # Initialize model object
+    fm = SpectralModel()
 
     # Define frequency range across which to model the spectrum
     freq_range = [3, 40]
 
-    # Model the power spectrum with FOOOF, and print out a report
+    # Parameterize the power spectrum, and print out a report
     fm.report(freqs, spectrum, freq_range)
 
-FOOOF.report() fits the model, plots the original power spectrum with the associated FOOOF model fit,
+SpectralModel.report() fits the model, plots the original power spectrum with the associated model fit,
 and prints out the parameters of the model fit for both the aperiodic component, and parameters for
 any identified peaks, reflecting periodic components.
 
-Example output for the report of a FOOOF fit on an individual power spectrum:
+Example output for the report of a parameterized fit on an individual power spectrum:
 
 .. image:: https://raw.githubusercontent.com/fooof-tools/fooof/main/doc/img/FOOOF_report.png
 
@@ -224,9 +224,9 @@ These settings can be defined when initializing the model, for example:
 
 .. code-block:: python
 
-    # Initialize a FOOOF model object with defined settings
-    fm = FOOOF(peak_width_limits=[1.0, 8.0], max_n_peaks=6, min_peak_height=0.1,
-               peak_threshold=2.0, aperiodic_mode='fixed')
+    # Initialize a model object with defined settings
+    fm = SpectralModel(peak_width_limits=[1.0, 8.0], max_n_peaks=6, min_peak_height=0.1,
+                       peak_threshold=2.0, aperiodic_mode='fixed')
 
 **Fitting a Group of Power Spectra**
 
@@ -236,19 +236,19 @@ We can fit the group of power spectra by doing:
 
 .. code-block:: python
 
-    # Initialize a FOOOFGroup object, specifying some parameters
-    fg = FOOOFGroup(peak_width_limits=[1.0, 8.0], max_n_peaks=8)
+    # Initialize a SpectralGroupModel object, specifying some parameters
+    fg = SpectralGroupModel(peak_width_limits=[1.0, 8.0], max_n_peaks=8)
 
-    # Fit FOOOF model across the matrix of power spectra
+    # Fit models across the matrix of power spectra
     fg.fit(freqs, spectra)
 
     # Create and save out a report summarizing the results across the group of power spectra
     fg.save_report()
 
-    # Save out FOOOF results for further analysis later
-    fg.save(file_name='fooof_group_results', save_results=True)
+    # Save out results for further analysis later
+    fg.save(file_name='group_results', save_results=True)
 
-Example output from using FOOOFGroup across a group of power spectra:
+Example output from using SpectralGroupModel across a group of power spectra:
 
 .. image:: https://raw.githubusercontent.com/fooof-tools/fooof/main/doc/img/FOOOFGroup_report.png
 

data/README.txt

@@ -1,4 +1,4 @@
 Data
 ====
 
-Example data files for the FOOOF module.
+Example data files for the module.

doc/Makefile

@@ -7,7 +7,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = fooof
+SPHINXPROJ    = specparam
 SOURCEDIR     = .
 BUILDDIR      = _build
 
@@ -44,7 +44,7 @@ check:
 	make SPHINXOPTS="-n" html
 	make linkcheck
 
-# Create the plots used in the FOOOF documentation
+# Create the plots used in the documentation
 plots:
 	python make_doc_plots.py