Fix Readme & Doc example

- Fix formatting of some examples
- Minor demo.ipynb clean

Author: donishadsmith

CHANGELOG.md

@@ -16,6 +16,11 @@ noted in the changelog (i.e new functions or parameters, changes in parameter de
 improvements/enhancements. Fixes and modifications will be backwards compatible.
 - *.postN* : Consists of only metadata-related changes, such as updates to type hints or doc strings/documentation.
 
+## [0.18.6] - 2024-11-18
+- Minor code cleaning
+### 📖 Documentation
+- Readme example fix
+
 ## [0.18.5] - 2024-11-16
 ## ♻ Changed
 - Updated Dependencies:

README.md

@@ -1,7 +1,7 @@
 # neurocaps
 [![Latest Version](https://img.shields.io/pypi/v/neurocaps.svg)](https://pypi.python.org/pypi/neurocaps/)
 [![Python Versions](https://img.shields.io/pypi/pyversions/neurocaps.svg)](https://pypi.python.org/pypi/neurocaps/)
-[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.11642615-teal)](https://doi.org/10.5281/zenodo.14174119)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.11642615-teal)](https://doi.org/10.5281/zenodo.14178104)
 [![Github Repository](https://img.shields.io/badge/Source%20Code-neurocaps-purple)](https://github.com/donishadsmith/neurocaps)
 [![Test Status](https://github.com/donishadsmith/neurocaps/actions/workflows/testing.yaml/badge.svg)](https://github.com/donishadsmith/neurocaps/actions/workflows/testing.yaml)
 [![codecov](https://codecov.io/github/donishadsmith/neurocaps/graph/badge.svg?token=WS2V7I16WF)](https://codecov.io/github/donishadsmith/neurocaps)
@@ -119,7 +119,7 @@ from neurocaps.extraction import TimeseriesExtractor
 from neurocaps.analysis import CAP
 
 # Set specific confounds for nuisance regression
-confounds = ['Cosine*', 'Rot*']
+confounds = ["Cosine*", "aComp*", "Rot*"]
 
 # Set parcellation
 parcel_approach = {"Schaefer": {"n_rois": 100, "yeo_networks": 7, "resolution_mm": 2}}
@@ -131,18 +131,17 @@ extractor = TimeseriesExtractor(parcel_approach=parcel_approach,
                                 detrend=True,
                                 low_pass=0.15,
                                 high_pass=0.01,
-                                confound_names=confounds,
-                                n_acompcor_separate=2)
+                                confound_names=confounds)
 
 bids_dir = "tests/ds000031_R1.0.4_ses001-022/ds000031_R1.0.4"
 
 # If there are multiple pipelines in the derivatives folder, you can specify a specific pipeline
-pipeline_name = fmriprep_1.0.0/fmriprep
+pipeline_name = "fmriprep_1.0.0/fmriprep"
 
 # Extract timeseries for subjects in the BIDS directory
 extractor.get_bold(bids_dir=bids_dir,
                    task="rest",
-                   session='002',
+                   session="002",
                    pipeline_name=pipeline_name
                    verbose=True,
                    flush=True)
@@ -277,16 +276,15 @@ radialaxis={"showline": True,
             "tickvals": [0.1,"","",0.4, "","", 0.6]}
 
 legend = {"yanchor": "top",
-        "y": 0.99,
-        "x": 0.99,
-        "title_font_family": "Times New Roman",
-        "font": {"size": 12, "color": "black"}}
+          "y": 0.99,
+          "x": 0.99,
+          "title_font_family": "Times New Roman",
+          "font": {"size": 12, "color": "black"}}
 
-colors =  {"High Amplitude": "black", "Low Amplitude": "orange"}
+colors =  {"High Amplitude": "black", "Low Amplitude": "orange"}git c
 
-
-kwargs = {"radialaxis": radial, "fill": "toself", "legend": legend,
-"color_discrete_map": colors, "height": 400, "width": 600}
+kwargs = {"radialaxis": radial, "fill": "toself", "legend": legend, "color_discrete_map": colors,
+          "height": 400, "width": 600}
 
 cap_analysis.caps2radar(output_dir=output_dir, **kwargs)
 ```

demo.ipynb

@@ -12,7 +12,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -103,7 +103,7 @@
     "# combination per session. `TimeseriesExtractor.get_bold().clear()`` can be used to clear the cache. Use `n_cores` to\n",
     "# speed up extraction\n",
     "extractor.get_bold(bids_dir=bids_dir,\n",
-    "                   session='002', \n",
+    "                   session=\"002\", \n",
     "                   runs=\"001\",\n",
     "                   task=\"rest\", \n",
     "                   pipeline_name=pipeline_name, \n",

docs/examples/analysis.rst

@@ -181,19 +181,19 @@ Plotting CAPs to Radar
 .. code-block:: python
 
     radialaxis={"showline": True,
-            "linewidth": 2,
-            "linecolor": "rgba(0, 0, 0, 0.25)",
-            "gridcolor": "rgba(0, 0, 0, 0.25)",
-            "ticks": "outside" ,
-            "tickfont": {"size": 14, "color": "black"},
-            "range": [0,0.6],
-            "tickvals": [0.1,"","",0.4, "","", 0.6]}
+                "linewidth": 2,
+                "linecolor": "rgba(0, 0, 0, 0.25)",
+                "gridcolor": "rgba(0, 0, 0, 0.25)",
+                "ticks": "outside" ,
+                "tickfont": {"size": 14, "color": "black"},
+                "range": [0,0.6],
+                "tickvals": [0.1,"","",0.4, "","", 0.6]}
 
     legend = {"yanchor": "top",
-            "y": 0.99,
-            "x": 0.99,
-            "title_font_family": "Times New Roman",
-            "font": {"size": 12, "color": "black"}}
+              "y": 0.99,
+              "x": 0.99,
+              "title_font_family": "Times New Roman",
+              "font": {"size": 12, "color": "black"}}
 
     colors =  {"High Amplitude": "red", "Low Amplitude": "blue"}
 

docs/examples/extraction.rst

@@ -21,7 +21,7 @@ Extracting Timeseries
 
     confounds=["Cosine*", "aComp*", "Rot*"]
 
-    parcel_approach = {"Schaefer": {"n_rois": 100, "yeo_networks": 7}}
+    parcel_approach = {"Schaefer": {"n_rois": 100, "yeo_networks": 7, "resolution_mm": 2}}
 
     extractor = TimeseriesExtractor(parcel_approach=parcel_approach,
                                     standardize="zscore_sample",
@@ -35,8 +35,9 @@ Extracting Timeseries
 
     # Can use the `n_cores` parameter for multiprocessing
     pipeline_name = "fmriprep_1.0.0/fmriprep"
+
     extractor.get_bold(bids_dir=bids_dir,
-                       session='002',
+                       session="002",
                        task="rest",
                        pipeline_name=pipeline_name,
                        tr=1.2)

docs/introduction.rst

@@ -9,7 +9,7 @@
    :alt: Python Versions
 
 .. image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.11642615-teal
-   :target: https://doi.org/10.5281/zenodo.14174119
+   :target: https://doi.org/10.5281/zenodo.14178104
    :alt: DOI
 
 .. image:: https://img.shields.io/badge/Source%20Code-neurocaps-purple
@@ -39,7 +39,7 @@ Citing
 ------
 ::
 
-  Smith, D. (2024). neurocaps. Zenodo. https://doi.org/10.5281/zenodo.14174119
+  Smith, D. (2024). neurocaps. Zenodo. https://doi.org/10.5281/zenodo.14178104
 
 Usage
 -----

neurocaps/__init__.py

@@ -3,4 +3,4 @@
 __all__=["analysis", "extraction"]
 
 # Version in single place
-__version__ = "0.18.5"
+__version__ = "0.18.6"