small fixes and version update (#10)

LegrandNico · web-flow · commit f80ca5dd4844 · 2023-11-09T21:03:18.000+01:00
diff --git a/README.rst b/README.rst
@@ -58,13 +58,13 @@ Systole can be installed using pip:
 
 The following packages are required to use Systole:
 
-* `Numpy <https://numpy.org/>`_ (>=1.15)
+* `Numpy <https://numpy.org/>`_ (>=1.21,<=1.26)
 * `SciPy <https://www.scipy.org/>`_ (>=1.3.0)
 * `Pandas <https://pandas.pydata.org/>`_ (>=0.24)
-* `Numba <http://numba.pydata.org/>`_ (>=0.51.2)
+* `Numba <http://numba.pydata.org/>`_ (>=0.58.0)
 * `Seaborn <https://seaborn.pydata.org/>`_ (>=0.9.0)
 * `Matplotlib <https://matplotlib.org/>`_ (>=3.0.2)
-* `Bokeh <https://docs.bokeh.org/en/latest/index.html#>`_ (>=2.3.3)
+* `Bokeh <https://docs.bokeh.org/en/latest/index.html#>`_ (>=3.0.0)
 * `pyserial <https://pyserial.readthedocs.io/en/latest/pyserial.html>`_ (>=3.4)
 * `setuptools <https://setuptools.pypa.io/en/latest/>`_ (>=38.4)
 * `requests <https://docs.python-requests.org/en/latest/>`_ (>=2.26.0)
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -117,7 +117,7 @@ Interactive data labelling and peaks correction
 
 .. currentmodule:: systole.interact
 
-.. _reports:
+.. _interact:
 
 .. autosummary::
    :toctree: generated/interact
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -26,11 +26,19 @@
 image_scrapers = ("matplotlib",)
 
 sphinx_gallery_conf = {
-    "examples_dirs": "./examples/",
+    "examples_dirs": "examples",
     "backreferences_dir": "api",
+    'gallery_dirs': 'auto_examples',
     "image_scrapers": image_scrapers,
 }
 
+exclude_patterns = [
+    # exclude .py and .ipynb files in auto_examples generated by sphinx-gallery
+    # this is to prevent sphinx from complaining about duplicate source files
+    "auto_examples/**/*.ipynb",
+    "auto_examples/**/*.py",
+]
+
 bibtex_bibfiles = ['refs.bib']
 bibtex_reference_style = "author_year"
 bibtex_default_style = "unsrt"
@@ -54,7 +62,6 @@
     "jupyter_sphinx",
     "sphinx_design",
     "myst_nb",
-    "sphinx_gallery.load_style",
     "sphinxcontrib.bibtex"
 ]
 
@@ -79,11 +86,6 @@
 # The master toctree document.
 master_doc = "index"
 
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
-
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages. See the documentation for
@@ -99,9 +101,9 @@
             icon="fa-brands fa-square-github",
         ),
         dict(
-            name="Twitter",
-            url="https://twitter.com/visceral_mind",
-            icon="fa-brands fa-square-twitter",
+            name="Mastodon",
+            url="https://mastodon.social/@nicolegrand",
+            icon="fa-brands fa-mastodon",
         ),
         dict(
             name="Pypi",
diff --git a/docs/source/examples/Plots/plot_circular.py b/docs/source/examples/Plots/plot_circular.py
@@ -1,5 +1,4 @@
 """
-
 Plot circular
 =============
 The density function can be represented using the area of the bars, the height or
diff --git a/docs/source/examples/Plots/plot_ectopic.py b/docs/source/examples/Plots/plot_ectopic.py
@@ -1,5 +1,4 @@
 """
-
 Plot ectopic beats
 ==================
 
diff --git a/docs/source/examples/Plots/plot_events.py b/docs/source/examples/Plots/plot_events.py
@@ -1,5 +1,4 @@
 """
-
 Plot events
 ===========
 
diff --git a/docs/source/examples/Plots/plot_evoked.py b/docs/source/examples/Plots/plot_evoked.py
@@ -1,5 +1,4 @@
 """
-
 Plot evoked
 ===========
 
diff --git a/docs/source/examples/Plots/plot_frequency.py b/docs/source/examples/Plots/plot_frequency.py
@@ -1,5 +1,4 @@
 """
-
 Plot frequency
 ==============
 
diff --git a/docs/source/examples/Plots/plot_pointcare.py b/docs/source/examples/Plots/plot_pointcare.py
@@ -1,5 +1,4 @@
 """
-
 Plot pointcare
 ==============
 
diff --git a/docs/source/examples/Plots/plot_raw.py b/docs/source/examples/Plots/plot_raw.py
@@ -1,5 +1,4 @@
 """
-
 Plot raw physiological signal
 =============================
 
diff --git a/docs/source/examples/Plots/plot_rr.py b/docs/source/examples/Plots/plot_rr.py
@@ -1,5 +1,4 @@
 """
-
 Plot instantaneous heart rate
 =============================
 
@@ -27,8 +26,8 @@
 # -----------------------------------------------------------------------------------------------------------------------------
 plot_rr(rr=rr, input_type="rr_ms", unit="bpm", points=False);
 #%%
-# Use Bokeh as a plotting backend, only show the scatterplt and highlight artefacts in the RR intervals
-# -----------------------------------------------------------------------------------------------------
+# Use Bokeh as a plotting backend, only show the scatterplot and highlight artefacts in the RR intervals
+# ------------------------------------------------------------------------------------------------------
 output_notebook()
 
 show(
diff --git a/docs/source/examples/Plots/plot_shortlong.py b/docs/source/examples/Plots/plot_shortlong.py
@@ -1,5 +1,4 @@
 """
-
 Plot short and long invertvals
 ==============================
 
diff --git a/docs/source/examples/Plots/plot_subspace.py b/docs/source/examples/Plots/plot_subspace.py
@@ -1,5 +1,4 @@
 """
-
 Plot subspaces to vivualize short/long and ectopic beats
 ========================================================
 
diff --git a/docs/source/examples/README.txt b/docs/source/examples/README.txt
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
@@ -16,13 +16,13 @@ If you want to download the `dev` branch instead and try the last features that
 
 The following packages are required to use Systole:
 
-* `Numpy <https://numpy.org/>`_ (>=1.15)
+* `Numpy <https://numpy.org/>`_ (>=1.21,<=1.26)
 * `SciPy <https://www.scipy.org/>`_ (>=1.3.0)
 * `Pandas <https://pandas.pydata.org/>`_ (>=0.24)
-* `Numba <http://numba.pydata.org/>`_ (>=0.51.2)
+* `Numba <http://numba.pydata.org/>`_ (>=0.58.0)
 * `Seaborn <https://seaborn.pydata.org/>`_ (>=0.9.0)
 * `Matplotlib <https://matplotlib.org/>`_ (>=3.0.2)
-* `Bokeh <https://docs.bokeh.org/en/latest/index.html#>`_ (>=2.3.3)
+* `Bokeh <https://docs.bokeh.org/en/latest/index.html#>`_ (>=3.0.0)
 * `pyserial <https://pyserial.readthedocs.io/en/latest/pyserial.html>`_ (>=3.4)
 * `setuptools <https://setuptools.pypa.io/en/latest/>`_ (>=38.4)
 * `requests <https://docs.python-requests.org/en/latest/>`_ (>=2.26.0)
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -167,7 +167,7 @@ Contributors
 
 ================
 
-|AU| |lundbeck| |lab|
+|AU|
 
 .. |AU| image::  https://github.com/LegrandNico/systole/raw/master/docs/source/images/au_clinisk_logo.png
    :width: 100%
diff --git a/docs/source/notebooks/1-PhysiologicalSignals.ipynb b/docs/source/notebooks/1-PhysiologicalSignals.ipynb
@@ -22,7 +22,7 @@
     "%%capture\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    ! pip install systole"
+    "    !pip install systole"
    ]
   },
   {
diff --git a/docs/source/notebooks/1-PhysiologicalSignals.md b/docs/source/notebooks/1-PhysiologicalSignals.md
@@ -22,7 +22,7 @@ Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
 %%capture
 import sys
 if 'google.colab' in sys.modules:
-    ! pip install systole
+    !pip install systole
 ```
 
 ```{code-cell} ipython3
diff --git a/docs/source/notebooks/2-DetectingCycles.ipynb b/docs/source/notebooks/2-DetectingCycles.ipynb
@@ -24,7 +24,7 @@
     "%%capture\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    ! pip install systole"
+    "    !pip install systole"
    ]
   },
   {
diff --git a/docs/source/notebooks/2-DetectingCycles.md b/docs/source/notebooks/2-DetectingCycles.md
@@ -22,7 +22,7 @@ Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
 %%capture
 import sys
 if 'google.colab' in sys.modules:
-    ! pip install systole
+    !pip install systole
 ```
 
 ```{code-cell} ipython3
diff --git a/docs/source/notebooks/3-DetectingAndCorrectingArtefacts.ipynb b/docs/source/notebooks/3-DetectingAndCorrectingArtefacts.ipynb
@@ -24,7 +24,7 @@
     "%%capture\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    ! pip install systole"
+    "    !pip install systole"
    ]
   },
   {
@@ -1117,7 +1117,7 @@
    "id": "8a67ca80",
    "metadata": {},
    "source": [
-    "This concludes the tutorial on using Systole to detect and correct more complex artefacts. In the next tutorial we will introduce more advanced signal processing techniques for estimating low and high-frequency heart-rate variability. "
+    "This concludes the tutorial on using Systole to detect and correct more complex artefacts. In the next tutorial we will introduce more advanced signal processing techniques for estimating low and high-frequency heart-rate variability."
    ]
   },
   {
@@ -1297,7 +1297,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.9.16"
   },
   "vscode": {
    "interpreter": {
diff --git a/docs/source/notebooks/3-DetectingAndCorrectingArtefacts.md b/docs/source/notebooks/3-DetectingAndCorrectingArtefacts.md
@@ -5,7 +5,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.14.1
+    jupytext_version: 1.15.1
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
@@ -22,7 +22,7 @@ Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
 %%capture
 import sys
 if 'google.colab' in sys.modules:
-    ! pip install systole
+    !pip install systole
 ```
 
 ```{code-cell} ipython3
@@ -257,7 +257,7 @@ plot_evoked(rr=peaks, triggers_idx=triggers_idx, ci=68, palette=["#55a868"],
 plt.ylim(-20, 20);
 ```
 
-This concludes the tutorial on using Systole to detect and correct more complex artefacts. In the next tutorial we will introduce more advanced signal processing techniques for estimating low and high-frequency heart-rate variability. 
+This concludes the tutorial on using Systole to detect and correct more complex artefacts. In the next tutorial we will introduce more advanced signal processing techniques for estimating low and high-frequency heart-rate variability.
 
 +++
 
diff --git a/docs/source/notebooks/4-HeartRateVariability.ipynb b/docs/source/notebooks/4-HeartRateVariability.ipynb
@@ -24,7 +24,7 @@
     "%%capture\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    ! pip install systole"
+    "    !pip install systole"
    ]
   },
   {
@@ -806,7 +806,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,
diff --git a/docs/source/notebooks/4-HeartRateVariability.md b/docs/source/notebooks/4-HeartRateVariability.md
@@ -5,7 +5,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.14.1
+    jupytext_version: 1.15.1
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
@@ -22,7 +22,7 @@ Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
 %%capture
 import sys
 if 'google.colab' in sys.modules:
-    ! pip install systole
+    !pip install systole
 ```
 
 ```{code-cell} ipython3
diff --git a/docs/source/notebooks/5-InstantaneousHeartRate.ipynb b/docs/source/notebooks/5-InstantaneousHeartRate.ipynb
@@ -24,7 +24,7 @@
     "%%capture\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    ! pip install systole"
+    "    !pip install systole"
    ]
   },
   {
@@ -889,7 +889,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,
diff --git a/docs/source/notebooks/5-InstantaneousHeartRate.md b/docs/source/notebooks/5-InstantaneousHeartRate.md
@@ -5,7 +5,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.14.1
+    jupytext_version: 1.15.1
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
@@ -22,7 +22,7 @@ Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
 %%capture
 import sys
 if 'google.colab' in sys.modules:
-    ! pip install systole
+    !pip install systole
 ```
 
 ```{code-cell} ipython3
diff --git a/docs/source/notebooks/6-WorkingWithBIDSFolders.ipynb b/docs/source/notebooks/6-WorkingWithBIDSFolders.ipynb
@@ -24,7 +24,7 @@
     "%%capture\n",
     "import sys\n",
     "if 'google.colab' in sys.modules:\n",
-    "    ! pip install systole"
+    "    !pip install systole"
    ]
   },
   {
@@ -395,7 +395,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.9.16"
   },
   "vscode": {
    "interpreter": {
diff --git a/docs/source/notebooks/6-WorkingWithBIDSFolders.md b/docs/source/notebooks/6-WorkingWithBIDSFolders.md
@@ -5,7 +5,7 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.14.1
+    jupytext_version: 1.15.1
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
@@ -22,7 +22,7 @@ Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
 %%capture
 import sys
 if 'google.colab' in sys.modules:
-    ! pip install systole
+    !pip install systole
 ```
 
 Starting in version `0.2.3`, Systole provides tools to interact with large datasets of physiological recordings. The functionalities interface with folders that are structured following the [BIDS standards](https://bids-specification.readthedocs.io/en/stable/) and this is the format we recommend using if you are following this tutorial.
@@ -232,7 +232,7 @@ This function will create a JSON file (using the path specified in the `correcte
 * `corrected_peaks` : the peaks indexes after correction.
 * `bad_segments` : a list of `start` and `end` indexed of bad segments.
 
-+++ {"tags": []}
++++
 
 ### Using the Viewer to navigate preprocessed folder
 
diff --git a/docs/source/refs.bib b/docs/source/refs.bib
diff --git a/requirements-docs.txt b/requirements-docs.txt

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot circular`
`4`	`3`	`=============`
`5`	`4`	`The density function can be represented using the area of the bars, the height or`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot ectopic beats`
`4`	`3`	`==================`
`5`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot events`
`4`	`3`	`===========`
`5`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot evoked`
`4`	`3`	`===========`
`5`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot frequency`
`4`	`3`	`==============`
`5`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot pointcare`
`4`	`3`	`==============`
`5`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot raw physiological signal`
`4`	`3`	`=============================`
`5`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot short and long invertvals`
`4`	`3`	`==============================`
`5`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`"""`
`2`		`-`
`3`	`2`	`Plot subspaces to vivualize short/long and ectopic beats`
`4`	`3`	`========================================================`
`5`	`4`
Original file line number	Diff line number	Diff line change
`@@ -22,7 +22,7 @@`
`22`	`22`	`"%%capture\n",`
`23`	`23`	`"import sys\n",`
`24`	`24`	`"if 'google.colab' in sys.modules:\n",`
`25`		`- " ! pip install systole"`
	`25`	`+ " !pip install systole"`
`26`	`26`	`]`
`27`	`27`	`},`
`28`	`28`	`{`