Merge branch 'doc/test' into r/0.38

christianbrodbeck · Sep 5, 2022 · 6de46c3 · 6de46c3
2 parents 0d4671e + 5a31c02
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diff --git a/doc/index.rst b/doc/index.rst
@@ -56,7 +56,9 @@ and incorporates icons from the `Tango Desktop Project <http://tango.freedesktop
 
 Eelbrain is maintained by `Christian Brodbeck <http://christianbrodbeck.net>`_.
 Current funding:
-`NSF <http://nsf.gov>`_ `1754284 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=1754284>`_ (2020-);
+`University of Connecticut <https://uconn.edu>`_ (2021-);
+`NSF <http://nsf.gov>`_ `2043950 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=2043950>`_ (2021-);
 Past funding:
+`NSF <http://nsf.gov>`_ `1754284 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=1754284>`_ (2020-2021);
 `NIH <https://www.nih.gov>`_ R01-DC-014085 (2016-2020);
 `NYU Abu Dhabi Institute <http://nyuad.nyu.edu/en/research/nyuad-institute.html>`_ G1001 (2011-2016).
diff --git a/doc/publications.bib b/doc/publications.bib
@@ -685,3 +685,33 @@ @article{schubert2022individual
     doi = "10.1101/2022.04.22.489224",
     google_result_id = "zyzRBRZ6n7UJ"
 }
+
+@article{tezcan2022tradeoff,
+    author = "Tezcan, Filiz and Weissbart, Hugo and Martin, Andrea E",
+    title = "A tradeoff between acoustic and linguistic feature encoding in spoken language comprehension",
+    journal = "bioRxiv",
+    year = "2022",
+    publisher = "Cold Spring Harbor Laboratory",
+    doi = "10.1101/2022.08.17.504234",
+    google_result_id = "DydMiMelnaYJ"
+}
+
+@article{gillis2022linguistic,
+    author = "Gillis, Marlies and Kries, Jill and Vandermosten, Maaike and Francart, Tom",
+    title = "Linguistic speech processing decreases with advancing age",
+    journal = "bioRxiv",
+    year = "2022",
+    publisher = "Cold Spring Harbor Laboratory",
+    doi = "10.1101/2022.07.29.501978",
+    google_result_id = "Tnb_P_A4WiAJ"
+}
+
+@article{de2022beyond,
+    author = "De Clercq, Pieter and Vanthornhout, Jonas and Vandermosten, Maaike and Francart, Tom",
+    title = "Beyond Linear Neural Envelope Tracking: A Mutual Information Approach",
+    journal = "bioRxiv",
+    year = "2022",
+    publisher = "Cold Spring Harbor Laboratory",
+    doi = "10.1101/2022.08.11.503600",
+    google_result_id = "uX8c_LpxGisJ"
+}
diff --git a/doc/recipes.rst b/doc/recipes.rst
@@ -23,14 +23,36 @@ Style
 
 In order to produce multiple plots with consistent style it is useful to set
 some :mod:`matplotlib` options globally. One way to do this is by updating
-``rcParams`` inside a script, e.g.::
-
-    import matplotlib
-
-    matplotlib.rcParams['font.family'] = 'sans-serif'
-    matplotlib.rcParams['font.size'] = 9
-    # The size of saved figures depends on the figure size (w, h) and DPI
-    matplotlib.rcParams['savefig.dpi'] = 300
+:attr:`matplotlib.rcParams` at the beginning of a script/notebook, e.g.::
+
+    from matplotlib import pyplot
+
+    FONT = 'Arial'
+    FONT_SIZE = 8
+    LINEWIDTH = 0.5
+    pyplot.rcParams.update({
+        'figure.dpi': 150,
+        'savefig.dpi': 300,
+        'savefig.transparent': True,
+        # Font
+        'font.family': 'sans-serif',
+        'font.sans-serif': FONT,
+        'font.size': FONT_SIZE,
+        'axes.labelsize': FONT_SIZE,
+        'axes.titlesize': FONT_SIZE,
+        'xtick.labelsize': FONT_SIZE,
+        'ytick.labelsize': FONT_SIZE,
+        'legend.fontsize': FONT_SIZE,
+        # line width
+        'axes.linewidth': LINEWIDTH,
+        'grid.linewidth': LINEWIDTH,
+        'lines.linewidth': LINEWIDTH,
+        'patch.linewidth': LINEWIDTH,
+        'xtick.major.width': LINEWIDTH,
+        'xtick.minor.width': LINEWIDTH,
+        'ytick.major.width': LINEWIDTH,
+        'ytick.minor.width': LINEWIDTH,
+    })
 
 
 Plot sizes

diff --git a/doc/scripts/bibtex.pickle b/doc/scripts/bibtex.pickle
diff --git a/doc/scripts/cache.json b/doc/scripts/cache.json
diff --git a/doc/scripts/find_publications.py b/doc/scripts/find_publications.py
@@ -6,7 +6,7 @@
 
 !! Run from interpreter to retain data for debugging access
 
-run find_publications.py, then copy-paste download function
+run find_publications.py with command
 
 """
 from argparse import ArgumentParser
@@ -31,6 +31,9 @@
 BIBTEX_CACHE = DIR / 'bibtex.pickle'
 # Parse
 DST = DIR.parent / 'publications.bib'
+OBSOLETE = """
+Qm4WZWrznhEJ
+""".split()
 BIORXIV_OBSOLETE = """
 10.1101/326785
 2018/10/09/439158
@@ -162,6 +165,8 @@ def parse():
     for result_id, raw_bibtex in bibtex_entries.items():
         if not selection.get(result_id, False):
             continue
+        elif result_id in OBSOLETE:
+            continue
         raw_bibtex = re.sub(rb'[^\x00-\x7F]+', b' ', raw_bibtex)
         # parse entry
         data = parse_bytes(raw_bibtex, 'bibtex')

diff --git a/doc/scripts/selection.json b/doc/scripts/selection.json
@@ -70,5 +70,10 @@
  "FSefJe40PsgJ": false,
  "zyzRBRZ6n7UJ": true,
  "7_12qdwe3r4J": true,
- "QMt_-oHCdi0J": true
+ "QMt_-oHCdi0J": true,
+ "DydMiMelnaYJ": true,
+ "Tnb_P_A4WiAJ": true,
+ "V3JR8DvqOQcJ": false,
+ "h123-VpM2bwJ": false,
+ "uX8c_LpxGisJ": true
 }
diff --git a/examples/mass-univariate-statistics/simulate-N400.py b/examples/mass-univariate-statistics/simulate-N400.py
@@ -2,8 +2,8 @@
 """
 .. _exa-generate-ndvar:
 
-Generate :class:`NDVar` (with artificial data)
-==============================================
+Generate NDVar (with artificial data)
+=====================================
 
 .. currentmodule:: eelbrain
 

diff --git a/examples/plots/utsstat.py b/examples/plots/utsstat.py
@@ -15,8 +15,8 @@
 """
 .. _exa-utsstat:
 
-UTS-statistics (``UTSStat``)
-============================
+UTS-statistics (plot.UTSStat)
+=============================
 
 """
 # sphinx_gallery_thumbnail_number = 5