Merge branch 'main' into add_HOOMD_burst_example

glotzerlab · Jul 8, 2024 · 6665029 · 6665029
2 parents bc17a25 + ead4ad6
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diff --git a/docs/citing.rst b/docs/citing.rst
@@ -6,8 +6,7 @@ Please acknowledge the use of this software within the body of your publication
 
 *Event detection for this publication used the dupin library[1].*
 
-The following is a BibTex citation for the current pre-print.
-Before submitting please check to see if this has been updated with the submitted journal paper::
+The following is a BibTex citation for the dupin paper::
 
     @article{butler2023change,
       title = {Change point detection of events in molecular simulations using dupin},

diff --git a/docs/module-preprocessing-signal.rst b/docs/module-preprocessing-signal.rst
@@ -8,12 +8,12 @@ dupin.preprocessing.signal
 .. autosummary::
     :nosignatures:
 
-    fft_smoothing
+    high_frequency_smoothing
     moving_average
 
 .. rubric:: Details
 
 .. automodule:: dupin.preprocessing.signal
     :synopsis: Functions for transforming feature signals across time.
-    :members: fft_smoothing,
+    :members: high_frequency_smoothing,
         moving_average
diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -6,4 +6,6 @@ Tutorials
    :maxdepth: 1
 
    /tutorials/00-Introducing-dupin/00-index
+   /tutorials/01-Custom-generators/Custom-generator
    /tutorials/02-HOOMD-burst-writer-with-online-detection/HOOMD-burst-with-online
+   /tutorials/03-Logging-particles-undergoing-detection/Logging-particles-example
diff --git a/docs/tutorials/00-Introducing-dupin/03-collecting-data.ipynb b/docs/tutorials/00-Introducing-dupin/03-collecting-data.ipynb
@@ -33,7 +33,7 @@
     "\n",
     "import dupin as du\n",
     "\n",
-    "FILENAME = \"lj-sim.gsd\""
+    "FILENAME = \"../data/lj-sim.gsd\""
    ]
   },
   {
@@ -396,7 +396,7 @@
     "    for frame in traj:\n",
     "        signal_aggregator.accumulate(frame, nlist_kwargs)\n",
     "df = signal_aggregator.to_dataframe()\n",
-    "df.to_hdf(\"./lj-data.h5\", \"data\")\n",
+    "df.to_hdf(\"lj-data.h5\", \"data\")\n",
     "display_dataframe(df)"
    ]
   },

diff --git a/docs/tutorials/01-Custom-generators/Custom-generator.ipynb b/docs/tutorials/01-Custom-generators/Custom-generator.ipynb
diff --git a/docs/tutorials/03-Logging-particles-undergoing-detection/Logging-particles-example.ipynb b/docs/tutorials/03-Logging-particles-undergoing-detection/Logging-particles-example.ipynb
diff --git a/...tutorials/00-Introducing-dupin/lj-sim.gsd → docs/tutorials/data/lj-sim.gsd b/...tutorials/00-Introducing-dupin/lj-sim.gsd → docs/tutorials/data/lj-sim.gsd