Merge pull request #391 from pynapple-org/dev

Bump 0.8.0

.github/workflows/main.yml

@@ -31,7 +31,8 @@ jobs:
           black --check pynapple
           isort --check pynapple --profile black
           flake8 pynapple --max-complexity 10
-          
+          black --check tests
+          isort --check tests --profile black
   test:
     needs: lint
     runs-on: ${{ matrix.os }}
@@ -84,7 +85,7 @@ jobs:
         with:
           directory: "./doc/_build/html"
           # The directory to scan
-          arguments: --checks Links,Scripts --ignore-urls "https://fonts.gstatic.com,https://mkdocs-gallery.github.io,./doc/_build/html/_static/" --assume-extension --check-external-hash --ignore-status-codes 403 --ignore-files "/.+\/html\/_static\/.+/"
+          arguments: --checks Links,Scripts --ignore-urls "https://fonts.gstatic.com,https://mkdocs-gallery.github.io,./doc/_build/html/_static/,https://www.nature.com/articles/s41593-022-01020-w" --assume-extension --check-external-hash --ignore-status-codes 403 --ignore-files "/.+\/html\/_static\/.+/"
           # The arguments to pass to HTMLProofer
 
 

.gitignore

@@ -8,6 +8,10 @@
 /docs/generated/gallery/*.py
 /docs/generated/gallery/*.zip
 
+/doc/generated
+/doc/examples/nwb-cache
+/doc/_build
+
 /tests/npzfilestest
 
 # Byte-compiled / optimized / DLL files
@@ -152,4 +156,7 @@ tutorials/data/KA28-190405/
 
 old
 data
-your
+your
+
+# Ignore npz files from testing:
+tests/*.npz

README.md

@@ -1,10 +1,4 @@
-<!-- ![pic1](banner_logo.png) -->
-<p align="center">
-  <img width="60%" src="docs/images/banner_logo.png">
-</p>
-
 
-<!-- ========================== -->
 
 [![image](https://img.shields.io/pypi/v/pynapple.svg)](https://pypi.python.org/pypi/pynapple)
 [![pynapple CI](https://github.com/pynapple-org/pynapple/actions/workflows/main.yml/badge.svg)](https://github.com/pynapple-org/pynapple/actions/workflows/main.yml)
@@ -157,7 +151,7 @@ Shown below, the final figure from the example code displays the firing rate of
 
 <!-- ![pic1](readme_figure.png) -->
 <p align="center">
-  <img width="80%" src="docs/images/readme_figure.png">
+  <img width="80%" src="doc/_static/readme_figure.png">
 </p>
 
 

doc/api.rst

@@ -8,7 +8,7 @@ Core objects
 
 .. rubric:: Time Series
 
-.. currentmodule:: pynapple.core.time_series
+.. currentmodule:: pynapple
 
 .. autosummary::
     :toctree: generated/
@@ -22,7 +22,7 @@ Core objects
 
 .. rubric:: Intervals
 
-.. currentmodule:: pynapple.core.interval_set
+.. currentmodule:: pynapple
 
 .. autosummary::
     :toctree: generated/
@@ -34,7 +34,7 @@ Core objects
 
 .. rubric:: Timestamps
 
-.. currentmodule:: pynapple.core.time_series
+.. currentmodule:: pynapple
 
 .. autosummary::
     :toctree: generated/
@@ -45,7 +45,7 @@ Core objects
 
 .. rubric:: Group of timestamps
 
-.. currentmodule:: pynapple.core.ts_group
+.. currentmodule:: pynapple
 
 .. autosummary::
     :toctree: generated/
@@ -58,7 +58,7 @@ Core objects
 Input-Ouput
 -----------
 
-.. currentmodule:: pynapple.io.interface_nwb
+.. currentmodule:: pynapple.io
 
 .. rubric:: Neurodata Without Borders (NWB)
 
@@ -70,7 +70,7 @@ Input-Ouput
     NWBFile
 
 
-.. currentmodule:: pynapple.io.interface_npz
+.. currentmodule:: pynapple.io
 
 .. rubric:: Numpy files
 

doc/examples/tutorial_HD_dataset.md

@@ -116,7 +116,7 @@ tuning_curves = nap.compute_1d_tuning_curves(
     group=spikes_adn, 
     feature=angle, 
     nb_bins=61, 
-    ep = epochs['wake'],
+    ep=epochs[epochs.tags == "wake"],
     minmax=(0, 2 * np.pi)
     )
 ```
@@ -199,7 +199,7 @@ To decode the population activity, we will be using a Bayesian Decoder as implem
 decoded, proba_feature = nap.decode_1d(
     tuning_curves=tuning_curves,
     group=spikes_adn,
-    ep=epochs["wake"],
+    ep=epochs[epochs.tags == "wake"],
     bin_size=0.1,  # second
     feature=angle,
 )

doc/index.rst

@@ -64,7 +64,7 @@ pynapple: python neural analysis package
 
    .. grid-item-card:: Time Series
       :text-align: center
-      :link: ./user_guide/04_core_methods.html
+      :link: ./user_guide/03_core_methods.html
 
       .. image:: _static/example_thumbs/timeseries.svg         
          :class: dark-light
@@ -97,7 +97,7 @@ pynapple: python neural analysis package
       .. image:: _static/example_thumbs/tuningcurves.svg         
          :class: dark-light
 
-   .. grid-item-card:: Wavelets
+   .. grid-item-card:: Spectrogram
       :text-align: center
       :link: ./user_guide/11_wavelets.html
 
@@ -120,5 +120,11 @@ This package is supported by the Center for Computational Neuroscience, in the F
 
 .. image:: _static/CCN-logo-wText.png
    :width: 200px
+   :class: only-light
+   :target: https://www.simonsfoundation.org/flatiron/center-for-computational-neuroscience/
+
+.. image:: _static/logo_flatiron_white.svg
+   :width: 200px
+   :class: only-dark
    :target: https://www.simonsfoundation.org/flatiron/center-for-computational-neuroscience/
 

doc/releases.md

@@ -18,6 +18,11 @@ of the Flatiron institute.
 
 ## Releases
 
+### 0.8.0 (2025-01-15)
+
+- New private class: `_MetadataMixin` (core/metadata_class.py). Can be inherited by `IntervalSet`, `TsdFrame` and `TsGroup`.
+- `decode_1d` and `decode_2d` now accepts `TsdFrame` as input. 
+
 ### 0.7.1 (2024-09-24)
 
 - Fixing nan issue when computing 1d tuning curve (See issue #334).

doc/user_guide.md

@@ -20,7 +20,11 @@ Interaction with numpy <user_guide/03_interacting_with_numpy>
 ```
 
 ```{toctree}
-Core methods <user_guide/04_core_methods>
+Core methods <user_guide/03_core_methods>
+```
+
+```{toctree}
+Metadata <user_guide/03_metadata>
 ```
 :::