Param matching

.github/workflows/deploy.yml

@@ -8,20 +8,25 @@ jobs:
     name: Build and test package
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - name: Checkout with full history and tags
+      uses: actions/checkout@v4
         # this is necessary for setuptools_scm to work properly with github
         # actions, see https://github.com/pypa/setuptools_scm/issues/480 and
         # https://stackoverflow.com/a/68959339
       with:
         fetch-depth: 0
+        tags: true
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
         python-version: 3.x
+
     - name: Build package
       run: |
         pip install build
         python -m build --outdir dist/ --sdist --wheel
+
     - name: Check there's only one sdist and one whl file created
       shell: bash
         # because the following two tests will be weird otherwise. see
@@ -31,6 +36,7 @@ jobs:
       run: |
         [[ $(find dist/ -type f -name "*whl" -printf x | wc -c) == 1 ]] || exit 1
         [[ $(find dist/ -type f -name "*tar.gz" -printf x | wc -c) == 1 ]] || exit 1
+
     - name: Check setuptools_scm version against git tag
       shell: bash
       run: |
@@ -40,6 +46,7 @@ jobs:
         # ends in the most recent git tag, fail if it does not.
         TAG=$(git describe --tags)
         [[ "$(ls dist/*tar.gz)" =~ "-${TAG:1}.tar.gz" ]]
+
     - name: Check we can install from wheel
         # note that this is how this works in bash (different shells might be
         # slightly different). we've checked there's only one .whl file in an
@@ -50,10 +57,12 @@ jobs:
       shell: bash
       run: |
         pip install "$(ls dist/*whl)[dev]"
+
     - name: Run some tests
         # modify the following as necessary to e.g., run notebooks
       run: |
         pytest tests/
+
     - uses: actions/upload-artifact@v4
       with:
         path: dist/*

.github/workflows/documentation.yml

@@ -22,6 +22,10 @@ jobs:
         # https://stackoverflow.com/a/68959339
         with:
           fetch-depth: 0
+          tags: true
+      # Ensure all tags are present
+      - run: git fetch --tags
+
       - uses: actions/setup-python@v5
       - name: Install dependencies
         run: |

.github/workflows/main.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - name: Install dependencies
         run: |
           echo "testing: ${{github.ref}}"
@@ -33,8 +33,22 @@ jobs:
           flake8 pynapple --max-complexity 10
           black --check tests
           isort --check tests --profile black
+  check-param-naming:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: Install pynapple
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      - name: Check parameter name consistency
+        run: python scripts/check_parameter_naming.py
   test:
-    needs: lint
+    needs: [lint, check-param-naming]
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -90,7 +104,13 @@ 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/,https://www.nature.com/articles/s41593-022-01020-w" --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,https://elifesciences.org/reviewed-preprints/85786" 
+            --assume-extension 
+            --check-external-hash 
+            --ignore-status-codes 403 
+            --ignore-files "/.+\/html\/_static\/.+/"
           # The arguments to pass to HTMLProofer
 
   check:
@@ -99,6 +119,7 @@ jobs:
     - lint
     - test
     - documentation
+    - check-param-naming
     runs-on: ubuntu-latest
     steps:
     - name: Decide whether all tests and notebooks succeeded

.gitignore

@@ -165,3 +165,5 @@ your
 # Ignore npz files from testing:
 tests/*.npz
 .vscode/settings.json
+doc/user_guide/MyProject/sub-A2929/A2929-200711/stimulus-fish.json
+doc/user_guide/memmap.dat

README.md

@@ -19,9 +19,25 @@ pynapple is a light-weight python library for neurophysiological data analysis.
 
 ------------------------------------------------------------------------
 
+
+Learning pynapple
+-----------------
+
+Workshops are regularly organized by the [center for Computational Neuroscience ](https://www.simonsfoundation.org/flatiron/center-for-computational-neuroscience/) of the Flatiron institute 
+to teach pynapple & [NeMos](https://nemos.readthedocs.io/en/latest/) to new users. 
+
+**The next workshop will take place in New York City on February 2 - 5, 2026. Register [here](https://www.simonsfoundation.org/event/flatiron-ccn-neural-data-analysis-workshop/).**
+
+
 New release :fire:
 ------------------
 
+### pynapple >= 0.10.0
+
+Tuning curves computation have been generalized to n-dimensions with the function `compute_tuning_curves`.
+It can now return a [xarray DataArray](https://docs.xarray.dev/en/stable/) instead of a Pandas DataFrame.
+
+
 ### pynapple >= 0.8.2
 
 The objects `IntervalSet`, `TsdFrame` and `TsGroup` inherits a new metadata class. It is now possible to add labels for 
@@ -38,27 +54,6 @@ nap.apply_bandpass_filter(signal, (10, 20), fs=1250)
 ```
 New functions includes power spectral density and Morlet wavelet decomposition. See the [documentation](https://pynapple-org.github.io/pynapple/reference/process/) for more details.
 
-### pynapple >= 0.6
-
-Starting with 0.6, [`IntervalSet`](https://pynapple-org.github.io/pynapple/reference/core/interval_set/) objects are behaving as immutable numpy ndarray. Before 0.6, you could select an interval within an `IntervalSet` object with:
-
-```python
-new_intervalset = intervalset.loc[[0]] # Selecting first interval
-```
-
-With pynapple>=0.6, the slicing is similar to numpy and it returns an `IntervalSet`
-
-```python
-new_intervalset = intervalset[0]
-```
-
-### pynapple >= 0.4
-
-Starting with 0.4, pynapple rely on the [numpy array container](https://numpy.org/doc/stable/user/basics.dispatch.html) approach instead of Pandas for the time series. Pynapple builtin functions will remain the same except for functions inherited from Pandas. 
-
-This allows for a better handling of returned objects.
-
-Additionaly, it is now possible to define time series objects with more than 2 dimensions with `TsdTensor`. You can also look at this [notebook](https://pynapple-org.github.io/pynapple/generated/gallery/tutorial_pynapple_numpy/) for a demonstration of numpy compatibilities.
 
 Community
 ---------
@@ -73,13 +68,11 @@ Getting Started
 The best way to install pynapple is with pip inside a new [conda](https://docs.conda.io/en/latest/) environment:
 
 ``` {.sourceCode .shell}
-$ conda create --name pynapple pip python=3.8
+$ conda create --name pynapple pip python=3.11
 $ conda activate pynapple
 $ pip install pynapple
 ```
 
-> **Note**
-> The package uses a pyproject.toml file for installation and dependencies management.
 
 Running `pip install pynapple` will install all the dependencies, including: 
 
@@ -90,13 +83,14 @@ Running `pip install pynapple` will install all the dependencies, including:
 -   pynwb 2.0
 -   tabulate
 -   h5py
+-   xarray
 
 For development, see the [contributor guide](CONTRIBUTING.md) for steps to install from source code.
 
 <!-- For spyder users, it is recommended to install spyder after installing pynapple with :
 
 ``` {.sourceCode .shell}
-$ conda create --name pynapple pip python=3.8
+$ conda create --name pynapple pip python=3.11
 $ conda activate pynapple
 $ pip install pynapple
 $ pip install spyder
@@ -130,18 +124,20 @@ head_direction = data["ry"]
 wake_ep = data["position_time_support"]
 
 # COMPUTING TUNING CURVES
-tuning_curves = nap.compute_1d_tuning_curves(
-    spikes, head_direction, 120, ep=wake_ep, minmax=(0, 2 * np.pi)
+tuning_curves = nap.compute_tuning_curves(
+    spikes, head_direction, 120, epochs=wake_ep, range=(0, 2 * np.pi)
 )
 
-
 # PLOT
-plt.figure()
-for i in spikes:
-    plt.subplot(3, 5, i + 1, projection="polar")
-    plt.plot(tuning_curves[i])
-    plt.xticks([0, np.pi / 2, np.pi, 3 * np.pi / 2])
-
+g=tuning_curves.plot(
+    row="unit", 
+    col_wrap=5, 
+    subplot_kws={"projection": "polar"}, 
+    sharey=False
+)
+plt.xticks([0, np.pi / 2, np.pi, 3 * np.pi / 2])
+g.set_titles("")
+g.set_xlabels("")
 plt.show()
 ```
 Shown below, the final figure from the example code displays the firing rate of 15 neurons as a function of the direction of the head of the animal in the horizontal plane.

doc/conf.py

@@ -22,7 +22,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "pynapple"
-copyright = f'2021-{time.strftime("%Y")}'
+copyright = f"2021-{time.strftime('%Y')}"
 author = "Guillaume Viejo"
 from importlib.metadata import version
 
@@ -42,6 +42,7 @@
     "sphinx.ext.coverage",
     "sphinx.ext.viewcode",  # Links to source code
     "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
     "sphinx_copybutton",  # Adds copy button to code blocks
     "sphinx_design",  # For layout components
     "myst_nb",
@@ -75,6 +76,16 @@
     "show-inheritance": True,
 }
 
+# Intersphinx setup
+intersphinx_mapping = {
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "python": ("https://docs.python.org/3/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+}
+
 # apidoc_module_dir = '../pynapple'
 # apidoc_output_dir = 'reference'
 # apidoc_excluded_paths = ['tests']

doc/examples.md

@@ -24,15 +24,7 @@ Streaming data from Dandi <examples/tutorial_pynapple_dandi>
 :::{card} 
 ```{toctree}
 :maxdepth: 3
-Computing calcium imaging tuning curves <examples/tutorial_calcium_imaging>
-```
-:::
-
-
-:::{card} 
-```{toctree}
-:maxdepth: 3
-Example perievent <examples/tutorial_human_dataset>
+Analyzing calcium imaging data <examples/tutorial_calcium_imaging>
 ```
 :::