Merge pull request #472 from pynapple-org/dev

Bump 0.9.2

Author: gviejo

.github/workflows/documentation.yml

@@ -37,4 +37,4 @@ jobs:
           publish_branch: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: _build/
-          force_orphan: true
+          force_orphan: true

.github/workflows/main.yml

@@ -82,6 +82,9 @@ jobs:
         run: |          
           cd doc
           make html
+      - name: Start tmate session for debugging
+        if: failure()
+        uses: mxschmitt/action-tmate@v3
       - name: Check html
         uses: chabad360/htmlproofer@master
         with:

.gitignore

@@ -100,6 +100,9 @@ ipython_config.py
 # pyenv
 .python-version
 
+# pre-commit
+.pre-commit-config.yaml
+
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
 #   However, in case of collaboration, if having platform-specific dependencies or dependencies
@@ -125,6 +128,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+uv.lock
 
 # Spyder project settings
 .spyderproject

CONTRIBUTING.md

@@ -0,0 +1,69 @@
+# Contributing
+
+In general, we welcome contributions from the community, including bug fixes and documentation improvements. Please see the Issues tab for discussion.
+
+## Development environment
+
+To get started, clone the repository and set up your local environment:
+
+```bash
+# Clone the repository
+git clone https://github.com/pynapple-org/pynapple.git
+cd pynapple
+
+# Create a new conda environment
+conda create --name pynapple pip python=3.8
+conda activate pynapple
+
+# Install in editable mode with dev dependencies
+pip install -e ".[dev,docs]"
+```
+
+Note: If you're an external contributor, you'll likely want to fork the repository first with your own GitHub account, and then set up an `upstream` remote branch:
+
+```
+# Replace username with your GitHub username
+git clone https://github.com/<username>/pynapple.git
+git remote add upstream https://github.com/pynapple-org/pynapple
+```
+
+## Git workflow
+
+In general, we recommend developing changes on feature branches, and then opening a pull request against the `dev` branch for review.
+
+```bash
+# Create a new branch
+git checkout dev
+git pull origin dev # or git pull upstream dev
+git checkout -b your-branch-name
+
+# Commit and push changes
+git commit -m "Your commit message"
+git push origin your-branch-name
+```
+
+## Testing and linting
+
+You can run the tests and code linters locally using `tox`. This is generally kept in sync with the Github Actions defined in `.github/workflows` via the [`tox.ini`](tox.ini) file.
+
+```bash
+# Install tox
+pip install tox tox-conda
+
+# Run tests and linter
+tox
+```
+
+## Generating docs
+
+The user documentation is generated using Sphinx and can be built using the Makefile in the `doc/` folder:
+
+```bash
+cd doc && make html
+```
+
+You can also start a development server that will watch for changes with `sphinx-autobuild`:
+
+```bash
+sphinx-autobuild . _build/html
+```

README.md

@@ -70,30 +70,18 @@ Getting Started
 
 ### Installation
 
-The best way to install pynapple is with pip within a new [conda](https://docs.conda.io/en/latest/) environment :
-
+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 activate pynapple
 $ pip install pynapple
 ```
 
-or directly from the source code:
-
-``` {.sourceCode .shell}
-$ conda create --name pynapple pip python=3.8
-$ conda activate pynapple
-$ # clone the repository
-$ git clone https://github.com/pynapple-org/pynapple.git
-$ cd pynapple
-$ # Install in editable mode with `-e` or, equivalently, `--editable`
-$ pip install -e .
-```
 > **Note**
-> The package is now using a pyproject.toml file for installation and dependencies management. If you want to run the tests, use pip install -e .[dev]
+> The package uses a pyproject.toml file for installation and dependencies management.
 
-This procedure will install all the dependencies including 
+Running `pip install pynapple` will install all the dependencies, including: 
 
 -   pandas
 -   numpy
@@ -103,6 +91,8 @@ This procedure will install all the dependencies including
 -   tabulate
 -   h5py
 
+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}
@@ -174,3 +164,7 @@ This package was developped by Guillaume Viejo
 (<https://github.com/gviejo>) and other members of the Peyrache Lab.
 
 <!-- Logo: Sofia Skromne Carrasco, 2021. -->
+
+## Contributing
+
+We welcome contributions, including documentation improvements. For more information, see the [contributor guide](CONTRIBUTING.md).

doc/conf.py

@@ -14,45 +14,46 @@
 import time
 from pathlib import Path
 
-sys.path.insert(0, os.path.abspath('..'))
-sys.path.insert(0, os.path.abspath('sphinxext'))
+sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath("sphinxext"))
 
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'pynapple'
+project = "pynapple"
 copyright = f'2021-{time.strftime("%Y")}'
-author = 'Guillaume Viejo'
+author = "Guillaume Viejo"
 from importlib.metadata import version
+
 release: str = version("pynapple")
 # this will grab major.minor.patch (excluding any .devN afterwards, which should only
 # show up when building locally during development)
-version: str = ".".join(release.split('.')[:3])
+version: str = ".".join(release.split(".")[:3])
 
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',  # Links to source code
-    'sphinx.ext.doctest',
-    'sphinx_copybutton',  # Adds copy button to code blocks
-    'sphinx_design',  # For layout components
-    'myst_nb',
-    'sphinx_contributors',
-    'matplotlib.sphinxext.plot_directive'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.coverage",
+    "sphinx.ext.viewcode",  # Links to source code
+    "sphinx.ext.doctest",
+    "sphinx_copybutton",  # Adds copy button to code blocks
+    "sphinx_design",  # For layout components
+    "myst_nb",
+    "sphinx_contributors",
+    "matplotlib.sphinxext.plot_directive",
     # 'sphinxcontrib.apidoc'
-    # 'sphinx_gallery.gen_gallery',    
+    # 'sphinx_gallery.gen_gallery',
     # 'myst_sphinx_gallery',
 ]
 
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 
 # The Root document
@@ -62,17 +63,17 @@
 # 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 = ['_build', 'docstrings', 'nextgen', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "docstrings", "nextgen", "Thumbs.db", ".DS_Store"]
 
 
 # Generate the API documentation when building
 autosummary_generate = True
 numpydoc_show_class_members = True
 autodoc_default_options = {
-    'members': True,
-    'inherited-members': True,
-    'show-inheritance': True,
-    }
+    "members": True,
+    "inherited-members": True,
+    "show-inheritance": True,
+}
 
 # apidoc_module_dir = '../pynapple'
 # apidoc_output_dir = 'reference'
@@ -84,7 +85,7 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 
 html_logo = "_static/Logo/Pynapple_final_logo.png"
 html_favicon = "_static/Icon/Pynapple_final_icon.png"
@@ -116,37 +117,36 @@
 
 html_sidebars = {
     "index": [],
-    "installing":[],
-    "about":[],
-    "releases":[],
-    "external":[],
-    "pynajax":[],
-    "citing":[],
+    "installing": [],
+    "about": [],
+    "releases": [],
+    "external": [],
+    "pynajax": [],
+    "citing": [],
     "**": ["search-field.html", "sidebar-nav-bs.html"],
 }
 
 # # Path for static files (custom stylesheets or JavaScript)
-html_static_path = ['_static']
-html_css_files = ['custom.css']
+html_static_path = ["_static"]
+html_css_files = ["custom.css"]
 
 # Copybutton settings (to hide prompt)
 copybutton_prompt_text = r">>> |\$ |# "
 copybutton_prompt_is_regexp = True
 
 # Enable markdown and notebook support
-myst_enable_extensions = ["colon_fence"]  # For improved markdown 
+myst_enable_extensions = ["colon_fence"]  # For improved markdown
 
 # # ----------------------------------------------------------------------------
 # # -- Autodoc and Napoleon Options -------------------------------------------------
 autodoc_default_options = {
-    'members': True,
-    'undoc-members': True,
-    'show-inheritance': True,
+    "members": True,
+    "undoc-members": True,
+    "show-inheritance": True,
 }
 napoleon_numpy_docstring = True
 
 
-
 nitpicky = True
 
 # Set timeout in seconds (e.g., 15 minutes)
@@ -155,8 +155,3 @@
 # Execute notebooks during the build:
 nb_execution_mode = "cache"
 nb_execution_raise_on_error = True
-
-
-
-
-

doc/examples/tutorial_calcium_imaging.md

@@ -161,7 +161,7 @@ plt.show()
 
 It looks like this could be a head-direction cell. One important property of head-directions cells however, is that their firing with respect to head-direction is stable. To check for their stability, we can split our recording in two and compute a tuning curve for each half of the recording.
 
-We start by finding the midpoint of the recording, using the function `get_intervals_center`. Using this, then create one new IntervalSet with two rows, one for each half of the recording.
+We start by finding the midpoint of the recording, using the function [`get_intervals_center`](pynapple.IntervalSet.get_intervals_center). Using this, then create one new IntervalSet with two rows, one for each half of the recording.
 
 
 ```{code-cell} ipython3