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Spellcheck pass
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7 files changed

+132
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‎cspell.json

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// cSpell Settings
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//https://github.com/streetsidesoftware/vscode-spell-checker
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{
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"version": "0.2", // Version of the setting file. Always 0.2
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"language": "en", // language - current active spelling language
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"enabledLanguageIds": [
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"markdown", "yaml", "python"
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],
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// flagWords - list of words to be always considered incorrect
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// This is useful for offensive words and common spelling errors.
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// For example "hte" should be "the"
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"flagWords": [],
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"allowCompoundWords": true,
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"ignorePaths": [
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"./element_array_ephys.egg-info/*",
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"./images/*"
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],
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"words": [
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"aggr",
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"apmeta",
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"arange",
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"asarray",
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"astype",
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"autocorrelogram",
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"bbins",
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"bdist",
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"Binarize",
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"catgt",
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"cbar",
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"cbin",
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"cdat",
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"Chans",
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"chans",
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"chns",
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"cmap",
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"correlogram",
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"correlograms",
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"decomp",
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"DISTRO",
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"djbase",
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"dtype",
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"ecephys",
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"elif",
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"Ephys",
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"gblcar",
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"gfix",
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"hstack",
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"ibllib",
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"ifnull",
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"Imax",
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"IMAX",
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"imax",
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"imec",
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"imread",
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"imro",
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"imrotbl",
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"imshow",
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"inlinehilite",
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"ipywidgets",
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"kcoords",
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"lfmeta",
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"linenums",
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"mdict",
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"mkdocs",
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"mkdocstrings",
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"mtscomp",
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"Nchan",
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"nchan",
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"ndarray",
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"ndim",
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"ndimage",
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"NEURO",
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"Neuropix",
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"NeuroPixels",
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"oebin",
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"openephys",
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"openephys",
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"openpyxl",
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"phylog",
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"plotly",
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"pykilosort",
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"pymdownx",
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"pynwb",
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"pyopenephys",
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"pyplot",
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"pytest",
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"repolarization",
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"Roboto",
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"scipy",
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"sdist",
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"sess",
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"SGLX",
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"spikeglx",
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"spkcount",
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"Stereotaxic","acorr",
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"tcat",
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"tickvals",
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"tofile",
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"vline",
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"Vmax",
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"vmax",
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"xanchor",
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"xaxes",
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"xaxis",
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"xcoords",
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"xcorr",
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"xlabel",
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"xlim",
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"XPOS",
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"xtick",
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"yaxes",
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"yaxis",
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"ycoord",
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"ycoords",
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"ylabel",
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"ylim",
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"YPOS",
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"yref",
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"yticks"
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]
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}

‎docs/mkdocs.yaml

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# HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
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# ```
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# 02. Site analytics depend on a local environment variable GOOGLE_ANALYTICS_KEY
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# You can find this in LastPass or declare with any string to suprress errors
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# You can find this in LastPass or declare with any string to suppress errors
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# 03. The API section will pull docstrings.
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# A. Follow google styleguide e.g.,
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# https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html

‎element_array_ephys/ephys_acute.py

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Args:
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ephys_schema_name (str): A string containing the name of the ephys schema.
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probe_schema_name (str): A string containing the name of the probe scehma.
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probe_schema_name (str): A string containing the name of the probe schema.
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create_schema (bool): If True, schema will be created in the database.
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create_tables (bool): If True, tables related to the schema will be created in the database.
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linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.

‎element_array_ephys/ephys_chronic.py

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Args:
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ephys_schema_name (str): A string containing the name of the ephys schema.
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probe_schema_name (str): A string containing the name of the probe scehma.
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probe_schema_name (str): A string containing the name of the probe schema.
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create_schema (bool): If True, schema will be created in the database.
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create_tables (bool): If True, tables related to the schema will be created in the database.
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linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.

‎element_array_ephys/ephys_no_curation.py

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Args:
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ephys_schema_name (str): A string containing the name of the ephys schema.
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probe_schema_name (str): A string containing the name of the probe scehma.
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probe_schema_name (str): A string containing the name of the probe schema.
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create_schema (bool): If True, schema will be created in the database.
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create_tables (bool): If True, tables related to the schema will be created in the database.
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linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.

‎element_array_ephys/ephys_precluster.py

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Args:
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ephys_schema_name (str): A string containing the name of the ephys schema.
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probe_schema_name (str): A string containing the name of the probe scehma.
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probe_schema_name (str): A string containing the name of the probe schema.
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create_schema (bool): If True, schema will be created in the database.
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create_tables (bool): If True, tables related to the schema will be created in the database.
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linking_module (str): A string containing the module name or module containing the required dependencies to activate the schema.
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@schema
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class PreClusterTask(dj.Manual):
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"""Defines a pre-clusting task ready to be run.
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"""Defines a pre-clustering task ready to be run.
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Attributes:
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EphysRecording (foreign key): EphysRecording primary key.

‎element_array_ephys/plotting/qc.py

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key (dict, optional): key from ephys.QualityMetric table. Defaults to None.
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scale (float, optional): Scale at which to render figure. Defaults to 1.4.
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fig_width (int, optional): Figure width in pixels. Defaults to 800.
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amplitude_cutoff_maximum (float, optional): Cutoff for unit ampliude in
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amplitude_cutoff_maximum (float, optional): Cutoff for unit amplitude in
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visualizations. Defaults to None.
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presence_ratio_minimum (float, optional): Cutoff for presence ratio in
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visualizations. Defaults to None.
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def key(self, key: dict):
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"""Use class_instance.key = your_key to reset key"""
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if key not in self._ephys.QualityMetrics.fetch("KEY"):
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# If not already full key, check if unquely identifies entry
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# If not already full key, check if uniquely identifies entry
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key = (self._ephys.QualityMetrics & key).fetch1("KEY")
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self._key = key
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def _format_fig(
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self, fig: go.Figure = None, scale: float = None, ratio: float = 1.0
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) -> go.Figure:
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"""Return formatted figure or apply prmatting to existing figure
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"""Return formatted figure or apply formatting to existing figure
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fig (go.Figure, optional): Apply formatting to this plotly graph object
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"""Plot grid of histograms as subplots in go.Figure using n_columns
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n_columns (int, optional): Number of colums in grid. Defaults to 4.
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n_columns (int, optional): Number of column in grid. Defaults to 4.
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scale (float, optional): Scale to render fig. Defaults to scale at class
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init, 1.
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@property
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def plot_list(self):
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"""List of plots that can be rendered inidividually by name or as grid"""
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"""List of plots that can be rendered individually by name or as grid"""
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if not self._plots:
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_ = self.plots
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return [plot for plot in self._plots]

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