Add quotes in the conversion gallery installation (#956)

Co-authored-by: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
catalystneuro · Jul 11, 2024 · 5986a72 · 5986a72
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diff --git a/dockerfiles/neuroconv_latest_release_dockerfile b/dockerfiles/neuroconv_latest_release_dockerfile
@@ -2,5 +2,5 @@ FROM python:3.11.7-slim
 LABEL org.opencontainers.image.source=https://github.com/catalystneuro/neuroconv
 LABEL org.opencontainers.image.description="A docker image for the most recent official release of the NeuroConv package."
 RUN apt update && apt install musl-dev python3-dev -y
-RUN pip install neuroconv[full]
+RUN pip install "neuroconv[full]"
 CMD ["python -m"]
diff --git a/docs/conversion_examples_gallery/behavior/audio.rst b/docs/conversion_examples_gallery/behavior/audio.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading audio d
 
 .. code-block:: bash
 
-    pip install neuroconv[audio]
+    pip install "neuroconv[audio]"
 
 This interface can handle conversions from `WAV` format to NWB using the
 :py:class:`~neuroconv.datainterfaces.behavior.audio.audiointerface.AudioInterface` class.

diff --git a/docs/conversion_examples_gallery/behavior/deeplabcut.rst b/docs/conversion_examples_gallery/behavior/deeplabcut.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading DeepLab
 
 .. code-block:: bash
 
-    pip install neuroconv[deeplabcut]
+    pip install "neuroconv[deeplabcut]"
 
 Convert DeepLabCut pose estimation data to NWB using :py:class:`~neuroconv.datainterfaces.behavior.deeplabcut.deeplabcutdatainterface.DeepLabCutInterface`.
 

diff --git a/docs/conversion_examples_gallery/behavior/fictrac.rst b/docs/conversion_examples_gallery/behavior/fictrac.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading `FicTra
 
 .. code-block:: bash
 
-    pip install neuroconv[fictrac]
+    pip install "neuroconv[fictrac]"
 
 Convert FicTrac spherical motion and fictive animal path data in a FicTrac ``.dat`` file to NWB using :py:class:`~neuroconv.datainterfaces.behavior.fictrac.fictracdatainterface.FicTracDataInterface`.
 

diff --git a/docs/conversion_examples_gallery/behavior/lightningpose.rst b/docs/conversion_examples_gallery/behavior/lightningpose.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Lightni
 
 .. code-block:: bash
 
-    pip install neuroconv[lightningpose]
+    pip install "neuroconv[lightningpose]"
 
 Convert LightningPose pose estimation data to NWB using :py:class:`~neuroconv.datainterfaces.behavior.lightningpose.lightningposeconverter.LightningPoseConverter`.
 

diff --git a/docs/conversion_examples_gallery/behavior/sleap.rst b/docs/conversion_examples_gallery/behavior/sleap.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading SLEAP d
 
 .. code-block:: bash
 
-    pip install neuroconv[sleap]
+    pip install "neuroconv[sleap]"
 
 Convert SLEAP pose estimation data to NWB using :py:class:`~neuroconv.datainterfaces.behavior.sleap.sleapdatainterface.SLEAPInterface`.
 

diff --git a/docs/conversion_examples_gallery/behavior/video.rst b/docs/conversion_examples_gallery/behavior/video.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading multime
 
 .. code-block:: bash
 
-    pip install neuroconv[video]
+    pip install "neuroconv[video]"
 
 This interface can handle conversions from avi, mov, mp4, wmv, flv and most FFmpeg_ supported formats to NWB using the
 :py:class:`~neuroconv.datainterfaces.behavior.video.videodatainterface.VideoInterface` class.

diff --git a/docs/conversion_examples_gallery/imaging/brukertiff.rst b/docs/conversion_examples_gallery/imaging/brukertiff.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Bruker
 
 .. code-block:: bash
 
-    pip install neuroconv[brukertiff]
+    pip install "neuroconv[brukertiff]"
 
 **Convert single imaging plane**
 

diff --git a/docs/conversion_examples_gallery/imaging/hdf5imaging.rst b/docs/conversion_examples_gallery/imaging/hdf5imaging.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading HDF5 da
 
 .. code-block:: bash
 
-    pip install neuroconv[hdf5]
+    pip install "neuroconv[hdf5]"
 
 Convert HDF5 imaging data to NWB using :py:class:`~neuroconv.datainterfaces.ophys.hdf5.hdf5datainterface.Hdf5ImagingInterface`.
 

diff --git a/docs/conversion_examples_gallery/imaging/micromanagertiff.rst b/docs/conversion_examples_gallery/imaging/micromanagertiff.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Micro-M
 
 .. code-block:: bash
 
-    pip install neuroconv[micromanagertiff]
+    pip install "neuroconv[micromanagertiff]"
 
 Convert Micro-Manager TIFF imaging data to NWB using
 :py:class:`~neuroconv.datainterfaces.ophys.micromanagertiff.micromanagertiffdatainterface.MicroManagerTiffImagingInterface`.

diff --git a/docs/conversion_examples_gallery/imaging/miniscope.rst b/docs/conversion_examples_gallery/imaging/miniscope.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Minisco
 
 .. code-block:: bash
 
-    pip install neuroconv[miniscope]
+    pip install "neuroconv[miniscope]"
 
 Miniscope simultaneously records optical physiology and behavior in the form of video data.
 The :py:class:`~neuroconv.datainterfaces.ophys.miniscope.miniscopeconverter.MiniscopeConverter` combines the two data streams

diff --git a/docs/conversion_examples_gallery/imaging/scanbox.rst b/docs/conversion_examples_gallery/imaging/scanbox.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Scanbox
 
 .. code-block:: bash
 
-    pip install neuroconv[scanbox]
+    pip install"neuroconv[scanbox]"
 
 Convert Scanbox imaging data to NWB using
 :py:class:`~neuroconv.datainterfaces.ophys.sbx.sbxdatainterface.SbxImagingInterface`.

diff --git a/docs/conversion_examples_gallery/imaging/scanimage.rst b/docs/conversion_examples_gallery/imaging/scanimage.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading ScanIma
 
 .. code-block:: bash
 
-    pip install neuroconv[scanimage]
+    pip install "neuroconv[scanimage]"
 
 Convert single plane single file imaging data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/docs/conversion_examples_gallery/imaging/tiff.rst b/docs/conversion_examples_gallery/imaging/tiff.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading TIFF da
 
 .. code-block:: bash
 
-    pip install neuroconv[tiff]
+    pip install "neuroconv[tiff]"
 
 Convert TIFF imaging data to NWB using
 :py:class:`~neuroconv.datainterfaces.ophys.tiff.tiffdatainterface.TiffImagingInterface`.

diff --git a/docs/conversion_examples_gallery/recording/abf.rst b/docs/conversion_examples_gallery/recording/abf.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading ABF dat
 
 .. code-block:: bash
 
-    pip install neuroconv[abf]
+    pip install "neuroconv[abf]"
 
 Convert ABF intracellular electrophysiology data to NWB using :py:class:`~neuroconv.datainterfaces.icephys.abf.abfdatainterface.AbfInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/alphaomega.rst b/docs/conversion_examples_gallery/recording/alphaomega.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading AlphaOm
 
 .. code-block:: bash
 
-    pip install neuroconv[alphaomega]
+    pip install "neuroconv[alphaomega]"
 
 Convert AlphaOmega data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.alphaomega.alphaomegadatainterface.AlphaOmegaRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/axona.rst b/docs/conversion_examples_gallery/recording/axona.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Axona d
 
 .. code-block:: bash
 
-    pip install neuroconv[axona]
+    pip install "neuroconv[axona]"
 
 Convert axona data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.axona.axonadatainterface.AxonaRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/biocam.rst b/docs/conversion_examples_gallery/recording/biocam.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Biocam
 
 .. code-block:: bash
 
-    pip install neuroconv[biocam]
+    pip install "neuroconv[biocam]"
 
 Convert Biocam data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.biocam.biocamdatainterface.BiocamRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/blackrock.rst b/docs/conversion_examples_gallery/recording/blackrock.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Blackro
 
 .. code-block:: bash
 
-    pip install neuroconv[blackrock]
+    pip install "neuroconv[blackrock]"
 
 Convert Blackrock data to NWB using
 :py:class:`~neuroconv.datainterfaces.ecephys.blackrock.blackrockdatainterface.BlackrockRecordingInterface`.

diff --git a/docs/conversion_examples_gallery/recording/edf.rst b/docs/conversion_examples_gallery/recording/edf.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading EDF dat
 
 .. code-block:: bash
 
-    pip install neuroconv[edf]
+    pip install "neuroconv[edf]"
 
 Convert edf data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.edf.edfdatainterface.EDFRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/intan.rst b/docs/conversion_examples_gallery/recording/intan.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Intan d
 
 .. code-block:: bash
 
-    pip install neuroconv[intan]
+    pip install "neuroconv[intan]"
 
 Convert Intan data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.intan.intandatainterface.IntanRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/maxone.rst b/docs/conversion_examples_gallery/recording/maxone.rst
@@ -9,7 +9,7 @@ Install NeuroConv with the additional dependencies necessary for reading MaxOne
 
 .. code-block:: bash
 
-    pip install neuroconv[maxwell]
+    pip install "neuroconv[maxwell]"
 
 Convert MaxOne data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.maxwell.maxonedatainterface.MaxOneRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/mcsraw.rst b/docs/conversion_examples_gallery/recording/mcsraw.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading MCSRaw
 
 .. code-block:: bash
 
-    pip install neuroconv[mcsraw]
+    pip install "neuroconv[mcsraw]"
 
 Convert MCSRaw data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.mcsraw.mcsrawdatainterface.MCSRawRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/mearec.rst b/docs/conversion_examples_gallery/recording/mearec.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading MEArec
 
 .. code-block:: bash
 
-    pip install neuroconv[mearec]
+    pip install "neuroconv[mearec]"
 
 Convert MEArec data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.mearec.mearecdatainterface.MEArecRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/neuralynx.rst b/docs/conversion_examples_gallery/recording/neuralynx.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Neuraly
 
 .. code-block:: bash
 
-    pip install neuroconv[neuralynx]
+    pip install "neuroconv[neuralynx]"
 
 Convert Neuralynx data to NWB using
 :py:class:`~.neuroconv.datainterfaces.ecephys.neuralynx.neuralynxdatainterface.NeuralynxRecordingInterface`.

diff --git a/docs/conversion_examples_gallery/recording/neuroscope.rst b/docs/conversion_examples_gallery/recording/neuroscope.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading NeuroSc
 
 .. code-block:: bash
 
-    pip install neuroconv[neuroscope]
+    pip install "neuroconv[neuroscope]"
 
 Convert NeuroScope data to NWB using
 :py:class:`~neuroconv.datainterfaces.ecephys.neuroscope.neuroscopedatainterface.NeuroScopeRecordingInterface`.

diff --git a/docs/conversion_examples_gallery/recording/openephys.rst b/docs/conversion_examples_gallery/recording/openephys.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading OpenEph
 
 .. code-block:: bash
 
-    pip install neuroconv[openephys]
+    pip install "neuroconv[openephys]"
 
 Convert OpenEphys data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.openephys.openephysdatainterface.OpenEphysRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/recording/plexon.rst b/docs/conversion_examples_gallery/recording/plexon.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Plexon
 
 .. code-block:: bash
 
-    pip install neuroconv[plexon]
+    pip install "neuroconv[plexon]"
 
 Convert Plexon recording data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.plexon.plexondatainterface.PlexonRecordingInterface`. Currently, only .plx is supported.
 

diff --git a/docs/conversion_examples_gallery/recording/spike2.rst b/docs/conversion_examples_gallery/recording/spike2.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Spike2
 
 .. code-block:: bash
 
-    pip install neuroconv[spike2]
+    pip install "neuroconv[spike2]"
 
 Convert Spike2 data to NWB using
 :py:class:`~neuroconv.datainterfaces.ecephys.spike2.spike2datainterface.Spike2RecordingInterface`.

diff --git a/docs/conversion_examples_gallery/recording/spikegadgets.rst b/docs/conversion_examples_gallery/recording/spikegadgets.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Spikega
 
 .. code-block:: bash
 
-    pip install neuroconv[spikegadgets]
+    pip install "neuroconv[spikegadgets]"
 
 Convert spikegadgets data to NWB using
 :py:class:`~neuroconv.datainterfaces.ecephys.spikegadgets.spikegadgetsdatainterface.SpikeGadgetsRecordingInterface`.

diff --git a/docs/conversion_examples_gallery/recording/spikeglx.rst b/docs/conversion_examples_gallery/recording/spikeglx.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading SpikeGL
 
 .. code-block:: bash
 
-    pip install neuroconv[spikeglx]
+    pip install "neuroconv[spikeglx]"
 
 
 

diff --git a/docs/conversion_examples_gallery/recording/tdt.rst b/docs/conversion_examples_gallery/recording/tdt.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading TDT dat
 
 .. code-block:: bash
 
-    pip install neuroconv[tdt]
+    pip install "neuroconv[tdt]"
 
 Convert TDT data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.tdt.tdtdatainterface.TdtRecordingInterface`.
 

diff --git a/docs/conversion_examples_gallery/segmentation/caiman.rst b/docs/conversion_examples_gallery/segmentation/caiman.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading CaImAn
 
 .. code-block:: bash
 
-    pip install neuroconv[caiman]
+    pip install "neuroconv[caiman]"
 
 Convert CaImAn segmentation data to NWB using :py:class:`~neuroconv.datainterfaces.ophys.caiman.caimandatainterface.CaimanSegmentationInterface`.
 

diff --git a/docs/conversion_examples_gallery/segmentation/cnmfe.rst b/docs/conversion_examples_gallery/segmentation/cnmfe.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading CNMF-E
 
 .. code-block:: bash
 
-    pip install neuroconv[cnmfe]
+    pip install "neuroconv[cnmfe]"
 
 Convert CNMFE segmentation data to NWB using :py:class:`~neuroconv.datainterfaces.ophys.cnmfe.cnmfedatainterface.CnmfeSegmentationInterface`.
 

diff --git a/docs/conversion_examples_gallery/segmentation/extract.rst b/docs/conversion_examples_gallery/segmentation/extract.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading EXTRACT
 
 .. code-block:: bash
 
-    pip install neuroconv[extract]
+    pip install "neuroconv[extract]"
 
 Convert EXTRACT segmentation data to NWB using :py:class:`~neuroconv.datainterfaces.ophys.extract.extractdatainterface.ExtractSegmentationInterface`.
 

diff --git a/docs/conversion_examples_gallery/segmentation/suite2p.rst b/docs/conversion_examples_gallery/segmentation/suite2p.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading suite2p
 
 .. code-block:: bash
 
-    pip install neuroconv[suite2p]
+    pip install "neuroconv[suite2p]"
 
 Convert suite2p segmentation data to NWB using
 :py:class:`~neuroconv.datainterfaces.ophys.suite2p.suite2pdatainterface.Suite2pSegmentationInterface`.

diff --git a/docs/conversion_examples_gallery/sorting/blackrock.rst b/docs/conversion_examples_gallery/sorting/blackrock.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Blackro
 
 .. code-block:: bash
 
-    pip install neuroconv[blackrock]
+    pip install "neuroconv[blackrock]"
 
 Convert Blackrock sorting data to NWB using
 :py:class:`~neuroconv.datainterfaces.ecephys.blackrock.blackrockdatainterface.BlackrockSortingInterface`.

diff --git a/docs/conversion_examples_gallery/sorting/cellexplorer.rst b/docs/conversion_examples_gallery/sorting/cellexplorer.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading CellExp
 
 .. code-block:: bash
 
-    pip install neuroconv[cellexplorer]
+    pip install "neuroconv[cellexplorer]"
 
 Convert CellExplorer sorting data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.cellexplorer.cellexplorerdatainterface.CellExplorerSortingInterface`.
 

diff --git a/docs/conversion_examples_gallery/sorting/kilosort.rst b/docs/conversion_examples_gallery/sorting/kilosort.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading kilosor
 
 .. code-block:: bash
 
-    pip install neuroconv[kilosort]
+    pip install "neuroconv[kilosort]"
 
 Convert KiloSort data to NWB using
 :py:class:`~neuroconv.datainterfaces.ecephys.kilosort.kilosortdatainterface.KiloSortSortingInterface`.

diff --git a/docs/conversion_examples_gallery/sorting/neuralynx.rst b/docs/conversion_examples_gallery/sorting/neuralynx.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading neuraly
 
 .. code-block:: bash
 
-    pip install neuroconv[neuralynx]
+    pip install "neuroconv[neuralynx]"
 
 Convert Neuralynx data to NWB using
 :py:class:`~neuroconv.datainterfaces.ecephys.neuralynx.neuralynxdatainterface.NeuralynxSortingInterface`.

diff --git a/docs/conversion_examples_gallery/sorting/neuroscope.rst b/docs/conversion_examples_gallery/sorting/neuroscope.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading neurosc
 
 .. code-block:: bash
 
-    pip install neuroconv[neuroscope]
+    pip install "neuroconv[neuroscope]"
 
 Convert NeuroScope sorting data to NWB using
 :py:class:`~neuroconv.datainterfaces.ecephys.neuroscope.neuroscopedatainterface.NeuroScopeSortingInterface`.

diff --git a/docs/conversion_examples_gallery/sorting/phy.rst b/docs/conversion_examples_gallery/sorting/phy.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Phy dat
 
 .. code-block:: bash
 
-    pip install neuroconv[phy]
+    pip install "neuroconv[phy]"
 
 Convert Phy data to NWB using :py:class:`~.neuroconv.datainterfaces.ecephys.phy.phydatainterface.PhySortingInterface`.
 

diff --git a/docs/conversion_examples_gallery/sorting/plexon.rst b/docs/conversion_examples_gallery/sorting/plexon.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Plexon
 
 .. code-block:: bash
 
-    pip install neuroconv[plexon]
+    pip install "neuroconv[plexon]"
 
 Convert Plexon spiking data (.plx) to NWB using :py:class:`~.neuroconv.datainterfaces.ecephys.plexon.plexondatainterface.PlexonSortingInterface`.
 

diff --git a/docs/conversion_examples_gallery/text/excel.rst b/docs/conversion_examples_gallery/text/excel.rst
@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading Excel d
 
 .. code-block:: bash
 
-    pip install neuroconv[excel]
+    pip install "neuroconv[excel]"
 
 Convert Excel data to NWB using
 :py:class:`~neuroconv.datainterfaces.text.excel.exceltimeintervalsinterface.ExcelTimeIntervalsInterface`.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,7 +5,7 @@ Install NeuroConv with the additional dependencies necessary for reading SpikeGL

		.. code-block:: bash

		pip install neuroconv[spikeglx]
		pip install "neuroconv[spikeglx]"



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