Project-OSmOSE · Gautzilla · Sep 23, 2025 · Sep 24, 2025 · Sep 24, 2025 · Sep 24, 2025
diff --git a/docs/source/analysis.rst b/docs/source/analysis.rst
@@ -3,12 +3,16 @@ Analysis
 
 .. _analysis:
 
+Analysis
+========
+
 .. autoclass:: osekit.public_api.analysis.Analysis
    :members:
 
-===============
-
 .. _analysis_Type:
 
+AnalysisType
+============
+
 .. autoclass:: osekit.public_api.analysis.AnalysisType
    :members:
diff --git a/docs/source/audiodata.rst b/docs/source/audiodata.rst
@@ -1,7 +1,7 @@
+.. _audiodata:
+
 AudioData
 ---------
 
-.. _audiodata:
-
 .. autoclass:: osekit.core_api.audio_data.AudioData
    :members:
diff --git a/docs/source/audiodataset.rst b/docs/source/audiodataset.rst
@@ -1,7 +1,7 @@
+.. _audiodataset:
+
 AudioDataset
 ------------
 
-.. _audiodataset:
-
 .. autoclass:: osekit.core_api.audio_dataset.AudioDataset
    :members:
diff --git a/docs/source/audiofile.rst b/docs/source/audiofile.rst
@@ -1,7 +1,7 @@
+.. _audiofile:
+
 AudioFile
 ---------
 
-.. _audiofile:
-
 .. autoclass:: osekit.core_api.audio_file.AudioFile
    :members:
diff --git a/docs/source/audiofilemanager.rst b/docs/source/audiofilemanager.rst
@@ -3,5 +3,5 @@ AudioFileManager
 
 .. _audiofilemanager:
 
-.. autoclass:: osekit.core_api.audio_file_manager.AudioFileManager
+.. autoclass:: osekit.audio_backend.audio_file_manager.AudioFileManager
    :members:
diff --git a/docs/source/audioitem.rst b/docs/source/audioitem.rst
@@ -1,7 +1,7 @@
+.. _audioitem:
+
 AudioItem
 ---------
 
-.. _audioitem:
-
 .. autoclass:: osekit.core_api.audio_item.AudioItem
    :members:
diff --git a/docs/source/basedata.rst b/docs/source/basedata.rst
@@ -1,7 +1,7 @@
+.. _basedata:
+
 BaseData
 --------
 
-.. _basedata:
-
 .. autoclass:: osekit.core_api.base_data.BaseData
    :members:
diff --git a/docs/source/basedataset.rst b/docs/source/basedataset.rst
@@ -1,7 +1,7 @@
+.. _basedataset:
+
 BaseDataset
 -----------
 
-.. _basedataset:
-
 .. autoclass:: osekit.core_api.base_dataset.BaseDataset
    :members:
diff --git a/docs/source/basefile.rst b/docs/source/basefile.rst
@@ -1,7 +1,7 @@
+.. _basefile:
+
 BaseFile
 --------
 
-.. _basefile:
-
 .. autoclass:: osekit.core_api.base_file.BaseFile
    :members:
diff --git a/docs/source/baseitem.rst b/docs/source/baseitem.rst
@@ -1,7 +1,7 @@
+.. _baseitem:
+
 BaseItem
 --------
 
-.. _baseitem:
-
 .. autoclass:: osekit.core_api.base_item.BaseItem
    :members:
diff --git a/docs/source/coreapi.rst b/docs/source/coreapi.rst
@@ -1,8 +1,8 @@
+.. _coreapi:
+
 Core API
 ----------
 
-.. _coreapi:
-
 .. toctree::
    :maxdepth: 1
 
@@ -22,4 +22,4 @@ Core API
    spectrodataset
    ltasdata
    audiofilemanager
-   frequencyscale
+   frequencyscale
diff --git a/docs/source/coreapi_home.rst b/docs/source/coreapi_home.rst
@@ -1,8 +1,8 @@
+.. _coreapi_home:
+
 Core API
 --------
 
-.. _coreapi_home:
-
 For an introduction to how **OSEkit** works, please refer to the :ref:`introduction section <coreapi_introduction>`.
 
 For a tutorial on how to use **OSEkit**'s ``Core API``, please refer to the :ref:`usage section <coreapi_usage>`.
@@ -11,4 +11,4 @@ For a tutorial on how to use **OSEkit**'s ``Core API``, please refer to the :ref
    :maxdepth: 1
 
    coreapi_introduction
-   coreapi_usage
+   coreapi_usage
diff --git a/docs/source/coreapi_introduction.rst b/docs/source/coreapi_introduction.rst
@@ -9,20 +9,20 @@ The audio data is decoupled from audio files: audio data can be fetched across m
 The ``Core API`` provides ways of computing and plotting spectrograms, which are also treated as time-bound data that can be joined with
 audio (or any other type of) data.
 
+.. _event:
+
 Event
 """""
 
-.. _event:
-
 The :class:`osekit.core_api.event.Event` represent anything that is time-bound: an ``Event`` has a begin and an end, which are described as `pandas Timestamps <https://pandas.pydata.org/docs/reference/api/pandas.Timestamp.html>`_.
 
 Almost every other class in **OSEkit** inherits from ``Event``.
 
+.. _data_files:
+
 Data and Files
 """"""""""""""
 
-.. _data_files:
-
 Decoupling data from files is the cornerstone of **OSEkit**'s behaviour.
 Users can define data events from any list of files without worrying of whether the data events scatter across multiple files,
 nor if it contains empty time periods between files.
@@ -52,4 +52,4 @@ are managed in bases classes:
 - :class:`osekit.core_api.base_data.BaseData` represent any **data**
 
 These base classes are then derived through inheritance to specialized classes for any data type. For example, **audio data** is manipulated through the
-:class:`osekit.core_api.audio_data.AudioData` class.
+:class:`osekit.core_api.audio_data.AudioData` class.
diff --git a/docs/source/coreapi_usage.rst b/docs/source/coreapi_usage.rst
@@ -1,8 +1,8 @@
+.. _coreapi_usage:
+
 Usage
 -----
 
-.. _coreapi_usage:
-
 Audio File
 ^^^^^^^^^^
 
@@ -164,11 +164,11 @@ requested normalization flag:
         incorrect_normalization = Normalization.RAW | Normalization.PEAK
         incorrect_normalization = Normalization.DC_REJECT | Normalization.RAW | Normalization.PEAK
 
+.. _instrument_calibration:
+
 Calibration
 """""""""""
 
-.. _instrument_calibration:
-
 The :class:`osekit.core_api.instrument.Instrument` class can be used to provide calibration info to your audio data.
 This can be used to convert raw WAV data to the recorded acoustic pressure.
 
@@ -419,11 +419,11 @@ The resulting figure presents the full-scale spectrogram at the top (from 0 to 7
 .. image:: _static/spectrograms/frequency_scale.png
 
 
+.. _ltas:
+
 LTAS Data
 ^^^^^^^^^
 
-.. _ltas:
-
 OSEkit provides the :class:`osekit.core_api.ltas_data.LTASData` class for computing and plotting LTAS (**L**\ ong-\ **T**\ erm **A**\ verage **S**\ pectrum).
 
 LTAS are suitable when a spectrum is computed over a very long time and that the spectrum matrix time dimension reach a really high value.

diff --git a/docs/source/dataset.rst b/docs/source/dataset.rst
@@ -1,7 +1,7 @@
+.. _dataset:
+
 Dataset
 -------
 
-.. _dataset:
-
 .. autoclass:: osekit.public_api.dataset.Dataset
    :members:
diff --git a/docs/source/event.rst b/docs/source/event.rst
@@ -1,7 +1,7 @@
+.. _event-api:
+
 Event
 -----
 
-.. _event:
-
 .. autoclass:: osekit.core_api.event.Event
    :members:
diff --git a/docs/source/example_ltas.rst b/docs/source/example_ltas.rst
@@ -1,8 +1,8 @@
+.. _example_ltas:
+
 Computing a Long-Term Average Spectrum
 ======================================
 
-.. _example_ltas:
-
 In this example, we want to compute a :ref:`LTAS <ltas>` of audio data over a long period of time.
 
 For the sake of the example, the audio will not actually span over a long time period, but LTASes are meant

diff --git a/docs/source/example_multiple_spectrograms.rst b/docs/source/example_multiple_spectrograms.rst
@@ -1,8 +1,8 @@
+.. _example_multiple_spectrograms:
+
 Computing multiple spectrograms (timestamped files)
 ===================================================
 
-.. _example_multiple_spectrograms:
-
 In this example, we want to export spectrograms drawn from the sample audio dataset with the following requirements:
 
 * First spectrogram starts at ``2022-09-25 22:35:15``

diff --git a/docs/source/example_multiple_spectrograms_id.rst b/docs/source/example_multiple_spectrograms_id.rst
@@ -1,8 +1,8 @@
+.. _example_multiple_spectrograms_id:
+
 Computing multiple spectrograms (ID files)
 ==========================================
 
-.. _example_multiple_spectrograms_id:
-
 In this example, we want to export spectrograms drawn from the sample audio dataset with the following requirements:
 
 * Start timestamps of the audio files are unknown

diff --git a/docs/source/example_reshaping_multiple_files.rst b/docs/source/example_reshaping_multiple_files.rst
@@ -1,8 +1,8 @@
+.. _example_reshaping_multiple_files:
+
 Reshaping multiple files
 ========================
 
-.. _example_reshaping_multiple_files:
-
 In this example, we want to export reshaped files from the sample audio dataset with the following requirements:
 
 * First file starts at ``2022-09-25 22:35:15``

diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -1,8 +1,8 @@
+.. _examples:
+
 🐳 Examples
 ===========
 
-.. _examples:
-
 This section gathers **OSEkit** jupyter notebooks that complete typical tasks.
 
 Example tasks will be completed with both the :ref:`Public <publicapi_usage>` and :ref:`Core API <coreapi_usage>` (see the :ref:`usage <usage>` section

diff --git a/docs/source/export_analysis.rst b/docs/source/export_analysis.rst
@@ -1,7 +1,7 @@
+.. _export_analysis:
+
 Export Analysis
 ---------------
 
-.. _export_analysis:
-
 .. automodule:: osekit.public_api.export_analysis
    :members:
diff --git a/docs/source/frequencyscale.rst b/docs/source/frequencyscale.rst
@@ -1,10 +1,10 @@
+.. _frequencyscale:
+
 Custom Frequency Scale
 ----------------------
 
-.. _frequencyscale:
-
 .. autoclass:: osekit.core_api.frequency_scale.Scale
    :members:
 
 .. autoclass:: osekit.core_api.frequency_scale.ScalePart
-   :members:
+   :members:
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -1,8 +1,8 @@
+.. _installation:
+
 🐳 Installation
 ===============
 
-.. _installation:
-
 To use **OSEkit**, you first need to install it using one of the following:
 
 With pip
@@ -19,6 +19,7 @@ Alternatively, you can install it with a wheel file for any of our releases:
 
     pip install osmose-x.x.x.-py3-none-any.whl
 
+.. _from-git:
 
 From Git
 --------
@@ -40,3 +41,45 @@ You can now install the package using uv from the cloned repository: ::
     uv sync
 
 This will create a virtual environment within your cloned repository and install all required dependencies for using and contributing to **OSEkit**.
+
+MSEED (MiniSEED) support
+------------------------
+
+**OSEkit** is primarily designed for standard audio formats (WAV, FLAC, OGG, etc.) used in bioacoustics workflows.
+
+Support for **MiniSEED** (.mseed) files is experimental and relies on the `ObsPy <https://docs.obspy.org/>`_ third-party library.
+
+**MiniSEED** is a seismological data format and may contain:
+
+* multiple traces
+* gaps or overlaps in time
+* inconsistent metadata
+
+For these reasons, **MiniSEED** support in **OSEkit** is provided on a best-effort basis.
+
+Installation with the mseed optional dependency
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+With pip
+""""""""
+
+::
+
+    pip install osekit[mseed]
+
+
+From Git
+""""""""
+
+Follow the same instructions as in the :ref:`From Git <from-git>` section above, but replace the uv command with:
+
+::
+
+    uv sync --extra mseed
+
+.. warning::
+
+    Installing ObsPy on Windows might be a stairway to hell.
+    If installation fails, we recommand either:
+    * Using Linux or `WSL <https://learn.microsoft.com/en-us/windows/wsl/install/>`_
+    * Converting MiniSEED files to WAV/FLAC prior to processing
diff --git a/docs/source/instrument.rst b/docs/source/instrument.rst
@@ -1,7 +1,7 @@
+.. _instrument:
+
 Instrument
 ----------
 
-.. _instrument:
-
 .. autoclass:: osekit.core_api.instrument.Instrument
    :members:
diff --git a/docs/source/job.rst b/docs/source/job.rst
@@ -1,7 +1,7 @@
+.. _job:
+
 Job
 ---
 
-.. _job:
-
 .. automodule:: osekit.utils.job
     :members: JobConfig, JobBuilder, Job