add mdformat-mkdocs

.pre-commit-config.yaml

@@ -13,6 +13,7 @@ repos:
         types: [markdown]
         args: [--wrap, "80", --number]
         additional_dependencies:
+          - mdformat-mkdocs
           - mdformat-toc
           - mdformat-beautysh
           - mdformat-config

CHANGELOG.md

@@ -26,17 +26,17 @@
 ### Pipelines
 
 - Common:
-  - Added support multiple cameras per epoch. #557
-  - Removed `common_backup` schema. #631
-  - Added support for multiple position objects per NWB in `common_behav` via
-    PositionSource.SpatialSeries and RawPosition.PosObject #628, #616. _Note:_
-    Existing functions have been made compatible, but column labels for
-    `RawPosition.fetch1_dataframe` may change.
+    - Added support multiple cameras per epoch. #557
+    - Removed `common_backup` schema. #631
+    - Added support for multiple position objects per NWB in `common_behav` via
+        PositionSource.SpatialSeries and RawPosition.PosObject #628, #616. _Note:_
+        Existing functions have been made compatible, but column labels for
+        `RawPosition.fetch1_dataframe` may change.
 - Spike sorting:
-  - Added pipeline populator. #637, #646, #647
-  - Fixed curation functionality for `nn_isolation`. #597, #598
+    - Added pipeline populator. #637, #646, #647
+    - Fixed curation functionality for `nn_isolation`. #597, #598
 - Position: Added position interval/epoch mapping via PositionIntervalMap. #620,
-  #621, #627
+    #621, #627
 - LFP: Refactored pipeline. #594, #588, #605, #606, #607, #608, #615, #629
 
 ## [0.4.1] (June 30, 2023)
@@ -47,41 +47,41 @@
 ## [0.4.0] (May 22, 2023)
 
 - Updated call to `spikeinterface.preprocessing.whiten` to use dtype np.float16.
-  #446,
+    #446,
 - Updated default spike sorting metric parameters. #447
 - Updated whitening to be compatible with recent changes in spikeinterface when
-  using mountainsort. #449
+    using mountainsort. #449
 - Moved LFP pipeline to `src/spyglass/lfp/v1` and addressed related usability
-  issues. #468, #478, #482, #484, #504
+    issues. #468, #478, #482, #484, #504
 - Removed whiten parameter for clusterless thresholder. #454
 - Added plot to plot all DIO events in a session. #457
 - Added file sharing functionality through kachery_cloud. #458, #460
 - Pinned numpy version to `numpy<1.24`
 - Added scripts to add guests and collaborators as users. #463
 - Cleaned up installation instructions in repo README. #467
 - Added checks in decoding visualization to ensure time dimensions are the
-  correct length.
+    correct length.
 - Fixed artifact removed valid times. #472
 - Added codespell workflow for spell checking and fixed typos. #471
 - Updated LFP code to save LFP as `pynwb.ecephys.LFP` type. #475
 - Added artifact detection to LFP pipeline. #473
 - Replaced calls to `spikeinterface.sorters.get_default_params` with
-  `spikeinterface.sorters.get_default_sorter_params`. #486
+    `spikeinterface.sorters.get_default_sorter_params`. #486
 - Updated position pipeline and added functionality to handle pose estimation
-  through DeepLabCut. #367, #505
+    through DeepLabCut. #367, #505
 - Updated `environment_position.yml`. #502
 - Renamed `FirFilter` class to `FirFilterParameters`. #512
 
 ## [0.3.4] (March 30, 2023)
 
 - Fixed error in spike sorting pipeline referencing the "probe_type" column
-  which is no longer accessible from the `Electrode` table. #437
+    which is no longer accessible from the `Electrode` table. #437
 - Fixed error when inserting an NWB file that does not have a probe
-  manufacturer. #433, #436
+    manufacturer. #433, #436
 - Fixed error when adding a new `DataAcquisitionDevice` and a new `ProbeType`.
-  #436
+    #436
 - Fixed inconsistency between capitalized/uncapitalized versions of "Intan" for
-  DataAcquisitionAmplifier and DataAcquisitionDevice.adc_circuit. #430, #438
+    DataAcquisitionAmplifier and DataAcquisitionDevice.adc_circuit. #430, #438
 
 ## [0.3.3] (March 29, 2023)
 

docs/README.md

@@ -6,7 +6,7 @@
 section of this file. New pages should be either:
 
 1. A markdown file in the `docs/` directory.
-2. A Jupyter notebook in the `notebooks/` directory.
+1. A Jupyter notebook in the `notebooks/` directory.
 
 The remainder of `mkdocs.yml` specifies the site's
 [configuration](https://www.mkdocs.org/user-guide/configuration/)

docs/src/contribute.md

@@ -17,20 +17,20 @@ for features that will involve multiple contributors.
 
 - Tables are grouped into schemas by topic (e.g., `common_metrics`)
 - Schemas
-  - Are defined in a `py` pile.
-  - Correspond to MySQL 'databases'.
-  - Are organized into modules (e.g., `common`) by folders.
+    - Are defined in a `py` pile.
+    - Correspond to MySQL 'databases'.
+    - Are organized into modules (e.g., `common`) by folders.
 - The _common_ module
-  - In principle, contains schema that are shared across all projects.
-  - In practice, contains shared tables (e.g., Session) and the first draft of
-    schemas that have since been split into their own modality-specific\
-    modules
-    (e.g., `lfp`)
-  - Should not be added to without discussion.
+    - In principle, contains schema that are shared across all projects.
+    - In practice, contains shared tables (e.g., Session) and the first draft of
+        schemas that have since been split into their own
+        modality-specific\
+        modules (e.g., `lfp`)
+    - Should not be added to without discussion.
 - A pipeline
-  - Refers to a set of tables used for processing data of a particular modality
-    (e.g., LFP, spike sorting, position tracking).
-  - May span multiple schema.
+    - Refers to a set of tables used for processing data of a particular modality
+        (e.g., LFP, spike sorting, position tracking).
+    - May span multiple schema.
 - For analysis that will be only useful to you, create your own schema.
 
 ## Types of tables
@@ -54,7 +54,7 @@ Tables shared across multiple pipelines for shared data types.
 - Naming convention: None
 - Data tier: `dj.Manual`
 - Examples: `IntervalList` (time interval for any analysis), `AnalysisNwbfile`
-  (analysis NWB files)
+    (analysis NWB files)
 
 _Note_: Because these are stand-alone tables not part of the dependency
 structure, developers should include enough information to link entries back to
@@ -72,8 +72,8 @@ should be included in the `make` method of `Session`.
 - Non-primary key: `object_id`, the unique hash of an object in the NWB file.
 - Examples: `Raw`, `Institution`, etc.
 - Required methods:
-  - `make`: must read information from an NWB file and insert it to the table.
-  - `fetch_nwb`: retrieve the data specified by the object ID.
+    - `make`: must read information from an NWB file and insert it to the table.
+    - `fetch_nwb`: retrieve the data specified by the object ID.
 
 ### Parameters
 
@@ -99,8 +99,8 @@ session.
 - Naming convention: end with `Selection`
 - Data tier: `dj.Manual`
 - Primary key(s): Foreign key references to
-  - one or more NWB or data tables
-  - optionally, one or more parameter tables
+    - one or more NWB or data tables
+    - optionally, one or more parameter tables
 - Non-primary key: None
 - Examples: `MetricSelection`, `LFPSElection`
 
@@ -119,16 +119,17 @@ method that carries out the computation specified in the Selection table when
 - Data tier: `dj.Computed`
 - Primary key: Foreign key reference to a Selection table.
 - Non-primary key: `analysis_file_name` inherited from `AnalysisNwbfile` table
-  (i.e., name of the analysis NWB file that will hold the output of the
-  computation).
+    (i.e., name of the analysis NWB file that will hold the output of the
+    computation).
 - Required methods:
-  - `make`: carries out the computation and insert a new entry; must also create
-    an analysis NWB file and insert it to the `AnalysisNwbfile` table. Note that
-    this method is never called directly; it is called via `populate`. Multiple
-    entries can be run in parallel when called with `reserve_jobs=True`.
-  - `delete`: extension of the `delete` method that checks user privilege before
-    deleting entries as a way to prevent accidental deletion of computations
-    that take a long time (see below).
+    - `make`: carries out the computation and insert a new entry; must also create
+        an analysis NWB file and insert it to the `AnalysisNwbfile` table. Note
+        that this method is never called directly; it is called via `populate`.
+        Multiple entries can be run in parallel when called with
+        `reserve_jobs=True`.
+    - `delete`: extension of the `delete` method that checks user privilege before
+        deleting entries as a way to prevent accidental deletion of computations
+        that take a long time (see below).
 - Example: `QualityMetrics`, `LFPV1`
 
 ### Merge
@@ -154,28 +155,28 @@ all analyses.
 
 - Naming: `{animal name}YYYYMMDD.nwb`
 - Storage:
-  - On disk, directory identified by `settings.py` as `raw_dir` (e.g.,
-    `/stelmo/nwb/raw`)
-  - In database, in the `Nwbfile` table
+    - On disk, directory identified by `settings.py` as `raw_dir` (e.g.,
+        `/stelmo/nwb/raw`)
+    - In database, in the `Nwbfile` table
 - Copies:
-  - made with an underscore `{animal name}YYYYMMDD_.nwb`
-  - stored in the same `raw_dir`
-  - contain pointers to objects in original file
-  - permit adding new parts to the NWB file without risk of corrupting the
-    original data
+    - made with an underscore `{animal name}YYYYMMDD_.nwb`
+    - stored in the same `raw_dir`
+    - contain pointers to objects in original file
+    - permit adding new parts to the NWB file without risk of corrupting the
+        original data
 
 ### Analysis files
 
 Hold the results of intermediate steps in the analysis.
 
 - Naming: `{animal name}YYYYMMDD_{10-character random string}.nwb`
 - Storage:
-  - On disk, directory identified by `settings.py` as `analysis_dir` (e.g.,
-    `/stelmo/nwb/analysis`). Items are further sorted into folders matching
-    original NWB file name
-  - In database, in the `AnalysisNwbfile` table.
+    - On disk, directory identified by `settings.py` as `analysis_dir` (e.g.,
+        `/stelmo/nwb/analysis`). Items are further sorted into folders matching
+        original NWB file name
+    - In database, in the `AnalysisNwbfile` table.
 - Examples: filtered recordings, spike times of putative units after sorting, or
-  waveform snippets.
+    waveform snippets.
 
 _Note_: Because NWB files and analysis files exist both on disk and listed in
 tables, these can become out of sync. You can 'equalize' the database table
@@ -194,16 +195,16 @@ HDF5 format. This duplication should be resolved in the future.
 The following objects should be uniquely named.
 
 - _Recordings_: Underscore-separated concatenations of uniquely defining
-  features,
-  `NWBFileName_IntervalName_ElectrodeGroupName_PreprocessingParamsName`.
+    features,
+    `NWBFileName_IntervalName_ElectrodeGroupName_PreprocessingParamsName`.
 - _SpikeSorting_: Adds `SpikeSorter_SorterParamName` to the name of the
-  recording.
+    recording.
 - _Waveforms_: Adds `_WaveformParamName` to the name of the sorting.
 - _Quality metrics_: Adds `_MetricParamName` to the name of the waveform.
 - _Analysis NWB files_:
-  `NWBFileName_IntervalName_ElectrodeGroupName_PreprocessingParamsName.nwb`
+    `NWBFileName_IntervalName_ElectrodeGroupName_PreprocessingParamsName.nwb`
 - Each recording and sorting is given truncated UUID strings as part of
-  concatenations.
+    concatenations.
 
 Following broader Python conventions, methods a method that will not be
 explicitly called by the user should start with `_`
@@ -217,35 +218,35 @@ faulty connection.
 
 - Intervals can be nested for a set of disjoint intervals.
 - Some recordings have explicit
-  [PTP timestamps](https://en.wikipedia.org/wiki/Precision_Time_Protocol)
-  associated with each sample. Some older recordings are missing PTP times, and
-  times must be inferred from the TTL pulses from the camera.
+    [PTP timestamps](https://en.wikipedia.org/wiki/Precision_Time_Protocol)
+    associated with each sample. Some older recordings are missing PTP times,
+    and times must be inferred from the TTL pulses from the camera.
 
 ## Misc
 
 - During development, we suggest using a Docker container. See
-  [example](./notebooks/00_Setup.ipynb).
+    [example](./notebooks/00_Setup.ipynb).
 - DataJoint is unable to set delete permissions on a per-table basis. If a user
-  is able to delete entries in a given table, she can delete entries in any
-  table in the schema. The `SpikeSorting` table extends the built-in `delete`
-  method to check if the username matches a list of allowed users when `delete`
-  is called. Issues #226 and #586 track the progress of generalizing this
-  feature.
+    is able to delete entries in a given table, she can delete entries in any
+    table in the schema. The `SpikeSorting` table extends the built-in `delete`
+    method to check if the username matches a list of allowed users when
+    `delete` is called. Issues #226 and #586 track the progress of generalizing
+    this feature.
 - `numpy` style docstrings will be interpreted by API docs. To check for
-  compliance, monitor the std out when building docs (see `docs/README.md`)
+    compliance, monitor the std out when building docs (see `docs/README.md`)
 - `fetch_nwb` is currently reperated across many tables. For progress on a fix,
-  follow issue #530
+    follow issue #530
 
 ## Making a release
 
 Spyglass follows [Semantic Versioning](https://semver.org/) with versioning of
 the form `X.Y.Z` (e.g., `0.4.2`).
 
 1. In `CITATION.cff`, update the `version` key.
-2. Make a pull request with changes.
-3. After the pull request is merged, pull this merge commit and tag it with
-   `git tag {version}`
-4. Publish the new release tag. Run `git push origin {version}`. This will
-   rebuild docs and push updates to PyPI.
-5. Make a new
-   [release on GitHub](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository).
+1. Make a pull request with changes.
+1. After the pull request is merged, pull this merge commit and tag it with
+    `git tag {version}`
+1. Publish the new release tag. Run `git push origin {version}`. This will
+    rebuild docs and push updates to PyPI.
+1. Make a new
+    [release on GitHub](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository).

docs/src/misc/database_management.md

@@ -34,7 +34,7 @@ schema/database prefix.
 
 - `SELECT` privileges allow users to read, write, and delete data.
 - `ALL` privileges allow users to create, alter, or drop tables and schemas in
-  addition to operations above.
+    addition to operations above.
 
 In practice, DataJoint only permits alerations of secondary keys on existing
 tables, and more derstructive operations would require using DataJoint to
@@ -76,7 +76,7 @@ migrate the contents to another server. Some conventions to note:
 - `.host`: files used in the host's context
 - `.container`: files used inside the database Docker container
 - `.env`: files used to set environment variables used by the scripts for
-  database name, backup name, and backup credentials
+    database name, backup name, and backup credentials
 
 ### mysql.env.host