.github/pull_request_template.md

@@ -1,4 +1,4 @@
 * [ ] fix #(issue number)
 * [ ] description of feature/fix
 * [ ] tests added/passed
-* [ ] add an entry to the [latest changes](../docs/changes/latest.inc)
+* [ ] add an entry for the latest changes

.github/workflows/docs-preview.yml

@@ -22,6 +22,7 @@ jobs:
     - name: Checkout source
       uses: actions/checkout@v3
       with:
+        fetch-depth: 0
         submodules: true
     - name: Set up Python 3.10
       uses: actions/setup-python@v4

docs/Makefile

@@ -12,16 +12,34 @@ BUILDDIR      ?= _build
 help:
 	@$(SPHINXBUILD) --help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+.PHONY: help Makefile clean local news _build_local _html
 
 clean:
 	rm -rf $(BUILDDIR)/*
 	rm -rf auto_examples/
 
 # For local build
-local:
+local: news
+	make _build_local; STATUS=$$?; make news_cleanup; exit $$STATUS
+
+news: 
+	@echo "Generating whats_new.rst"
+	cd ../ && towncrier build --keep
+
+news_cleanup:
+	@echo "Cleaning up whats_new.rst"
+	git restore --staged whats_new.rst
+	git restore whats_new.rst
+
+_build_local:
 	sphinx-build "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
+html: news
+	make _html; STATUS=$$?; make news_cleanup; exit $$STATUS
+
+_html:
+	$(SPHINXBUILD) "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS)
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile

docs/_static/css/custom.css

@@ -14,4 +14,10 @@
 #versions {
   display: none;
   overflow: hidden;
+}
+
+/* Reduce font size of "What's New" section */
+#what-s-new li,
+#what-s-new a {
+  font-size: medium;
 }

docs/changes/0.0.1.inc

@@ -1,115 +0,0 @@
-v0.0.1
-------
-
-Enhancements
-~~~~~~~~~~~~
-
-- Create the repository based on the mockup by `Fede Raimondo`_.
-
-- Implement :class:`junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber` datagrabber
-  (:gh:`52` by `Fede Raimondo`_).
-
-- Add comments to :class:`junifer.datagrabber.DataladDataGrabber` datagrabber and change to
-  use ``datalad-clone`` instead of ``datalad-install`` (:gh:`55` by `Benjamin Poldrack`_).
-
-- Add an example how to use junifer and julearn in one pipeline to extract features
-  and do machine learning (:gh:`40` by `Leonard Sasse`_, `Nicolas Nieto`_, and `Sami Hamdan`_).
-
-- Implement matrix storage in SQliteFeatureStorage (:gh:`42` by `Fede Raimondo`_).
-
-- Implement :class:`junifer.markers.FunctionalConnectivityParcels` marker for functional
-  connectivity using a parcellation (:gh:`41` by `Amir Omidvarnia`_ and `Kaustubh R. Patil`_).
-
-- Add documentation for the datagrabbers (by `Leonard Sasse`_,
-  `Nicolas Nieto`_, and `Sami Hamdan`_).
-
-- Implement coordinate register, list and load (:gh:`11` by `Fede Raimondo`_).
-
-- Add :class:`junifer.datagrabber.DataladAOMICID1000` datagrabber for AOMIC ID1000 dataset
-  including tests and creation of mock dataset for testing (:gh:`60` by `Vera Komeyer`_, `Xuan Li`_).
-
-- Add support to access other input in the data object in the ``compute`` method
-  (by `Fede Raimondo`_).
-
-- Implement :class:`junifer.markers.RSSETSMarker` marker (:gh:`51` by `Leonard Sasse`_,
-  `Nicolas Nieto`_, `Sami Hamdan`_).
-
-- Implement :class:`junifer.markers.SphereAggregation` marker (by `Fede Raimondo`_).
-
-- Implement :class:`junifer.datagrabber.DataladAOMICPIOP1` and
-  :class:`junifer.datagrabber.DataladAOMICPIOP2` datagrabbers for AOMIC PIOP1 and PIOP2 datasets
-  respectively and refactor :class:`junifer.datagrabber.DataladAOMICID1000` slightly
-  (:gh:`94` by `Leonard Sasse`_)
-
-- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladCamCANVBM` datagrabber
-  (:gh:`99` by `Leonard Sasse`_)
-
-- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladIXIVBM` CAT output
-  datagrabber for juseless (:gh:`48` by `Leonard Sasse`_).
-
-- Upgrade storage interface for storage-like objects (:gh:`84` by `Synchon Mandal`_).
-
-- Add missing type annotations (:gh:`74` by `Synchon Mandal`_).
-
-- Add ``junifer wtf`` to report environment details (:gh:`33` by `Synchon Mandal`_).
-
-- Add ``junifer selftest`` to report environment details (:gh:`9` by `Synchon Mandal`_).
-
-- Refactor markers ``on`` attribute and ``get_valid_inputs`` to verify that the marker can
-  be computed on the input data types (by `Fede Raimondo`_)
-
-- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladAOMICID1000VBM`
-  datagrabber for accessing AOMIC ID1000 VBM from juseless (:gh:`57` by `Felix Hoffstaedter`_
-  and `Synchon Mandal`_)
-
-- Add test for :class:`junifer.datagrabber.DataladHCP1200` datagrabber (:gh:`93` by `Synchon Mandal`_).
-
-- Change documentation template to furo. Fix references and standardize documentation (:gh:`114` by `Fede Raimondo`_).
-
-- Add :class:`junifer.preprocess.fMRIPrepConfoundRemover` (:gh:`111` by `Fede Raimondo`_ and `Leonard Sasse`_).
-
-- Implement :class:`junifer.markers.CrossParcellationFC` marker (:gh:`85` by `Leonard Sasse`_
-  and `Kaustubh R. Patil`_)
-
-- Add :class:`junifer.configs.juseless.datagrabbers.JuselessUCLA` datagrabber for the UCLA dataset
-  available on juseless (:gh:`118` by `Leonard Sasse`_).
-
-- Rename "atlas" to "parcellation" (:gh:`116` by `Fede Raimondo`_).
-
-- Refactor the :class:`junifer.datagrabber.BaseDataGrabber` class to allow for easier subclassing (:gh:`123` by `Fede Raimondo`_).
-
-- Allow custom aggregation method for :class:`junifer.markers.SphereAggregation` (:gh:`102` by `Synchon Mandal`_).
-
-- Add support for "masks" (:gh:`79` by `Fede Raimondo`_).
-
-- Allow :class:`junifer.markers.ParcelAggregation` to apply multiple parcellations at once (:gh:`131` by `Fede Raimondo`_).
-
-- Introduce a singleton decorator for marker computations (:gh:`151` by `Synchon Mandal`_).
-
-- Refactor :class:`junifer.pipeline.PipelineStepMixin` to improve its implementation and validation for pipeline steps
-  (:gh:`152` by `Synchon Mandal`_).
-
-- Implement :class:`junifer.markers.ReHoParcels` and :class:`junifer.markers.ReHoSpheres` markers (:gh:`36` by `Synchon Mandal`_).
-
-- Implement :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels` and
-  :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres` markers (:gh:`35` by `Fede Raimondo`_).
-
-Bugs
-~~~~
-
-- Fix a bug in which a :class:`junifer.datagrabber.PatternDataGrabber` would now work with relative ``datadir`` paths.
-  (:gh:`96` by `Leonard Sasse`_, fixed in :gh:`98` by `Fede Raimondo`_).
-
-- Fix a bug in which :class:`junifer.datagrabber.DataladAOMICPIOP2` datagrabber did not use user input to
-  constrain elements based on tasks (:gh:`105` by `Leonard Sasse`_)
-
-- Fix a bug in which a datalad dataset could remove a user-cloned dataset (:gh:`53` by `Fede Raimondo`_)
-
-- Fix a bug in which CLI command would not work using elements with more than one field (by `Fede Raimondo`_).
-
-- Fix a bug in which the generated DAG for HTCondor will not work (:gh:`143` by `Fede Raimondo`_).
-
-API changes
-~~~~~~~~~~~
-
-- Change the ``single_output`` default parameter in storage classes from ``False`` to ``True`` (:gh:`134` by `Fede Raimondo`_).

docs/changes/latest.inc

@@ -1,106 +0,0 @@
-.. NOTE: we are now using links to highlight new functions and classes.
-   Please follow the examples below like
-   :func:`julearn.api.run_cross_validation`, so the
-   whats_new page will have a link to the function/class documentation.
-
-.. NOTE: there are 3 separate sections for changes, based on type:
-   - "Enhancements" for new features
-   - "Bugs" for bug fixes
-   - "API changes" for backward-incompatible changes
-
-.. NOTE: add the contributors and reference to the github issue/PR at the end
-   Example:
-     - Implemented feature X (:gh:`151` by `Sami Hamdan`_).
-
-.. _current:
-
-Current (0.0.2.dev)
--------------------
-
-Enhancements
-~~~~~~~~~~~~
-
-- Allow :class:`junifer.testing.datagrabbers.PartlyCloudyTestingDataGrabber` to be accessible
-  via ``import junifer.testing.registry`` (:gh:`160` by `Synchon Mandal`_).
-
-- Update docstrings and fix typo in log message (:gh:`165` by `Synchon Mandal`_).
-
-- Add support for ``Power`` coordinates (:gh:`167` by `Synchon Mandal`_).
-
-- Add support for ``Dosenbach`` coordinates (:gh:`168` by `Synchon Mandal`_).
-
-- Organize functional connectivity markers in ``junifer.markers.functional_connectivity``
-  (:gh:`107` by `Synchon Mandal`_).
-
-- Add :class:`junifer.markers.EdgeCentricFCParcels` and :class:`junifer.markers.EdgeCentricFCSpheres`
-  (:gh:`64` by `Leonard Sasse`_).
-
-- Change HCP datagrabber tests to decrease CI running time (:gh:`155` by `Fede Raimondo`_).
-
-- Add support for nilearn computed masks (``compute_epi_mask``, ``compute_brain_mask``, ``compute_background_mask``,
-  ``fetch_icbm152_brain_gm_mask``) (:gh:`175` by `Fede Raimondo`_).
-
-- Add fMRIPrep brain masks to the datagrabber patterns for all datagrabbers in the aomic sub-package
-  (:gh:`177` by `Leonard Sasse`_).
-
-- Add :class:`junifer.markers.TemporalSNRParcels` and :class:`junifer.markers.TemporalSNRSpheres`
-  (:gh:`163` by `Leonard Sasse`_).
-
-- Add support for HDF5 feature storage via :class:`junifer.storage.HDF5FeatureStorage`
-  (:gh:`147` by `Synchon Mandal`_).
-
-- Add ``pre_run`` parameter to ``_queue_condor`` (:gh:`188` by `Fede Raimondo`_).
-
-- Allow for empty spheres in :class:`junifer.external.nilearn.JuniferNiftiSpheresMasker`, that will result in NaNs (:gh:`190` by `Fede Raimondo`_).
-
-- Expose ``allow_overlap`` parameter in  :class:`junifer.markers.SphereAggregation` and related markers (:gh:`190` by `Fede Raimondo`_).
-
-- Add aggregation function :func:`junifer.stats.count` that returns the number of elements in a given axis. This allows to count the number of voxels per sphere/parcel when used as ``method`` in markers (:gh:`190` by `Fede Raimondo`_).
-
-- Modify the behaviour of the ``collect`` parameter in HTCondor ``queue`` function to run a collect job even if some of the previous jobs fail. This is useful to collect the results of a pipeline even if some of the jobs fail (:gh:`190` by `Fede Raimondo`_).
-
-- Allow for empty parcels in :class:`junifer.markers.ParcelAggregation`, that will result in NaNs (:gh:`194` by `Fede Raimondo`_).
-
-- Improve metadata and data I/O for :class:`junifer.storage.HDF5FeatureStorage` (:gh:`196` by `Synchon Mandal`_).
-
-- Force datalad to be non-interactive on _queued_ jobs (:gh:`201` by `Fede Raimondo`_).
-
-- Add more documentation on registering parcellations, coordinates, and masks (:gh:`166` by `Leonard Sasse`_)
-
-- Expose a :func:`junifer.data.parcellations.merge_parcellations` function to merge a list of parcellations (:gh:`146` by `Leonard Sasse`_).
-
-- Add copy button to documentation code blocks (:gh:`205` by `Synchon Mandal`_).
-
-- Add func:`junifer.stats.select` as an aggregation function that allows to select a subset of elements (:gh:`204` by `Fede Raimondo`_).
-
-- Add ``time_method`` and ``time_method_params`` to  :class:`junifer.markers.ParcelAggregation` and  :class:`junifer.markers.SphereAggregation`, allowing to apply an aggregation on the time axis after the aggregation on the parcels and spheres respectively (:gh:`204` by `Fede Raimondo`_).
-
-Bugs
-~~~~
-
-- Fix ``junifer run`` to respect preprocess step specified in the pipeline (:gh:`159` by `Synchon Mandal`_).
-
-- Fix :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels`, :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres`
-  :class:`junifer.markers.ReHoSpheres` and :class:`junifer.markers.ReHoParcels` pass the ``extra_input`` parameter (:gh:`187` by `Fede Raimondo`_).
-
-- Fix several markers that did not properly handle the ``extra_input`` parameter (:gh:`189` by `Fede Raimondo`_).
-
-- Fix an issue with datalad cache and locks in which the user-specific configuration might create a conflict in high throughput systems (:gh:`192` by `Fede Raimondo`_).
-
-- Fix a bug in which :func:`junifer.stats.count` will not be correctly applied across an axis (:gh:`195` by `Fede Raimondo`_).
-
-- Fix an issue with datalad cache and locks in which the overriden settings in Junifer were not propagated to subprocesses, resulting in using the default settings (:gh:`199` by `Fede Raimondo`_).
-
-- Fix a bug in which :class:`junifer.markers.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique (:gh:`194` by `Fede Raimondo`_).
-
-- Fix a bug in which :func:`junifer.data.masks.get_mask` fails for FunctionalConnectivityBase class, because of missing extra_input parameter (:gh:`200` by `Leonard Sasse`_)
-
-API changes
-~~~~~~~~~~~
-
-- Add ``confounds_format`` parameter to :class:`junifer.datagrabber.PatternDataGrabber` constructor for
-  improved handling of confounds specified via ``BOLD_confounds`` data type (:gh:`158` by `Synchon Mandal`_).
-
-- Rename ``store_table()`` to ``store_vector()`` for storage-like objects and adapt marker-like objects to
-  use ``"vector"`` in place of ``"table"`` for storage. Also, improve the logic of storing vectors
-  (:gh:`181` by `Synchon Mandal`_).

docs/changes/newsfragments/.gitignore

@@ -0,0 +1 @@
+!.gitignore

docs/changes/newsfragments/107.enh

@@ -0,0 +1 @@
+Organize functional connectivity markers in ``junifer.markers.functional_connectivity`` by `Synchon Mandal`_

docs/changes/newsfragments/146.feature

@@ -0,0 +1 @@
+Expose a :func:`junifer.data.parcellations.merge_parcellations` function to merge a list of parcellations by `Leonard Sasse`_

docs/changes/newsfragments/147.feature

@@ -0,0 +1 @@
+Add support for HDF5 feature storage via :class:`junifer.storage.HDF5FeatureStorage` by `Synchon Mandal`_

docs/changes/newsfragments/155.enh

@@ -0,0 +1 @@
+Change HCP datagrabber tests to decrease CI running time by `Fede Raimondo`_

docs/changes/newsfragments/158.change

@@ -0,0 +1 @@
+Add ``confounds_format`` parameter to :class:`junifer.datagrabber.PatternDataGrabber` constructor for improved handling of confounds specified via ``BOLD_confounds`` data type by `Synchon Mandal`_

docs/changes/newsfragments/159.bugfix

@@ -0,0 +1 @@
+Fix ``junifer run`` to respect preprocess step specified in the pipeline by `Synchon Mandal`_

docs/changes/newsfragments/160.enh

@@ -0,0 +1 @@
+Allow :class:`junifer.testing.datagrabbers.PartlyCloudyTestingDataGrabber` to be accessible via ``import junifer.testing.registry`` by `Synchon Mandal`_

docs/changes/newsfragments/163.feature

@@ -0,0 +1 @@
+Add :class:`junifer.markers.TemporalSNRParcels` and :class:`junifer.markers.TemporalSNRSpheres` by `Leonard Sasse`_

docs/changes/newsfragments/165.enh

@@ -0,0 +1 @@
+Update docstrings and fix typo in log message by `Synchon Mandal`_

docs/changes/newsfragments/166.doc

@@ -0,0 +1 @@
+Add more documentation on registering parcellations, coordinates, and masks by `Leonard Sasse`_

docs/changes/newsfragments/167.feature

@@ -0,0 +1 @@
+Add support for ``Power`` coordinates by `Synchon Mandal`_

docs/changes/newsfragments/168.feature

@@ -0,0 +1 @@
+Add support for ``Dosenbach`` coordinates by `Synchon Mandal`_

docs/changes/newsfragments/175.feature

@@ -0,0 +1 @@
+Add support for nilearn computed masks (``compute_epi_mask``, ``compute_brain_mask``, ``compute_background_mask``, ``fetch_icbm152_brain_gm_mask``) by `Fede Raimondo`_

docs/changes/newsfragments/177.enh

@@ -0,0 +1 @@
+Add fMRIPrep brain masks to the datagrabber patterns for all datagrabbers in the aomic sub-package by `Leonard Sasse`_

docs/changes/newsfragments/181.change

@@ -0,0 +1 @@
+Rename ``store_table()`` to ``store_vector()`` for storage-like objects and adapt marker-like objects to use ``"vector"`` in place of ``"table"`` for storage. Also, improve the logic of storing vectors by `Synchon Mandal`_

docs/changes/newsfragments/187.bugfix

@@ -0,0 +1 @@
+Fix :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels`, :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres`, :class:`junifer.markers.ReHoSpheres` and :class:`junifer.markers.ReHoParcels` pass the ``extra_input`` parameter by `Fede Raimondo`_

docs/changes/newsfragments/188.change

@@ -0,0 +1 @@
+Add ``pre_run`` parameter to ``_queue_condor`` by `Fede Raimondo`_

docs/changes/newsfragments/189.bugfix

@@ -0,0 +1 @@
+Fix several markers that did not properly handle the ``extra_input`` parameter by `Fede Raimondo`_

docs/changes/newsfragments/190.change

@@ -0,0 +1 @@
+Expose ``allow_overlap`` parameter in  :class:`junifer.markers.SphereAggregation` and related markers by `Fede Raimondo`_

docs/changes/newsfragments/190.enh

@@ -0,0 +1 @@
+Allow for empty spheres in :class:`junifer.external.nilearn.JuniferNiftiSpheresMasker`, that will result in NaNs. Also, modify the behaviour of the ``collect`` parameter in HTCondor ``queue`` function to run a collect job even if some of the previous jobs fail. This is useful to collect the results of a pipeline even if some of the jobs fail by `Fede Raimondo`_

docs/changes/newsfragments/190.feature

@@ -0,0 +1 @@
+Add aggregation function :func:`junifer.stats.count` that returns the number of elements in a given axis. This allows to count the number of voxels per sphere/parcel when used as ``method`` in markers by `Fede Raimondo`_

docs/changes/newsfragments/192.bugfix

@@ -0,0 +1 @@
+Fix an issue with datalad cache and locks in which the user-specific configuration might create a conflict in high throughput systems by `Fede Raimondo`_

docs/changes/newsfragments/194.bugfix

@@ -0,0 +1 @@
+Fix a bug in which :class:`junifer.markers.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique by `Fede Raimondo`_

docs/changes/newsfragments/194.enh

@@ -0,0 +1 @@
+Allow for empty parcels in :class:`junifer.markers.ParcelAggregation`, that will result in NaNs by `Fede Raimondo`_

docs/changes/newsfragments/195.bugfix

@@ -0,0 +1 @@
+Fix a bug in which :func:`junifer.stats.count` will not be correctly applied across an axis by `Fede Raimondo`_

docs/changes/newsfragments/196.enh

@@ -0,0 +1 @@
+Improve metadata and data I/O for :class:`junifer.storage.HDF5FeatureStorage` by `Synchon Mandal`_

docs/changes/newsfragments/199.bugfix

@@ -0,0 +1 @@
+Fix an issue with datalad cache and locks in which the overriden settings in Junifer were not propagated to subprocesses, resulting in using the default settings by `Fede Raimondo`_

docs/changes/newsfragments/200.bugfix

@@ -0,0 +1 @@
+Fix a bug in which :func:`junifer.data.masks.get_mask` fails for FunctionalConnectivityBase class, because of missing extra_input parameter by `Leonard Sasse`_

docs/changes/newsfragments/201.enh

@@ -0,0 +1 @@
+Force datalad to be non-interactive on _queued_ jobs by `Fede Raimondo`_

docs/changes/newsfragments/203.doc

@@ -0,0 +1 @@
+Migrate and document changelog creation and maintenance via ``towncrier`` by `Synchon Mandal`_

docs/changes/newsfragments/205.doc

@@ -0,0 +1 @@
+Add copy button to documentation code blocks by `Synchon Mandal`_

docs/changes/newsfragments/64.feature

@@ -0,0 +1 @@
+Add :class:`junifer.markers.EdgeCentricFCParcels` and :class:`junifer.markers.EdgeCentricFCSpheres` by `Leonard Sasse`_

docs/contribution.rst

@@ -8,61 +8,68 @@ Contributing to junifer
 Setting up the local development environment
 --------------------------------------------
 
-1. Fork the https://github.com/juaml/junifer repository on GitHub. If you
+#. Fork the https://github.com/juaml/junifer repository on GitHub. If you
    have never done this before, `follow the official guide
    <https://guides.github.com/activities/forking/>`_.
-2. Clone your fork locally as described in the same guide.
-3. Install your local copy into a Python virtual environment. You can `read
+#. Clone your fork locally as described in the same guide but also add the
+   flag to sync the submodules as well by appending the following to the
+   clone commmand:
+
+   .. code-block:: bash
+
+      ... --recurse-submodules
+
+#. Install your local copy into a Python virtual environment. You can `read
    this guide to learn more
    <https://realpython.com/python-virtual-environments-a-primer/>`_ about them
    and how to create one.
 
-   .. code-block:: console
+   .. code-block:: bash
 
        pip install -e ".[dev]"
 
-4. Create a branch for local development using the ``main`` branch as a
+#. Create a branch for local development using the ``main`` branch as a
    starting point. Use ``fix``, ``refactor``, or ``feat`` as a prefix.
 
-   .. code-block:: console
+   .. code-block:: bash
 
        git checkout main
        git checkout -b <prefix>/<name-of-your-branch>
 
    Now you can make your changes locally.
 
-5. When making changes locally, it is helpful to ``git commit`` your work
+#. When making changes locally, it is helpful to ``git commit`` your work
    regularly. On one hand to save your work and on the other hand, the smaller
    the steps, the easier it is to review your work later. Please use `semantic
    commit messages
    <http://karma-runner.github.io/2.0/dev/git-commit-msg.html>`_.
 
-   .. code-block:: console
+   .. code-block:: bash
 
        git add .
        git commit -m "<prefix>: <summary of changes>"
 
-6. When you're done making changes, check that your changes pass our test suite.
+#. When you're done making changes, check that your changes pass our test suite.
    This is all included with ``tox``.
 
-   .. code-block:: console
+   .. code-block:: bash
 
        tox
 
    You can also run all ``tox`` tests in parallel. As of ``tox 3.7``, you can run
 
-   .. code-block:: console
+   .. code-block:: bash
 
        tox --parallel
 
 
-7. Push your branch to GitHub.
+#. Push your branch to GitHub.
 
-   .. code-block:: console
+   .. code-block:: bash
 
        git push origin <prefix>/<name-of-your-branch>
 
-8. Open the link displayed in the message when pushing your new branch in order
+#. Open the link displayed in the message when pushing your new branch in order
    to submit a pull request. Please follow the template presented to you in the
    web interface to complete your pull request.
 
@@ -72,17 +79,38 @@ GitHub Pull Request guidelines
 
 Before you submit a pull request, check that it meets these guidelines:
 
-1. The pull request should include tests in the respective ``tests`` directory.
+#. The pull request should include tests in the respective ``tests`` directory.
    Except in rare circumstances, code coverage must not decrease (as reported
    by codecov which runs automatically when you submit your pull request).
-2. If the pull request adds functionality, the docs should be
+#. If the pull request adds functionality, the docs should be
    updated. Consider creating a Python file that demonstrates the usage in
    ``examples/`` directory.
-3. The pull request should also include a short one-liner of your contribution
-   in ``docs/changes/latest.inc``. If it's your first contribution, also add
-   yourself to ``docs/changes/contributors.inc``.
-4. The pull request will be tested against several Python versions.
-5. Someone from the core team will review your work and guide you to a successful
+#. Make sure to create a Draft Pull Request. If you are not sure how to do it,
+   check `here <https://github.blog/2019-02-14-introducing-draft-pull-requests/>`_.
+#. Note the pull request ID assigned after completing the previous step and create
+   a short one-liner file of your contribution named as ``<pull-request-ID>.<type>``
+   in ``docs/changes/newsfragments/``, ``<type>`` being as per the following
+   convention:
+
+   * API change : ``change``
+   * Bug fix : ``bugfix``
+   * Enhancement : ``enh``
+   * Feature : ``feature``
+   * Documentation improvement : ``doc``
+   * Miscellaneous : ``misc``
+   * Deprecation and API removal : ``removal``
+
+   For example, a basic documentation improvement can be recorded in a file
+   ``101.doc`` with the content:
+
+   .. code-block::
+
+       Fixed a typo in intro by `junifer's biggest fan`_
+
+#. If it's your first contribution, also add yourself to
+   ``docs/changes/contributors.inc``.
+#. The pull request will be tested against several Python versions.
+#. Someone from the core team will review your work and guide you to a successful
    contribution.
 
 
@@ -95,7 +123,7 @@ tests that make sure that the code runs as intended.
 
 To run all tests
 
-.. code-block:: console
+.. code-block:: bash
 
     tox -e test
 
@@ -105,7 +133,7 @@ Adding and building documentation
 
 Building the documentation requires some extra packages and can be installed by
 
-.. code-block:: console
+.. code-block:: bash
 
     pip install -e ".[docs]"
 

docs/maintaining.rst

@@ -24,41 +24,61 @@ Releasing a new version
 -----------------------
 
 Once the milestone is reached (all issues closed), it is time to do a new
-release.
+release. Make sure you have
+`towncrier <https://towncrier.readthedocs.io/en/stable/index.html>`_ installed
+before proceeding.
 
-1. Open a PR to update documentation:
-    - `docs/changes/latest.inc` should now be renamed to the version to be
-      released.
-    - `docs/whats_new.rst` must update the link to the new version.
-
-2. Merge PR
-
-3. Make sure you are in sync with the main branch.
+#. Make sure you are in sync with the main branch.
 
 .. code-block:: bash
 
     git checkout main
     git pull --rebase origin main
 
-4. Create tag (replace ``X.Y.Z`` with the proper version).
+#. Run the following to check changelog is properly generated:
+
+.. code-block:: bash
+
+   towncrier build --draft
+
+#. Then, run:
+
+.. code-block:: bash
+
+   towncrier
+
+to generate the proper changelog that should be reflected in
+``docs/whats_new.rst``.
+
+#. Commit the chages, make a PR and merge via a merge commit.
+
+#. Make sure you are in sync with the main branch.
+
+.. code-block:: bash
+
+    git checkout main
+    git pull --rebase origin main
+
+#. Create tag (replace ``X.Y.Z`` with the proper version) on the merged PR's
+   merge commit.
 
 .. code-block:: bash
 
     git tag -a vX.Y.Z -m "Release X.Y.Z"
 
-5. Check that the build system is creating the proper version
+#. Check that the build system is creating the proper version
 
 .. code-block:: bash
 
     SETUPTOOLS_SCM_DEBUG=1 python -m build --source --binary --out-dir dist/ .
 
-6. Push the tag
+#. Push the tag
 
 .. code-block:: bash
 
     git push origin --follow-tags
 
-7. Optional: bump the *MAJOR* or *MINOR* segment of next release (replace ``D.E.0`` with the proper version).
+#. Optional: bump the *MAJOR* or *MINOR* segment of next release (replace ``D.E.0`` with the proper version).
 
 .. code-block:: bash
 

docs/whats_new.rst

@@ -1,9 +1,160 @@
+.. include:: links.inc
+.. include:: changes/contributors.inc
+
 .. _whats_new:
 
 What's new
 ==========
 
-.. include:: changes/latest.inc
-.. include:: changes/0.0.1.inc
-.. include:: changes/contributors.inc
-.. include:: links.inc
+.. towncrier release notes start
+
+junifer 0.0.1 (2022-12-20)
+--------------------------
+
+API Changes
+^^^^^^^^^^^
+
+- Change the ``single_output`` default parameter in storage classes from
+  ``False`` to ``True`` by `Fede Raimondo`_ (:gh:`134`)
+
+Bugfixes
+^^^^^^^^
+
+- Fix a bug in which a :class:`junifer.datagrabber.PatternDataGrabber` would
+  now work with relative ``datadir`` paths (reported by `Leonard Sasse`_,
+  fixed by `Fede Raimondo`_) (:gh:`96`, :gh:`98`)
+
+- Fix a bug in which :class:`junifer.datagrabber.DataladAOMICPIOP2` datagrabber
+  did not use user input to constrain elements based on tasks by
+  `Leonard Sasse`_ (:gh:`105`)
+
+- Fix a bug in which a datalad dataset could remove a user-cloned dataset by
+  `Fede Raimondo`_ (:gh:`53`)
+
+- Fix a bug in which CLI command would not work using elements with more than
+  one field by `Fede Raimondo`_
+
+- Fix a bug in which the generated DAG for HTCondor will not work by
+  `Fede Raimondo`_ (:gh:`143`)
+
+Improved Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+- Add an example how to use ``junifer`` and ``julearn`` in one pipeline to
+  extract features and do machine learning by `Leonard Sasse`_,
+  `Nicolas Nieto`_, and `Sami Hamdan`_ (:gh:`40`)
+
+- Add documentation for the datagrabbers by `Leonard Sasse`_,
+  `Nicolas Nieto`_, and `Sami Hamdan`_
+
+- Change documentation template to furo. Fix references and standardize
+  documentation by `Fede Raimondo`_ (:gh:`114`)
+
+Enhancements
+^^^^^^^^^^^^
+
+- Add comments to :class:`junifer.datagrabber.DataladDataGrabber` datagrabber
+  and change to use ``datalad-clone`` instead of ``datalad-install`` by
+  `Benjamin Poldrack`_ (:gh:`55`)
+
+- Upgrade storage interface for storage-like objects by `Synchon Mandal`_
+  (:gh:`84`)
+
+- Add missing type annotations by `Synchon Mandal`_ (:gh:`74`)
+
+- Refactor markers ``on`` attribute and ``get_valid_inputs`` to verify that the
+  marker can be computed on the input data types by `Fede Raimondo`_
+
+- Add test for :class:`junifer.datagrabber.DataladHCP1200` datagrabber by
+  `Synchon Mandal`_ (:gh:`93`)
+
+- Rename "atlas" to "parcellation" by `Fede Raimondo`_ (:gh:`116`)
+
+- Refactor the :class:`junifer.datagrabber.BaseDataGrabber` class to allow for
+  easier subclassing by `Fede Raimondo`_ (:gh:`123`)
+
+- Allow custom aggregation method for :class:`junifer.markers.SphereAggregation`
+  by `Synchon Mandal`_ (:gh:`102`)
+
+- Add support for "masks" by `Fede Raimondo`_ (:gh:`79`)
+
+- Allow :class:`junifer.markers.ParcelAggregation` to apply multiple
+  parcellations at once by `Fede Raimondo`_ (:gh:`131`)
+
+- Refactor :class:`junifer.pipeline.PipelineStepMixin` to improve its
+  implementation and validation for pipeline steps by `Synchon Mandal`_
+  (:gh:`152`)
+
+Features
+^^^^^^^^
+
+- Implement :class:`junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`
+  datagrabber by `Fede Raimondo`_ (:gh:`52`)
+
+- Implement matrix storage in SQliteFeatureStorage by `Fede Raimondo`_
+  (:gh:`42`)
+
+- Implement :class:`junifer.markers.FunctionalConnectivityParcels` marker for
+  functional connectivity using a parcellation by `Amir Omidvarnia`_ and
+  `Kaustubh R. Patil`_ (:gh:`41`)
+
+- Implement coordinate register, list and load by `Fede Raimondo`_ (:gh:`11`)
+
+- Add :class:`junifer.datagrabber.DataladAOMICID1000` datagrabber for AOMIC
+  ID1000 dataset including tests and creation of mock dataset for testing by
+  `Vera Komeyer`_ and `Xuan Li`_ (:gh:`60`)
+
+- Add support to access other input in the data object in the ``compute`` method
+  by `Fede Raimondo`_
+
+- Implement :class:`junifer.markers.RSSETSMarker` marker by `Leonard Sasse`_,
+  `Nicolas Nieto`_ and `Sami Hamdan`_ (:gh:`51`)
+
+- Implement :class:`junifer.markers.SphereAggregation` marker by
+  `Fede Raimondo`_
+
+- Implement :class:`junifer.datagrabber.DataladAOMICPIOP1` and
+  :class:`junifer.datagrabber.DataladAOMICPIOP2` datagrabbers for AOMIC PIOP1
+  and PIOP2 datasets respectively and refactor
+  :class:`junifer.datagrabber.DataladAOMICID1000` slightly by `Leonard Sasse`_
+  (:gh:`94`)
+
+- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladCamCANVBM`
+  datagrabber by `Leonard Sasse`_ (:gh:`99`)
+
+- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladIXIVBM`
+  CAT output datagrabber for juseless by `Leonard Sasse`_ (:gh:`48`)
+
+- Add ``junifer wtf`` to report environment details by `Synchon Mandal`_
+  (:gh:`33`)
+
+- Add ``junifer selftest`` to report environment details by `Synchon Mandal`_
+  (:gh:`9`)
+
+- Implement :class:`junifer.configs.juseless.datagrabbers.JuselessDataladAOMICID1000VBM`
+  datagrabber for accessing AOMIC ID1000 VBM from juseless by `Felix Hoffstaedter`_
+  and `Synchon Mandal`_ (:gh:`57`)
+
+- Add :class:`junifer.preprocess.fMRIPrepConfoundRemover` by `Fede Raimondo`_
+  and `Leonard Sasse`_ (:gh:`111`)
+
+- Implement :class:`junifer.markers.CrossParcellationFC` marker by
+  `Leonard Sasse`_ and `Kaustubh R. Patil`_ (:gh:`85`)
+
+- Add :class:`junifer.configs.juseless.datagrabbers.JuselessUCLA` datagrabber
+  for the UCLA dataset available on juseless by `Leonard Sasse`_ (:gh:`118`)
+
+- Introduce a singleton decorator for marker computations by `Synchon Mandal`_
+  (:gh:`151`)
+
+- Implement :class:`junifer.markers.ReHoParcels` and
+  :class:`junifer.markers.ReHoSpheres` markers by `Synchon Mandal`_ (:gh:`36`)
+
+- Implement :class:`junifer.markers.AmplitudeLowFrequencyFluctuationParcels` and
+  :class:`junifer.markers.AmplitudeLowFrequencyFluctuationSpheres` markers by
+  `Fede Raimondo`_ (:gh:`35`)
+
+Misc
+^^^^
+
+- Create the repository based on the mockup by `Fede Raimondo`_

pyproject.toml

@@ -70,6 +70,7 @@ docs = [
     "numpydoc>=1.5.0,<1.6",
     "julearn==0.2.5",
     "sphinx-copybutton==0.5.1",
+    "towncrier==22.12.0",
 ]
 
 ################
@@ -96,3 +97,46 @@ extend-exclude = """
 [tool.pytest.ini_options]
 minversion = "7.0"
 addopts = "--ignore=junifer/external/h5io -vv"
+
+[tool.towncrier]
+directory = "docs/changes/newsfragments"
+filename = "docs/whats_new.rst"
+package = "junifer"
+# to use gh_substitutions
+issue_format = ":gh:`{issue}`"
+# modify to have proper toctree
+underlines = "-^~"
+# set line length to 79
+wrap = true
+
+# Need to put default explicitly as custom is not combined with default
+
+[tool.towncrier.fragment.bugfix]
+name = "Bugfixes"
+showcontent = true
+
+[tool.towncrier.fragment.doc]
+name = "Improved Documentation"
+showcontent = true
+
+[tool.towncrier.fragment.feature]
+name = "Features"
+showcontent = true
+
+[tool.towncrier.fragment.misc]
+name = "Misc"
+showcontent = true
+
+[tool.towncrier.fragment.removal]
+name = "Deprecations and Removals"
+showcontent = true
+
+# Add custom towncrier fragment for enhancements
+[tool.towncrier.fragment.enh]
+name = "Enhancements"
+showcontent = true
+
+# Add custom towncrier fragment for API changes
+[tool.towncrier.fragment.change]
+name = "API Changes"
+showcontent = true