Merge pull request #156 from juaml/release/0.0.1

release: 0.0.1
juaml · Dec 20, 2022 · c6508a7 · c6508a7
2 parents 49b17f9 + c939d21
commit c6508a7
Show file tree

Hide file tree

Showing 7 changed files with 141 additions and 105 deletions.
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-![Junifer logo](docs/images/junifer_logo.png)
+![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 
 # junifer - JUelich NeuroImaging FEature extractoR
 
@@ -46,6 +46,12 @@ pip install junifer
 
 If you use junifer in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project [URL](https://juaml.github.io/junifer).
 
+## Funding
+
+We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
+[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of Junifer.
+(The funding sources had no role in the design, implementation and evaluation of the pipeline.)
+
 ## Contribution
 
 Contributions are welcome and greatly appreciated. Please read the [guidelines](https://juaml.github.io/junifer/main/contributing.html) to get started.

diff --git a/docs/changes/0.0.1.inc b/docs/changes/0.0.1.inc
@@ -0,0 +1,115 @@
+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`_).
diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc
@@ -14,107 +14,14 @@
 
 .. _current:
 
-Current (0.0.0.dev)
+Current (0.0.2.dev)
 -------------------
 
 Enhancements
 ~~~~~~~~~~~~
 
-- Created a the repository based on the mockup by `Fede Raimondo`_.
-
-- Implemented SPM Auditory testing datagrabber X (:gh:`52` by `Fede Raimondo`_).
-
-- Added comments to datalad grabber and changed to use datalad-clone instead of
-  datalad-install (:gh:`55` by `Benjamin Poldrack`_).
-
-- Added an example how to use junifer and julearn (:gh:`40` by `Leonard Sasse`_,
-  `Nicolas Nieto`_, and `Sami Hamdan`_) in one pipeline to extract features
-  and do machine learning.
-
-- Implement matrix storage in SQliteFeatureStorage (:gh:`42` by `Fede Raimondo`_).
-
-- Marker for functional connectivity using a parcellation (:gh:`41` by
-  `Amir Omidvarnia`_ and `Kaustubh R. Patil`_).
-
-- Added documentation for the datagrabbers (by `Leonard Sasse`_,
-  `Nicolas Nieto`_, and `Sami Hamdan`_).
-
-- Implement coordinate register, list and load (:gh:`11` by `Fede Raimondo`_).
-
-- Added datagrabber for AOMIC1000 dataset including tests and creation of mock
-  dataset for testing (:gh:`60` by `Vera Komeyer`_, `Xuan Li`_).
-
-- Added support to access other input in the data object in the `compute` method
-  (by `Fede Raimondo`_).
-
-- Implemented the edge time series RSS marker (:gh:`51` by `Leonard Sasse`_,
-  `Nicolas Nieto`_, `Sami Hamdan`_).
-
-- Implement SphereAggregation marker (by `Fede Raimondo`_).
-
-- Implement PIOP1 and PIOP2 AOMIC datasets and refactor AOMICID1000 slightly
-  (:gh:`94` by `Leonard Sasse`_)
-
-- Implement a JuselessDataladCamCANVBM datagrabber class (:gh:`99` by `Leonard Sasse`_)
-
-- Implement IXI 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 JuselessDataladAOMICID1000VBM datagrabber for accessing AOMIC ID 1000 VBM from juseless (:gh:`57` by `Felix Hoffstaedter`_ and `Synchon Mandal`_)
-
-- Add test for 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 CrossParcellationFC marker (:gh:`85` by `Leonard Sasse`_ and `Kaustubh R. Patil`_)
-
-- Add datagrabber implementation 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 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 AOMIC PIOP2 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`_).
diff --git a/docs/index.rst b/docs/index.rst
@@ -41,3 +41,11 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
+
+
+Funding
+=======
+
+We thank the `Helmholtz Imaging Platform <https://helmholtz-imaging.de/>`_ and
+`SMHB <https://www.fz-juelich.de/en/smhb>`_ for supporting development of Junifer.
+(The funding sources had no role in the design, implementation and evaluation of the pipeline.)
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -65,16 +65,16 @@ find a list of all external dependencies that are required for specific markers.
 AFNI
 ----
 
-To install AFNI, you can always follow the `AFNI official instructions 
+To install AFNI, you can always follow the `AFNI official instructions
 <https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/main_toc.html>`_. Additionally, you can also follow
 the following steps to install and configure the AFNI Docker container in your local system.
 
-.. important:: 
+.. important::
 
-  The AFNI Docker container wrappers add the commands required by Junifer. Using this commands have
-  some limitations, mostly related to handling files and paths. Junifer knows about this and uses this
-  commands in the proper way. Keep this in mind if you try to use the AFNI Docker wrappers outside of junifer. This
-  caveats and limitations are not documented.
+  The AFNI Docker container wrappers add the commands required by junifer. Using these commands have
+  some limitations, mostly related to handling files and paths. Junifer knows about this and uses these
+  commands in the proper way. Keep this in mind if you try to use the AFNI Docker wrappers outside of junifer.
+  These caveats and limitations are not documented.
 
 1. Install Docker. You can follow the `Docker official instructions <https://docs.docker.com/get-docker/>`_.
 2. Pull the AFNI Docker image from `Docker Hub <https://hub.docker.com/r/afni/afni>`_:
@@ -89,7 +89,7 @@ the following steps to install and configure the AFNI Docker container in your l
 
   junifer setup afni-docker
 
-Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file. 
+Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
 
 Or, alternatively, you can exceute this command which will update the ``~/.bashrc`` for you:
 

diff --git a/docs/maintaining.rst b/docs/maintaining.rst
@@ -18,7 +18,7 @@ pre-release.
 
 The CI scripts will publish every tag with the format *v.X.Y.Z* to Pypi as
 version "X.Y.Z". Additionally, for every push to main, it will be published
-as pre-release to TestPypi.
+as pre-release to PyPI.
 
 Releasing a new version
 -----------------------
@@ -64,4 +64,3 @@ release.
 
     git tag -a vD.E.0.dev -m "Set next release to D.E.0"
     git push origin --follow-tags
-
diff --git a/docs/whats_new.rst b/docs/whats_new.rst
@@ -4,5 +4,6 @@ What's new
 ==========
 
 .. include:: changes/latest.inc
+.. include:: changes/0.0.1.inc
 .. include:: changes/contributors.inc
-.. include:: links.inc
+.. include:: links.inc