From e65e1d7489835eb783724173e9582d11627043a5 Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Wed, 17 Oct 2018 10:35:29 -0400 Subject: [PATCH 1/5] Update README.md Added notes for creating a conda environment for use with tedana Added links to dependencies --- README.md | 27 +++++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 8341b6f4e..9b08de508 100644 --- a/README.md +++ b/README.md @@ -40,12 +40,12 @@ More information and documentation can be found at https://tedana.readthedocs.io You'll need to set up a working development environment to use `tedana`. To set up a local environment, you will need Python >=3.6 and the following packages will need to be installed: -mdp -nilearn -nibabel>=2.1.0 -numpy -scikit-learn -scipy +[mdp](https://pypi.org/project/MDP/) +[numpy](http://www.numpy.org/) +[scikit-learn](http://scikit-learn.org/stable/) +[scipy](https://www.scipy.org/) +[nilearn](https://nilearn.github.io/) +[nibabel>=2.1.0](http://nipy.org/nibabel/) You can then install `tedana` with @@ -53,6 +53,21 @@ You can then install `tedana` with pip install tedana ``` +### Creating a miniconda environment for use with tedana +In order to use tedana, you can configure a miniconda environment for your user profile in Mac and Linux systems. (Systems administrators: note that global installation of miniconda in /usr/local/ may cause some trouble for individual users; user installations are recommended; pip installation will require root privileges otherwise. Some users may need you to adjust their home directory permissions during a miniconda install). This also makes it straightforward to install nibabel and nilearn. You can use [miniconda3](https://conda.io/miniconda.html). Then, use the following commands to create the environment: + +``` +conda create -n ENVIRONMENT_NAME python=3 pip mdp numpy scikit-learn scipy +source activate ENVIRONMENT_NAME +pip install nilearn nibabel tedana +``` + +At this stage tedana will be added to your path, while allowing any existing tedana installations, such as the one packaged with AfNI, to remain untouched. To leave this environment, use + +``` +source deactivate +``` + ## Getting involved We :yellow_heart: new contributors ! From f8744b30c4416ab4f878f09242532c7055ff8854 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Thu, 1 Nov 2018 08:25:08 -0400 Subject: [PATCH 2/5] Add Support and Communication page to docs. --- docs/contributing.rst | 20 ++++++++++++++++++-- docs/index.rst | 3 ++- docs/installation.rst | 16 ---------------- docs/support.rst | 10 ++++++++++ 4 files changed, 30 insertions(+), 19 deletions(-) create mode 100644 docs/support.rst diff --git a/docs/contributing.rst b/docs/contributing.rst index caf9399f6..12a16201a 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -1,3 +1,19 @@ +Getting involved +---------------- + +We 💛 new contributors! +To get started, check out `our contributing guidelines`_. + +Want to learn more about our plans for developing ``tedana``? +Have a question, comment, or suggestion? +Open or comment on one of `our issues`_! + +We ask that all contributions to ``tedana`` respect our `code of conduct`_. + +.. _our contributing guidelines: https://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md +.. _our issues: https://github.com/ME-ICA/tedana/issues +.. _code of conduct: https://github.com/ME-ICA/tedana/blob/master/CODE_OF_CONDUCT.md + Contributing to tedana ====================== @@ -11,7 +27,7 @@ For a more general guide to the tedana development, please see our Style Guide ------------ +=========== Code ```` @@ -44,7 +60,7 @@ This tells the development team that your pull request is a "work-in-progress", and that you plan to continue working on it. Release Checklist ------------------ +================= This is the checklist of items that must be completed when cutting a new release of tedana. These steps can only be completed by a project maintainer, but they are a good resource for diff --git a/docs/index.rst b/docs/index.rst index 326178cfe..c523af10c 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -129,11 +129,12 @@ tedana is licensed under GNU Lesser General Public License version 2.1. :maxdepth: 2 :caption: Contents: + installation multi-echo usage - installation approach outputs + support contributing api diff --git a/docs/installation.rst b/docs/installation.rst index 82fc724a0..7645b9859 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -17,19 +17,3 @@ You can then install ``tedana`` with: .. code-block:: bash pip install tedana - -Getting involved ----------------- - -We 💛 new contributors! -To get started, check out `our contributing guidelines`_. - -Want to learn more about our plans for developing ``tedana``? -Have a question, comment, or suggestion? -Open or comment on one of `our issues`_! - -We ask that all contributions to ``tedana`` respect our `code of conduct`_. - -.. _our contributing guidelines: https://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md -.. _our issues: https://github.com/ME-ICA/tedana/issues -.. _code of conduct: https://github.com/ME-ICA/tedana/blob/master/CODE_OF_CONDUCT.md diff --git a/docs/support.rst b/docs/support.rst new file mode 100644 index 000000000..b2343d622 --- /dev/null +++ b/docs/support.rst @@ -0,0 +1,10 @@ +Support and Communication +------------------------- +All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/poldracklab/fmriprep/issues. + +If you would like to ask a question about usage or tedana's outputs, please submit a question to `NeuroStars`_ with the ``multi-echo`` tag. + +All previous tedana-related questions are available `here`_. + +.. _NeuroStars: https://neurostars.org +.. _here: https://neurostars.org/tags/multi-echo From 0cb003e5e711635a83d1cedc369b5fa9eacc14bb Mon Sep 17 00:00:00 2001 From: Elizabeth DuPre Date: Thu, 1 Nov 2018 13:49:55 -0400 Subject: [PATCH 3/5] Update line lengths, remove sys admin information --- README.md | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 25e646aa8..848b7fd57 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,4 @@ -tedana: TE Dependent ANAlysis -============================= +# tedana: TE Dependent ANAlysis The ``tedana`` package is part of the ME-ICA pipeline, performing TE-dependent analysis of multi-echo functional magnetic resonance imaging (fMRI) data. @@ -15,16 +14,12 @@ multi-echo functional magnetic resonance imaging (fMRI) data. [![Codecov](https://codecov.io/gh/me-ica/tedana/branch/master/graph/badge.svg)](https://codecov.io/gh/me-ica/tedana) [![Join the chat at https://gitter.im/ME-ICA/tedana](https://badges.gitter.im/ME-ICA/tedana.svg)](https://gitter.im/ME-ICA/tedana?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) -About ------ +## About ``tedana`` originally came about as a part of the [ME-ICA](https://github.com/me-ica/me-ica) pipeline. The ME-ICA pipeline originally performed both pre-processing and TE-dependent analysis of multi-echo fMRI data; however, ``tedana`` now assumes that you're working with data which has been previously preprocessed. -If you're in need of a preprocessing pipeline, we recommend -[fmriprep](https://github.com/poldracklab/fmriprep/), which has been tested -for compatibility with multi-echo fMRI data and ``tedana``. ![http://tedana.readthedocs.io/](https://user-images.githubusercontent.com/7406227/40031156-57b7cbb8-57bc-11e8-8c51-5b29f2e86a48.png) @@ -48,23 +43,28 @@ You can then install `tedana` with pip install tedana ``` -### Creating a miniconda environment for use with tedana -In order to use tedana, you can configure a miniconda environment for your user profile in Mac and Linux systems. (Systems administrators: note that global installation of miniconda in /usr/local/ may cause some trouble for individual users; user installations are recommended; pip installation will require root privileges otherwise. Some users may need you to adjust their home directory permissions during a miniconda install). This also makes it straightforward to install nibabel and nilearn. You can use [miniconda3](https://conda.io/miniconda.html). Then, use the following commands to create the environment: +### Creating a miniconda environment for use with `tedana` +In using `tedana`, you can optionally configure [a conda environment](https://conda.io/docs/user-guide/tasks/manage-environments.html). -``` -conda create -n ENVIRONMENT_NAME python=3 pip mdp numpy scikit-learn scipy +We recommend using [miniconda3](https://conda.io/miniconda.html). +After installation, you can use the following commands to create an environment for `tedana`: + +```bash +conda create -n ENVIRONMENT_NAME python=3 pip mdp numpy scikit-learn scipy nilearn nibabel source activate ENVIRONMENT_NAME -pip install nilearn nibabel tedana +pip install tedana ``` -At this stage tedana will be added to your path, while allowing any existing tedana installations, such as the one packaged with AfNI, to remain untouched. To leave this environment, use +`tedana` will then be available in your path. +This will also allow any previously existing tedana installations to remain untouched. -``` +To exit this conda environment, use + +```bash source deactivate ``` -Getting involved ----------------- +## Getting involved We :yellow_heart: new contributors! To get started, check out [our contributing guidelines](https://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md). From 4ad04424ee5645e584fe90f9b72e3a4c5bdb7573 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Thu, 1 Nov 2018 13:57:32 -0400 Subject: [PATCH 4/5] Fix old link. --- docs/support.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/support.rst b/docs/support.rst index b2343d622..0828ea5c8 100644 --- a/docs/support.rst +++ b/docs/support.rst @@ -1,6 +1,6 @@ Support and Communication ------------------------- -All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/poldracklab/fmriprep/issues. +All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/ME-ICA/tedana/issues. If you would like to ask a question about usage or tedana's outputs, please submit a question to `NeuroStars`_ with the ``multi-echo`` tag. From 73cf8c82e81461401b2749f15aaade02dc56ae28 Mon Sep 17 00:00:00 2001 From: Elizabeth DuPre Date: Thu, 1 Nov 2018 14:34:14 -0400 Subject: [PATCH 5/5] [DOC] Remove getting started section --- docs/contributing.rst | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/docs/contributing.rst b/docs/contributing.rst index 12a16201a..42bfc6acc 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -1,19 +1,3 @@ -Getting involved ----------------- - -We 💛 new contributors! -To get started, check out `our contributing guidelines`_. - -Want to learn more about our plans for developing ``tedana``? -Have a question, comment, or suggestion? -Open or comment on one of `our issues`_! - -We ask that all contributions to ``tedana`` respect our `code of conduct`_. - -.. _our contributing guidelines: https://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md -.. _our issues: https://github.com/ME-ICA/tedana/issues -.. _code of conduct: https://github.com/ME-ICA/tedana/blob/master/CODE_OF_CONDUCT.md - Contributing to tedana ======================