Merge pull request #132 from effigies/rel/0.3.0

REL: 0.3.0

CHANGES.rst

@@ -1,3 +1,25 @@
+0.3.0 (April 19, 2019)
+======================
+
+This release restores reports at the second level and higher, and enables isotropic
+smoothing with the nistats backend. Reporting has also been refactored to reduce
+clutter in the outputs.
+
+With thanks to Karolina Finc, Rastko Ciric and Mathias Goncalves for contributions.
+
+* FIX: Restore level 2+ reports (https://github.com/poldracklab/fitlins/pull/130)
+* FIX: Remove uninformative metadata from derivative filenames (https://github.com/poldracklab/fitlins/pull/129)
+* FIX: Re-enable analysis level selection (https://github.com/poldracklab/fitlins/pull/120)
+* FIX: Switch plot colors to conventional blue for negative, red for positive (https://github.com/poldracklab/fitlins/pull/108)
+* ENH: Save crashfiles as text in working directory (https://github.com/poldracklab/fitlins/pull/121)
+* ENH: Add naive isotropic smoothing (https://github.com/poldracklab/fitlins/pull/104)
+* REF: Delegate isotropic smoothing to nistats (https://github.com/poldracklab/fitlins/pull/118)
+* DOC: Update README with latest help text, remove smoothing disclaimer (https://github.com/poldracklab/fitlins/pull/119)
+* MAINT: Add contributors to Zenodo (https://github.com/poldracklab/fitlins/pull/122)
+* MAINT: Consolidate configuration (https://github.com/poldracklab/fitlins/pull/113)
+* MAINT: Pybids 0.8 compatibility (https://github.com/poldracklab/fitlins/pull/109)
+* MAINT: Use numpy 1.15 to accommodate pytables (https://github.com/poldracklab/fitlins/pull/106)
+
 0.2.0 (February 1, 2019)
 =======================
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,77 @@
+# FitLins Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting Chris Markiewicz at <[email protected]>, the project
+lead.
+All complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

CONTRIBUTING.md

@@ -1,19 +1,145 @@
-# Contributing
+# Contributing to FitLins
 
-**Are you new to open source and GitHub?**
-If so, reading the "[How to submit a contribution](
-https://opensource.guide/how-to-contribute/#how-to-submit-a-contribution)"
-guide will provide a great introduction to contributing to MODELFIT and other
-Open Source projects.
-All the MODELFIT-specific contributing instructions listed below will make much
-more sense after reading this guide.
+Welcome to the FitLins repository!
+We're excited you're here and want to contribute.
 
-If you are new to the project don't forget to add your name and affiliation to
-the `.zenodo.json` file.
+## Practical guide to submitting your contribution
 
-## Code style guide
+These guidelines are designed to make it as easy as possible to get involved.
+If you have any questions that aren't discussed below,
+please let us know by opening an [issue][link_issues]!
 
-### Function and variable names
+Before you start you'll need to set up a free [GitHub][link_github] account and sign in.
+Here are some [instructions][link_signupinstructions].
+
+Already know what you're looking for in this guide? Jump to the following sections:
+
+* [Joining the conversation](#joining-the-conversation)
+* [Contributing through Github](#contributing-through-github)
+* [Understanding issues](#understanding-issues)
+* [Making a change](#making-a-change)
+* [Structuring contributions](#FitLins-coding-style-guide)
+* [Licensing](#licensing)
+* [Recognizing contributors](#recognizing-contributions)
+
+
+## Joining the conversation
+
+FitLins is maintained by a growing group of enthusiastic developers—
+and we're excited to have you join!
+Most of our discussions will take place on open [issues][link_issues].
+
+We also encourage users to report any difficulties they encounter on [NeuroStars][link_stars],
+a community platform for discussing neuroimaging.
+
+We actively monitor both spaces and look forward to hearing from you in either venue!
+
+
+## Contributing through GitHub
+
+[git][link_git] is a really useful tool for version control.
+[GitHub][link_github] sits on top of git and supports collaborative and distributed working.
+
+If you're not yet familiar with `git`, there are lots of great resources to help you *git* started!
+Some of our favorites include the [git Handbook][link_handbook] and
+the [Software Carpentry introduction to git][link_swc_intro].
+
+On GitHub, You'll use [Markdown][markdown] to chat in issues and pull requests.
+You can think of Markdown as a few little symbols around your text that will allow GitHub
+to render the text with a little bit of formatting.
+For example you could write words as bold (`**bold**`), or in italics (`*italics*`),
+or as a [link][rick_roll] (`[link](https://https://youtu.be/dQw4w9WgXcQ)`) to another webpage.
+
+GitHub has a really helpful page for getting started with
+[writing and formatting Markdown on GitHub][writing_formatting_github].
+
+
+## Understanding issues
+
+Every project on GitHub uses [issues][link_issues] slightly differently.
+
+The following outlines how the FitLins developers think about these tools.
+
+* **Issues** are individual pieces of work that need to be completed to move the project forwards.
+A general guideline: if you find yourself tempted to write a great big issue that
+is difficult to describe as one unit of work, please consider splitting it into two or more issues.
+
+    Issues are assigned [labels](#issue-labels) which explain how they relate to the overall project's
+    goals and immediate next steps.
+
+
+### Issue Labels
+
+The current list of issue labels are [here][link_labels] and include:
+
+* [![Help Wanted](https://img.shields.io/badge/-help%20wanted-159818.svg)][link_helpwanted] *These issues contain a task that a member of the team has determined we need additional help with.*
+
+    If you feel that you can contribute to one of these issues,
+    we especially encourage you to do so!
+
+* [![Bugs](https://img.shields.io/badge/-bugs-fc2929.svg)][link_bugs] *These issues point to problems in the project.*
+
+    If you find new a bug, please give as much detail as possible in your issue,
+    including steps to recreate the error.
+    If you experience the same bug as one already listed,
+    please add any additional information that you have as a comment.
+
+* [![Enhancement](https://img.shields.io/badge/-enhancement-84b6eb.svg)][link_feature] *These issues are asking for new features to be added to the project.*
+
+    Please try to make sure that your requested feature is distinct from any others
+    that have already been requested or implemented.
+    If you find one that's similar but there are subtle differences,
+    please reference the other request in your issue.
+
+
+## Making a change
+
+We appreciate all contributions to FitLins,
+but those accepted fastest will follow a workflow similar to the following:
+
+**1. Comment on an existing issue or open a new issue referencing your addition.**
+
+This allows other members of the FitLins development team to confirm that you aren't
+overlapping with work that's currently underway and that everyone is on the same page
+with the goal of the work you're going to carry out.
+
+[This blog][link_pushpullblog] is a nice explanation of why putting this work in up front
+is so useful to everyone involved.
+
+**2. [Fork][link_fork] the [FitLins repository][link_FitLins] to your profile.**
+
+This is now your own unique copy of FitLins.
+Changes here won't effect anyone else's work, so it's a safe space to explore edits to the code!
+
+Make sure to [keep your fork up to date][link_updateupstreamwiki] with the master repository.
+
+**3. Make the changes you've discussed, following the [FitLins coding style guide](#FitLins-coding-style-guide).**
+
+Try to keep the changes focused.
+If you feel tempted to "branch out" then please make a [new branch][link_branches].
+
+**4. Submit a [pull request][link_pullrequest].**
+
+A member of the development team will review your changes to confirm
+that they can be merged into the main code base.
+
+Pull requests titles should begin with a descriptive prefix:
+
+* ``ENH``: enhancements or new features
+* ``FIX``: bug fixes
+* ``TST``: new or updated tests
+* ``DOC``: new or updated documentation
+* ``STY``: style changes
+* ``REF``: refactoring existing code
+* ``CI``: updates to continous integration infrastructure
+* ``MAINT``: general maintenance
+
+For example: `[ENH] Support for naive thresholding`
+
+For works-in-progress, add the ``WIP`` tag in addition to the descriptive prefix.
+Pull-requests tagged with ``[WIP]`` will not be merged until the tag is removed.
+
+## FitLins coding style guide
 
 Whenever possible, instances of Nodes and Workflows should use the same names
 as the variables they are assigned to.
@@ -56,3 +182,56 @@ myworkflow1_wf = init_workflow_wf(name='myworkflow1_wf')
 myworkflow_lh_wf = init_workflow_wf(name='myworkflow_lh_wf')
 myworkflow_rh_wf = init_workflow_wf(name='myworkflow_rh_wf')
 ```
+
+
+## Licensing
+
+FitLins is licensed under the [Apache License, 2.0][link_license].
+By contributing to FitLins,
+you acknowledge that any contributions will be licensed under the same terms.
+
+
+## Recognizing contributions
+
+We welcome and recognize all contributions from documentation to testing to code development.
+You can see a list of current contributors in our [zenodo file][link_zenodo].
+If you are new to the project, don't forget to add your name and affiliation there!
+
+## Thank you!
+
+You're awesome. :wave::smiley:
+
+<br>
+
+*&mdash; Based on contributing guidelines from the [STEMMRoleModels][link_stemmrolemodels] project.*
+
+[link_github]: https://github.com/
+[link_FitLins]: https://github.com/poldracklab/fitlins
+[link_signupinstructions]: https://help.github.com/articles/signing-up-for-a-new-github-account
+
+[link_stars]: https://neurostars.org/
+
+[link_git]: https://git-scm.com/
+[link_handbook]: https://guides.github.com/introduction/git-handbook/
+[link_swc_intro]: http://swcarpentry.github.io/git-novice/
+
+[writing_formatting_github]: https://help.github.com/articles/getting-started-with-writing-and-formatting-on-github
+[markdown]: https://daringfireball.net/projects/markdown
+[rick_roll]: https://www.youtube.com/watch?v=dQw4w9WgXcQ
+
+[link_issues]: https://github.com/poldracklab/fitlins/issues
+[link_labels]: https://github.com/poldracklab/fitlins/labels
+[link_discussingissues]: https://help.github.com/articles/discussing-projects-in-issues-and-pull-requests
+
+[link_bugs]: https://github.com/poldracklab/fitlins/labels/bug
+[link_helpwanted]: https://github.com/poldracklab/fitlins/labels/help%20wanted
+[link_feature]: https://github.com/poldracklab/fitlins/labels/feature
+
+[link_pullrequest]: https://help.github.com/articles/creating-a-pull-request/
+[link_fork]: https://help.github.com/articles/fork-a-repo/
+[link_pushpullblog]: https://www.igvita.com/2011/12/19/dont-push-your-pull-requests/
+[link_branches]: https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/
+[link_updateupstreamwiki]: https://help.github.com/articles/syncing-a-fork/
+[link_stemmrolemodels]: https://github.com/KirstieJane/STEMMRoleModels
+[link_zenodo]: https://github.com/poldracklab/fitlins/blob/master/.zenodo.json
+[link_license]: https://github.com/poldracklab/fitlins/blob/master/LICENSE

fitlins/__init__.py

@@ -3,6 +3,10 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
+import warnings
+warnings.filterwarnings('ignore', r'numpy.ufunc size changed')
+warnings.filterwarnings('ignore', r'resolve package from __spec__')
+
 try:
     import matplotlib
 except ImportError: