Merge pull request #8 from nipreps/fix/leftovers-poldracklab-org

FIX: Update outdated references to ``poldracklab`` organization

Author: oesteban

docs/apps/docker.md

@@ -51,7 +51,7 @@ role="ref"}).-->
 Taking *fMRIPrep* to illustrate the usage, first you might want to make sure of the exact version of the tool to be used:
 
 ``` Shell
-$ docker pull poldracklab/fmriprep:<latest-version>
+$ docker pull nipreps/fmriprep:<latest-version>
 ```
 
 You can run *NiPreps* interacting directly with the Docker Engine via the `docker run` interface.
@@ -67,7 +67,7 @@ When you run `fmriprep-docker`, it will generate a Docker command line for you,
 ``` Shell
 $ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
 RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
-    -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
+    -v /path/to_output/dir:/out nipreps/fmriprep:20.2.2 \
     /data /out participant
 ...
 ```
@@ -118,7 +118,7 @@ You may also invoke `docker` directly:
 $ docker run -ti --rm \
     -v path/to/data:/data:ro \
     -v path/to/output:/out \
-    poldracklab/fmriprep:<latest-version> \
+    nipreps/fmriprep:<latest-version> \
     /data /out/out \
     participant
 ```
@@ -130,7 +130,7 @@ $ docker run -ti --rm \
     -v $HOME/ds005:/data:ro \
     -v $HOME/ds005/derivatives:/out \
     -v $HOME/tmp/ds005-workdir:/work \
-    poldracklab/fmriprep:<latest-version> \
+    nipreps/fmriprep:<latest-version> \
     /data /out/fmriprep-<latest-version> \
     participant \
     -w /work
@@ -146,7 +146,7 @@ $ docker run -ti --rm \                      # These lines
     -v $HOME/ds005:/data:ro \                # are equivalent to
     -v $HOME/ds005/derivatives:/out \        # a call to the App's
     -v $HOME/tmp/ds005-workdir:/work \       # entry-point.
-    poldracklab/fmriprep:<latest-version> \  #
+    nipreps/fmriprep:<latest-version> \  #
     \
     /data /out/fmriprep-<latest-version> \   # These lines correspond
     participant \                            # to the particular BIDS

docs/apps/singularity.md

@@ -12,7 +12,7 @@ directly on the system. This is as simple as:
 
 ``` Shell
 $ singularity build /my_images/fmriprep-<version>.simg \
-                    docker://poldracklab/fmriprep:<version>
+                    docker://nipreps/fmriprep:<version>
 ```
 
 where `<version>` should be replaced with the desired version of
@@ -30,7 +30,7 @@ $ docker run --privileged -t --rm \
     -v /var/run/docker.sock:/var/run/docker.sock \
     -v D:\host\path\where\to\output\singularity\image:/output \
     singularityware/docker2singularity \
-    poldracklab/fmriprep:<version>
+    nipreps/fmriprep:<version>
 ```
 
 Where `<version>` should be replaced with the desired version of
@@ -44,14 +44,14 @@ $ docker run --privileged -t --rm \
     -v /var/run/docker.sock:/var/run/docker.sock \
     -v /absolute/path/to/output/folder:/output \
     singularityware/docker2singularity \
-    poldracklab/fmriprep:<version>
+    nipreps/fmriprep:<version>
 ```
 
 Transfer the resulting Singularity image to the HPC, for example, using
 `scp` or `rsync`:
 
 ``` Shell
-$ scp poldracklab_fmriprep*.img [email protected]:/my_images
+$ scp nipreps_fmriprep*.img [email protected]:/my_images
 ```
 
 ## Running a Singularity Image
@@ -159,7 +159,7 @@ $ singularity run --cleanenv -B /work:/work fmriprep.simg \
     generally recommended to use binding scarcely and granting very limited
     access to the minimum necessary resources. In other words, it is
     preferred to bind just one subdirectory of `$HOME` than the full `$HOME`
-    directory of the host (see [poldracklab/fmriprep#1778 (comment)](https://github.com/poldracklab/fmriprep/issues/1778\#issuecomment-538009563)).
+    directory of the host (see [nipreps/fmriprep#1778 (comment)](https://github.com/nipreps/fmriprep/issues/1778\#issuecomment-538009563)).
 
 
 **Relevant aspects of the** `$HOME` **directory within the container**:
@@ -237,7 +237,7 @@ endpoints), then you can try the following:
 
 * `VerifiedHTTPSConnection ... Failed to establish a new connection: [Errno 110] Connection timed out`.
   If you encounter an error like this, probably you'll need to set up an
-  http proxy exporting `SINGULARITYENV_http_proxy` (see [poldracklab/fmriprep#1778 (comment)](https://github.com/poldracklab/fmriprep/issues/1778\#issuecomment-532297622).
+  http proxy exporting `SINGULARITYENV_http_proxy` (see [nipreps/fmriprep#1778 (comment)](https://github.com/nipreps/fmriprep/issues/1778\#issuecomment-532297622).
   For example:
 
     ```Shell

docs/assets/fmriprep.slurm

@@ -14,7 +14,7 @@
 # ------------------------------------------
 
 BIDS_DIR="$STUDY/data"
-DERIVS_DIR="derivatives/fmriprep-1.5.0"
+DERIVS_DIR="derivatives/fmriprep-20.2.2"
 LOCAL_FREESURFER_DIR="$STUDY/data/derivatives/freesurfer-6.0.1"
 
 # Prepare some writeable bind-mount points.
@@ -31,7 +31,7 @@ export SINGULARITYENV_FS_LICENSE=$HOME/.freesurfer.txt
 
 # Designate a templateflow bind-mount point
 export SINGULARITYENV_TEMPLATEFLOW_HOME="/templateflow"
-SINGULARITY_CMD="singularity run --cleanenv -B $BIDS_DIR:/data -B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} -B $L_SCRATCH:/work -B ${LOCAL_FREESURFER_DIR}:/fsdir $STUDY/images/poldracklab_fmriprep_1.5.0.simg"
+SINGULARITY_CMD="singularity run --cleanenv -B $BIDS_DIR:/data -B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} -B $L_SCRATCH:/work -B ${LOCAL_FREESURFER_DIR}:/fsdir $STUDY/images/fmriprep_20.2.2.simg"
 
 # Parse the participants.tsv file and extract one subject ID from the line corresponding to this SLURM task.
 subject=$( sed -n -E "$((${SLURM_ARRAY_TASK_ID} + 1))s/sub-(\S*)\>.*/\1/gp" ${BIDS_DIR}/participants.tsv )

docs/community/CONTRIBUTING.md

@@ -121,19 +121,19 @@ is difficult to describe as one unit of work, please consider splitting it into
 
 The current list of issue labels are [here][link_labels] and include:
 
-* [![Good first issue](https://img.shields.io/github/labels/poldracklab/fmriprep/good%20first%20issue)][link_firstissue] *These issues contain a task that is amenable to new contributors because it doesn't entail a steep learning curve.*
+* [![Good first issue](https://img.shields.io/github/labels/nipreps/fmriprep/good%20first%20issue)][link_firstissue] *These issues contain a task that is amenable to new contributors because it doesn't entail a steep learning curve.*
 
     If you feel that you can contribute to one of these issues,
     we especially encourage you to do so!
 
-* [![Bug](https://img.shields.io/github/labels/poldracklab/fmriprep/bug)][link_bugs] *These issues point to problems in the project.*
+* [![Bug](https://img.shields.io/github/labels/nipreps/fmriprep/bug)][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.
 
-* [![Feature](https://img.shields.io/github/labels/poldracklab/fmriprep/feature)][link_enhancement] *These issues are asking for new features and improvements to be considered by the project.*
+* [![Feature](https://img.shields.io/github/labels/nipreps/fmriprep/feature)][link_enhancement] *These issues are asking for new features and improvements to be considered by the project.*
 
     Please try to make sure that your requested feature is distinct from any others
     that have already been requested or implemented.
@@ -145,22 +145,22 @@ we have two sets of special labels:
 
 | Label                                                                                           | Description                                                                                           |
 |--------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------|
-| ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/impact%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/impact%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/impact%3A%20low)    | Estimation of the downstream impact the proposed feature/bugfix will have.                |
-| ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/effort%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/effort%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/effort%3A%20low)    | Estimation of effort required to implement the requested feature or fix the reported bug. |
+| ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/impact%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/impact%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/impact%3A%20low)    | Estimation of the downstream impact the proposed feature/bugfix will have.                |
+| ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/effort%3A%20high) <br> ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/effort%3A%20medium) <br> ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/effort%3A%20low)    | Estimation of effort required to implement the requested feature or fix the reported bug. |
 
 One way to understand these labels is to consider how they would apply to an imaginary issue.
 For example, if -- after a release -- a bug is identified that re-introduces a previously solved issue
 (i.e., its regresses the code outputs to some undesired behavior), we might assign it the following labels:
-![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/bug)
-![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/impact%3A%20high)
-![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/effort%3A%20low).
+![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/bug)
+![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/impact%3A%20high)
+![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/effort%3A%20low).
 Its development priority would then be "high", since it is a low-effort, high-impact change.
 
 Long-term goals may be labelled as a combination of:
-![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/effort%3A%20high) and  ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/impact%3A%20medium) or ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/impact%3A%20high)
+![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/effort%3A%20high) and  ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/impact%3A%20medium) or ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/impact%3A%20high)
 since they will have a high-impact on the code-base, but require a medium or high amount of effort.
 Of note, issues with the labels:
- ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/impact%3A%20low) or ![GitHub labels](https://img.shields.io/github/labels/poldracklab/fmriprep/effort%3A%20high)
+ ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/impact%3A%20low) or ![GitHub labels](https://img.shields.io/github/labels/nipreps/fmriprep/effort%3A%20high)
 are less likely to be addressed because they are less likely to impact the code-base, or because they will require a very high activation energy to do so.
 
 ## Making a change
@@ -190,7 +190,7 @@ but those accepted fastest will follow a workflow similar to the following:
   add the ["upstream" NiPreps repository as a remote][link_addremote]
   to your locally cloned repository.
     ```Shell
-    git remote add upstream https://github.com/poldracklab/fmriprep.git
+    git remote add upstream https://github.com/nipreps/fmriprep.git
     ```
     Make sure to [keep your fork up to date][link_updateupstreamwiki] with the upstream repository.<br />
     For example, to update your master branch on your local cloned repository:
@@ -339,7 +339,7 @@ You're awesome. :wave::smiley:
     [MetPy project](https://github.com/Unidata/MetPy).
 
 [link_github]: https://github.com/
-[link_fMRIPrep]: https://github.com/poldracklab/fmriprep
+[link_fMRIPrep]: https://github.com/nipreps/fmriprep
 [link_signupinstructions]: https://help.github.com/articles/signing-up-for-a-new-github-account
 
 [link_neurostars]: https://neurostars.org/tags/fmriprep
@@ -352,13 +352,13 @@ You're awesome. :wave::smiley:
 [markdown]: https://daringfireball.net/projects/markdown
 [rick_roll]: https://www.youtube.com/watch?v=dQw4w9WgXcQ
 
-[link_issues]: https://github.com/poldracklab/fmriprep/issues
-[link_labels]: https://github.com/poldracklab/fmriprep/labels
+[link_issues]: https://github.com/nipreps/fmriprep/issues
+[link_labels]: https://github.com/nipreps/fmriprep/labels
 [link_discussingissues]: https://help.github.com/articles/discussing-projects-in-issues-and-pull-requests
 
-[link_bugs]: https://github.com/poldracklab/fmriprep/labels/bug
-[link_firstissue]: https://github.com/poldracklab/fmriprep/labels/good%20first%20issue
-[link_enhancement]: https://github.com/poldracklab/fmriprep/labels/enhancement
+[link_bugs]: https://github.com/nipreps/fmriprep/labels/bug
+[link_firstissue]: https://github.com/nipreps/fmriprep/labels/good%20first%20issue
+[link_enhancement]: https://github.com/nipreps/fmriprep/labels/enhancement
 
 [link_pullrequest]: https://help.github.com/articles/creating-a-pull-request-from-a-fork
 [link_fork]: https://help.github.com/articles/fork-a-repo/
@@ -372,19 +372,19 @@ You're awesome. :wave::smiley:
 [link_add_commit_push]: https://help.github.com/articles/adding-a-file-to-a-repository-using-the-command-line
 [link_updateupstreamwiki]: https://help.github.com/articles/syncing-a-fork/
 [link_stemmrolemodels]: https://github.com/KirstieJane/STEMMRoleModels
-[link_zenodo]: https://github.com/poldracklab/fmriprep/blob/master/.zenodo.json
-[link_update_script]: https://github.com/poldracklab/fmriprep/blob/master/.maintenance/update_zenodo.py
+[link_zenodo]: https://github.com/nipreps/fmriprep/blob/master/.zenodo.json
+[link_update_script]: https://github.com/nipreps/fmriprep/blob/master/.maintenance/update_zenodo.py
 [link_devel]: https://fmriprep.readthedocs.io/en/latest/contributors.html
 [link_fmriprep]: http://fmriprep.org
 [link_bidsapps]: https://bids-apps.neuroimaging.io
 [link_mattermost]: https://mattermost.brainhack.org/brainhack/channels/fmriprep
 [link_aroma]: https://fmriprep.readthedocs.io/en/stable/workflows.html#ica-aroma
 
-[enh_ex]: https://github.com/poldracklab/fmriprep/pull/1508
-[fix_ex]: https://github.com/poldracklab/fmriprep/pull/1378
-[tst_ex]: https://github.com/poldracklab/fmriprep/pull/1098
-[doc_ex]: https://github.com/poldracklab/fmriprep/pull/1515
-[sty_ex]: https://github.com/poldracklab/fmriprep/pull/675
-[ref_ex]: https://github.com/poldracklab/fmriprep/pull/816
-[ci_ex]: https://github.com/poldracklab/fmriprep/pull/1048
-[maint_ex]: https://github.com/poldracklab/fmriprep/pull/1239
+[enh_ex]: https://github.com/nipreps/fmriprep/pull/1508
+[fix_ex]: https://github.com/nipreps/fmriprep/pull/1378
+[tst_ex]: https://github.com/nipreps/fmriprep/pull/1098
+[doc_ex]: https://github.com/nipreps/fmriprep/pull/1515
+[sty_ex]: https://github.com/nipreps/fmriprep/pull/675
+[ref_ex]: https://github.com/nipreps/fmriprep/pull/816
+[ci_ex]: https://github.com/nipreps/fmriprep/pull/1048
+[maint_ex]: https://github.com/nipreps/fmriprep/pull/1239

docs/community/features.md

@@ -1,7 +1,7 @@
 
 > The one bit that worries me is that *fMRIPrep* may become a Swiss army knife. I think instead it should just be a paring knife (small, efficient, and works for many things).
 >
-> -- <cite>Satra ([source](https://github.com/poldracklab/fmriprep/issues/1963#issuecomment-584455061))</cite>
+> -- <cite>Satra ([source](https://github.com/nipreps/fmriprep/issues/1963#issuecomment-584455061))</cite>
 
 When projects grow large, many forking paths created by newly implemented features start
 to open up.
@@ -14,7 +14,7 @@ Defining such a scope also aids the implementation of the ease-of-use principle:
 > in the acquisition, *NiPreps* should not add many additional knobs to those
 > for them to be considered a viable *augmentation* or extension of the scanner hw/sw.
 >
-> -- <cite>Oscar ([source](https://github.com/poldracklab/fmriprep/issues/1963#issuecomment-584455061))</cite>
+> -- <cite>Oscar ([source](https://github.com/nipreps/fmriprep/issues/1963#issuecomment-584455061))</cite>
 
 ## The problem of feature creep
 To avert [feature creep](https://en.wikipedia.org/wiki/Feature_creep) and
@@ -23,7 +23,7 @@ guidelines, with the hopes of keeping these tools in a healthy state.
 
 > I'm worried *fMRIPrep* is catching a case of featuritis
 >
-> -- <cite>Mathias ([source](https://github.com/poldracklab/fmriprep/issues/1985#issuecomment-588493059))</cite>
+> -- <cite>Mathias ([source](https://github.com/nipreps/fmriprep/issues/1985#issuecomment-588493059))</cite>
 
 These guidelines should also serve the community to transparently drive the process
 of including proposals into the road-map, set the ground for healthy conversation,
@@ -38,7 +38,7 @@ possible to rigorously follow them:
 > guarantee (or rule out) specific features when working with a small
 > development team.
 >
-> -- <cite>Elizabeth ([source](https://github.com/poldracklab/fmriprep/issues/1963#issuecomment-582453941))</cite>.
+> -- <cite>Elizabeth ([source](https://github.com/nipreps/fmriprep/issues/1963#issuecomment-582453941))</cite>.
 
 ## Proposing a new feature
 
@@ -52,7 +52,7 @@ particular *NiPrep* repository.
 If no previous discussion about the new idea is found,
 the next step is ensuring the new feature aligns with the vision and
 the scope of the target tool, as
-[Elizabeth points out](https://github.com/poldracklab/fmriprep/issues/1963#issuecomment-582453941).
+[Elizabeth points out](https://github.com/nipreps/fmriprep/issues/1963#issuecomment-582453941).
 Taking a look into the Development Road-map of the particular project
 (if it exists), may help finding an answer.
 
@@ -62,7 +62,7 @@ go ahead and post an issue requesting feedback on your proposal.
 Please make sure to clearly state why the new feature should be considered.
 
 ### Some questions will always be asked about a new feature
-[These questions by James](https://github.com/poldracklab/fmriprep/issues/1963#issuecomment-582220173)
+[These questions by James](https://github.com/nipreps/fmriprep/issues/1963#issuecomment-582220173)
 will certainly help build up the discourse in support of the new feature,
 as the *NiPreps* maintainers will consider them:
 
@@ -75,7 +75,7 @@ as the *NiPreps* maintainers will consider them:
     > Especially when the CLI is affected, and yet another option is added,
     > that makes the tool more complex to use.
     >
-    > -- <cite>Alejandro ([source](https://github.com/poldracklab/fmriprep/    issues/1963#issuecomment-582174814))</cite>.
+    > -- <cite>Alejandro ([source](https://github.com/nipreps/fmriprep/    issues/1963#issuecomment-582174814))</cite>.
 
   * Does the new feature substantially **increase the internal complexity**?
     Maintainers and developers will attempt to consolidate tools and lower the internal
@@ -97,7 +97,7 @@ as the *NiPreps* maintainers will consider them:
       * if so, can the procedure/value be determined algorithmically?
 
   * Does the feature **interact with other settings**?
-    For instance, [fmriprep#1962](https://github.com/poldracklab/fmriprep/pull/1962)
+    For instance, [fmriprep#1962](https://github.com/nipreps/fmriprep/pull/1962)
     interacts with the a/tCompCor implementation.
 
   * What is the **difficulty of implementing the procedure outside** of a *NiPrep*?