So there is indeed uncomitted difference in the state of mriqc even locally which also show up remotely, but reproman run complains about them only after "assuring" the same state on remote end. I wonder if complain should be issued upon analysis of the local space if there is a requirement to be "clean"?
the diff
```shell
(git)smaug:~/.reproman/run-root/4b3524f6-b98d-11e9-95c1-8019340ce7f2[master]
$> git status
On branch master
Changes not staged for commit:
(use "git add ..." to update what will be committed)
(use "git checkout -- ..." to discard changes in working directory)
modified: data/mriqc (new commits)
no changes added to commit (use "git add" and/or "git commit -a")
1 10154.....................................:Wed 07 Aug 2019 11:40:01 PM EDT:.
(git)smaug:~/.reproman/run-root/4b3524f6-b98d-11e9-95c1-8019340ce7f2[master]
$> datalad diff -r
modified(dataset): data/mriqc
modified(file): data/mriqc/.gitattributes
1 10155.....................................:Wed 07 Aug 2019 11:40:18 PM EDT:.
(git)smaug:~/.reproman/run-root/4b3524f6-b98d-11e9-95c1-8019340ce7f2[master]
$> git -C data/mriqc show
commit 8df32f9288d31c58f3bcf12195f87527e491c662 (HEAD -> master)
Author: Yaroslav Halchenko
Date: Wed Aug 7 23:33:44 2019 -0400
Instruct annex to add text files to Git
diff --git a/.gitattributes b/.gitattributes
index c3aaefe..8e9a246 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,4 @@
* annex.backend=MD5E
-**/.git* annex.largefiles=nothing
\ No newline at end of file
+**/.git* annex.largefiles=nothing
+* annex.largefiles=(not(mimetype=text/*))
\ No newline at end of file
```
Trying to run #438 (as of v0.1.0-519-g1588f76) using #408 (as of v0.1.0-546-gac14277) to ERROR out with
full log
```shell (git)hopa:~/proj/repronim/reproman-master[doc-usecases]docs/usecases $> ./bids-fmriprep-workflow-NP.sh bids-fmriprep-workflow-NP/out3 [INFO ] Creating a new annex repo at /home/yoh/proj/repronim/reproman-master/docs/usecases/bids-fmriprep-workflow-NP/out3 create(ok): /home/yoh/proj/repronim/reproman-master/docs/usecases/bids-fmriprep-workflow-NP/out3 (dataset) [INFO ] Running procedure cfg_text2git [INFO ] == Command start (output follows) ===== [INFO ] == Command exit (modification check follows) ===== [INFO ] Cloning http://datasets.datalad.org/repronim/containers [1 other candidates] into '/home/yoh/proj/repronim/reproman-master/docs/usecases/bids-fmriprep-workflow-NP/out3/containers' install(ok): containers (dataset) action summary: add (ok: 2) install (ok: 1) save (ok: 1) add(ok): .datalad/config (file) save(ok): containers (dataset) add(ok): containers (file) save(ok): . (dataset) action summary: add (ok: 2) save (ok: 2) [INFO ] Cloning https://github.com/ReproNim/ds000003-demo [1 other candidates] into '/home/yoh/proj/repronim/reproman-master/docs/usecases/bids-fmriprep-workflow-NP/out3/data/bids' [INFO ] Remote origin not usable by git-annex; setting annex-ignore [INFO ] access to 1 dataset sibling s3-PRIVATE not auto-enabled, enable with: | datalad siblings -d "/home/yoh/proj/repronim/reproman-master/docs/usecases/bids-fmriprep-workflow-NP/out3/data/bids" enable -s s3-PRIVATE install(ok): data/bids (dataset) action summary: add (ok: 2) install (ok: 1) save (ok: 1) add(ok): licenses/.gitignore (file) add(ok): licenses/README.md (file) save(ok): . (dataset) action summary: add (ok: 2) save (ok: 1) [INFO ] Creating a new annex repo at /home/yoh/proj/repronim/reproman-master/docs/usecases/bids-fmriprep-workflow-NP/out3/data/mriqc create(ok): data/mriqc (dataset) [INFO ] Running procedure cfg_text2git [INFO ] == Command start (output follows) ===== [INFO ] == Command exit (modification check follows) ===== action summary: add (ok: 2) create (ok: 1) save (ok: 1) 2019-08-07 23:33:47,131 [INFO ] No root directory supplied for smaug; using '/home/yoh/.reproman/run-root' [INFO ] Connecting ... ECDSA host key for IP address '129.170.233.9' not in list of known hosts. [INFO ] Considering to create a target dataset /home/yoh/proj/repronim/reproman-master/docs/usecases/bids-fmriprep-workflow-NP/out3 at /home/yoh/.reproman/run-root/4b3524f6-b98d-11e9-95c1-8019340ce7f2 of smaug [INFO ] Fetching updates forwhich is apparently due to https://github.com/datalad/datalad/issues/3591 - leaving super-dataset dirty, if subdataset was created with
-cprocedure call.So there is indeed uncomitted difference in the state of mriqc even locally which also show up remotely, but
reproman runcomplains about them only after "assuring" the same state on remote end. I wonder if complain should be issued upon analysis of the local space if there is a requirement to be "clean"?the diff
```shell (git)smaug:~/.reproman/run-root/4b3524f6-b98d-11e9-95c1-8019340ce7f2[master] $> git status On branch master Changes not staged for commit: (use "git add