diff --git a/.zenodo.json b/.zenodo.json index fd8891f7c3..1058e3b150 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -15,45 +15,45 @@ "name": "Ziegler, Erik", "orcid": "0000-0003-1857-8129" }, + { + "affiliation": "The University of Iowa", + "name": "Ellis, David Gage", + "orcid": "0000-0002-3718-6836" + }, { "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland", "name": "Notter, Michael Philipp", "orcid": "0000-0002-5866-047X" }, { - "name": "Burns, Christopher" - }, - { - "affiliation": "The University of Iowa", - "name": "Ellis, David Gage", - "orcid": "0000-0002-3718-6836" + "affiliation": "Stanford University", + "name": "Markiewicz, Christopher J.", + "orcid": "0000-0002-6533-164X" }, { "affiliation": "University of Iowa", "name": "Johnson, Hans", "orcid": "0000-0001-9513-2660" }, + { + "name": "Burns, Christopher" + }, { "affiliation": "Klinikum rechts der Isar, TUM. ACPySS", "name": "Manh\u00e3es-Savio, Alexandre", "orcid": "0000-0002-6608-6885" }, - { - "name": "Hamalainen, Carlo", - "orcid": "0000-0001-7655-3830" - }, { "affiliation": "MIT", "name": "Jarecka, Dorota", "orcid": "0000-0003-1857-8129" }, { - "name": "Yvernault, Benjamin" + "name": "Hamalainen, Carlo", + "orcid": "0000-0001-7655-3830" }, { - "affiliation": "Stanford University", - "name": "Markiewicz, Christopher J.", - "orcid": "0000-0002-6533-164X" + "name": "Yvernault, Benjamin" }, { "affiliation": "Florida International University", @@ -64,6 +64,10 @@ "affiliation": "Department of Psychology, Stanford University", "name": "Waskom, Michael" }, + { + "affiliation": "MIT", + "name": "Goncalves, Mathias" + }, { "affiliation": "Developer", "name": "Clark, Daniel", @@ -76,21 +80,22 @@ { "name": "Loney, Fred" }, - { - "name": "Madison, Cindee" - }, { "name": "Modat, Marc" }, - { - "affiliation": "MIT", - "name": "Goncalves, Mathias" - }, { "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University", "name": "Dewey, Blake E", "orcid": "0000-0003-4554-5058" }, + { + "affiliation": "University of California, San Francisco", + "name": "Jordan, Kesshi", + "orcid": "0000-0001-6313-0580" + }, + { + "name": "Madison, Cindee" + }, { "affiliation": "National Institutes of Health", "name": "Clark, Michael G. " @@ -111,13 +116,18 @@ "orcid": "0000-0002-3982-4416" }, { - "name": "Pinsard, Basile" + "affiliation": "Dartmouth College", + "name": "Visconti di Oleggio Castello, Matteo", + "orcid": "0000-0001-7931-5272" }, { "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay", "name": "Gramfort, Alexandre", "orcid": "0000-0001-9791-4404" }, + { + "name": "Pinsard, Basile" + }, { "name": "Berleant, Shoshana" }, @@ -136,11 +146,6 @@ "name": "Cipollini, Ben", "orcid": "0000-0002-7782-0790" }, - { - "affiliation": "National Institute of Mental Health", - "name": "Nielson, Dylan M.", - "orcid": "0000-0003-4613-6643" - }, { "affiliation": "Montreal Neurological Institute and Hospital", "name": "Markello, Ross", @@ -156,24 +161,14 @@ "name": "Wassermann , Demian", "orcid": "0000-0001-5194-6056" }, + { + "name": "Moloney, Brendan" + }, { "affiliation": "Dartmouth College: Hanover, NH, United States", "name": "Halchenko, Yaroslav O.", "orcid": "0000-0003-3456-2493" }, - { - "affiliation": "Dartmouth College", - "name": "Visconti di Oleggio Castello, Matteo", - "orcid": "0000-0001-7931-5272" - }, - { - "affiliation": "MIT", - "name": "Kaczmarzyk, Jakub", - "orcid": "0000-0002-5544-7577" - }, - { - "name": "Moloney, Brendan" - }, { "affiliation": "Otto-von-Guericke-University Magdeburg, Germany", "name": "Hanke, Michael", @@ -188,6 +183,11 @@ "affiliation": "Molecular Imaging Research Center, CEA, France", "name": "Bougacha, Salma" }, + { + "affiliation": "MIT", + "name": "Kaczmarzyk, Jakub", + "orcid": "0000-0002-5544-7577" + }, { "affiliation": "Vrije Universiteit, Amsterdam", "name": "Gilles de Hollander", @@ -234,6 +234,9 @@ "name": "DuPre, Elizabeth", "orcid": "0000-0003-1358-196X" }, + { + "name": "Dubois, Mathieu" + }, { "affiliation": "Child Mind Institute", "name": "Frohlich, Caroline" @@ -266,6 +269,11 @@ "name": "Kastman, Erik", "orcid": "0000-0001-7221-9042" }, + { + "affiliation": "SRI International", + "name": "Nichols, B. Nolan", + "orcid": "0000-0003-1099-3328" + }, { "name": "Ginsburg, Daniel" }, @@ -282,40 +290,15 @@ { "name": "Kent, James" }, - { - "name": "Perez-Guevara, Martin" - }, { "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland", "name": "Gillman, Ashley", "orcid": "0000-0001-9130-1092" }, - { - "affiliation": "Molecular Imaging Research Center, CEA, France", - "name": "Bougacha, Salma" - }, - { - "name": "Forbes, Jessica" - }, - { - "affiliation": "Montreal Neurological Institute and Hospital", - "name": "DuPre, Elizabeth", - "orcid": "0000-0003-1358-196X" - }, - { - "affiliation": "SRI International", - "name": "Nichols, B. Nolan", - "orcid": "0000-0003-1099-3328" - }, { "affiliation": "Child Mind Institute", "name": "Giavasis, Steven" }, - { - "affiliation": "University of California, San Francisco", - "name": "Jordan, Kesshi", - "orcid": "0000-0001-6313-0580" - }, { "affiliation": "UniversityHospital Heidelberg, Germany", "name": "Kleesiek, Jens" @@ -326,6 +309,9 @@ { "name": "K\u00fcttner, Ren\u00e9" }, + { + "name": "Liem, Franz" + }, { "name": "Haselgrove, Christian" }, @@ -336,14 +322,13 @@ "name": "Ghayoor, Ali" }, { - "name": "Millman, Jarrod" + "name": "Perez-Guevara, Martin" }, { - "name": "Haehn, Daniel" + "name": "Millman, Jarrod" }, { - "affiliation": "MPI CBS Leipzig, Germany", - "name": "Lampe, Leonie" + "name": "Haehn, Daniel" }, { "name": "Lai, Jeff" @@ -377,9 +362,8 @@ "orcid": "0000-0002-9546-1306" }, { - "affiliation": "University of California, San Francisco", - "name": "Jordan, Kesshi", - "orcid": "0000-0001-6313-0580" + "affiliation": "MPI CBS Leipzig, Germany", + "name": "Lampe, Leonie" }, { "affiliation": "Leibniz Institute for Neurobiology", @@ -397,11 +381,6 @@ { "name": "McDermottroe, Conor" }, - { - "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging", - "name": "Chetverikov, Andrey", - "orcid": "0000-0003-2767-6310" - }, { "name": "Salvatore, John" }, @@ -414,22 +393,27 @@ { "name": "Poldrack, Russell" }, - { - "affiliation": "University of California, San Francisco", - "name": "Jordan, Kesshi", - "orcid": "0000-0001-6313-0580" - }, { "affiliation": "Child Mind Institute", "name": "Craddock, R. Cameron", "orcid": "0000-0002-4950-1303" }, + { + "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging", + "name": "Chetverikov, Andrey", + "orcid": "0000-0003-2767-6310" + }, { "name": "Inati, Souheil" }, { "name": "Hinds, Oliver" }, + { + "affiliation": "Technical University Munich", + "name": "Molina-Romero, Miguel", + "orcid": "0000-0001-8054-0426" + }, { "affiliation": "University of Newcastle, Australia", "name": "Cooper, Gavin", @@ -498,9 +482,8 @@ "name": "Sharp, Paul" }, { - "affiliation": "University College London", - "name": "Mancini, Matteo", - "orcid": "0000-0001-7194-4568" + "affiliation": "Vrije Universiteit Amsterdam", + "name": "Ort, Eduard" }, { "name": "Weinstein, Alejandro" @@ -530,11 +513,6 @@ { "name": "Arias, Jaime" }, - { - "affiliation": "Dartmouth College", - "name": "Visconti di Oleggio Castello, Matteo", - "orcid": "0000-0001-7931-5272" - }, { "affiliation": "CEA", "name": "Papadopoulos Orfanos, Dimitri", @@ -554,9 +532,6 @@ { "name": "Brett, Matthew" }, - { - "name": "Dubois, Mathieu" - }, { "name": "Falkiewicz, Marcel" }, @@ -582,9 +557,6 @@ { "name": "Flandin, Guillaume" }, - { - "name": "Liem, Franz" - }, { "affiliation": "Stereotaxy Core, Brain & Spine Institute", "name": "P\u00e9rez-Garc\u00eda, Fernando", @@ -605,15 +577,6 @@ "affiliation": "MIT, HMS", "name": "Ghosh, Satrajit", "orcid": "0000-0002-5312-6729" - }, - { - "affiliation": "Vrije Universiteit Amsterdam", - "name": "Ort, Eduard" - }, - { - "affiliation": "Technical University Munich", - "name": "Molina-Romero, Miguel", - "orcid": "0000-0001-8054-0426" } ], "keywords": [ diff --git a/CHANGES b/doc/changelog/0.X.X-changelog similarity index 95% rename from CHANGES rename to doc/changelog/0.X.X-changelog index 56a5fc7490..b1c16318b2 100644 --- a/CHANGES +++ b/doc/changelog/0.X.X-changelog @@ -1,32 +1,3 @@ -1.0.0 (January 24, 2018) -======================== - -###### [Full changelog](https://github.com/nipy/nipype/milestone/16?closed=1) - -* FIX: Change to interface workdir within ``Interface.run()`` instead Node (https://github.com/nipy/nipype/pull/2384) -* FIX: PBS plugin submissions (https://github.com/nipy/nipype/pull/2344) -* FIX: Graph plugins submissions (https://github.com/nipy/nipype/pull/2359) -* FIX: Logging error if % in interface command (https://github.com/nipy/nipype/pull/2364) -* FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373) -* FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369) -* FIX: Errors parsing ``$DISPLAY`` (https://github.com/nipy/nipype/pull/2363) -* FIX: MultiProc starting workers at dubious wd (https://github.com/nipy/nipype/pull/2368) -* FIX: Explicitly collect MultiProc job IDs (https://github.com/nipy/nipype/pull/2378) -* FIX: Correct Windows environment canonicalization (https://github.com/nipy/nipype/pull/2328) -* FIX: Linked libraries (https://github.com/nipy/nipype/pull/2322) -* REF+FIX: Move BIDSDataGrabber to `interfaces.io` + fix correct default behavior (https://github.com/nipy/nipype/pull/2336) -* REF+MAINT: Simplify hashing (https://github.com/nipy/nipype/pull/2383) -* MAINT: Cleanup Interfaces base (https://github.com/nipy/nipype/pull/2387) -* MAINT: Cleanup EngineBase (https://github.com/nipy/nipype/pull/2376) -* MAINT: Cleaning / simplify ``Node`` (https://github.com/nipy/nipype/pull/2325) -* MAINT+ENH: Update and extend MRtrix3 interfaces (https://github.com/nipy/nipype/pull/2338) -* ENH: Add AFNI interface for 3dConvertDset (https://github.com/nipy/nipype/pull/2337) -* ENH: Allow specific interface command prefixes (https://github.com/nipy/nipype/pull/2379) -* STY: Cleanup of PEP8 violations (https://github.com/nipy/nipype/pull/2358) -* STY: Cleanup of trailing spaces and adding of missing newlines at end of files (https://github.com/nipy/nipype/pull/2355) -* STY: Apply yapf to codebase (https://github.com/nipy/nipype/pull/2371) -* DOC: Updated guide for contributing (https://github.com/nipy/nipype/pull/2393) - 0.14.0 (November 29, 2017) ========================== diff --git a/doc/changelog/1.X.X-changelog b/doc/changelog/1.X.X-changelog new file mode 100644 index 0000000000..49b8790ff9 --- /dev/null +++ b/doc/changelog/1.X.X-changelog @@ -0,0 +1,61 @@ +1.0.1 (February 27, 2018) +========================= + +###### [Full changelog](https://github.com/nipy/nipype/milestone/16?closed=1) + +* FIX: Small bug in freesurfer label2annot fill_thresh specs [#2377](https://github.com/nipy/nipype/pull/2377) +* FIX: Error creating gradients in DTIRecon [#2460](https://github.com/nipy/nipype/pull/2460) +* FIX: improve matlab_cmd [#2452](https://github.com/nipy/nipype/pull/2452) +* FIX: Extract unit information from image header in CompCor [#2458](https://github.com/nipy/nipype/pull/2458) +* FIX: Update pybids data directory, unbundle out-of-date numpydoc [#2437](https://github.com/nipy/nipype/pull/2437) +* FIX: Out_file bugs in Afni.Zcat and Afni.Merge interfaces [#2424](https://github.com/nipy/nipype/pull/2424) +* FIX: Re-enable spm.Realign to take lists of lists of files [#2409](https://github.com/nipy/nipype/pull/2409) +* FIX: Remove deprecated output from ICC interface [#2422](https://github.com/nipy/nipype/pull/2422) +* FIX: Argstr for mask in Afni.BlurToFWHM [#2418](https://github.com/nipy/nipype/pull/2418) +* FIX: Default value for sbatch_args (SLURMGraph) [#2417](https://github.com/nipy/nipype/pull/2417) +* FIX: Ortvec argstr for Afni.Deconvolve [#2415](https://github.com/nipy/nipype/pull/2415) +* FIX: Bug fixes for afni.model [#2398](https://github.com/nipy/nipype/pull/2398) +* DOC: Add brief neurodocker tutorial [#2464](https://github.com/nipy/nipype/pull/2464) +* DOC: Fix tutorials [#2459](https://github.com/nipy/nipype/pull/2459) +* ENH: antsRegistrationSyNQuick interface [#2453](https://github.com/nipy/nipype/pull/2453) +* ENH: Automate updates of CHANGES [#2440](https://github.com/nipy/nipype/pull/2440) +* ENH: Add SPM Fieldmap Tool wrapper [#1905](https://github.com/nipy/nipype/pull/1905) +* ENH: Additional option for DataGrabber [#1915](https://github.com/nipy/nipype/pull/1915) +* ENH: Add 3dTproject AFNI interface, Fix OneDToolPy, Add -noFDR flag to 3dDeconvolve [#2426](https://github.com/nipy/nipype/pull/2426) +* ENH: c3d/c4d interface [#2430](https://github.com/nipy/nipype/pull/2430) +* ENH: Allow input weight for AFNI's volreg. [#2396](https://github.com/nipy/nipype/pull/2396) +* ENH: Delay crashing if exception is raised in local hash check [#2410](https://github.com/nipy/nipype/pull/2410) +* CI: Add doctests to pytest script [#2449](https://github.com/nipy/nipype/pull/2449) +* CI: Ignore tests in calculating coverage [#2443](https://github.com/nipy/nipype/pull/2443) +* CI: Saturate Circle workflow [#2386](https://github.com/nipy/nipype/pull/2386) +* REF: Update and factor mount table parsing [#2444](https://github.com/nipy/nipype/pull/2444) +* REF: Make ignore_exception a class attribute [#2414](https://github.com/nipy/nipype/pull/2414) + +1.0.0 (January 24, 2018) +======================== + +###### [Full changelog](https://github.com/nipy/nipype/milestone/16?closed=1) + +* FIX: Change to interface workdir within ``Interface.run()`` instead Node (https://github.com/nipy/nipype/pull/2384) +* FIX: PBS plugin submissions (https://github.com/nipy/nipype/pull/2344) +* FIX: Graph plugins submissions (https://github.com/nipy/nipype/pull/2359) +* FIX: Logging error if % in interface command (https://github.com/nipy/nipype/pull/2364) +* FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373) +* FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369) +* FIX: Errors parsing ``$DISPLAY`` (https://github.com/nipy/nipype/pull/2363) +* FIX: MultiProc starting workers at dubious wd (https://github.com/nipy/nipype/pull/2368) +* FIX: Explicitly collect MultiProc job IDs (https://github.com/nipy/nipype/pull/2378) +* FIX: Correct Windows environment canonicalization (https://github.com/nipy/nipype/pull/2328) +* FIX: Linked libraries (https://github.com/nipy/nipype/pull/2322) +* REF+FIX: Move BIDSDataGrabber to `interfaces.io` + fix correct default behavior (https://github.com/nipy/nipype/pull/2336) +* REF+MAINT: Simplify hashing (https://github.com/nipy/nipype/pull/2383) +* MAINT: Cleanup Interfaces base (https://github.com/nipy/nipype/pull/2387) +* MAINT: Cleanup EngineBase (https://github.com/nipy/nipype/pull/2376) +* MAINT: Cleaning / simplify ``Node`` (https://github.com/nipy/nipype/pull/2325) +* MAINT+ENH: Update and extend MRtrix3 interfaces (https://github.com/nipy/nipype/pull/2338) +* ENH: Add AFNI interface for 3dConvertDset (https://github.com/nipy/nipype/pull/2337) +* ENH: Allow specific interface command prefixes (https://github.com/nipy/nipype/pull/2379) +* STY: Cleanup of PEP8 violations (https://github.com/nipy/nipype/pull/2358) +* STY: Cleanup of trailing spaces and adding of missing newlines at end of files (https://github.com/nipy/nipype/pull/2355) +* STY: Apply yapf to codebase (https://github.com/nipy/nipype/pull/2371) +* DOC: Updated guide for contributing (https://github.com/nipy/nipype/pull/2393) diff --git a/doc/conf.py b/doc/conf.py index 22467090af..c0c66cbc1e 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -82,7 +82,7 @@ # The short X.Y version. version = nipype.__version__ # The full version, including alpha/beta/rc tags. -release = "1.0.0" +release = "1.0.1" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/nipype/info.py b/nipype/info.py index 8a7e3b4348..1daa382e24 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -11,7 +11,7 @@ # full release. '.dev' as a version_extra string means this is a development # version # Remove -dev for release -__version__ = '1.0.1-dev' +__version__ = '1.0.1' def get_nipype_gitversion():