Merge pull request #144 from nipreps/dev/1.4.0

Massive merge of the new 2.0 API

.circleci/config.yml

@@ -48,9 +48,9 @@ jobs:
             - env-v2-
       - restore_cache:
           keys:
-            - data-v2-{{ .Branch }}-
-            - data-v2-master-
-            - data-v2-
+            - data-v4-{{ .Branch }}-
+            - data-v4-master-
+            - data-v4-
 
       - run:
           name: Setup git-annex
@@ -67,7 +67,7 @@ jobs:
           name: Setup DataLad & TemplateFlow
           command: |
             python -m pip install --no-cache-dir -U pip
-            python -m pip install --no-cache-dir -U datalad
+            python -m pip install --no-cache-dir -U datalad datalad-osf
             python -m pip install --no-cache-dir -U templateflow
             python -c "from templateflow import api as tfapi; \
                        tfapi.get('MNI152NLin2009cAsym', resolution=2, desc='brain', suffix='mask'); \
@@ -86,19 +86,33 @@ jobs:
       - run:
           name: Install ds001600
           command: |
-            datalad install https://github.com/OpenNeuroDatasets/ds001600.git
-            datalad update --merge -d ds001600/
-            datalad get -r -d ds001600/
+            datalad install -r https://github.com/nipreps-data/ds001600.git
+            datalad update -r --merge -d ds001600/
+            datalad get -r -d ds001600/ ds001600/sub-1/
+
       - run:
-          name: Get testdata
+          name: Install HCP/sub-101006
           command: |
-            if [[ ! -d /tmp/data/testdata ]]; then
-              wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-                  -O testdata.zip "https://files.osf.io/v1/resources/9sy2a/providers/osfstorage/5d44b940bcd6d900198ed6be/?zip="
-              unzip testdata.zip -d /tmp/data/testdata
-            fi
+            datalad install -r https://github.com/nipreps-data/HCP101006.git
+            datalad update -r --merge -d HCP101006/
+            datalad get -r -d HCP101006
+
+      - run:
+          name: Install ds001771
+          command: |
+            datalad install -r https://github.com/nipreps-data/ds001771.git
+            datalad update --merge -d ds001771/
+            datalad get -r -d ds001771/ ds001771/sub-36/fmap/*
+
+      - run:
+          name: Install ds000054
+          command: |
+            datalad install -r https://github.com/nipreps-data/ds000054.git
+            datalad update --merge -d ds000054/
+            datalad get -r -d ds000054/ ds000054/sub-100185/fmap/*
+
       - save_cache:
-          key: data-v2-{{ .Branch }}-{{ .BuildNum }}
+          key: data-v4-{{ .Branch }}-{{ .BuildNum }}
           paths:
             - /tmp/data
             - /tmp/templateflow
@@ -241,9 +255,9 @@ jobs:
             - freesurfer-v1-
       - restore_cache:
           keys:
-            - data-v2-{{ .Branch }}-
-            - data-v2-master-
-            - data-v2-
+            - data-v4-{{ .Branch }}-
+            - data-v4-master-
+            - data-v4-
       - restore_cache:
           keys:
             - workdir-v2-{{ .Branch }}-

.circleci/version.py

@@ -1,3 +1,4 @@
 """Get sdcflows version."""
 import sdcflows
+
 print(sdcflows.__version__, end="", file=open("/tmp/.docker-version.txt", "w"))

.github/workflows/travis.yml

@@ -89,6 +89,11 @@ jobs:
         datalad install -r https://github.com/nipreps-data/ds001771.git
         datalad update --merge -d ds001771/
         datalad get -r -d ds001771/ ds001771/sub-36/fmap/*
+
+        # ds000054
+        datalad install -r https://github.com/nipreps-data/ds000054.git
+        datalad update --merge -d ds000054/
+        datalad get -r -d ds000054/ ds000054/sub-100185/fmap/*
     - uses: actions/cache@v2
       with:
         path: /var/lib/apt

.mailmap

@@ -0,0 +1,68 @@
+Adriana Rivera-Dompenciel <[email protected]>
+Adriana Rivera-Dompenciel <[email protected]> <[email protected]>
+Alejandro de la Vega <[email protected]>
+Alejandro de la Vega <[email protected]> delavega4
+Anibal Sólon Heinsfeld <[email protected]>
+Asier Erramuzpe <[email protected]>
+Basile Pinsard <[email protected]>
+Basile Pinsard <[email protected]> basile <[email protected]>
+Basile Pinsard <[email protected]> <[email protected]>
+Blaise Frederick <[email protected]>
+Blaise Frederick <[email protected]> bbfrederick <[email protected]>
+Christopher J. Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>
+Daniel J. Lurie <[email protected]>
+Elizabeth DuPre <[email protected]>
+Franklin Feingold <[email protected]>
+Franklin Feingold <[email protected]> <[email protected]>
+Franz Liem <[email protected]>
+Gabriel A. Devenyi <[email protected]>
+Ilkay Isik <[email protected]>
+James D. Kent <[email protected]>
+James D. Kent <[email protected]> <[email protected]>
+James D. Kent <[email protected]> Fred Mertz <[email protected]>
+Jarod Roland <[email protected]>
+Joseph B. Wexler <[email protected]>
+Joseph B. Wexler <[email protected]> Joe B. Wexler
+Joseph B. Wexler <[email protected]> jbwexler
+Karolina Finc <[email protected]>
+Karolina Finc <[email protected]> kfinc
+Kevin Sitek <[email protected]>
+Kevin Sitek <[email protected]> sitek <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> <filo@filo-dtc-laptop>
+Krzysztof J. Gorgolewski <[email protected]> <filo@filo-Precision-M6500.(none)>
+Krzysztof J. Gorgolewski <[email protected]> <filo@filo-Precision-M6500>
+Krzysztof J. Gorgolewski <[email protected]> <filo@filolaptop>
+Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
+Marc Bue <[email protected]>
+Markus H. Sneve <[email protected]> <[email protected]>
+Mathias Goncalves <[email protected]>
+Mathias Goncalves <[email protected]> <[email protected]>
+Mathias Goncalves <[email protected]> <[email protected]>
+Matteo Visconti di Oleggio Castello <[email protected]>
+Marc Bue <[email protected]>
+Marc Bue <[email protected]> marcbue <[email protected]>
+Mikael Naveau <[email protected]>
+Nir Jacoby <[email protected]>
+Nir Jacoby <[email protected]> <[email protected]>
+Noah C. Benson <[email protected]>
+Noah C. Benson <[email protected]> noahbenson
+Oscar Esteban <[email protected]>
+Oscar Esteban <[email protected]> <[email protected]>
+Pablo Velasco <[email protected]>
+Rastko Ciric <[email protected]>
+Rastko Ciric <[email protected]> <[email protected]>
+Rastko Ciric <[email protected]> <[email protected]>
+Romain Valabregue <[email protected]>
+Ross Blair <[email protected]>
+Ross Blair <[email protected]> <[email protected]>
+Saren Seeley <[email protected]>
+Sebastian Urchs <[email protected]>
+Sebastien Naze <[email protected]>
+Shoshana Berleant <[email protected]>  <[email protected]>
+Soichi Hayashi <[email protected]>
+William Hedley Thompson <[email protected]>
+William Hedley Thompson <[email protected]> <[email protected]>

.maint/contributors.json

@@ -0,0 +1,32 @@
+[
+  {
+    "affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
+    "name": "Adebimpe, Azeez",
+    "orcid": "0000-0001-9049-0135"
+  },
+  {
+    "affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
+    "name": "Cieslak, Matthew",
+    "orcid": "0000-0002-1931-4734"
+  },
+  {
+    "affiliation": "Cyceron, UMS 3408 (CNRS - UCBN), France",
+    "name": "Naveau, Mikaël",
+    "orcid": "0000-0001-6948-9068"
+  },
+  {
+    "affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
+    "name": "Satterthwaite, Theodore D.",
+    "orcid": "0000-0001-7072-9399"
+  },
+  {
+    "affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University",
+    "name": "Sitek, Kevin R.",
+    "orcid": "0000-0002-2172-5786"
+  },
+  {
+    "affiliation": "Center for Lifespan Changes in Brain and Cognition, University of Oslo",
+    "name": "Sneve, Markus H.",
+    "orcid": "0000-0001-7644-7915"
+  }
+]

.maint/developers.json

@@ -0,0 +1,32 @@
+[
+  {
+    "affiliation": "Department of Psychology, Stanford University",
+    "name": "Blair, Ross W.",
+    "orcid": "0000-0003-3007-1056"
+  },
+  {
+    "affiliation": "Dept. of Radiology, Lausanne University Hospital, University of Lausanne",
+    "name": "Esteban, Oscar",
+    "orcid": "0000-0001-8435-6191"
+  },
+  {
+    "affiliation": "Department of Psychology, Stanford University",
+    "name": "Goncalves, Mathias",
+    "orcid": "0000-0002-7252-7771"
+  },
+  {
+    "affiliation": "Department of Psychology, Stanford University",
+    "name": "Gorgolewski, Krzysztof J.",
+    "orcid": "0000-0003-3321-7583"
+  },
+  {
+    "affiliation": "Department of Psychology, Stanford University",
+    "name": "Markiewicz, Christopher J.",
+    "orcid": "0000-0002-6533-164X"
+  },
+  {
+    "affiliation": "Department of Psychology, Stanford University",
+    "name": "Poldrack, Russell A.",
+    "orcid": "0000-0001-6755-0259"
+  }
+]

.maint/former.json

@@ -0,0 +1,5 @@
+[
+  {
+    "name": "Berleant, Shoshana"
+  }
+]

.maint/paper_author_list.py

@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+"""Generate an author list for a new paper or abstract."""
+import sys
+from pathlib import Path
+import json
+from update_zenodo import get_git_lines, sort_contributors
+
+
+# These authors should go last
+AUTHORS_LAST = ["Gorgolewski, Krzysztof J.", "Satterthwaite, Theodore D.", "Poldrack, Russell A.", "Esteban, Oscar"]
+
+
+def _aslist(inlist):
+    if not isinstance(inlist, list):
+        return [inlist]
+    return inlist
+
+
+if __name__ == "__main__":
+    devs = json.loads(Path(".maint/developers.json").read_text())
+    contribs = json.loads(Path(".maint/contributors.json").read_text())
+
+    author_matches, unmatched = sort_contributors(
+        devs + contribs,
+        get_git_lines(),
+        exclude=json.loads(Path(".maint/former.json").read_text()),
+        last=AUTHORS_LAST,
+    )
+    # Remove position
+    affiliations = []
+    for item in author_matches:
+        del item["position"]
+        for a in _aslist(item.get("affiliation", "Unaffiliated")):
+            if a not in affiliations:
+                affiliations.append(a)
+
+    aff_indexes = [
+        ", ".join(
+            [
+                "%d" % (affiliations.index(a) + 1)
+                for a in _aslist(author.get("affiliation", "Unaffiliated"))
+            ]
+        )
+        for author in author_matches
+    ]
+
+    print(
+        "Some people made commits, but are missing in .maint/ "
+        "files: %s." % ", ".join(unmatched),
+        file=sys.stderr,
+    )
+
+    print("Authors (%d):" % len(author_matches))
+    print(
+        "%s."
+        % "; ".join(
+            [
+                "%s \\ :sup:`%s`\\ " % (i["name"], idx)
+                for i, idx in zip(author_matches, aff_indexes)
+            ]
+        )
+    )
+
+    print(
+        "\n\nAffiliations:\n%s"
+        % "\n".join(
+            ["{0: >2}. {1}".format(i + 1, a) for i, a in enumerate(affiliations)]
+        )
+    )