Merge pull request #3336 from nipy/rel/1.6.1

REL: 1.6.1
nipy · Jun 16, 2021 · 0289137 · 0289137
2 parents 935d209 + 9fd9785
commit 0289137
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Showing 15 changed files with 159 additions and 117 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -204,61 +204,6 @@ jobs:
             - /tmp/docker/cache/Dockerfile.base-pruned
           key: dockerfile-cache-v1-{{ .Branch }}-{{ checksum "/tmp/docker/cache/Dockerfile.base-pruned" }}
 
-  pypi_precheck:
-    machine: *machine_kwds
-    working_directory: /home/circleci/nipype
-    steps:
-      - checkout:
-          path: /home/circleci/nipype
-      - run:
-          name: Check pypi preconditions
-          command: |
-            pyenv local 3.6.5
-            pip install --upgrade pip twine future wheel readme_renderer setuptools
-            python setup.py sdist bdist_wheel
-            twine check dist/*
-      - run:
-          name: Validate Python 3 installation
-          command: |
-            pyenv local 3.6.5
-            pip install --upgrade pip
-            pip install dist/nipype-*-py3-none-any.whl
-      - run:
-          name: Validate Python 3.7 installation
-          command: |
-            pyenv local 3.7.0
-            pip install --upgrade pip
-            # Pre-install a version of numpy that will not pass
-            pip install numpy==1.15.0
-            pip install dist/nipype-*-py3-none-any.whl
-            # Numpy should be upgraded to >= 1.15.3
-            test "$(pip show numpy | grep Version)" \> "Version: 1.15.2"
-      - run:
-          name: Check python_requires prevents installation on Python 3.3
-          command: |
-            pyenv install 3.3.7
-            pyenv local 3.3.7
-            FAIL=false
-            pip install dist/nipype-*-py2.py3-none-any.whl || FAIL=true
-            $FAIL
-      - store_artifacts:
-          path: /home/circleci/nipype/dist
-
-  deploy_pypi:
-    machine: *machine_kwds
-    working_directory: /home/circleci/nipype
-    steps:
-      - checkout:
-          path: /home/circleci/nipype
-      - run:
-          name: Deploy to PyPI
-          command: |
-            pyenv local 3.6.5
-            pip install --upgrade twine wheel readme_renderer setuptools
-            python setup.py check -r -s
-            python setup.py sdist bdist_wheel
-            twine upload dist/*
-
   update_feedstock:
     machine: *machine_kwds
     working_directory: /home/circleci/nipype
@@ -295,12 +240,6 @@ workflows:
   version: 2
   build_test_deploy:
     jobs:
-      - pypi_precheck:
-          filters:
-            branches:
-              only: /(rel|dev)\/.*/
-            tags:
-              only: /.*/
       - compare_base_dockerfiles:
           filters:
             branches:
@@ -325,19 +264,10 @@ workflows:
               only: /.*/
           requires:
             - test_pytest
-      - deploy_pypi:
-          filters:
-            branches:
-              ignore: /.*/
-            tags:
-              only: /.*/
-          requires:
-            - pypi_precheck
-            - test_pytest
       - update_feedstock:
           context: nipybot
           filters:
             branches:
-              only: /rel\/.*/
+              only: /rel\/\d.*/
             tags:
               only: /.*/
diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
@@ -0,0 +1,61 @@
+name: Packaging
+
+on:
+  push:
+    branches:
+      - master
+      - maint/*
+      - rel/*
+    tags:
+      - '*'
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  package:
+    # Build packages and upload
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python-version: 3.8
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Create virtual environment
+        run: tools/ci/create_venv.sh
+      - name: Build sdist
+        run: tools/ci/build_archive.sh
+        env:
+          INSTALL_TYPE: sdist
+      - name: Build wheel
+        run: tools/ci/build_archive.sh
+        env:
+          INSTALL_TYPE: wheel
+      ### Temporary
+      - name: Check packages with twine
+        run: |
+          pip install twine
+          twine check dist/*
+      ### Switch back to this if we figure out who has permissions on test.pypi.org
+      # - name: Test PyPI upload
+      #   uses: pypa/gh-action-pypi-publish@master
+      #   with:
+      #     user: __token__
+      #     password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+      #     repository_url: https://test.pypi.org/legacy/
+      #     skip_existing: true
+      - name: Upload to PyPI (on tags)
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.mailmap b/.mailmap
@@ -55,6 +55,7 @@ David Mordom <[email protected]>
 David Welch <[email protected]> <[email protected]>
 Dimitri Papadopoulos Orfanos <[email protected]>
 Dmytro Belevtsoff <[email protected]>
+Dorian Vogel <[email protected]>
 Dylan M. Nielson <[email protected]>
 Dylan M. Nielson <[email protected]> <[email protected]>
 Eduard Ort <[email protected]>
@@ -73,6 +74,7 @@ Gilles de Hollander <[email protected]>
 Gio Piantoni <[email protected]>
 Guillaume Flandin <[email protected]>
 Hans Johnson <[email protected]> <[email protected]>
+Henry Jones <[email protected]>
 Horea Christian <[email protected]> <[email protected]>
 Hrvoje Stojic <[email protected]>
 Isaac Schwabacher <[email protected]>
@@ -153,6 +155,8 @@ Ranjit Khanuja <[email protected]>
 Rastko Ćirić <[email protected]>
 Rastko Ćirić <[email protected]> <[email protected]>
 Rastko Ćirić <[email protected]> <[email protected]>
+Raunak Jalan <[email protected]>
+Raunak Jalan <[email protected]> <[email protected]>
 Ross Markello <[email protected]> <[email protected]>
 Russell Poldrack <[email protected]>
 Russell Poldrack <[email protected]>
@@ -175,6 +179,9 @@ Steven Giavasis <[email protected]> <[email protected]
 Steven Giavasis <[email protected]> <[email protected]>
 Steven Tilley <[email protected]> <[email protected]>
 Sulantha Mathotaarachchi <[email protected]>
+Tim Robert-Fitzgerald <[email protected]>
+Tom Close <[email protected]>
+Tom Close <[email protected]> <[email protected]>
 Tristan Glatard <[email protected]> <[email protected]>
 Victor Férat <[email protected]>
 Victor Férat <[email protected]> <[email protected]>

diff --git a/.zenodo.json b/.zenodo.json
@@ -230,6 +230,11 @@
       "name": "Mancini, Matteo",
       "orcid": "0000-0001-7194-4568"
     },
+    {
+      "affiliation": "University of Sydney",
+      "name": "Close, Thomas",
+      "orcid": "0000-0002-4160-2134"
+    },
     {
       "affiliation": "National Institute of Mental Health",
       "name": "Nielson, Dylan M.",
@@ -246,15 +251,30 @@
     {
       "name": "Mordom, David"
     },
+    {
+      "affiliation": "CIBIT, UC",
+      "name": "Machado, F\u00e1tima",
+      "orcid": "0000-0001-8878-1750"
+    },
     {
       "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
       "name": "Guillon, Je\u0301re\u0301my",
       "orcid": "0000-0002-2672-7510"
     },
+    {
+      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
+      "name": "Waller, Lea",
+      "orcid": "0000-0002-3239-6957"
+    },
     {
       "affiliation": "Indiana University, IN, USA",
       "name": "Koudoro, Serge"
     },
+    {
+      "affiliation": "Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania",
+      "name": "Robert-Fitzgerald, Timothy",
+      "orcid": "0000-0001-8303-8001"
+    },
     {
       "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
       "name": "Chetverikov, Andrey",
@@ -334,6 +354,11 @@
     {
       "name": "Schwartz, Yannick"
     },
+    {
+      "affiliation": "The University of Iowa",
+      "name": "Ghayoor, Ali",
+      "orcid": "0000-0002-8858-1254"
+    },
     {
       "affiliation": "NIMH IRP",
       "name": "Lee, John A.",
@@ -403,13 +428,12 @@
       "orcid": "0000-0003-2766-8425"
     },
     {
-      "affiliation": "University of Iowa",
-      "name": "Welch, David"
+      "affiliation": "Sagol School of Neuroscience, Tel Aviv University",
+      "name": "Baratz, Zvi"
     },
     {
-      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
-      "name": "Waller, Lea",
-      "orcid": "0000-0002-3239-6957"
+      "affiliation": "University of Iowa",
+      "name": "Welch, David"
     },
     {
       "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences",
@@ -421,11 +445,6 @@
       "name": "Triplett, William",
       "orcid": "0000-0002-9546-1306"
     },
-    {
-      "affiliation": "The University of Iowa",
-      "name": "Ghayoor, Ali",
-      "orcid": "0000-0002-8858-1254"
-    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Craddock, R. Cameron",
@@ -614,6 +633,9 @@
       "name": "Lee, Nat",
       "orcid": "0000-0001-9308-9988"
     },
+    {
+      "name": "Jalan, Raunak"
+    },
     {
       "name": "Inati, Souheil"
     },
@@ -697,10 +719,6 @@
       "name": "Andberg, Sami Kristian",
       "orcid": "0000-0002-5650-3964"
     },
-    {
-      "affiliation": "Sagol School of Neuroscience, Tel Aviv University",
-      "name": "Baratz, Zvi"
-    },
     {
       "name": "Matsubara, K"
     },
@@ -711,11 +729,6 @@
     {
       "name": "Marina, Ana"
     },
-    {
-      "affiliation": "University of Sydney",
-      "name": "Close, Thomas",
-      "orcid": "0000-0002-4160-2134"
-    },
     {
       "name": "Davison, Andrew"
     },
@@ -741,9 +754,19 @@
     {
       "name": "Shachnev, Dmitry"
     },
+    {
+      "affiliation": "University of Applied Sciences and Arts Northwestern Switzerland",
+      "name": "Vogel, Dorian",
+      "orcid": "0000-0003-3445-576X"
+    },
     {
       "name": "Flandin, Guillaume"
     },
+    {
+      "affiliation": "Stanford University and the University of Chicago",
+      "name": "Jones, Henry",
+      "orcid": "0000-0001-7719-3646"
+    },
     {
       "affiliation": "Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA",
       "name": "Gonzalez, Ivan",
@@ -790,22 +813,19 @@
       "name": "Broderick, William",
       "orcid": "0000-0002-8999-9003"
     },
-    {
-      "name": "Tambini, Arielle"
-    },
     {
       "affiliation": "Weill Cornell Medicine",
       "name": "Xie, Xihe",
       "orcid": "0000-0001-6595-2473"
     },
+    {
+      "name": "Tambini, Arielle"
+    },
     {
       "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.",
       "name": "Mihai, Paul Glad",
       "orcid": "0000-0001-5715-6442"
     },
-    {
-      "name": "Jalan, Raunak",
-    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Gorgolewski, Krzysztof J.",
@@ -815,11 +835,6 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
-    },
-    {
-      "affiliation": "CIBIT, UC",
-      "name": "Machado, Fátima",
-      "orcid": "0000-0001-8878-1750"
     }
   ],
   "keywords": [