Merge branch 'master' into interface/cat12

Author: mfmachado

.circleci/config.yml

@@ -52,6 +52,7 @@ _build_main_image_py36: &build_main_image_py36
         --rm=false \
         --tag nipype/nipype:latest \
         --tag nipype/nipype:py36 \
+        $(test -z "${CIRCLE_TAG}" || echo --tag nipype/nipype:"${CIRCLE_TAG}") \
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
         --build-arg VERSION="${CIRCLE_TAG}" /home/circleci/nipype
@@ -192,6 +193,7 @@ jobs:
             docker push nipype/nipype:base
             docker push nipype/nipype:latest
             docker push nipype/nipype:py36
+            test -z "${CIRCLE_TAG}" || docker push nipype/nipype:"${CIRCLE_TAG}"
       - run:
           name: Move pruned Dockerfile to /tmp/docker/cache directory
           command: |
@@ -289,44 +291,10 @@ jobs:
               ssh-add ~/.ssh/id_ed25519
               /home/circleci/nipype/tools/feedstock.sh
 
-  build_docs:
-    docker:
-      - image: python:3.7.4
-    working_directory: /tmp/src/nipype
-    environment:
-      - FSLOUTPUTTYPE: 'NIFTI'
-    steps:
-      - checkout
-      - run:
-          name: Check Python version and upgrade pip
-          command: |
-            python --version
-            python -m pip install -U pip
-      - run:
-          name: Install graphviz
-          command: |
-              apt-get update
-              apt-get install -y graphviz
-      - run:
-          name: Install Requirements (may contain pinned versions)
-          command: python -m pip install -r doc/requirements.txt
-      - run:
-          name: Install NiPype
-          command: python -m pip install ".[doc]"
-      - run:
-          name: Build documentation
-          command: make -C doc html
-      - store_artifacts:
-          path: /tmp/src/nipype/doc/_build/html
-
 workflows:
   version: 2
   build_test_deploy:
     jobs:
-      - build_docs:
-          filters:
-            tags:
-              only: /.*/
       - pypi_precheck:
           filters:
             branches:
@@ -353,6 +321,8 @@ workflows:
           filters:
             branches:
               only: master
+            tags:
+              only: /.*/
           requires:
             - test_pytest
       - deploy_pypi:

.github/workflows/main.yml

@@ -87,7 +87,7 @@ function generate_main_dockerfile() {
     --label maintainer="The nipype developers https://github.com/nipy/nipype" \
     --env MKL_NUM_THREADS=1 \
           OMP_NUM_THREADS=1 \
-    --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \
+    --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=8 BUILD_DATE VCS_REF VERSION \
     --user neuro \
     --workdir /home/neuro \
     --miniconda create_env=neuro \

.travis.yml

@@ -162,7 +162,7 @@ def get_nipype_gitversion():
 EXTRA_REQUIRES = {
     "data": ["datalad"],
     "doc": [
-        "dipy",
+        "dipy!=1.4.1",
         "ipython",
         "matplotlib",
         "nbsphinx",
@@ -172,7 +172,7 @@ def get_nipype_gitversion():
         "sphinxcontrib-napoleon",
     ],
     "duecredit": ["duecredit"],
-    "nipy": ["nitime", "nilearn", "dipy", "nipy", "matplotlib"],
+    "nipy": ["nitime", "nilearn", "dipy!=1.4.1", "nipy", "matplotlib"],
     "profiler": ["psutil>=5.0"],
     "pybids": ["pybids>=0.7.0"],
     "specs": ["black"],

docker/generate_dockerfiles.sh

@@ -362,7 +362,9 @@ def _list_outputs(self):
             splits.extend(self.inputs.splits)
             splits = np.cumsum(splits)
             for i in range(len(splits) - 1):
-                val = np.array(self.inputs.inlist)[splits[i] : splits[i + 1]].tolist()
+                val = np.array(self.inputs.inlist, dtype=object)[
+                    splits[i] : splits[i + 1]
+                ].tolist()
                 if self.inputs.squeeze and len(val) == 1:
                     val = val[0]
                 outputs["out%d" % (i + 1)] = val
@@ -407,7 +409,9 @@ class Select(IOBase):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        out = np.array(self.inputs.inlist)[np.array(self.inputs.index)].tolist()
+        out = np.array(self.inputs.inlist, dtype=object)[
+            np.array(self.inputs.index)
+        ].tolist()
         outputs["out"] = out
         return outputs
 

nipype/info.py

@@ -543,7 +543,9 @@ def _submit_job(self, node, updatehash=False):
         pyscript = create_pyscript(node, updatehash=updatehash)
         batch_dir, name = os.path.split(pyscript)
         name = ".".join(name.split(".")[:-1])
-        batchscript = "\n".join((self._template, "%s %s" % (sys.executable, pyscript)))
+        batchscript = "\n".join(
+            (self._template.rstrip("\n"), "%s %s" % (sys.executable, pyscript))
+        )
         batchscriptfile = os.path.join(batch_dir, "batchscript_%s.sh" % name)
         with open(batchscriptfile, "wt") as fp:
             fp.writelines(batchscript)