Merge branch 'master' of github.com:nipy/nipype into enh/euler-number

Author: mgxd

.circleci/config.yml

@@ -172,103 +172,6 @@ jobs:
           paths:
             - docker
 
-  test_fmri_fsl_spm:
-    machine: *machine_kwds
-    working_directory: /home/circleci/nipype
-    steps:
-      - checkout:
-          path: /home/circleci/nipype
-      - attach_workspace:
-          at: /tmp
-      - run: *set_pr_number
-      - run: *generate_dockerfiles
-      - run: *modify_nipype_version
-      - run: *get_base_image
-      - run: *build_main_image_py36
-      - run: *_get_codecov
-      - run: *_download_test_data
-      - run: *prepare_working_directory
-      - run:
-          name: Run FSL reuse pipeline
-          no_output_timeout: 40m
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_fmri_fsl_reuse_linear_l1.sh
-      - run:
-          name: Run SPM test workflow - 3D inputs
-          no_output_timeout: 40m
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_fmri_spm_linear_3d.sh
-      - run:
-          name: Run SPM test workflow - 4D inputs
-          no_output_timeout: 40m
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_fmri_spm_linear_4d.sh
-      - run: *_run_codecov_smoke
-      - store_artifacts: *store_artifacts_kwds
-
-  test_fmri_spm_dartel_multiproc:
-    machine: *machine_kwds
-    working_directory: /home/circleci/nipype
-    steps:
-      - checkout:
-          path: /home/circleci/nipype
-      - attach_workspace:
-          at: /tmp
-      - run: *set_pr_number
-      - run: *generate_dockerfiles
-      - run: *modify_nipype_version
-      - run: *get_base_image
-      - run: *build_main_image_py36
-      - run: *_get_codecov
-      - run: *_download_test_data
-      - run: *prepare_working_directory
-      - run:
-          name: Run SPM DARTEL Level 1 pipeline
-          no_output_timeout: 1h
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_fmri_spm_dartel_multiproc_l1.sh
-      - run:
-          name: Run SPM DARTEL Level 2 pipeline
-          no_output_timeout: 30m
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_fmri_spm_dartel_multiproc_l2.sh
-      - run: *_run_codecov_smoke
-      - store_artifacts: *store_artifacts_kwds
-
-  test_fmri_spm_nested_fsl_feeds:
-    machine: *machine_kwds
-    working_directory: /home/circleci/nipype
-    steps:
-      - checkout:
-          path: /home/circleci/nipype
-      - attach_workspace:
-          at: /tmp
-      - run: *set_pr_number
-      - run: *generate_dockerfiles
-      - run: *modify_nipype_version
-      - run: *get_base_image
-      - run: *build_main_image_py36
-      - run: *_get_codecov
-      - run: *_download_test_data
-      - run: *prepare_working_directory
-      - run:
-          name: Run SPM Nested Level 1 pipeline
-          no_output_timeout: 1h
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_fmri_spm_nested_multiproc_l1.sh
-      - run:
-          name: Run SPM Nested Level 2 pipeline
-          no_output_timeout: 30m
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_fmri_spm_nested_multiproc_l2.sh
-      - run:
-          name: Run FSL FEEDS pipeline
-          no_output_timeout: 40m
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/test_fmri_fsl_feeds_linear_l1.sh
-      - run: *_run_codecov_smoke
-      - store_artifacts: *store_artifacts_kwds
-
   deploy_dockerhub:
     docker:
       - image: docker:17.10.0-ce-git
@@ -446,36 +349,12 @@ workflows:
               only: /.*/
           requires:
             - compare_base_dockerfiles
-      - test_fmri_fsl_spm:
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-          requires:
-            - compare_base_dockerfiles
-      - test_fmri_spm_dartel_multiproc:
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-          requires:
-            - compare_base_dockerfiles
-      - test_fmri_spm_nested_fsl_feeds:
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-          requires:
-            - compare_base_dockerfiles
       - deploy_dockerhub:
           filters:
             branches:
               only: master
           requires:
             - test_pytest
-            - test_fmri_spm_nested_fsl_feeds
-            - test_fmri_fsl_spm
-            - test_fmri_spm_dartel_multiproc
       - deploy_pypi:
           filters:
             branches:

.circleci/test_fmri_fsl_feeds_linear_l1.sh

@@ -6,8 +6,8 @@ These guidelines are designed to make it as easy as possible to get involved. If
 
 Before you start you'll need to set up a free [GitHub][link_github] account and sign in. Here are some [instructions][link_signupinstructions].
 If you are not familiar with version control systems such as git,
- [introductions and tutorials](http://www.reproducibleimaging.org/module-reproducible-basics/02-vcs/)
- may be found on [ReproducibleImaging.org](https://www.reproducibleimaging.org/).
+we recommend the [VCS module](http://www.reproducibleimaging.org/module-reproducible-basics/02-vcs/)
+available from [ReproNim](http://www.reproducibleimaging.org/).
 
 Already know what you're looking for in this guide? Jump to the following sections:
 * [Understanding issue labels](#issue-labels)
@@ -22,7 +22,7 @@ The current list of issue labels are [here][link_labels] and include:
 
 * [![Bugs](https://img.shields.io/badge/-bugs-fc2929.svg)][link_bugs] *These issues point to problems in the project.*
 
-    If you find new a bug, please provide as much information as possible to recreate the error.
+    If you find a new bug, please provide as much information as possible to recreate the error.
     The [issue template][link_issue_template] will automatically populate any new issue you open, and contains information we've found to be helpful in addressing bug reports.
     Please fill it out to the best of your ability!
 

.circleci/test_fmri_fsl_reuse_linear_l1.sh

@@ -1 +1,2 @@
 /documentation.zip
+_static/python

.circleci/test_fmri_spm_dartel_multiproc_l1.sh

@@ -24,7 +24,7 @@ help:
 	@echo "  doctest   run all doctests embedded in the documentation"
 
 clean:
-	-rm -rf _build/* *~ api/generated interfaces/generated users/examples documentation.zip
+	-rm -rf _build/* *~ api/generated interfaces/generated users/examples documentation.zip _static/python
 
 htmlonly:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html

.circleci/test_fmri_spm_dartel_multiproc_l2.sh

@@ -13,18 +13,39 @@
 # serve to show the default.
 
 import os
+from pathlib import Path
+from tempfile import TemporaryDirectory
+import shutil
 from packaging.version import Version
 import nipype
+import subprocess as sp
 
-doc_path = os.path.abspath(os.path.dirname(__file__))
-os.makedirs('users/examples', exist_ok=True)
+# Disable etelemetry during doc builds
+os.environ["NIPYPE_NO_ET"] = "1"
 
-os.chdir(os.path.join(doc_path, 'users', 'examples'))
-os.system("""python ../../../tools/ex2rst -x ../../../examples/test_spm.py \
---project Nipype --outdir . ../../../examples""")
-os.system("""python ../../../tools/ex2rst --project Nipype --outdir . \
-../../../examples/frontiers_paper""")
-os.chdir(doc_path)
+conf_py = Path(__file__)
+
+example_dir = conf_py.parent / 'users' / 'examples'
+shutil.rmtree(example_dir, ignore_errors=True)
+example_dir.mkdir(parents=True)
+python_dir = conf_py.parent / "_static" / "python"
+shutil.rmtree(python_dir, ignore_errors=True)
+
+ex2rst = str(conf_py.parent.parent / "tools" / "ex2rst")
+
+with TemporaryDirectory() as tmpdir:
+    sp.run(["git", "clone", "--depth", "1", "https://github.com/niflows/nipype1-examples.git",
+            tmpdir], check=True)
+    source_dir = Path(tmpdir) / "package" / "niflow" / "nipype1" / "examples"
+    shutil.copytree(source_dir, python_dir)
+
+sp.run(["python", ex2rst, "--outdir", str(example_dir), str(python_dir),
+        "-x", str(python_dir / "test_spm.py"),
+        "-x", str(python_dir / "__init__.py"),
+        "-x", str(python_dir / "cli.py")],
+       check=True)
+sp.run(["python", ex2rst, "--outdir", str(example_dir), str(python_dir / "frontiers_paper")],
+       check=True)
 
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -98,7 +119,7 @@
 
 # General information about the project.
 project = u'nipype'
-copyright = u'2009-19, Neuroimaging in Python team'
+copyright = u'2009-20, Neuroimaging in Python team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

.circleci/test_fmri_spm_linear_3d.sh

@@ -0,0 +1,7 @@
+The examples directory previously held a set of
+[literate programming](https://en.wikipedia.org/wiki/Literate_programming) documents that
+demonstrated solutions to various problems using Nipype.
+
+These examples have been moved to the
+[Nipype1 Examples Niflow](https://github.com/niflows/nipype1-examples). Please refer to
+that repository for more information, and report any issues with the examples there.