Merge pull request #3172 from effigies/enh/move_examples

ENH: Remove examples from repository

.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:

doc/.gitignore

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

doc/Makefile

@@ -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

doc/conf.py

@@ -13,18 +13,37 @@
 # 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)
 
-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 +117,7 @@
 
 # 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

examples/README.md

@@ -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.