Merge branch 'master' into mnt/nipype_interf_convert_cont

Author: djarecka

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,3 +1,6 @@
+## Acknowledgment
+- [ ] I acknowledge that this contribution will be available under the Apache 2 license.
+
 ## Types of changes
 <!--- What types of changes does your code introduce? Put an `x` in all the boxes that apply: -->
 - [ ] Bug fix (non-breaking change which fixes an issue)
@@ -16,6 +19,3 @@
 (we are using `black`: you can `pip install pre-commit`,
 run `pre-commit install` in the `pydra` directory
 and `black` will be run automatically with each commit)
-
-## Acknowledgment
-- [ ] I acknowledge that this contribution will be available under the Apache 2 license.

.github/workflows/publish.yml

@@ -5,7 +5,7 @@ name: Upload to PyPI
 
 on:
   release:
-    types: [created]
+    types: [published]
 
 jobs:
   deploy:
@@ -14,7 +14,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: '3.x'
     - name: Install dependencies

.github/workflows/testallowfail.yml

@@ -12,13 +12,15 @@ jobs:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
         python-version: [3.7, 3.8]
-        install: [min-req, install, develop, wheel]
+        install: [install, develop, wheel]
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
 
     steps:
     - uses: actions/checkout@v2
+    - name: Disable etelemetry
+      run:  echo ::set-env name=NO_ET::TRUE
     - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
       uses: actions/setup-python@v2
       with:
@@ -27,9 +29,10 @@ jobs:
       run: python -m pip install --upgrade pip setuptools
 
 
-    - name: Install dependencies (min-requirements.txt)
-      if: matrix.install == 'min-req'
-      run: pip install -r min-requirements.txt
+    - name: Install Pydra tests dependencies (develop or setup.py install)
+      if: matrix.install == 'develop' || matrix.install == 'install'
+      run: pip install ".[test]"
+
 
     - name: Install dependencies (setup.py install)
       if: matrix.install == 'install'
@@ -42,15 +45,7 @@ jobs:
         pip install dist/*.whl
 
 
-    - name: Install Pydra (min-requirements.txt or setup.py install)
-      if: matrix.install == 'min-req' || matrix.install == 'install'
-      run: pip install ".[test]"
-
-    - name: Install Pydra (setup.py develop)
-      if: matrix.install == 'develop'
-      run: pip install -e ".[test]"
-
-    - name: Install Pydra (wheel)
+    - name: Install Pydra tests dependencies (wheel)
       if: matrix.install == 'wheel'
       run: pip install "$( ls dist/pydra*.whl )[test]"
 

.github/workflows/testpydra.yml

@@ -15,6 +15,7 @@ jobs:
       - name: Set env
         run: |
           echo ::set-env name=RELEASE_VERSION::v3.5.0
+          echo ::set-env name=NO_ET::TRUE
       - name: Setup Singularity
         uses: actions/checkout@v2
         with:
@@ -60,6 +61,6 @@ jobs:
 
 
       - name: Pytest
-        run: pytest -vs --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml --doctest-modules pydra
+        run: pytest -vs --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml pydra/engine/tests/test_singularity.py
       - name: Upload to codecov
         run: codecov -f cov.xml -F unittests -e GITHUB_WORKFLOW

.github/workflows/testsingularity.yml

@@ -9,12 +9,14 @@ jobs:
       DOCKER_IMAGE: mgxd/slurm:19.05.1
 
     steps:
+    - name: Disable etelemetry
+      run: echo ::set-env name=NO_ET::TRUE
     - uses: actions/checkout@v2
     - name: Pull docker image
       run: |
         docker pull $DOCKER_IMAGE
         # Have image running in background
-        docker run `bash <(curl -s https://codecov.io/env)` -itd -h ernie --name slurm -v `pwd`:/pydra $DOCKER_IMAGE
+        docker run `bash <(curl -s https://codecov.io/env)` -itd -h ernie --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE
     - name: Display previous jobs with sacct
       run: |
         echo "Allowing ports/daemons time to start" && sleep 10
@@ -29,6 +31,7 @@ jobs:
         fi
     - name: Setup Python
       run: |
+        docker exec slurm bash -c "echo $NO_ET"
         docker exec slurm bash -c "ls -la && echo list top level dir"
         docker exec slurm bash -c "ls -la /pydra && echo list pydra dir"
         docker exec slurm bash -c "pip install -e /pydra[test] && python -c 'import pydra; print(pydra.__version__)'"

.github/workflows/testslurm.yml

@@ -20,12 +20,10 @@ jobs:
     - name: Update build tools
       run: python -m pip install --upgrade pip setuptools
 
-    - name: Install dependencies
-      run: pip install -r min-requirements.txt
     - name: Install Pydra
-      run: pip install ".[test]"
+      run: pip install ".[dev]"
 
     - name: Check Style
       run: |
         pip install black==19.3b0 codecov
-        black --check pydra tools setup.py
+        black --check pydra setup.py

.github/workflows/teststyle.yml

@@ -1,27 +1,32 @@
+|GHAction| |CircleCI| |codecov|
 
-.. image:: https://raw.githubusercontent.com/nipype/pydra/master/docs/logo/pydra_logo.jpg
-   :width: 50
-   :alt: pydra logo
-
-A simple dataflow engine with scalable semantics.
+|Pydralogo|
 
+.. |Pydralogo| image:: https://raw.githubusercontent.com/nipype/pydra/master/docs/logo/pydra_logo.jpg
+   :width: 200px
+   :alt: pydra logo
 
-.. image:: https://github.com/nipype/pydra/workflows/Pydra/badge.svg
+.. |GHAction| image:: https://github.com/nipype/pydra/workflows/Pydra/badge.svg
    :alt: GitHub Actions CI
    :target: https://github.com/nipype/Pydra/actions
 
-|CircleCI|	
+.. |CircleCI| image:: https://circleci.com/gh/nipype/pydra.svg?style=svg
+   :alt: CircleCI
 
-.. |CircleCI| image:: https://circleci.com/gh/nipype/pydra.svg?style=svg	
-   :alt: CircleCI	
+.. |codecov| image:: https://codecov.io/gh/nipype/pydra/branch/master/graph/badge.svg
+   :alt: codecov
 
+======================
+Pydra: Dataflow Engine
+======================
 
-|codecov|
+A simple dataflow engine with scalable semantics.
 
-.. |codecov| image:: https://codecov.io/gh/nipype/pydra/branch/master/graph/badge.svg
-   :alt: codecov
+Pydra is a rewrite of the Nipype engine with mapping and joining as
+first-class operations. It forms the core of the Nipype 2.0 ecosystem.
 
-The goal of pydra is to provide a lightweight Python dataflow engine for DAG construction, manipulation, and distributed execution.
+The goal of pydra is to provide a lightweight Python dataflow engine for DAG
+construction, manipulation, and distributed execution.
 
 Feature list:
 =============
@@ -59,10 +64,10 @@ Installation
 Note that installation fails with older versions of pip on Windows. Upgrade pip before installing:
 
 ::
-   
+
    pip install –upgrade pip
    pip install pydra
-   
+
 
 Developer installation
 ======================

README.rst

@@ -22,6 +22,7 @@
 
 
 def check_latest_version():
+
     import etelemetry
 
     return etelemetry.check_available_version("nipype/pydra", __version__, lgr=logger)