Merge https://github.com/nipype/pydra

Author: djarecka

.circleci/config.yml

@@ -46,7 +46,10 @@ jobs:
       - checkout
       - run:
           name: Install deps
-          command: pip install --no-cache-dir -r docs/requirements.txt
+          command: |
+            pip install --upgrade pip
+            pip install --no-cache-dir -r docs/requirements.txt
+            pip install --no-cache-dir .[doc]
       - run:
           name: Build only this commit
           command: make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" SPHINX_APIDOC_OPTIONS="members,undoc-members,show-inheritance,noindex" html

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+doctests = True
+exclude =
+    **/__init__.py
+    **/tests/*
+    *build/
+    docs/sphinxext/
+    docs/tools/
+    docs/conf.py
+    pydra/_version.py
+max-line-length=105
+ignore = E203,W503,F541

.gitattributes

@@ -20,12 +20,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build twine
 
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
       run: |
-        python setup.py bdist_wheel
+        python -m build
         twine upload dist/*

.github/workflows/publish.yml

@@ -16,7 +16,10 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        exclude:
+          - os: 'windows-latest'
+            python-version: '3.11'
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -30,7 +33,9 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Update build tools
-      run: python -m pip install --upgrade pip build
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install build wheel
 
     - name: Build pydra
       run: python -m build

.github/workflows/testpydra.yml

@@ -53,7 +53,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Update build tools
-        run: python -m pip install --upgrade pip setuptools
+        run: python -m pip install --upgrade pip
 
 
       - name: Checkout Pydra repo

.github/workflows/testsingularity.yml

@@ -38,7 +38,7 @@ jobs:
         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__)'"
+        docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test] && python -c 'import pydra; print(pydra.__version__)'"
     - name: Run pytest
       run: docker exec slurm bash -c "pytest --color=yes -vs -n auto --cov pydra --cov-config /pydra/.coveragerc --cov-report xml:/pydra/cov.xml --doctest-modules /pydra/pydra"
     - name: Upload to codecov

.github/workflows/testslurm.yml

@@ -17,3 +17,6 @@ cov.xml
 .idea
 
 .DS_Store
+
+# This can be generated in-tree. We never want to commit it.
+pydra/_version.py

.gitignore

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -16,8 +16,9 @@ repos:
     rev: v2.2.2
     hooks:
     -   id: codespell
-        exclude: ^(pydra/_version\.py|versioneer\.py)$
+        additional_dependencies:
+        - tomli
 -   repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build with Python 3.9 on the latest version of Ubuntu.
+build:
+  os: ubuntu-22.04
+  tools:
+    python: '3.9'
+
+# Build documentation in the docs/ directory with Sphinx.
+sphinx:
+  configuration: docs/conf.py
+
+# Install extra requirements for the documentation.
+python:
+  install:
+    - method: pip
+      path: '.'
+      extra_requirements:
+        - doc