misc framework updates

Author: casperdcl

.github/workflows/test.yml

@@ -2,17 +2,12 @@ name: Test
 on: [push, pull_request]
 jobs:
   check:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'NiftyPET'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: [3.6, 3.9]
-    name: Check py${{ matrix.python }}
+    name: Check
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python }}
     - name: set PYSHA
       run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
     - uses: actions/cache@v1
@@ -24,7 +19,7 @@ jobs:
         pip install -U pre-commit
         sudo apt-get install -yqq clang-format
     - uses: reviewdog/action-setup@v1
-    - if: github.event_name != 'schedule'
+    - if: github.event_name == 'push' || github.event_name == 'pull_request'
       name: comment
       run: |
         if [[ $EVENT == pull_request ]]; then
@@ -39,20 +34,23 @@ jobs:
         EVENT: ${{ github.event_name }}
     - run: pre-commit run -a --show-diff-on-failure
   test:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'NiftyPET'
+    name: Test py${{ matrix.python }}
     runs-on: [self-hosted, python, cuda, matlab]
-    name: Test
+    strategy:
+      matrix:
+        python: [3.6, 3.9]
     steps:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
     - name: Run setup-python
-      run: setup-python -p3.7
+      run: setup-python -p${{ matrix.python }}
     - run: pip install -U --no-binary nimpa -e .[dev]
     - run: pytest
-    - run: codecov
+    - uses: codecov/codecov-action@v1
     - name: Post Run setup-python
-      run: setup-python -p3.7 -Dr
+      run: setup-python -p${{ matrix.python }} -Dr
       if: ${{ always() }}
   deploy:
     needs: [check, test]

.pre-commit-config.yaml

@@ -21,10 +21,10 @@ repos:
   - id: todo
     name: Check TODO
     language: pygrep
+    args: [-i]
     entry: TODO
     types: [text]
     exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
-    args: [-i]
 - repo: https://gitlab.com/pycqa/flake8
   rev: 3.9.2
   hooks:
@@ -36,7 +36,7 @@ repos:
     - flake8-debugger
     - flake8-string-format
 - repo: https://github.com/google/yapf
-  rev: 6db9374
+  rev: v0.31.0
   hooks:
   - id: yapf
     args: [-i]
@@ -45,7 +45,7 @@ repos:
   hooks:
   - id: isort
 - repo: https://github.com/doublify/pre-commit-clang-format
-  rev: master
+  rev: '6230247'
   hooks:
   - id: clang-format
     files: \.(cc?|cuh?|cxx|cpp|h|hpp|hxx|java|js)$

setup.cfg

@@ -64,9 +64,13 @@ dev=
     pytest-cov
     pytest-timeout
     pytest-xdist
-    codecov
 examples=jupyter; ipywidgets; matplotlib; brainweb
 
+[flake8]
+max_line_length=99
+extend-ignore=W504,E225,E261,E701,P1
+exclude=.git,__pycache__,build,dist,.eggs
+
 [yapf]
 spaces_before_comment=15, 20
 arithmetic_precedence_indication=true
@@ -83,12 +87,6 @@ profile=black
 line_length=99
 known_first_party=niftypet,tests
 
-[flake8]
-statistics=True
-max_line_length=99
-extend-ignore=W504,E225,E261,E701,P1
-exclude=.git,__pycache__,build,dist,.eggs
-
 [tool:pytest]
 timeout=3600
 log_level=INFO