Merge pull request #11 from AMYPAD/devel

.github/workflows/test.yml

@@ -1,17 +1,15 @@
 name: Test
-on:
-- push
+on: [push, pull_request]
 jobs:
   check:
+    if: github.event_name != 'push' || github.ref != 'refs/heads/devel'
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [2.7, 3.6, 3.9]
     name: Check py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
     - uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python }}
@@ -21,54 +19,84 @@ jobs:
       with:
         path: ~/.cache/pre-commit
         key: pre-commit|${{ env.PYSHA }}|${{ hashFiles('.pre-commit-config.yaml') }}
-    - run: pip install -U .[dev]
-    - run: python setup.py sdist bdist_wheel
-    - run: twine check dist/*
+    - name: dependencies
+      run: pip install -U pre-commit
     - uses: reviewdog/action-setup@v1
     - if: github.event_name != 'schedule'
+      name: comment
       run: |
-        pre-commit run -a flake8 | reviewdog -f=pep8 -name=flake8 -tee -reporter=github-check -filter-mode nofilter
+        if [[ $EVENT == pull_request ]]; then
+          REPORTER=github-pr-review
+        else
+          REPORTER=github-check
+        fi
+        pre-commit run -a todo | reviewdog -efm="%f:%l: %m" -name=TODO -tee -reporter=$REPORTER -filter-mode nofilter
+        pre-commit run -a flake8 | reviewdog -f=pep8 -name=flake8 -tee -reporter=$REPORTER -filter-mode nofilter
       env:
         REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        EVENT: ${{ github.event_name }}
     - if: startsWith(matrix.python, '3')
       run: pre-commit run -a --show-diff-on-failure
-    - if: startsWith(matrix.python, '2')
-      run: pre-commit run -a --show-diff-on-failure isort
   test:
-    runs-on: [self-hosted, matlab]
+    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: [2.7, 3.6, 3.9]
+    name: Test py${{ matrix.python }}
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+    - run: pip install -U .[dev]
+    - if: startsWith(matrix.python, '3')
+      run: pytest --durations-min=1
+    - if: startsWith(matrix.python, '2')
+      run: pytest
+    - run: codecov
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  matlab:
+    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    runs-on: [self-hosted, python, matlab]
     name: Test matlab
     steps:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
+    - name: Run setup-python
+      run: setup-python -p3.7
     - run: pip install -U .[dev]
-    - run: pytest
+    - run: pytest --durations-min=1
     - run: codecov
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+    - name: Post Run setup-python
+      run: setup-python -p3.7 -Dr
+      if: ${{ always() }}
   deploy:
-    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-    needs: [check, test]
+    needs: [check, test, matlab]
     name: PyPI Deploy
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-    - uses: casperdcl/deploy-pypi@v1
+    - uses: actions/setup-python@v2
+    - id: dist
+      uses: casperdcl/deploy-pypi@v2
       with:
         build: true
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
-    - id: collect_assets
-      name: Collect assets
-      run: |
-        echo "::set-output name=asset_path::$(ls dist/*.whl)"
-        echo "::set-output name=asset_name::$(basename dist/*.whl)"
-        echo "::set-output name=asset_path_sig::$(ls dist/*.whl.asc 2>/dev/null)"
-        echo "::set-output name=asset_name_sig::$(basename dist/*.whl.asc 2>/dev/null)"
-        git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
-    - id: create_release
+        upload: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }}
+    - name: Changelog
+      run: git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
+    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      id: create_release
       uses: actions/create-release@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
@@ -77,20 +105,21 @@ jobs:
         release_name: spm12 ${{ github.ref }} beta
         body_path: _CHANGES.md
         draft: true
-    - uses: actions/upload-release-asset@v1
+    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+      uses: actions/upload-release-asset@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
         upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: ${{ steps.collect_assets.outputs.asset_path }}
-        asset_name: ${{ steps.collect_assets.outputs.asset_name }}
+        asset_path: dist/${{ steps.dist.outputs.whl }}
+        asset_name: ${{ steps.dist.outputs.whl }}
         asset_content_type: application/zip
     - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
       uses: actions/upload-release-asset@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
         upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: ${{ steps.collect_assets.outputs.asset_path_sig }}
-        asset_name: ${{ steps.collect_assets.outputs.asset_name_sig }}
+        asset_path: dist/${{ steps.dist.outputs.whl_asc }}
+        asset_name: ${{ steps.dist.outputs.whl_asc }}
         asset_content_type: text/plain

.pre-commit-config.yaml

@@ -2,31 +2,43 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v2.4.0
+  rev: v3.4.0
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
   - id: check-docstring-first
   - id: check-executables-have-shebangs
   - id: check-toml
+  - id: check-merge-conflict
   - id: check-yaml
+  - id: debug-statements
   - id: end-of-file-fixer
   - id: mixed-line-ending
+  - id: sort-simple-yaml
   - id: trailing-whitespace
-- hooks:
+- repo: local
+  hooks:
+  - id: todo
+    name: Check TODO
+    language: pygrep
+    entry: TODO
+    types: [text]
+    exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
+    args: [-i]
+- repo: https://gitlab.com/pycqa/flake8
+  rev: 3.8.4
+  hooks:
   - id: flake8
     additional_dependencies:
     - flake8-bugbear
     - flake8-comprehensions
     - flake8-debugger
     - flake8-string-format
-  repo: https://gitlab.com/pycqa/flake8
-  rev: 3.8.4
-- hooks:
-  - id: black
-  repo: https://github.com/psf/black
+- repo: https://github.com/psf/black
   rev: 19.10b0
-- hooks:
+  hooks:
+  - id: black
+- repo: https://github.com/PyCQA/isort
+  rev: 5.7.0
+  hooks:
   - id: isort
-  repo: https://github.com/timothycrosley/isort
-  rev: 5.6.4

setup.cfg

@@ -28,7 +28,6 @@ classifiers=
     Programming Language :: Python :: 2
     Programming Language :: Python :: 2.7
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.5
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
@@ -48,11 +47,13 @@ install_requires=
     scipy
 include_package_data=True
 packages=find:
+python_requires=>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*
 [options.extras_require]
 dev=
     pre-commit
     twine
     wheel
+    miutil[web]>=0.7.0
     pytest
     pytest-cov
     pytest-timeout
@@ -80,4 +81,7 @@ profile=black
 known_first_party=spm12,tests
 
 [tool:pytest]
-addopts=-v --tb=short -rxs -W=error --log-level=debug -n=auto --durations=0 --durations-min=1 --cov=spm12 --cov-report=term-missing --cov-report=xml
+timeout=300
+addopts=-v --tb=short -rxs -W=error --log-level=debug -n=auto --durations=0 --cov=spm12 --cov-report=term-missing --cov-report=xml
+filterwarnings=
+    ignore:numpy.ufunc size changed.*:RuntimeWarning

spm12/utils.py

@@ -1,11 +1,16 @@
 import logging
-from functools import lru_cache, wraps
+from functools import wraps
 from os import path
 from textwrap import dedent
 
 from miutil.mlab import get_engine
 from pkg_resources import resource_filename
 
+try:
+    from functools import lru_cache
+except ImportError:  # fix py2.7
+    from backports.functools_lru_cache import lru_cache
+
 __all__ = ["get_matlab", "ensure_spm"]
 PATH_M = resource_filename(__name__, "")
 log = logging.getLogger(__name__)
@@ -30,7 +35,7 @@ def ensure_spm(name=None, cache="~/.spm12", version=12):
     if path.exists(addpath):
         eng.addpath(addpath)
     if not eng.exist("spm_jobman"):
-        log.warn("MATLAB could not find SPM.")
+        log.warning("MATLAB could not find SPM.")
         try:
             from zipfile import ZipFile
 

tests/__main__.py

@@ -0,0 +1,22 @@
+import logging
+
+from miutil.fdio import extractall
+from miutil.web import urlopen_cached
+
+from .conftest import HOME
+
+log = logging.getLogger(__name__)
+DATA_URL = (
+    "https://zenodo.org/record/3877529/files/amyloidPET_FBP_TP0_extra.zip?download=1"
+)
+
+
+def main():
+    log.info(f"Downloading {DATA_URL}\nto ${{DATA_ROOT:-~}} ({HOME})")
+    with urlopen_cached(DATA_URL, HOME) as fd:
+        extractall(fd, HOME)
+
+
+if __name__ == "__main__":
+    logging.basicConfig(level=logging.INFO)
+    main()

tests/conftest.py

@@ -0,0 +1,54 @@
+from os import getenv
+from textwrap import dedent
+
+from miutil.fdio import Path
+from pytest import fixture, skip
+
+HOME = Path(getenv("DATA_ROOT", "~")).expanduser()
+
+
+@fixture(scope="session")
+def folder_in():
+    Ab_PET_mMR_test = HOME / "Ab_PET_mMR_test"
+    if not Ab_PET_mMR_test.is_dir():
+        skip(
+            dedent(
+                """\
+            Cannot find Ab_PET_mMR_test in ${DATA_ROOT:-~} (%s).
+            Try running `python -m tests` to download it.
+            """
+            )
+            % HOME
+        )
+    return Ab_PET_mMR_test
+
+
+@fixture(scope="session")
+def folder_ref(folder_in):
+    Ab_PET_mMR_ref = folder_in / "testing_reference" / "Ab_PET_mMR_ref"
+    if not Ab_PET_mMR_ref.is_dir():
+        skip(
+            dedent(
+                """\
+            Cannot find Ab_PET_mMR_ref in
+            ${DATA_ROOT:-~}/testing_reference (%s/testing_reference).
+            Try running `python -m tests` to download it.
+            """
+            )
+            % HOME
+        )
+    return Ab_PET_mMR_ref
+
+
+@fixture
+def PET(folder_ref):
+    res = folder_ref / "basic" / "17598013_t-3000-3600sec_itr-4_suvr.nii.gz"
+    assert res.is_file()
+    return res
+
+
+@fixture
+def MRI(folder_in):
+    res = folder_in / "T1w_N4" / "t1_S00113_17598013_N4bias_cut.nii.gz"
+    assert res.is_file()
+    return res

tests/test_main.py

@@ -1,9 +1,19 @@
 from miutil.mlab import matlabroot
-from pytest import skip
+from pytest import mark, skip
+
+try:
+    FileNotFoundError
+except NameError:  # fix py2.7
+    FileNotFoundError = OSError
+
+pytestmark = mark.filterwarnings("ignore:numpy.ufunc size changed.*:RuntimeWarning")
 
 
 def test_cli():
-    if matlabroot("None") == "None":
+    try:
+        if matlabroot("None") == "None":
+            raise FileNotFoundError
+    except FileNotFoundError:
         skip("MATLAB not installed")
     from spm12.cli import main