bump version, merge pull request #24 from AMYPAD/devel

.github/workflows/comment-bot.yml

@@ -29,6 +29,7 @@ jobs:
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "eyes"})
+        github-token: ${{ secrets.GH_TOKEN }}
     - name: Tag Commit
       run: |
         git clone https://${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY} repo
@@ -48,3 +49,4 @@ jobs:
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "rocket"})
+        github-token: ${{ secrets.GH_TOKEN }}

.github/workflows/test.yml

@@ -2,17 +2,14 @@ name: Test
 on: [push, pull_request]
 jobs:
   check:
-    if: github.event_name != 'push' || github.ref != 'refs/heads/devel'
+    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: [2.7, 3.6, 3.9]
-    name: Check py${{ matrix.python }}
+    name: Check
     steps:
     - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python }}
+        fetch-depth: 0
+    - uses: actions/setup-python@v2
     - name: set PYSHA
       run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
     - uses: actions/cache@v1
@@ -35,8 +32,7 @@ jobs:
       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
+    - run: pre-commit run -a --show-diff-on-failure
   test:
     if: github.event_name != 'pull_request' || github.head_ref != 'devel'
     runs-on: ubuntu-latest
@@ -57,10 +53,10 @@ jobs:
     - if: startsWith(matrix.python, '2')
       run: pytest
     - run: codecov
-  matlab:
+  cuda_matlab:
     if: github.event_name != 'pull_request' || github.head_ref != 'devel'
     runs-on: [self-hosted, python, cuda, matlab]
-    name: Test matlab & cuda
+    name: Test cuda & matlab
     steps:
     - uses: actions/checkout@v2
       with:
@@ -74,7 +70,7 @@ jobs:
       run: setup-python -p3.7 -Dr
       if: ${{ always() }}
   deploy:
-    needs: [check, test, matlab]
+    needs: [check, test, cuda_matlab]
     name: PyPI Deploy
     runs-on: ubuntu-latest
     steps:
@@ -85,37 +81,24 @@ jobs:
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:
+        requirements: twine setuptools wheel setuptools_scm[toml]
         build: true
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
-        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
+        upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}
+    - id: meta
+      name: Changelog
+      run: |
+        echo ::set-output name=tag::${GITHUB_REF#refs/tags/}
+        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.ref, 'refs/tags')
+      uses: softprops/action-gh-release@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
-        tag_name: ${{ github.ref }}
-        release_name: miutil ${{ github.ref }} beta
+        name: miutil ${{ steps.meta.outputs.tag }} beta
         body_path: _CHANGES.md
         draft: true
-    - 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: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: dist/${{ 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: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: dist/${{ steps.dist.outputs.whl_asc }}
-        asset_name: ${{ steps.dist.outputs.whl_asc }}
-        asset_content_type: text/plain
+        files: |
+          dist/${{ steps.dist.outputs.whl }}
+          dist/${{ steps.dist.outputs.whl_asc }}

.gitignore

@@ -1,9 +1,9 @@
 *.py[cod]
 __pycache__/
 /miutil/_dist_ver.py
-/.eggs/
-/*.egg-info/
+/*.egg*/
 /build/
 /dist/
 /.coverage*
 /coverage.xml
+/.pytest_cache/

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v4.0.1
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -21,24 +21,25 @@ 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: 3.8.4
+  rev: 3.9.2
   hooks:
   - id: flake8
+    args: [-j8]
     additional_dependencies:
     - flake8-bugbear
     - flake8-comprehensions
     - flake8-debugger
     - flake8-string-format
 - repo: https://github.com/psf/black
-  rev: 19.10b0
+  rev: 21.8b0
   hooks:
   - id: black
 - repo: https://github.com/PyCQA/isort
-  rev: 5.7.0
+  rev: 5.9.3
   hooks:
   - id: isort

README.rst

@@ -3,7 +3,7 @@ miutil
 
 Medical imaging utilities.
 
-|Version| |Py-Versions| |Tests| |Coverage| |DOI| |LICENCE|
+|Version| |Py-Versions| |Conda| |Tests| |Coverage| |DOI| |LICENCE|
 
 Basic functionality needed for `AMYPAD <https://github.com/AMYPAD/AMYPAD>`_
 and `NiftyPET <https://github.com/NiftyPET/NiftyPET>`_.
@@ -50,6 +50,8 @@ use the package name ``miutil[option1,option2]``.
    :target: https://github.com/AMYPAD/miutil/releases
 .. |Py-Versions| image:: https://img.shields.io/pypi/pyversions/miutil.svg?logo=python&logoColor=white
    :target: https://pypi.org/project/miutil
+.. |Conda| image:: https://img.shields.io/conda/v/conda-forge/miutil.svg?label=conda&logo=conda-forge
+   :target: https://anaconda.org/conda-forge/miutil
 .. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4281542.svg
    :target: https://doi.org/10.5281/zenodo.4281542
 .. |LICENCE| image:: https://img.shields.io/pypi/l/miutil.svg

miutil/fdio.py

@@ -1,4 +1,5 @@
 import logging
+import re
 from contextlib import contextmanager
 from os import makedirs
 from shutil import copyfileobj, rmtree
@@ -73,3 +74,14 @@ def extractall(fzip, dest, desc="Extracting"):
                 if mode:
                     (dest / i.filename).chmod(mode)
                     log.debug(oct((i.external_attr >> 16) & 0o777))
+
+
+def nsort(fnames):
+    """Sort a file list, automatically detecting embedded numbers"""
+
+    def path2parts(fname):
+        parts = re.split(r"([0-9][0-9.]*e[-+][0-9]+|[0-9]+\.[0-9]+|[0-9]+)", fname)
+        parts[1::2] = map(float, parts[1::2])
+        return parts
+
+    return sorted(fnames, key=path2parts)

setup.cfg

@@ -3,7 +3,7 @@ name=miutil
 description=Medical imaging utilities for the AMYPAD and NiftyPET projects
 long_description=file: README.rst
 long_description_content_type=text/x-rst
-license=Apache 2.0
+license=Apache-2.0
 license_file=LICENCE.md
 url=https://github.com/AMYPAD/miutil
 project_urls=
@@ -49,8 +49,6 @@ python_requires=>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*
 [options.extras_require]
 dev=
     pre-commit
-    twine
-    wheel
     pytest
     pytest-cov
     pytest-timeout

tests/test_fdio.py

@@ -62,3 +62,10 @@ def test_extractall(tmp_path):
         "Medical imaging utilities."
         in (tmpdir / "miutil-0.6.0" / "README.rst").read_text()
     )
+
+
+def test_nsort():
+    fnames = ["foo1_bar_21.nii.gz", "foo1_bar_1.2.nii.gz", "foo1_bar_1.nii.gz"]
+    assert fdio.nsort(fnames) == fnames[::-1]
+    fnames = [i[9:] for i in fnames]
+    assert fdio.nsort(fnames) == fnames[::-1]