Merge pull request #30 from AMYPAD/devel

next release v0.11.0

.github/workflows/comment-bot.yml

@@ -1,25 +1,23 @@
 name: Comment Bot
 on:
-  issue_comment:
-    types: [created]
-  pull_request_review_comment:
-    types: [created]
+  issue_comment: {types: [created]}
+  pull_request_review_comment: {types: [created]}
 jobs:
   tag:  # /tag <tagname> <commit>
     if: startsWith(github.event.comment.body, '/tag ')
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: React Seen
-      uses: actions/github-script@v2
+      uses: actions/github-script@v6
       with:
         script: |
-          const perm = await github.repos.getCollaboratorPermissionLevel({
+          const perm = await github.rest.repos.getCollaboratorPermissionLevel({
             owner: context.repo.owner, repo: context.repo.repo,
             username: context.payload.comment.user.login})
           post = (context.eventName == "issue_comment"
-            ? github.reactions.createForIssueComment
-            : github.reactions.createForPullRequestReviewComment)
+            ? github.rest.reactions.createForIssueComment
+            : github.rest.reactions.createForPullRequestReviewComment)
           if (!["admin", "write"].includes(perm.data.permission)){
             post({
               owner: context.repo.owner, repo: context.repo.repo,
@@ -40,12 +38,12 @@ jobs:
         BODY: ${{ github.event.comment.body }}
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
     - name: React Success
-      uses: actions/github-script@v2
+      uses: actions/github-script@v6
       with:
         script: |
           post = (context.eventName == "issue_comment"
-            ? github.reactions.createForIssueComment
-            : github.reactions.createForPullRequestReviewComment)
+            ? github.rest.reactions.createForIssueComment
+            : github.rest.reactions.createForPullRequestReviewComment)
           post({
             owner: context.repo.owner, repo: context.repo.repo,
             comment_id: context.payload.comment.id, content: "rocket"})

.github/workflows/test.yml

@@ -2,18 +2,19 @@ name: Test
 on:
   push:
   pull_request:
-  schedule:
-  - cron: '15 23 * * 6'  # M H d m w (Sat at 23:15)
+  schedule: [{cron: '15 23 * * 6'}]  # M H d m w (Sat at 23:15)
 jobs:
   check:
     if: github.event_name != 'pull_request' || !contains('OWNER,MEMBER,COLLABORATOR', github.event.pull_request.author_association)
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
     - name: set PYSHA
       run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
-    - uses: actions/cache@v1
+    - uses: actions/cache@v3
       with:
         path: ~/.cache/pre-commit
         key: pre-commit|${{ env.PYSHA }}|${{ hashFiles('.pre-commit-config.yaml') }}
@@ -40,36 +41,33 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [2.7, 3.6, 3.9]
+        python: [3.7, 3.11]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python }}
     - run: pip install -U .[dev,nii,web]
-    - if: startsWith(matrix.python, '3')
-      run: pytest --durations-min=1
-    - if: startsWith(matrix.python, '2')
-      run: pytest
-    - uses: codecov/codecov-action@v1
+    - run: pytest --durations-min=1
+    - uses: codecov/codecov-action@v3
   cuda_matlab:
     if: github.event_name != 'pull_request' || !contains('OWNER,MEMBER,COLLABORATOR', github.event.pull_request.author_association)
     name: CUDA MATLAB py${{ matrix.python }}
     runs-on: [self-hosted, python, cuda, matlab]
     strategy:
       matrix:
-        python: [3.7, 3.9]
+        python: [3.7, 3.8]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
     - name: Run setup-python
       run: setup-python -p${{ matrix.python }}
     - run: pip install -U .[dev,nii,cuda,web,mbeautify]
     - run: pytest --durations-min=1
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v3
     - name: Post Run setup-python
       run: setup-python -p${{ matrix.python }} -Dr
       if: ${{ always() }}
@@ -78,10 +76,12 @@ jobs:
     name: PyPI Deploy
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:
@@ -90,19 +90,11 @@ jobs:
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
         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---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
     - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-      uses: softprops/action-gh-release@v1
+      name: Release
+      run: |
+        changelog=$(git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD)
+        tag="${GITHUB_REF#refs/tags/}"
+        gh release create --title "miutil $tag beta" --draft --notes "$changelog" "$tag" dist/${{ steps.dist.outputs.whl }} dist/${{ steps.dist.outputs.whl_asc }}
       env:
-        GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
-      with:
-        name: miutil ${{ steps.meta.outputs.tag }} beta
-        body_path: _CHANGES.md
-        draft: true
-        files: |
-          dist/${{ steps.dist.outputs.whl }}
-          dist/${{ steps.dist.outputs.whl_asc }}
+        GH_TOKEN: ${{ github.token }}

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.1.0
+  rev: v4.4.0
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -25,8 +25,8 @@ repos:
     entry: TODO
     types: [text]
     exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
-- repo: https://gitlab.com/pycqa/flake8
-  rev: 3.9.2
+- repo: https://github.com/PyCQA/flake8
+  rev: 5.0.4
   hooks:
   - id: flake8
     args: [-j8]
@@ -44,6 +44,6 @@ repos:
     args: [-i]
     additional_dependencies: [toml]
 - repo: https://github.com/PyCQA/isort
-  rev: 5.10.1
+  rev: 5.12.0
   hooks:
   - id: isort

README.rst

@@ -42,7 +42,7 @@ To install extras and their dependencies,
 use the package name ``miutil[option1,option2]``.
 
 
-.. |Tests| image:: https://img.shields.io/github/workflow/status/AMYPAD/miutil/Test?logo=GitHub
+.. |Tests| image:: https://img.shields.io/github/actions/workflow/status/AMYPAD/miutil/test.yml?branch=master&logo=GitHub
    :target: https://github.com/AMYPAD/miutil/actions
 .. |Coverage| image:: https://codecov.io/gh/AMYPAD/miutil/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/AMYPAD/miutil

miutil/cuinfo.py

@@ -61,7 +61,11 @@ def memory(dev_id=-1):
 
 def name(dev_id=-1):
     """returns device name"""
-    return pynvml.nvmlDeviceGetName(get_handle(dev_id)).decode("U8")
+    res = pynvml.nvmlDeviceGetName(get_handle(dev_id))
+    try:
+        return res.decode("U8") # pynvml<11.5
+    except AttributeError:
+        return res
 
 
 def nvcc_flags(dev_id=-1):

miutil/fdio.py

@@ -1,24 +1,13 @@
 import logging
 import re
+from collections.abc import Iterable
 from contextlib import contextmanager
-from os import makedirs
+from os import fspath, makedirs
+from pathlib import Path
 from shutil import copyfileobj, rmtree
 from tempfile import mkdtemp
 from zipfile import ZipFile
 
-try:
-    from collections.abc import Iterable
-except ImportError:
-    from collections import Iterable
-try:
-    from os import fspath
-except ImportError:
-    fspath = str
-try:
-    from pathlib import Path
-except ImportError:
-    from pathlib2 import Path
-
 from tqdm.auto import tqdm
 from tqdm.utils import CallbackIOWrapper
 
@@ -32,7 +21,7 @@ def create_dir(pth):
         try:
             makedirs(fspath(pth))
         except Exception as exc:
-            log.warning("cannot create:%s:%s" % (pth, exc))
+            log.warning("cannot create:%s:%s", pth, exc)
 
 
 def is_iter(x):
@@ -78,7 +67,6 @@ def extractall(fzip, dest, desc="Extracting"):
 
 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])

miutil/imio/nii.py

@@ -173,7 +173,7 @@ def array2nii(im, A, fnii, descrip="", trnsp=None, flip=None, storage_as=None):
     if len(flip) == 3:
         im = im[::-flip[0], ::-flip[1], ::-flip[2], ...]
 
-    res = nib.Nifti1Image(im, A)
+    res = nib.Nifti1Image(im, A, dtype=im.dtype)
     hdr = res.header
     hdr.set_sform(None, code='scanner')
     hdr['cal_max'] = np.max(im) # np.percentile(im, 90) #

miutil/mlab/__init__.py

@@ -3,15 +3,12 @@
 import re
 import sys
 from ast import literal_eval
+from functools import lru_cache
 from os import getenv, path
 from platform import system
 from subprocess import STDOUT, CalledProcessError, check_output
 from textwrap import dedent
 
-try:
-    from functools import lru_cache
-except ImportError:
-    from backports.functools_lru_cache import lru_cache
 try:
     FileNotFoundError
 except NameError:
@@ -52,9 +49,9 @@ def check_output_u8(*args, **kwargs):
 
 def env_prefix(key, dir):
     try:
-        os.environ[key] = "%s%s%s" % (os.environ[key], os.pathsep, fspath(dir))
+        os.environ[key] = f"{os.environ[key]}{os.pathsep}{fspath(dir)}"
     except KeyError:
-        os.environ[key] = str(fspath(dir))
+        os.environ[key] = fspath(dir)
 
 
 @lru_cache()
@@ -91,14 +88,13 @@ def get_engine(name=None):
 
                 Alternatively, use `get_runtime()` instead of `get_engine()`.
                 """).format(matlabroot=matlabroot(default="matlabroot"), exe=sys.executable))
-    started = engine.find_matlab()
-    notify = False
-    if not started or (name and name not in started):
-        notify = True
-        log.debug("Starting MATLAB")
-    eng = engine.connect_matlab(name=name or getenv("SPM12_MATLAB_ENGINE", None))
-    if notify:
-        log.debug("MATLAB started")
+    log.debug("Starting MATLAB")
+    try:
+        eng = engine.connect_matlab(name=name or getenv("SPM12_MATLAB_ENGINE", None))
+    except engine.EngineError:
+        log.error("MATLAB hasn't properly cleaned up. Try restarting your computer.")
+        raise
+    log.debug("MATLAB started")
     return eng
 
 
@@ -152,7 +148,7 @@ def _install_engine():
 def get_runtime(cache="~/.mcr", version=99):
     cache = Path(cache).expanduser()
     mcr_root = cache
-    i = mcr_root / ("v%d"%version)
+    i = mcr_root / f"v{version}"
     if i.is_dir():
         mcr_root = i
     else:
@@ -174,8 +170,8 @@ def get_runtime(cache="~/.mcr", version=99):
                 if system() == "Linux":
                     install.chmod(0o755)
                     check_output_u8([
-                        fspath(install), "-P",
-                        'bean421.installLocation="%s"' % fspath(cache), "-silent"])
+                        fspath(install), "-P", f'bean421.installLocation="{fspath(cache)}"',
+                        "-silent"])
                 else:
                     raise NotImplementedError(
                         dedent("""\
@@ -185,7 +181,7 @@ def get_runtime(cache="~/.mcr", version=99):
                         """).format(fspath(install), system()))
             else:
                 raise IndexError(version)
-            mcr_root /= "v%d" % version
+            mcr_root /= f"v{version}"
             log.info("Installed")
 
     # bin

miutil/mlab/beautify.py

@@ -25,10 +25,10 @@
 def ensure_mbeautifier(*args, **kwargs):
     eng = get_engine(*args, **kwargs)
     fn = get_file(
-        "MBeautifier-%s.zip" % MBEAUTIFIER_REV[:7],
-        "https://github.com/davidvarga/MBeautifier/archive/%s.zip" % MBEAUTIFIER_REV,
+        f"MBeautifier-{MBEAUTIFIER_REV[:7]}.zip",
+        f"https://github.com/davidvarga/MBeautifier/archive/{MBEAUTIFIER_REV}.zip",
     )
-    outpath = path.join(path.dirname(fn), "MBeautifier-%s" % MBEAUTIFIER_REV)
+    outpath = path.join(path.dirname(fn), f"MBeautifier-{MBEAUTIFIER_REV}")
     if not path.exists(outpath):
         with ZipFile(fn) as fd:
             fd.extractall(path=path.dirname(outpath))

miutil/web.py

@@ -50,7 +50,7 @@ def get_file(fname, origin, cache_dir=None, chunk_size=None):
     fpath = path.join(cache_dir, fname)
 
     if not path.exists(fpath):
-        log.debug("Downloading %s from %s" % (fpath, origin))
+        log.debug("Downloading %s from %s", fpath, origin)
         try:
             d = requests.get(origin, stream=True)
             with tqdm(
@@ -93,7 +93,7 @@ def urlopen_cached(url, outdir, fname=None, mode="rb"):
     if fname is None:
         fname = Path(urlparse(url).path).name
     fout = outdir / fname
-    cache = outdir / (fspath(fname) + ".url")
+    cache = outdir / f"{fspath(fname)}.url"
     if not fout.is_file() or not cache.is_file() or cache.read_text().strip() != url:
         fi = urlopen(url)
         with fout.open("wb") as raw: