bump version, merge pull request #26 from AMYPAD/devel

AMYPAD · Oct 30, 2021 · f54cf4a · f54cf4a
2 parents 14ea116 + 601c0f3
commit f54cf4a
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,14 +1,15 @@
 name: Test
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: '15 23 * * 6'  # M H d m w (Sat at 23:15)
 jobs:
   check:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'AMYPAD'
     runs-on: ubuntu-latest
-    name: Check
     steps:
     - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
     - uses: actions/setup-python@v2
     - name: set PYSHA
       run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
@@ -19,7 +20,7 @@ jobs:
     - name: dependencies
       run: pip install -U pre-commit
     - 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
@@ -34,12 +35,12 @@ jobs:
         EVENT: ${{ github.event_name }}
     - run: pre-commit run -a --show-diff-on-failure
   test:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'AMYPAD'
+    name: py${{ matrix.python }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [2.7, 3.6, 3.9]
-    name: Test py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2
       with:
@@ -52,22 +53,25 @@ jobs:
       run: pytest --durations-min=1
     - if: startsWith(matrix.python, '2')
       run: pytest
-    - run: codecov
+    - uses: codecov/codecov-action@v1
   cuda_matlab:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'AMYPAD'
+    name: CUDA MATLAB py${{ matrix.python }}
     runs-on: [self-hosted, python, cuda, matlab]
-    name: Test cuda & matlab
+    strategy:
+      matrix:
+        python: [3.7, 3.9]
     steps:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
     - name: Run setup-python
-      run: setup-python -p3.7
+      run: setup-python -p${{ matrix.python }}
     - run: pip install -U .[dev,nii,cuda,web,mbeautify]
     - run: pytest --durations-min=1
-    - run: codecov
+    - uses: codecov/codecov-action@v1
     - name: Post Run setup-python
-      run: setup-python -p3.7 -Dr
+      run: setup-python -p${{ matrix.python }} -Dr
       if: ${{ always() }}
   deploy:
     needs: [check, test, cuda_matlab]

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -35,10 +35,11 @@ repos:
     - flake8-comprehensions
     - flake8-debugger
     - flake8-string-format
-- repo: https://github.com/psf/black
-  rev: 21.8b0
+- repo: https://github.com/google/yapf
+  rev: v0.31.0
   hooks:
-  - id: black
+  - id: yapf
+    args: [-i]
 - repo: https://github.com/PyCQA/isort
   rev: 5.9.3
   hooks:

diff --git a/miutil/__init__.py b/miutil/__init__.py
@@ -1,4 +1,4 @@
-from .fdio import *  # NOQA
+from .fdio import *  # yapf: disable # NOQA
 
 # version detector. Precedence: installed dist, git, 'UNKNOWN'
 try:

diff --git a/miutil/cuinfo.py b/miutil/cuinfo.py
@@ -18,13 +18,13 @@
 def nvmlDeviceGetCudaComputeCapability(handle):
     major = pynvml.c_int()
     minor = pynvml.c_int()
-    try:  # pynvml>=11
+    try:      # pynvml>=11
         get_fn = pynvml.nvml._nvmlGetFunctionPointer
     except AttributeError:
         get_fn = pynvml.get_func_pointer
     fn = get_fn("nvmlDeviceGetCudaComputeCapability")
     ret = fn(handle, pynvml.byref(major), pynvml.byref(minor))
-    try:  # pynvml>=11
+    try:      # pynvml>=11
         check_ret = pynvml.nvml._nvmlCheckReturn
     except AttributeError:
         check_ret = pynvml.check_return
@@ -66,8 +66,7 @@ def name(dev_id=-1):
 
 def nvcc_flags(dev_id=-1):
     return "-gencode=arch=compute_{0:d}{1:d},code=compute_{0:d}{1:d}".format(
-        *compute_capability(dev_id)
-    )
+        *compute_capability(dev_id))
 
 
 def main(*args, **kwargs):
@@ -86,12 +85,9 @@ def main(*args, **kwargs):
         noargs = False
     if noargs:
         for dev_id in devices:
-            print(
-                "Device {:2d}:{}:compute capability:{:d}.{:d}".format(
-                    dev_id, name(dev_id), *compute_capability(dev_id)
-                )
-            )
+            print("Device {:2d}:{}:compute capability:{:d}.{:d}".format(
+                dev_id, name(dev_id), *compute_capability(dev_id)))
 
 
-if __name__ == "__main__":  # pragma: no cover
+if __name__ == "__main__": # pragma: no cover
     main()
diff --git a/miutil/fdio.py b/miutil/fdio.py
@@ -57,14 +57,14 @@ def extractall(fzip, dest, desc="Extracting"):
     """zipfile.Zipfile(fzip).extractall(dest) with progress"""
     dest = Path(dest).expanduser()
     with ZipFile(fzip) as zipf, tqdm(
-        desc=desc,
-        unit="B",
-        unit_scale=True,
-        unit_divisor=1024,
-        total=sum(getattr(i, "file_size", 0) for i in zipf.infolist()),
+            desc=desc,
+            unit="B",
+            unit_scale=True,
+            unit_divisor=1024,
+            total=sum(getattr(i, "file_size", 0) for i in zipf.infolist()),
     ) as pbar:
         for i in zipf.infolist():
-            if not getattr(i, "file_size", 0):  # directory
+            if not getattr(i, "file_size", 0): # directory
                 zipf.extract(i, fspath(dest))
             else:
                 (dest / i.filename).parent.mkdir(parents=True, exist_ok=True)
@@ -78,7 +78,6 @@ 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])

diff --git a/miutil/imio/nii.py b/miutil/imio/nii.py
@@ -4,16 +4,20 @@
 import numbers
 import os.path
 import re
+import sys
 
 import nibabel as nib
 import numpy as np
-from six import string_types
 
 from ..fdio import create_dir, fspath, hasext
 from . import RE_NII_GZ
 
 RE_GZ = re.compile(r"^(.+)(\.gz)$", flags=re.I)
 log = logging.getLogger(__name__)
+if sys.version_info[0] < 3:
+    string_types = basestring, # NOQA: F821
+else:
+    string_types = str,
 
 
 def file_parts(fname, regex=RE_NII_GZ):
@@ -86,22 +90,20 @@ def getnii(fim, nan_replace=None, output="image"):
         flip = tuple(np.int8(ornt[:, 1]))
 
         # > voxel size
-        voxsize = nim.header.get("pixdim")[1 : nim.header.get("dim")[0] + 1]
+        voxsize = nim.header.get("pixdim")[1:nim.header.get("dim")[0] + 1]
         # > rearrange voxel size according to the orientation
         voxsize = voxsize[np.array(trnsp)]
 
         # > dimensions
-        dims = dim[1 : nim.header.get("dim")[0] + 1]
+        dims = dim[1:nim.header.get("dim")[0] + 1]
         dims = dims[np.array(trnsp)]
 
         # > flip y-axis and z-axis and then transpose.
         # Depends if dynamic (4 dimensions) or static (3 dimensions)
         if dimno == 4:
-            imr = np.transpose(
-                imr[:: -flip[0], :: -flip[1], :: -flip[2], :], (3,) + trnsp
-            )
+            imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2], :], (3,) + trnsp)
         elif dimno == 3:
-            imr = np.transpose(imr[:: -flip[0], :: -flip[1], :: -flip[2]], trnsp)
+            imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2]], trnsp)
 
     if output == "affine" or output == "all":
         # A = nim.get_sform()
@@ -111,17 +113,8 @@ def getnii(fim, nan_replace=None, output="image"):
 
     if output == "all":
         out = {
-            "im": imr,
-            "affine": A,
-            "fim": fim,
-            "dtype": nim.get_data_dtype(),
-            "shape": imr.shape,
-            "hdr": nim.header,
-            "voxsize": voxsize,
-            "dims": dims,
-            "transpose": trnsp,
-            "flip": flip,
-        }
+            "im": imr, "affine": A, "fim": fim, "dtype": nim.get_data_dtype(), "shape": imr.shape,
+            "hdr": nim.header, "voxsize": voxsize, "dims": dims, "transpose": trnsp, "flip": flip}
     elif output == "image":
         out = imr
     elif output == "affine":
@@ -161,11 +154,7 @@ def array2nii(im, A, fnii, descrip="", trnsp=None, flip=None, storage_as=None):
     # >>as obtained from getnii(..., output='all')
 
     # > permute the axis order in the image array
-    if (
-        isinstance(storage_as, dict)
-        and "transpose" in storage_as
-        and "flip" in storage_as
-    ):
+    if (isinstance(storage_as, dict) and "transpose" in storage_as and "flip" in storage_as):
 
         trnsp = (
             storage_as["transpose"].index(0),
@@ -186,12 +175,12 @@ def array2nii(im, A, fnii, descrip="", trnsp=None, flip=None, storage_as=None):
 
     # > perform flip of x,y,z axes after transposition into proper NIfTI order
     if len(flip) == 3:
-        im = im[:: -flip[0], :: -flip[1], :: -flip[2], ...]
+        im = im[::-flip[0], ::-flip[1], ::-flip[2], ...]
 
     res = nib.Nifti1Image(im, A)
     hdr = res.header
     hdr.set_sform(None, code="scanner")
-    hdr["cal_max"] = np.max(im)  # np.percentile(im, 90) #
+    hdr["cal_max"] = np.max(im) # np.percentile(im, 90) #
     hdr["cal_min"] = np.min(im)
     hdr["descrip"] = descrip
     nib.save(res, fspath(fnii))
@@ -266,12 +255,8 @@ def niisort(fims, memlim=True):
         raise ValueError("Input image(s) must be 3D.")
 
     out = {
-        "shape": _nii.shape[::-1],
-        "files": _fims,
-        "sortlist": sortlist,
-        "dtype": _nii.get_data_dtype(),
-        "N": Nim,
-    }
+        "shape": _nii.shape[::-1], "files": _fims, "sortlist": sortlist,
+        "dtype": _nii.get_data_dtype(), "N": Nim}
 
     if memlim and Nfrm > 50:
         imdic = getnii(_fims[0], output="all")
@@ -328,12 +313,11 @@ def nii_modify(nii_fd, fimout="", outpath="", fcomment="", voxel_range=None):
     log.debug("output floating and affine file names:%s", fout)
     fout = os.path.join(opth, fout)
 
-    if len(voxel_range) == 1:  # set max value
+    if len(voxel_range) == 1:                                               # set max value
         im = voxel_range[0] * dctnii["im"] / np.max(dctnii["im"])
-    elif len(voxel_range) == 2:  # set range
-        im = (dctnii["im"] - np.min(dctnii["im"])) * (
-            np.ptp(voxel_range) / np.ptp(dctnii["im"])
-        ) + voxel_range[0]
+    elif len(voxel_range) == 2:                                             # set range
+        im = (dctnii["im"] - np.min(dctnii["im"])) * (np.ptp(voxel_range) /
+                                                      np.ptp(dctnii["im"])) + voxel_range[0]
     else:
         return None