bump version, merge pull request #9 from AMYPAD/devel

.github/workflows/comment-bot.yml

@@ -4,7 +4,6 @@ on:
     types: [created]
   pull_request_review_comment:
     types: [created]
-
 jobs:
   tag:  # /tag <tagname> <commit>
     if: startsWith(github.event.comment.body, '/tag ')
@@ -21,7 +20,6 @@ jobs:
           post = (context.eventName == "issue_comment"
             ? github.reactions.createForIssueComment
             : github.reactions.createForPullRequestReviewComment)
-
           if (!["admin", "write"].includes(perm.data.permission)){
             post({
               owner: context.repo.owner, repo: context.repo.repo,

.github/workflows/test.yml

@@ -15,13 +15,27 @@ jobs:
     - uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python }}
+    - name: set PYSHA
+      run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
+    - uses: actions/cache@v1
+      with:
+        path: ~/.cache/pre-commit
+        key: pre-commit|${{ env.PYSHA }}|${{ hashFiles('.pre-commit-config.yaml') }}
     - run: pip install -U .[dev]
     - run: python setup.py sdist bdist_wheel
     - run: twine check dist/*
-    - run: flake8 .
+    - uses: reviewdog/action-setup@v1
+    - if: github.event_name != 'schedule'
+      run: |
+        set -o pipefail
+        pre-commit run -a flake8 | \
+          reviewdog -f=pep8 -name=flake8 -tee -reporter=github-check -filter-mode nofilter
+      env:
+        REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     - if: |
         ! startsWith(matrix.python, '2')
-      run: black --check .
+      run: pre-commit run -a --show-diff-on-failure black
+    - run: pre-commit run -a --show-diff-on-failure isort
   test:
     runs-on: ubuntu-latest
     strategy:
@@ -59,6 +73,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
     - uses: casperdcl/deploy-pypi@v1
       with:
         build: true

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.4.0
+  hooks:
+  - id: check-added-large-files
+  - id: check-case-conflict
+  - id: check-docstring-first
+  - id: check-executables-have-shebangs
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+  - id: trailing-whitespace
+- 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
+  rev: 19.10b0
+- hooks:
+  - id: isort
+  repo: https://github.com/timothycrosley/isort
+  rev: 5.6.4

.pre-commit-hooks.yaml

@@ -0,0 +1,9 @@
+- id: mbeautify
+  name: mbeautify
+  description: '`mbeautify` is a command-line utility for enforcing style consistency across Matlab projects.'
+  entry: mbeautify
+  language: python
+  additional_dependencies: ['.[mbeautify]']
+  types: [text]
+  files: \.(m)$
+  require_serial: true

LICENCE.md

@@ -1,7 +1,7 @@
 Copyright 2020 AMYPAD
 
 Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
+you may not use this project except in compliance with the License.
 You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0

README.rst

@@ -15,6 +15,14 @@ Install
 Intended for inclusion in requirements for other packages.
 The package name is ``miutil``. Extra install options include:
 
+- cuda
+
+  - provides `miutil.cuinfo <https://github.com/AMYPAD/miutil/blob/master/miutil/cuinfo.py>`_
+
+- mbeautify
+
+  - provides `miutil.mlab.beautify <https://github.com/AMYPAD/miutil/blob/master/miutil/mlab/beautify.py>`_
+
 - nii
 
   - provides `miutil.imio.nii <https://github.com/AMYPAD/miutil/blob/master/miutil/imio/nii.py>`_
@@ -25,9 +33,9 @@ The package name is ``miutil``. Extra install options include:
 
     - includes a useful 3D multi-volume ``imscroll`` function which depends only on ``matplotlib``
 
-- cuda
+- web
 
-  - provides `miutil.cuinfo <https://github.com/AMYPAD/miutil/blob/master/miutil/cuinfo.py>`_
+  - provides `miutil.web <https://github.com/AMYPAD/miutil/blob/master/miutil/web.py>`_
 
 
 To install extras and their dependencies,

miutil/cuinfo.py

@@ -1,14 +1,15 @@
+#!/usr/bin/env python3
 """CUDA helpers
 Usage:
-  miutil.cuinfo [options]
+  cuinfo [options]
 
 Options:
   -n, --num-devices   : print number of devices (ignores `-d`)
   -f, --nvcc-flags    : print out flags for use nvcc compilation
   -d ID, --dev-id ID  : select device ID [default: None:int] for all
 """
-from argopt import argopt
 import pynvml
+from argopt import argopt
 
 __all__ = ["num_devices", "compute_capability", "memory", "name", "nvcc_flags"]
 

miutil/fdio.py

@@ -1,13 +1,19 @@
+import logging
 from contextlib import contextmanager
 from os import makedirs, path
 from shutil import rmtree
 from tempfile import mkdtemp
 
+log = logging.getLogger(__name__)
+
 
 def create_dir(pth):
     """Equivalent of `mkdir -p`"""
-    if not path.exists(pth):
-        makedirs(pth)
+    if not path.isdir(pth):
+        try:
+            makedirs(pth)
+        except Exception as exc:
+            log.warn("cannot create:%s:%s" % (pth, exc))
 
 
 def hasext(fname, ext):

miutil/imio/__init__.py

@@ -4,16 +4,16 @@
 RE_NPYZ = re.compile(r"^(.+)(\.np[yz])$", flags=re.I)
 
 
-def imread(fname):
+def imread(fname, *args, **kwargs):
     """Read any supported filename"""
     if RE_NII_GZ.search(fname):
         from .nii import getnii
 
-        return getnii(fname)
+        return getnii(fname, *args, **kwargs)
     elif RE_NPYZ.search(fname):
         import numpy as np
 
-        res = np.load(fname)
+        res = np.load(fname, *args, **kwargs)
         if hasattr(res, "keys") and len(res.keys()) == 1:
             res = res[list(res.keys())[0]]
         return res

miutil/imio/nii.py

@@ -1,5 +1,4 @@
 """NIfTI I/O"""
-from six import string_types
 import gzip
 import logging
 import numbers
@@ -8,9 +7,10 @@
 
 import nibabel as nib
 import numpy as np
+from six import string_types
 
-from . import RE_NII_GZ
 from ..fdio import create_dir, hasext
+from . import RE_NII_GZ
 
 RE_GZ = re.compile(r"^(.+)(\.gz)$", flags=re.I)
 log = logging.getLogger(__name__)

miutil/mlab.py → miutil/mlab/__init__.py

@@ -1,13 +1,13 @@
+import logging
+import re
+import sys
 from ast import literal_eval
 from functools import lru_cache
 from os import getenv, path
-from subprocess import CalledProcessError, STDOUT, check_output
+from subprocess import STDOUT, CalledProcessError, check_output
 from textwrap import dedent
-import logging
-import re
-import sys
 
-from .fdio import tmpdir
+from ..fdio import tmpdir
 
 __all__ = ["get_engine"]
 IS_WIN = any(sys.platform.startswith(i) for i in ["win32", "cygwin"])

miutil/mlab/beautify.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+"""Usage:
+  mbeautify <mfile>...
+
+Arguments:
+  <mfile>  : Path to `*.m` file
+"""
+import logging
+from functools import lru_cache, wraps
+from os import path
+from zipfile import ZipFile
+
+from argopt import argopt
+from tqdm.contrib import tmap
+
+from ..web import get_file
+from . import get_engine
+
+log = logging.getLogger(__name__)
+MBEAUTIFIER_REV = "aad307c62532cd7c852aab9bac44fd6443b90bef"
+
+
+@lru_cache()
+@wraps(get_engine)
+def ensure_mbeautifier(*args, **kwargs):
+    eng = get_engine(*args, **kwargs)
+    fn = get_file(
+        "MBeautifier-aad307c.zip",
+        "https://github.com/davidvarga/MBeautifier/archive/%s.zip" % MBEAUTIFIER_REV,
+    )
+    outpath = path.join(path.dirname(fn), "MBeautifier-%s" % MBEAUTIFIER_REV)
+    if not path.exists(outpath):
+        with ZipFile(fn) as fd:
+            fd.extractall(path=path.dirname(outpath))
+    assert path.exists(outpath), "Error extracting"
+    log.debug("adding wrappers (%s) to MATLAB path", outpath)
+    eng.addpath(outpath, nargout=0)
+    return eng
+
+
+def main(*args, **kwargs):
+    args = argopt(__doc__).parse_args(*args, **kwargs)
+    logging.basicConfig(level=logging.INFO)
+    eng = ensure_mbeautifier()
+    formatter = eng.MBeautify.formatFileNoEditor
+
+    for fn in tmap(path.abspath, args.mfile):
+        log.debug("file:%s", fn)
+        formatter(fn, fn, nargout=0)
+
+
+if __name__ == "__main__":  # pragma: no cover
+    main()

miutil/plot.py

@@ -1,9 +1,39 @@
 from os import path
 from textwrap import dedent
+
 import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib import cm
 
 from .imio import imread
 
+show = plt.show  # convenience: for use after `imscroll`
+
+
+def apply_cmap(**kwargs):
+    """Apply different cmaps to inputs an average the results.
+
+    Args:
+      **kwargs: map named cmap to ndarray
+
+    >>> vol1 = np.random.random((10, 10, 10))
+    >>> vol2 = np.random.random((10, 10, 10))
+    >>> res = apply_cmap(magma=vol1, bone=vol2)
+    >>> assert res.shape == (10, 10, 10, 4)  # RGBA
+    >>> imscroll(res[None])  # (1, 10, 10, 10, 4) for (N, Z, Y, X, RGBA)
+    """
+    res = None
+    for v in kwargs.values():
+        if res is None:
+            res = np.zeros(v.shape + (4,), dtype=np.float32)
+        else:
+            assert v.shape == res.shape[:-1], "all inputs must have same shape"
+    for k, v in kwargs.items():
+        cmap = getattr(cm, k)
+        res += cmap(v)
+    res /= len(kwargs)
+    return res
+
 
 class imscroll:
     """
@@ -137,10 +167,7 @@ def _on_click(self, event):
             ]
         else:
             z = ndi.map_coordinates(
-                arr,
-                np.vstack((x, y)),
-                order=self.order,
-                mode="nearest",
+                arr, np.vstack((x, y)), order=self.order, mode="nearest"
             )
         self.picked = []
         self.key["control"] = False