bump version, merge pull request #32 from AMYPAD/devel

.github/workflows/test.yml

@@ -65,7 +65,7 @@ jobs:
         fetch-depth: 0
     - name: Run setup-python
       run: setup-python -p${{ matrix.python }}
-    - run: pip install -U .[dev,nii,cuda,web,mbeautify]
+    - run: pip install -U .[dev,nii,cuda,web,mbeautify] 'setuptools<66' # ignore matlab engine PEP440 non-compliance https://github.com/pypa/setuptools/issues/3772
     - run: pytest --durations-min=1
     - uses: codecov/codecov-action@v3
     - name: Post Run setup-python
@@ -85,8 +85,7 @@ jobs:
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:
-        requirements: twine setuptools wheel setuptools_scm[toml]
-        build: true
+        pip: true
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
         upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}

.pre-commit-config.yaml

@@ -36,9 +36,10 @@ repos:
     - flake8-comprehensions
     - flake8-debugger
     - flake8-isort
+    - flake8-pyproject
     - flake8-string-format
 - repo: https://github.com/google/yapf
-  rev: v0.32.0
+  rev: v0.33.0
   hooks:
   - id: yapf
     args: [-i]

LICENCE.md

@@ -1,4 +1,4 @@
-Copyright 2020 AMYPAD
+Copyright 2020-23 AMYPAD
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this project except in compliance with the License.

miutil/cuinfo.py

@@ -89,7 +89,7 @@ def main(*args, **kwargs):
         noargs = False
     if noargs:
         for dev_id in devices:
-            print("Device {:2d}:{}:compute capability:{:d}.{:d}".format(
+            print("Device {:2d}:{}:compute capability:{:d}.{:d}".format( # NOQA: P101
                 dev_id, name(dev_id), *compute_capability(dev_id)))
 
 

miutil/imio/nii.py

@@ -57,9 +57,9 @@ def nii_gzip(imfile, outpath=""):
 
 def getnii(fim, nan_replace=None, output='image'):
     """
-    Get PET image from NIfTI file.
+    Get image from NIfTI file.
     Arguments:
-        fim: input file name for the nifty image
+        fim: input file name for the NIfTI image
         nan_replace: the value to be used for replacing the NaNs in the image.
                      by default no change (None).
         output: option for choosing output: image, affine matrix or

miutil/mlab/__init__.py

@@ -78,16 +78,17 @@ def get_engine(name=None):
 install-matlab-engine-api-for-python-in-nondefault-locations.html
                 It's likely you need to do:
 
-                cd "{matlabroot}\\extern\\engines\\python"
-                {exe} setup.py build --build-base="BUILDDIR" install
+                cd "{setup_dir}"
+                {exe} -m pip install 'setuptools<66'
+                {exe} setup.py build --build-base="BUILDDIR" install --prefix="{pre}"
 
                 - Fill in any temporary directory name for BUILDDIR
                   (e.g. /tmp/builddir).
-                - If installation fails due to write permissions, try appending `--user`
-                  to the above command.
 
                 Alternatively, use `get_runtime()` instead of `get_engine()`.
-                """).format(matlabroot=matlabroot(default="matlabroot"), exe=sys.executable))
+                """).format(
+                    setup_dir=path.join(matlabroot(default="matlabroot"), "extern", "engines",
+                                        "python"), exe=sys.executable, pre=sys.prefix))
     log.debug("Starting MATLAB")
     try:
         eng = engine.connect_matlab(name=name or getenv("SPM12_MATLAB_ENGINE", None))
@@ -126,7 +127,8 @@ def matlabroot(default=None):
 
 def _install_engine():
     src = path.join(matlabroot(), "extern", "engines", "python")
-    with open(path.join(src, "setup.py")) as fd: # check version support
+    with open(path.join(src, "setup.py")) as fd:
+        # check version support
         supported = literal_eval(
             re.search(r"supported_version.*?=\s*(.*?)$", fd.read(), flags=re.M).group(1))
         if ".".join(map(str, sys.version_info[:2])) not in map(str, supported):
@@ -138,10 +140,21 @@ def _install_engine():
     with tmpdir() as td:
         cmd = [sys.executable, "setup.py", "build", "--build-base", td, "install"]
         try:
-            return check_output_u8(cmd, cwd=src)
+            return check_output_u8(cmd + ["--prefix", sys.prefix], cwd=src)
         except CalledProcessError:
             log.warning("Normal install failed. Attempting `--user` install.")
-            return check_output_u8(cmd + ["--user"], cwd=src)
+            try:
+                return check_output_u8(cmd + ["--user"], cwd=src)
+            except CalledProcessError:
+                ml_ver = src.split(path.sep)[-4].lstrip("R")
+                if ml_ver < '2020b':
+                    raise
+                eng_ver = {
+                    '2020b': '9.9', '2021a': '9.10', '2021b': '9.11', '2022a': '9.12',
+                    '2022b': '9.13', '2023a': '9.14'}
+                pin = f"=={eng_ver[ml_ver]}.*" if ml_ver in eng_ver else ""
+                return check_output_u8([
+                    sys.executable, "-m", "pip", "install", "matlabengine" + pin])
 
 
 @lru_cache()
@@ -176,8 +189,8 @@ def get_runtime(cache="~/.mcr", version=99):
                     raise NotImplementedError(
                         dedent("""\
                         Don't yet know how to handle
-                        {}
-                        for {!r}.
+                        {0}
+                        for {1!r}.
                         """).format(fspath(install), system()))
             else:
                 raise IndexError(version)

miutil/plot.py

@@ -78,7 +78,7 @@ def __init__(self, vol, view='t', fig=None, titles=None, order=0, sharexy=None,
                     3: single volume
                     4: multiple volumes
                     5: multiple RGB volumes
-                but got {}
+                but got {0}
                 """.format(ndim)))
 
         view = view.lower()
@@ -100,7 +100,7 @@ def __init__(self, vol, view='t', fig=None, titles=None, order=0, sharexy=None,
         self.axs = [axs] if len(vol) == 1 else list(axs.flat)
         for ax, i, t in zip(self.axs, vol, self.titles):
             ax.imshow(i[self.index], **kwargs)
-            ax.set_title(t or "slice #{}".format(self.index))
+            ax.set_title(t or f"slice #{self.index}")
         self.vols = vol
         # line profiles
         self.order = order
@@ -137,7 +137,7 @@ def set_index(self, index):
         self.index = int(index) % self.index_max
         for ax, vol, t in zip(self.axs, self.vols, self.titles):
             ax.images[0].set_array(vol[self.index])
-            ax.set_title(t or "slice #{}".format(self.index))
+            ax.set_title(t or f"slice #{self.index}")
         for ann in self._annotes:
             ann.remove()
         self._annotes = []

pyproject.toml

@@ -1,6 +1,94 @@
 [build-system]
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
+build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 write_to = "miutil/_dist_ver.py"
 write_to_template = "__version__ = '{version}'\n"
+
+[tool.setuptools.packages.find]
+exclude = ["tests"]
+
+[project.urls]
+documentation = "https://github.com/AMYPAD/miutil/#miutil"
+repository = "https://github.com/AMYPAD/miutil"
+changelog = "https://github.com/AMYPAD/miutil/releases"
+
+[project]
+name = "miutil"
+dynamic = ["version"]
+maintainers = [{name = "Casper da Costa-Luis", email = "casper.dcl@physics.org"}]
+description = "Medical imaging utilities for the AMYPAD and NiftyPET projects"
+readme = "README.rst"
+requires-python = ">=3.7"
+keywords = ["fMRI", "PET", "SPECT", "EEG", "MEG"]
+license = {text = "Apache-2.0"}
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Environment :: GPU",
+    "Environment :: GPU :: NVIDIA CUDA",
+    "Intended Audience :: Education",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Other Scripting Engines",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    "Topic :: Software Development :: Libraries",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Software Development :: User Interfaces",
+    "Topic :: System :: Installation/Setup",
+    "Topic :: Utilities"]
+dependencies = ["tqdm>=4.40.0"]
+
+[project.optional-dependencies]
+dev = ["pytest>=6", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+nii = ["nibabel>=4.0", "numpy"]
+plot = ["matplotlib", "numpy", "scipy"]
+cuda = ["argopt", "pynvml"]
+web = ["requests"]
+mbeautify = ["argopt", "tqdm>=4.42.0", "requests"]  # web
+
+[project.scripts]
+cuinfo = "miutil.cuinfo:main"
+mbeautify = "miutil.mlab.beautify:main"
+
+[tool.flake8]
+max_line_length = 99
+extend_ignore = ["E261"]
+exclude = [".git", "__pycache__", "build", "dist", ".eggs"]
+
+[tool.yapf]
+spaces_before_comment = [15, 20]
+arithmetic_precedence_indication = true
+allow_split_before_dict_value = false
+coalesce_brackets = true
+column_limit = 99
+each_dict_entry_on_separate_line = false
+space_between_ending_comma_and_closing_bracket = false
+split_before_named_assigns = false
+split_before_closing_bracket = false
+blank_line_before_nested_class_or_def = false
+
+[tool.isort]
+profile = "black"
+line_length = 99
+multi_line_output = 4
+known_first_party = ["miutil", "tests"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+timeout = 15
+log_level = "INFO"
+python_files = ["tests/test_*.py"]
+testpaths = ["tests"]
+addopts = "-v --tb=short -rxs -W=error --log-level=debug -n=auto --durations=0 --cov=miutil --cov-report=term-missing --cov-report=xml"