Merge pull request #1163 from ZviBaratz/docs

Fixed documentation build error and warnings

.github/workflows/misc.yml

@@ -24,7 +24,7 @@ jobs:
       matrix:
         python-version: ["3.10"]
         install: ['pip']
-        check: ['style', 'doc']
+        check: ['style', 'doctest']
         pip-flags: ['']
         depends: ['REQUIREMENTS']
     env:

doc-requirements.txt

@@ -1,6 +1,7 @@
-# Requirements for building docs
+# Auto-generated by tools/update_requirements.py
 -r requirements.txt
-sphinx<3
+matplotlib >= 1.5.3
 numpydoc
+sphinx ~= 5.3
 texext
-matplotlib >=1.3.1
+tomli; python_version < "3.11"

doc/source/conf.py

@@ -23,7 +23,10 @@
 from pathlib import Path
 from runpy import run_path
 
-import toml
+try:
+    import tomllib
+except ImportError:
+    import tomli as tomllib
 
 # Check for external Sphinx extensions we depend on
 try:
@@ -52,14 +55,15 @@
     fobj.write(rel['long_description'])
 
 # Load metadata from setup.cfg
-pyproject_dict = toml.load(Path("../../pyproject.toml"))
-metadata = pyproject_dict["project"]
+with open(Path("../../pyproject.toml"), 'rb') as fobj:
+    pyproject = tomllib.load(fobj)
+authors = pyproject["project"]["authors"][0]
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.doctest',
-              #'sphinx.ext.intersphinx',
+              'sphinx.ext.intersphinx',
               'sphinx.ext.todo',
               'sphinx.ext.mathjax',
               'sphinx.ext.inheritance_diagram',
@@ -69,9 +73,10 @@
               'matplotlib.sphinxext.plot_directive',
               ]
 
-# the following doesn't work with sphinx < 1.0, but will make a separate
-# sphinx-autogen run obsolete in the future
-#autosummary_generate = True
+# Autosummary always wants to use a `generated/` directory.
+# We generate with `make api-stamp`
+# This could change in the future
+autosummary_generate = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -87,9 +92,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-author_name = metadata["authors"][0]["name"]
-author_email = metadata["authors"][0]["email"]
-copyright = f"2006-2022, {author_name} <{author_email}>"
+copyright = f"2006-2022, {authors['name']} <{authors['email']}>"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -269,7 +272,7 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'https://docs.python.org/3/': None}
 
 # Config of plot_directive
 plot_include_source = True

doc/source/devel/biaps/biap_0003.rst

@@ -199,8 +199,8 @@ The base level header will usually also have image metadata fields giving
 information about the whole image. A field is an "image metadata field" if it
 is defined at the top level of the header.  For example::
 
->>> hdr = dict(nipy_header_version='1.0',
-...            Manufacturer="SIEMENS")
+      >>> hdr = dict(nipy_header_version='1.0',
+      ...            Manufacturer="SIEMENS")
 
 All image metadata fields are optional.
 
@@ -635,7 +635,7 @@ Use case
 ^^^^^^^^
 
 When doing motion correction on a 4D image, we calculate the required affine
-transformation from |--| say |--| the second image to the first image; the
+transformation from, say, the second image to the first image; the
 third image to the first image; etc. If there are N volumes in the 4D image,
 we would need to store N-1 affine transformations.  If we have registered to
 the mean volume of the volume series instead of one of the volumes in the

doc/source/devel/biaps/biap_0004.rst

@@ -221,6 +221,7 @@ Improving access to varying meta data through the Nifti
 
 Currently, when accessing varying meta data through the `get_meta` method 
 you can only get one value at a time::
+
     >>> echo_times = [nii.get_meta('EchoTime', (0, 0, 0, idx)) 
                       for idx in xrange(data.shape[-1])]
 

doc/source/devel/biaps/biap_0006.rst

@@ -193,7 +193,7 @@ In NIfTI:
 
 We saw above that the MGH format refers to a volume (in our sense) as a
 *frame*.  ECAT has the same usage - a frame is a 3D volume. The fmristat
-software uses frame in the same sense |--| e.g. `line 32 of example.m
+software uses frame in the same sense, e.g., `line 32 of example.m
 <https://github.com/matthew-brett/fmristat/blob/master/fmristat/example.m#L32>`_.
 
 Unfortunately DICOM appears to use "frame" to mean a 2D slice.  For example,

doc/source/devel/devdiscuss.rst

@@ -22,3 +22,7 @@ progress.
     spm_use
     modified_images
     data_pkg_design
+    data_pkg_discuss
+    data_pkg_uses
+    scaling
+    bv_formats

doc/source/devel/image_design.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 ########################
 The nibabel image object
 ########################

doc/source/installing_data.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 .. _installing-data:
 
 Installing data packages

doc/source/old/ioimplementation.rst

@@ -1,5 +1,7 @@
 .. -*- mode: rst -*-
 
+:orphan:
+
 ##################################################
 Relationship between images and io implementations
 ##################################################

doc/tools/build_modref_templates.py

@@ -83,6 +83,7 @@ def abort(error):
                                         r'\.info.*$',
                                         r'\.pkg_info.*$',
                                         r'\.py3k.*$',
+                                        r'\._version.*$',
                                         ]
     docwriter.write_api_docs(outdir)
     docwriter.write_index(outdir, 'index', relative_to=outdir)

nibabel/batteryrunners.py

@@ -20,6 +20,7 @@
 
 To run checks only, and return problem report objects:
 
+>>> from nibabel.batteryrunners import BatteryRunner, Report
 >>> def chk(obj, fix=False): # minimal check
 ...     return obj, Report()
 >>> btrun = BatteryRunner((chk,))

nibabel/ecat.py

@@ -523,7 +523,7 @@ def __init__(self, hdr, mlist, fileobj):
         there is one subheader for each frame in the ecat file
 
         Parameters
-        -----------
+        ----------
         hdr : EcatHeader
             ECAT main header
         mlist : array shape (N, 4)

nibabel/gifti/__init__.py

@@ -13,7 +13,6 @@
 .. autosummary::
    :toctree: ../generated
 
-   giftiio
    gifti
 """
 

nibabel/processing.py

@@ -327,11 +327,13 @@ def conform(
     Using the default arguments, this function is meant to replicate most parts
     of FreeSurfer's ``mri_convert --conform`` command. Specifically, this
     function:
+
         - Resamples data to ``output_shape``
         - Resamples voxel sizes to ``voxel_size``
         - Reorients to RAS (``mri_convert --conform`` reorients to LIA)
 
     Unlike ``mri_convert --conform``, this command does not:
+
         - Transform data to range [0, 255]
         - Cast to unsigned eight-bit integer
 

nibabel/quaternions.py

@@ -19,6 +19,7 @@
 they are applied on the left of the vector.  For example:
 
 >>> import numpy as np
+>>> from nibabel.quaternions import quat2mat
 >>> q = [0, 1, 0, 0] # 180 degree rotation around axis 0
 >>> M = quat2mat(q) # from this module
 >>> vec = np.array([1, 2, 3]).reshape((3,1)) # column vector

nibabel/spatialimages.py

@@ -91,6 +91,7 @@
 example, the Analyze data format needs an ``image`` and a ``header``
 file type for storage:
 
+   >>> import numpy as np
    >>> import nibabel as nib
    >>> data = np.arange(24, dtype='f4').reshape((2,3,4))
    >>> img = nib.AnalyzeImage(data, np.eye(4))

nibabel/tmpdirs.py

@@ -52,7 +52,7 @@ class InTemporaryDirectory(TemporaryDirectory):
     """Create, return, and change directory to a temporary directory
 
     Notes
-    ------
+    -----
     As its name suggests, the class temporarily changes the working
     directory of the Python process, and this is not thread-safe.  We suggest
     using it only for tests.

pyproject.toml

@@ -25,8 +25,7 @@ classifiers = [
   "Topic :: Scientific/Engineering",
 ]
 # Version from versioneer
-# optional-dependencies from setup.cfg (using ConfigParser features)
-dynamic = ["version", "optional-dependencies"]
+dynamic = ["version"]
 
 [project.urls]
 "Homepage" = "https://nipy.org/nibabel"
@@ -45,6 +44,32 @@ nib-trk2tck = "nibabel.cmdline.trk2tck:main"
 nib-roi = "nibabel.cmdline.roi:main"
 parrec2nii = "nibabel.cmdline.parrec2nii:main"
 
+[project.optional-dependencies]
+dicom = ["pydicom >=1.0.0"]
+dicomfs = ["nibabel[dicom]", "pillow"]
+dev = ["gitpython", "twine"]
+doc = [
+    "matplotlib >= 1.5.3",
+    "numpydoc",
+    "sphinx ~= 5.3",
+    "texext",
+    "tomli; python_version < \"3.11\"",
+]
+minc2 = ["h5py"]
+spm = ["scipy"]
+style = ["flake8"]
+test = [
+    "coverage",
+    "pytest !=5.3.4",
+    "pytest-cov",
+    "pytest-doctestplus",
+    "pytest-httpserver",
+    "pytest-xdist",
+]
+zstd = ["pyzstd >= 0.14.3"]
+doctest = ["nibabel[doc,test]"]
+all = ["nibabel[dicomfs,dev,doc,minc2,spm,style,test,zstd]"]
+
 [tool.setuptools]
 platforms = ["OS Independent"]
 provides = ["nibabel", "nisext"]

setup.cfg

@@ -1,43 +1,3 @@
-[options.extras_require]
-dicom =
-    pydicom >=1.0.0
-dicomfs =
-    %(dicom)s
-    pillow
-dev =
-    gitpython
-    twine
-doc =
-    matplotlib >= 1.5.3
-    numpydoc
-    sphinx ~= 5.3
-    texext
-    toml
-minc2 =
-    h5py
-spm =
-    scipy
-style =
-    flake8
-test =
-    coverage
-    pytest !=5.3.4
-    pytest-cov
-    pytest-doctestplus
-    pytest-httpserver
-    pytest-xdist
-zstd =
-    pyzstd >= 0.14.3
-all =
-    %(dicomfs)s
-    %(dev)s
-    %(doc)s
-    %(minc2)s
-    %(spm)s
-    %(style)s
-    %(test)s
-    %(zstd)s
-
 [flake8]
 max-line-length = 100
 extend-ignore = E203,E266,E402,E731

tools/ci/check.sh

@@ -16,9 +16,8 @@ export NIBABEL_DATA_DIR="$PWD/nibabel-data"
 if [ "${CHECK_TYPE}" == "style" ]; then
     # Run styles only on core nibabel code.
     flake8 nibabel
-elif [ "${CHECK_TYPE}" == "doc" ]; then
-    cd doc
-    make html && make doctest
+elif [ "${CHECK_TYPE}" == "doctest" ]; then
+    make -C doc html && make -C doc doctest
 elif [ "${CHECK_TYPE}" == "test" ]; then
     # Change into an innocuous directory and find tests from installation
     mkdir for_testing

tools/update_requirements.py

@@ -11,10 +11,12 @@
 pyproject_toml = repo_root / "pyproject.toml"
 reqs = repo_root / "requirements.txt"
 min_reqs = repo_root / "min-requirements.txt"
+doc_reqs = repo_root / "doc-requirements.txt"
 
 with open(pyproject_toml, 'rb') as fobj:
     config = tomli.load(fobj)
 requirements = config["project"]["dependencies"]
+doc_requirements = config["project"]["optional-dependencies"]["doc"]
 
 script_name = Path(__file__).relative_to(repo_root)
 
@@ -27,3 +29,7 @@
 # Write minimum requirements
 lines[1:-1] = [req.replace(">=", "==").replace("~=", "==") for req in requirements]
 min_reqs.write_text("\n".join(lines))
+
+# Write documentation requirements
+lines[1:-1] = ["-r requirements.txt"] + doc_requirements
+doc_reqs.write_text("\n".join(lines))