LICENSE

 The fslpy library
 
-Copyright 2016-2017 University of Oxford, Oxford, UK.
+Copyright 2016-2023 University of Oxford, Oxford, UK.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

MANIFEST.in

-include           LICENSE
+include           AUTHOR
+include           CHANGELOG.rst
 include           COPYRIGHT
-include           requirements.txt
-include           requirements-dev.txt
-include           requirements-extra.txt
-include           pytest.ini
-recursive-include doc      *
-recursive-exclude doc/html *
-recursive-include tests    *
+include           LICENSE
+include           README.rst
+include           conftest.py
+recursive-include doc       *
+recursive-include fsl/tests *

README.rst

 fslpy
 =====
 
+.. image:: https://img.shields.io/pypi/v/fslpy.svg
+   :target: https://pypi.python.org/pypi/fslpy/
 
-.. image:: https://git.fmrib.ox.ac.uk/fsl/fslpy/badges/master/build.svg
-   :target: https://git.fmrib.ox.ac.uk/fsl/fslpy/commits/master/
+.. image:: https://anaconda.org/conda-forge/fslpy/badges/version.svg
+   :target: https://anaconda.org/conda-forge/fslpy
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1470750.svg
+   :target: https://doi.org/10.5281/zenodo.1470750
 
 .. image:: https://git.fmrib.ox.ac.uk/fsl/fslpy/badges/master/coverage.svg
    :target: https://git.fmrib.ox.ac.uk/fsl/fslpy/commits/master/
 
-.. image:: https://img.shields.io/pypi/v/fslpy.svg
-   :target: https://pypi.python.org/pypi/fslpy/
-
 
 The ``fslpy`` project is a `FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_
 programming library written in Python. It is used by `FSLeyes
 <https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/>`_.
 
 
+``fslpy`` is tested against Python versions 3.10, 3.11, 3.12, and 3.13.
+
+
 Installation
 ------------
 
@@ -26,71 +31,107 @@ Install ``fslpy`` and its core dependencies via pip::
     pip install fslpy
 
 
+``fslpy`` is also available on `conda-forge <https://conda-forge.org/>`_::
+
+    conda install -c conda-forge fslpy
+
+
 Dependencies
 ------------
 
 
-All of the core dependencies of ``fslpy`` are listed in the `requirements.txt
-<requirements.txt>`_ file.
+All of the core dependencies of ``fslpy`` are listed in the
+`pyproject.toml <pyproject.toml>`_ file.
 
-Some extra dependencies are listed in `requirements.txt
-<requirements-extra.txt>`_ which provide addditional functionality:
+Some optional dependencies (labelled ``extra`` in ``pyproject.toml``) provide
+addditional functionality:
 
- - ``wxPython``: The `fsl.utils.idle <fsl/utils/idle.py>`_ module has
-   functionality  to schedule functions on the ``wx`` idle loop.
+- ``wxPython``: The `fsl.utils.idle <fsl/utils/idle.py>`_ module has
+  functionality  to schedule functions on the ``wx`` idle loop.
 
- - ``indexed_gzip``: The `fsl.data.image.Image <fsl/data/image.py>`_ class
-   can use ``indexed_gzip`` to keep large compressed images on disk instead
-   of decompressing and loading them into memory..
+- ``indexed_gzip``: The `fsl.data.image.Image <fsl/data/image.py>`_ class
+  can use ``indexed_gzip`` to keep large compressed images on disk instead
+  of decompressing and loading them into memory..
 
- - ``trimesh``/``rtree``: The `fsl.data.mesh.TriangleMesh <fsl/data/mesh.py>`_
-   class has some methods which use ``trimesh`` to perform geometric queries
-   on the mesh.
+- ``trimesh``/``rtree``: The `fsl.data.mesh.TriangleMesh <fsl/data/mesh.py>`_
+  class has some methods which use ``trimesh`` to perform geometric queries
+  on the mesh.
 
+- ``Pillow``: The `fsl.data.bitmap.Bitmap <fsl/data/bitmap.py>`_ class uses
+  ``Pillow`` to load image files.
 
 
-To install these additional dependencies, you first need to install wxPython,
-which is still in pre-relaes.
+If you are using Linux, you need to install wxPython first, as binaries are
+not available on PyPI. Install wxPython like so, changing the URL for your
+specific platform::
 
- - **macOS**: ``pip install --pre wxPython``
- - **Linux** (change the URL for your specific platform): ``pip install --only-binary wxpython -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython``
+    pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython
 
 
-The ``rtree`` library also assumes that ``libspatialindex`` is installed on
-your system.
+Once wxPython has been installed, you can type the following to install the
+remaining optional dependencies::
+
+    pip install "fslpy[extra]"
 
 
-Once wxPython has been installed, you can simply type the following to install
-the rest of the extra dependencies::
+Dependencies for testing and documentation are also listed in ``pyproject.toml``,
+and are respectively labelled as ``test`` and ``doc``.
 
-    pip install fslpy[extras]
+
+Non-Python dependencies
+^^^^^^^^^^^^^^^^^^^^^^^
+
+
+The `fsl.data.dicom <fsl/data/dicom.py>`_ module requires the presence of
+Chris Rorden's `dcm2niix <https://github.com/rordenlab/dcm2niix>`_ program.
+
+
+The ``rtree`` library assumes that ``libspatialindex`` is installed on
+your system.
+
+
+The `fsl.transform.x5 <fsl/transform/x5.py>`_ module uses `h5py
+<https://www.h5py.org/>`_, which requires ``libhdf5``.
 
 
 Documentation
 -------------
 
+API documentation for ``fslpy`` is hosted at
+https://open.win.ox.ac.uk/pages/fsl/fslpy/.
+
 ``fslpy`` is documented using `sphinx <http://http://sphinx-doc.org/>`_. You
 can build the API documentation by running::
 
-    python setup.py doc
+    pip install ".[doc]"
+    sphinx-build doc html
 
-The HTML documentation will be generated and saved in the ``doc/html/``
+The HTML documentation will be generated and saved in the ``html/``
 directory.
 
 
-If you are interested in contributing to ``fslpy``, check out the
-`contributing guide <doc/contributing.rst>`_.
-
-
 Tests
 -----
 
 Run the test suite via::
 
-    python setup.py test
+    pip install ".[test]"
+    pytest
 
-A test report will be generated at ``report.html``, and a code coverage report
-will be generated in ``htmlcov/``.
+
+Some tests will only pass if the test environment meets certain criteria -
+refer to the ``tool.pytest.init_options`` section of
+[``pyproject.toml``](pyproject.toml) for a list of [pytest
+marks](https://docs.pytest.org/en/7.1.x/example/markers.html) which can be
+selectively enabled or disabled.
+
+
+Contributing
+------------
+
+
+If you are interested in contributing to ``fslpy``, check out the
+`contributing guide <doc/contributing.rst>`_.
 
 
 Credits

tests/conftest.py → conftest.py

@@ -14,42 +14,24 @@ import numpy as np
 
 
 def pytest_addoption(parser):
-    parser.addoption('--niters',
-                     type=int,
-                     action='store',
-                     default=50,
-                     help='Number of test iterations for imagewrapper')
-    
     parser.addoption('--testdir',
                      action='store',
                      help='FSLeyes test data directory')
 
     parser.addoption('--seed',
                      type=int,
-                     help='Seed for random number generator') 
+                     help='Seed for random number generator')
 
 
-    
-@pytest.fixture
-def testdir(request):
-    """FSLeyes test data directory."""
-    return op.expanduser(request.config.getoption('--testdir'))
-
-
-@pytest.fixture
-def niters(request):
-    """Number of test iterations."""
-    return request.config.getoption('--niters')
-
 
 @pytest.fixture
 def seed(request):
-    
+
     seed = request.config.getoption('--seed')
 
     if seed is None:
-        seed = np.random.randint(2 ** 32)
-        
+        seed = np.random.randint(2 ** 30)
+
     np.random.seed(seed)
     random   .seed(seed)
     print('Seed for random number generator: {}'.format(seed))

doc/_static/theme_overrides.css

+/* override table width restrictions */
+.wy-table-responsive table td, .wy-table-responsive table th {
+    white-space: normal;
+}
+
+.wy-table-responsive {
+    margin-bottom: 24px;
+    max-width: 100%;
+    overflow: visible;
+}

doc/conf.py

@@ -12,12 +12,70 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+import glob
+import itertools as it
 import os
+import os.path as op
 import sys
 import datetime
 
 date = datetime.date.today()
 
+
+def check_for_missing_stubs():
+
+    docdir  = op.dirname(__file__)
+    basedir = op.join(docdir, '..')
+    modules = []
+
+    def tomodname(f):
+        if f.endswith('.py'):
+            f = f[:-3]
+        return op.relpath(op.join(dirpath, f), basedir).replace(op.sep, '.')
+
+    for dirpath, dirnames, filenames in os.walk(op.join(basedir, 'fsl')):
+        for d in dirnames:
+            if d == '__pycache__':
+                continue
+            if len(glob.glob(op.join(dirpath, d, '**', '*.py'), recursive=True)) == 0:
+                continue
+            modules.append(tomodname(d))
+
+        for f in filenames:
+            if not f.endswith('.py'):
+                continue
+            if f in ('__init__.py', '__main__.py'):
+                continue
+            modules.append(tomodname(f))
+
+    modules = [m for m in modules if not m.startswith('fsl.tests')]
+
+    # import fsl
+    # modules = recurse(fsl)
+    # modules = [m.name for m in modules]
+
+    # print()
+    # print()
+    # print()
+
+    for mod in modules:
+
+        docfile = op.join(docdir, f'{mod}.rst')
+
+        if not op.exists(docfile):
+            print(f'No doc file found for module: {mod}')
+
+    for docfile in glob.glob(op.join(docdir, '*.rst')):
+        docfile = op.relpath(docfile, basedir)
+        mod     = op.splitext(op.basename(docfile))[0]
+        if mod not in modules:
+            print(f'No module found for doc file: {docfile}')
+
+
+if __name__ == '__main__':
+    check_for_missing_stubs()
+
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -33,7 +91,8 @@ date = datetime.date.today()
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary', 
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosummary',
     'sphinx.ext.mathjax',
     'sphinx.ext.graphviz',
     'sphinx.ext.todo',
@@ -55,13 +114,13 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'fslpy'
-copyright = u'{}, Paul McCarthy, University of Oxford, Oxford, UK'.format(
+copyright = u'{}, FMRIB Centre, University of Oxford, Oxford, UK'.format(
     date.year)
 
 # Links to other things
 rst_epilog = """
 .. |fsleyes_apidoc| replace:: FSLeyes
-.. _fsleyes_apidoc: http://users.fmrib.ox.ac.uk/~paulmc/fsleyes_apidoc/index.html
+.. _fsleyes_apidoc: http://users.fmrib.ox.ac.uk/~paulmc/fsleyes/userdoc/latest/index.html
 """
 
 
@@ -121,6 +180,7 @@ pygments_style = 'sphinx'
 # a list of builtin themes.
 html_theme = 'sphinx_rtd_theme'
 
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
@@ -148,7 +208,11 @@ html_theme = 'sphinx_rtd_theme'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_static_path = ['_static']
+
+html_css_files = [
+    'theme_overrides.css',  # overrides for wide tables in RTD theme
+]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -353,26 +417,12 @@ epub_exclude_files = ['search.html']
 # special-members flag)
 autoclass_content = 'class'
 
-# Document private members and special members (e.g. __init__)
-autodocsourc_default_flags = ['private-members', 'special-members']
-
-# Documentation for python modules is in the same order
-# as the source code.
-autodoc_member_order = 'bysource'
-
-def autodoc_skip_member(app, what, name, obj, skip, options):
 
-    # Do not document the _sync_* properties
-    # that are added by the props package to
-    # all SyncableHasProperties classes.
-    if what == 'class':
-        attName = name.split('.')[-1]
-        return skip or attName.startswith('_sync_')
-    
-    return skip or False
-
-
-def setup(app):
-    app.connect('autodoc-skip-member', autodoc_skip_member)
+autodoc_default_options = {
+    'special-members' : True,
+    'private-members' : True,
+    'undoc-members'   : True,
+    'member-order'    : 'bysource',
+}
 
 graphviz_output_format = 'svg'

doc/contributing.rst

@@ -9,10 +9,10 @@ Development model
 -----------------
 
 
-- The master branch should always be stable and ready to release. All
-  development occurs on the master branch.
+- The main branch should always be stable and ready to release. All
+  development occurs on the main branch.
 
-- All changes to the master branch occur via merge requests. Individual
+- All changes to the main branch occur via merge requests. Individual
   developers are free to choose their own development workflow in their own
   repositories.
 
@@ -24,6 +24,27 @@ Development model
  - Coding conventions are adhered to (unless there is good reason not to).
 
 
+Commit messages
+---------------
+
+
+To aid readability, all commit messages should be prefixed with one or more of
+the following labels (this convention has been inherited from `nibabel
+<https://github.com/nipy/nibabel>`_):
+
+  * *BF*  : bug fix
+  * *RF*  : refactoring
+  * *ENH*:  enhancement/new feature
+  * *BW*  : addresses backward-compatibility
+  * *OPT* : optimization
+  * *BK*  : breaks something and/or tests fail
+  * *PL*  : making pylint happier
+  * *DOC* : for all kinds of documentation related commits
+  * *TEST*: for adding or changing tests
+  * *MNT* : for administrative/maintenance changes
+  * *CI*  : for continuous-integration changes
+
+
 Version number
 --------------
 
@@ -45,10 +66,10 @@ numbers::
   backwards-incompatible changes.
 
 
-The version number in the ``master`` branch should be of the form
-``major.minor.patch.dev``, to indicate that any releases made from this branch
-are development releases (although development releases are not part of the
-release model).
+The version number in the ``main`` branch should be of the form
+``major.minor.patch.dev0``, to indicate that any releases made from this
+branch are development releases (although development releases are not part of
+the release model).
 
 
 Releases
@@ -62,7 +83,7 @@ name for minor release ``1.0`` would be ``v1.0``.
 
 
 Patches and bugfixes may be added to these release branches as ``patch``
-releases.  These changes should be made on the master branch like any other
+releases.  These changes should be made on the main branch like any other
 change (i.e. via merge requests), and then cherry-picked onto the relevant
 release branch(es).
 
@@ -73,6 +94,44 @@ example, the first release off the ``v1.0`` branch would be tagged with
 ``1.0.1``, ``1.0.2``, etc.
 
 
+Major/minor releases
+^^^^^^^^^^^^^^^^^^^^
+
+
+Follow this process for major and minor releases. Steps 1 and 2 should be
+performed via a merge request onto the main branch, and step 4 via a merge
+request onto the relevant minor branch.
+
+
+1. Update the changelog on the main branch to include the new version number
+   and release date.
+2. On the main branch, update the version number in ``fsl/version.py`` to
+   a development version of **the next** minor release number. For example,
+   if you are about to release version ``1.3.0``, the version in the main
+   branch should be ``1.4.0.dev0``.
+3. Create the new minor release branch off the main branch.
+4. Update the version number on the release branch. If CI tests fail on the
+   release branch, postpone the release until they are fixed.
+5. Tag the new release on the minor release branch.
+
+
+Bugfix/patch releases
+^^^^^^^^^^^^^^^^^^^^^
+
+
+Follow this process for patch releases. Step 1 should be performed via
+a merge request onto the main branch, and step 2 via a merge request onto
+the relevant minor branch.
+
+
+1. Add the fix to the main branch, along with an updated changelog including
+   the version number and date for the bugfix release.
+2. Cherry-pick the relevant commit(s) from the main branch onto the minor
+   release branch, and update the version number on the minor release branch.
+   If CI tests fail on the release branch, go back to step 1.
+3. Tag the new release on the minor release branch.
+
+
 Testing
 -------
 
@@ -81,7 +140,7 @@ Unit and integration tests are currently run with ``py.test`` and
 ``coverage``.
 
 - Aim for 100% code coverage.
-- Tests must pass on python 2.7, 3.4, 3.5, and 3.6
+- Tests must pass on python 3.5, 3.6, and 3.7.
 
 
 Coding conventions
@@ -123,6 +182,7 @@ for a list of error codes):
 - E302: expected 2 blank lines, found 0
 - E303: too many blank lines (3)
 - E701: multiple statements on one line (colon)
+- W504: line break after binary operator
 
 
 The ``pylint`` tool can be *very* opinionated about how you write your code,
@@ -141,7 +201,7 @@ refactoring and convention messages, and a few select warnings (type ``pylint
 To check code with ``flake8`` and ``pylint``, I use the following commands::
 
 
-  flake8 --ignore=E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701 fsl
+  flake8 --ignore=E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504 fsl
   pylint --extension-pkg-whitelist=numpy,wx \
          --generated-members=np.int8,np.uint8,np.int16,np.uint16,np.int32,np.uint32,np.int64,np.uint64,np.float32,np.float64,np.float128,wx.PyDeadObjectError \
          --disable=R,C,W0511,W0703,W1202 fsl

doc/fsl.data.bitmap.rst

+``fsl.data.bitmap``
+===================
+
+.. automodule:: fsl.data.bitmap
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.data.cifti.rst

+``fsl.data.cifti``
+==================
+
+.. automodule:: fsl.data.cifti
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.data.rst

@@ -5,6 +5,8 @@
    :hidden:
 
    fsl.data.atlases
+   fsl.data.bitmap
+   fsl.data.cifti
    fsl.data.constants
    fsl.data.dicom
    fsl.data.dtifit
@@ -12,6 +14,7 @@
    fsl.data.featdesign
    fsl.data.featimage
    fsl.data.fixlabels
+   fsl.data.freesurfer
    fsl.data.gifti
    fsl.data.image
    fsl.data.imagewrapper
@@ -19,8 +22,10 @@
    fsl.data.melodicimage
    fsl.data.mesh
    fsl.data.mghimage
+   fsl.data.utils
    fsl.data.vest
    fsl.data.volumelabels
+   fsl.data.vtk
 
 .. automodule:: fsl.data
     :members:

doc/fsl.data.utils.rst

+``fsl.data.utils``
+==================
+
+.. automodule:: fsl.data.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.Text2Vest.rst

+``fsl.scripts.Text2Vest``
+=========================
+
+.. automodule:: fsl.scripts.Text2Vest
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.Vest2Text.rst

+``fsl.scripts.Vest2Text``
+=========================
+
+.. automodule:: fsl.scripts.Vest2Text
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.fsl_abspath.rst

+``fsl.scripts.fsl_abspath``
+===========================
+
+.. automodule:: fsl.scripts.fsl_abspath
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.fsl_apply_x5.rst

+``fsl.scripts.fsl_apply_x5``
+============================
+
+.. automodule:: fsl.scripts.fsl_apply_x5
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.fsl_convert_x5.rst

+``fsl.scripts.fsl_convert_x5``
+==============================
+
+.. automodule:: fsl.scripts.fsl_convert_x5
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.fsl_ents.rst

+``fsl.scripts.fsl_ents``
+========================
+
+.. automodule:: fsl.scripts.fsl_ents
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.imln.rst

+``fsl.scripts.imln``
+====================
+
+.. automodule:: fsl.scripts.imln
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.imrm.rst

+``fsl.scripts.imrm``
+====================
+
+.. automodule:: fsl.scripts.imrm
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.scripts.imtest.rst

+``fsl.scripts.imtest``
+======================
+
+.. automodule:: fsl.scripts.imtest
+    :members:
+    :undoc-members:
+    :show-inheritance: