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.
 
@@ -34,7 +34,7 @@ the following labels (this convention has been inherited from `nibabel
 
   * *BF*  : bug fix
   * *RF*  : refactoring
-  * *NF*  : new feature
+  * *ENH*:  enhancement/new feature
   * *BW*  : addresses backward-compatibility
   * *OPT* : optimization
   * *BK*  : breaks something and/or tests fail
@@ -66,10 +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
@@ -83,7 +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).
 
@@ -94,6 +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
 -------
 
@@ -102,7 +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
@@ -144,6 +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,
@@ -162,7 +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
@@ -20,6 +22,7 @@
    fsl.data.melodicimage
    fsl.data.mesh
    fsl.data.mghimage
+   fsl.data.utils
    fsl.data.vest
    fsl.data.volumelabels
    fsl.data.vtk

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.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:

doc/fsl.scripts.remove_ext.rst

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

doc/fsl.scripts.resample_image.rst

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

doc/fsl.scripts.rst

@@ -5,12 +5,26 @@
    :hidden:
 
    fsl.scripts.atlasq
+   fsl.scripts.fsl_abspath
+   fsl.scripts.fsl_apply_x5
+   fsl.scripts.fsl_convert_x5
    fsl.scripts.fsl_ents
    fsl.scripts.imcp
    fsl.scripts.imglob
+   fsl.scripts.imln
    fsl.scripts.immv
+   fsl.scripts.imrm
+   fsl.scripts.imtest
+   fsl.scripts.remove_ext
+   fsl.scripts.resample_image
+   fsl.scripts.Text2Vest
+   fsl.scripts.Vest2Text
 
-.. automodule:: fsl.scripts
-    :members:
-    :undoc-members:
-    :show-inheritance:
+
+The ``fsl.scripts`` package contains all of the executable scripts provided by
+``fslpy``, and other python-based FSL packages.
+
+
+The ``fsl.scripts`` package is a `native namespace package
+<https://packaging.python.org/guides/packaging-namespace-packages/>`_, which
+means that it can be used by other Python libraries.

doc/fsl.transform.affine.rst

+``fsl.transform.affine``
+========================
+
+.. automodule:: fsl.transform.affine
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.utils.transform.rst → doc/fsl.transform.flirt.rst

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

doc/fsl.transform.fnirt.rst

+``fsl.transform.fnirt``
+=======================
+
+.. automodule:: fsl.transform.fnirt
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/fsl.transform.nonlinear.rst

+``fsl.transform.nonlinear``
+===========================
+
+.. automodule:: fsl.transform.nonlinear
+    :members:
+    :undoc-members:
+    :show-inheritance: