🤝 Merge updates from v1.7.0-source into source

Author: shnizzedy

.circleci/config.yml

@@ -15,7 +15,7 @@ commands:
           command: |
             apt-get update && apt-get -y install git python-dev graphviz libgraphviz-dev pkg-config python3-sphinx
             pip install --user -r https://raw.githubusercontent.com/FCP-INDI/C-PAC/<< parameters.version >>/requirements.txt
-            pip install --user git+https://github.com/${CIRCLE_PROJECT_USERNAME}/C-PAC.git@<< parameters.version >> sphinx m2r numpydoc PyGithub sphinxcontrib-fulltoc sphinxcontrib-programoutput torch
+            pip install --user git+https://github.com/${CIRCLE_PROJECT_USERNAME}/C-PAC.git@<< parameters.version >> sphinx m2r numpydoc PyGithub sphinxcontrib-fulltoc sphinxcontrib-programoutput semver torch
             git clone https://github.com/${CIRCLE_PROJECT_USERNAME}/C-PAC.git /build/C-PAC
             cd /build/C-PAC
             git checkout << parameters.version >>

build_version.txt

@@ -0,0 +1 @@
+v1.7.0

docs/_sources/conf.py

@@ -14,6 +14,8 @@
 
 import m2r
 import os
+import re
+import semver
 import sys
 
 from CPAC import __version__
@@ -22,6 +24,76 @@
 from github.GithubException import RateLimitExceededException, \
     UnknownObjectException
 
+# "Dealing with Invalid Versions" from
+# https://python-semver.readthedocs.io/en/latest/usage.html
+
+
+def coerce(version):
+    """
+    Convert an incomplete version string into a semver-compatible VersionInfo
+    object
+
+    * Tries to detect a "basic" version string (``major.minor.patch``).
+    * If not enough components can be found, missing components are
+        set to zero to obtain a valid semver version.
+
+    :param str version: the version string to convert
+    :return: a tuple with a :class:`VersionInfo` instance (or ``None``
+        if it's not a version) and the rest of the string which doesn't
+        belong to a basic version.
+    :rtype: tuple(:class:`VersionInfo` | None, str)
+    """
+    BASEVERSION = re.compile(
+        r"""[vV]?
+            (?P<major>0|[1-9]\d*)
+            (\.
+            (?P<minor>0|[1-9]\d*)
+            (\.
+                (?P<patch>0|[1-9]\d*)
+            )?
+            )?
+        """,
+        re.VERBOSE,
+    )
+    
+    match = BASEVERSION.search(version)
+    if not match:
+        return (None, version)
+
+    ver = {
+        key: 0 if value is None else value for key, value in match.groupdict().items()
+    }
+    ver = semver.VersionInfo(**ver)
+    rest = match.string[match.end() :]  # noqa:E203
+    return ver, rest
+    
+    
+def compare_versions(new, old):
+    """
+    Function to compare two versions.
+    
+    Parameters
+    ----------
+    new: str
+    
+    old: str
+    
+    Returns
+    -------
+    bool
+        Is the "new" at least as new as "old"?
+    """
+    comparisons = list(zip(coerce(new), coerce(old)))
+    if any([v is None for v in comparisons[0]]):
+        return(False)
+    outright = semver.compare(str(comparisons[0][0]), str(comparisons[0][1]))
+    return (
+        bool(outright == 1) or bool(
+            (outright == 0) and comparisons[1][0] >= comparisons[1][1]
+        )
+    )
+    
+
 # 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.
@@ -110,6 +182,17 @@ def _gh_rate_limit():
     gh_tags = []
 gh_tags.sort(reverse=True)
 
+build_version_path = os.path.abspath(os.path.join(
+    __file__, os.pardir, os.pardir, os.pardir, 'build_version.txt'
+))
+# don't build release notes for newer releases
+if os.path.exists(build_version_path):
+    with open(build_version_path, 'r') as bvf:
+        build_version = bvf.read().strip()
+    gh_tags = [gh_tag for gh_tag in gh_tags if compare_versions(
+        build_version, gh_tag
+    )]
+
 # Try to get release notes from GitHub
 try:
     gh_releases = []
@@ -129,9 +212,9 @@ def _gh_rate_limit():
         t: {
             'name': t,
             'body': ''.join([
-                'See https://github.com/FCP-INDI/C-PAC/releases/tag/{t}',
-                ' for ',
-                'release notes.'
+                'See https://github.com/FCP-INDI/C-PAC/releases/tag/',
+                t,
+                ' for release notes.'
             ]),
             'published_at': None
         } for t in gh_tags
@@ -181,7 +264,7 @@ def _unireplace(release_note, unireplace):
             ).strip(),
             ' ({})'.format(
                 dparser.parse(gh_releaseNotes[t]['published_at']).date(
-                ).strftime('%b %w, %Y')
+                ).strftime('%b %d, %Y')
             ) if gh_releaseNotes[t]['published_at'] else ''
         )
         release_note = '\n'.join(_unireplace(
@@ -199,13 +282,11 @@ def _unireplace(release_note, unireplace):
             {}
         ))
 
-        release_notes_path = os.path.join(
-            release_notes_dir, '{}.rst'.format(t)
-        )
+        release_notes_path = os.path.join(release_notes_dir, f'{t}.rst')
         if gh_releaseNotes[t]['published_at'] and not os.path.exists(
             release_notes_path
         ) and not os.path.exists(
-            os.path.join(release_notes_dir, 'v{}.rst'.format(t))
+            os.path.join(release_notes_dir, f'v{t}.rst')
         ):
             with open(release_notes_path, 'w+') as f:
                 f.write(release_note)
@@ -243,49 +324,44 @@ def _unireplace(release_note, unireplace):
    {}
 
 """.format(
-    '\n'.join([
-        '.. include:: /user/release_notes/{}'.format(fp) for fp in rnd
-    ]),
-    '\n   '.join([
-        '/user/release_notes/{}'.format(d) for d in rnd
-    ])
-)
+    '\n'.join([f'.. include:: /user/release_notes/{fp}' for fp in rnd]),
+    '\n   '.join([f'/user/release_notes/{d}' for d in rnd]))
 with open(os.path.join(release_notes_dir, 'index.rst'), 'w+') as f:
     f.write(all_release_notes.strip())
 
 
 # The full version, including alpha/beta/rc tags.
-release = '{} Beta'.format(__version__)
+release = f'{__version__} Beta'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 # language = None
-#
+
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
 # today = ''
 # Else, today_fmt is used as the format for a strftime call.
 # today_fmt = '%B %d, %Y'
-#
+
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = ['futuredocs/*']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
 # default_role = None
-#
+
 # If true, '()' will be appended to :func: etc. cross-reference text.
 # add_function_parentheses = True
-#
+
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
 # add_module_names = True
-#
+
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
 # show_authors = False
-#
+
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
@@ -294,7 +370,7 @@ def _unireplace(release_note, unireplace):
 
 # -- Options for HTML output --------------------------------------------------
 
-# The theme to use for HTML and HTML Help pages. See the documentation for
+# The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_theme = 'classic'
 
@@ -317,12 +393,12 @@ def _unireplace(release_note, unireplace):
 ]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
-# "<project> v<release> documentation".
+# '<project> v<release> documentation'.
 # html_title = None
-#
+
 # A shorter title for the navigation bar.  Default is the same as html_title.
 # html_short_title = None
-#
+
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
 html_logo = '_static/cpac_logo_vertical.png'
@@ -334,17 +410,17 @@ def _unireplace(release_note, unireplace):
 
 # 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".
+# so a file named 'default.css' will overwrite the builtin 'default.css'.
 html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
 # html_last_updated_fmt = '%b %d, %Y'
-#
+
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
 # html_use_smartypants = True
-#
+
 # Custom sidebar templates, maps document names to template names.
 html_sidebars = {
   '**': [
@@ -357,30 +433,30 @@ def _unireplace(release_note, unireplace):
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
 # html_additional_pages = {}
-#
+
 # If false, no module index is generated.
 # html_domain_indices = True
-#
+
 # If false, no index is generated.
 # html_use_index = True
-#
+
 # If true, the index is split into individual pages for each letter.
 # html_split_index = False
-#
+
 # If true, links to the reST sources are added to the pages.
 # html_show_sourcelink = True
-#
-# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+
+# If true, 'Created using Sphinx' is shown in the HTML footer. Default is True.
 # html_show_sphinx = True
-#
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+
+# If true, '(C) Copyright ...' is shown in the HTML footer. Default is True.
 # html_show_copyright = True
-#
+
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
 # html_use_opensearch = ''
-#
+
 # This is the file name suffix for HTML files (e.g. '.xhtml').
 html_file_suffix = '.html'
 
@@ -415,20 +491,20 @@ def _unireplace(release_note, unireplace):
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
 # latex_logo = None
-#
-# For "manual" documents, if this is true, then toplevel headings are parts,
+
+# For 'manual' documents, if this is true, then toplevel headings are parts,
 # not chapters.
 # latex_use_parts = False
-#
+
 # If true, show page references after internal links.
 # latex_show_pagerefs = False
-#
+
 # If true, show URL addresses after external links.
 # latex_show_urls = False
-#
+
 # Documents to append as an appendix to all manuals.
 # latex_appendices = []
-#
+
 # If false, no module index is generated.
 # latex_domain_indices = True
 
@@ -454,10 +530,10 @@ def _unireplace(release_note, unireplace):
 
 # Documents to append as an appendix to all manuals.
 # texinfo_appendices = []
-#
+
 # If false, no module index is generated.
 # texinfo_domain_indices = True
-#
+
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
 # texinfo_show_urls = 'footnote'
 

scripts/link_to_set_version.py

@@ -1,6 +1,4 @@
-"""Python 2 version
-
-This script takes a version string as a commandline argument and updates
+"""This script takes a version string as a commandline argument and updates
 the links in `docs/{version}` that point to code in the `master` branch of
 FCP-INDI/C-PAC to code in the tagged version.
 
@@ -12,20 +10,7 @@
 import os
 import sys
 
-from fnmatch import filter as fnfilter
-
-
-def glob(pattern, recursive=True):
-    split_pattern = pattern.split('/')
-    filepath = '/'.join(split_pattern[0:-1])
-    pattern = split_pattern[-1]
-    del split_pattern
-
-    matches = []
-    for root, dirnames, filenames in os.walk(filepath):
-        for filename in fnfilter(filenames, pattern):
-            matches.append(os.path.join(root, filename))
-    return matches
+from glob import glob
 
 
 def set_version(version):