Merge pull request #167 from bioio-devs/bugfix/docs-changelog

Admin: Repair changelog and curate docs landing.

Author: BrianWhitneyAI

.gitchangelog.rc

@@ -1,293 +1,41 @@
 # -*- coding: utf-8; mode: python -*-
-##
-## Format
-##
-##   ACTION: COMMIT_MSG [!TAG ...]
-##
-## Description
-##
-##   ACTION is one of 'feature', 'bugfix', 'other'
-##
-##   COMMIT_MSG is ... well ... the commit message itself.
-##
-##   TAGs are additionnal adjective as 'refactor' 'minor' 'cosmetic'
-##
-##       They are preceded with a '!' or a '@' (prefer the former, as the
-##       latter is wrongly interpreted in github.) Commonly used tags are:
-##
-##       'refactor' is obviously for refactoring code only
-##       'minor' is for a very meaningless change (a typo, adding a comment)
-##       'cosmetic' is for cosmetic driven change (re-indentation, 80-col...)
-##       'wip' is for partial functionality but complete subfunctionality.
-##
-## Example:
-##
-##   feature/use-dask
-##
-##   Please note that multi-line commit message are supported, and only the
-##   first line will be considered as the "summary" of the commit message. So
-##   tags, and other rules only applies to the summary.  The body of the commit
-##   message will be displayed in the changelog without reformatting.
 
-
-##
-## ``ignore_regexps`` is a line of regexps
-##
-## Any commit having its full commit message matching any regexp listed here
-## will be ignored and won't be reported in the changelog.
-##
 ignore_regexps = [
     r'^(.{3,3}\s*:)?\s*[fF]irst commit.?\s*$',
     r'^[iI]ntial commit.?\s*$',
-    r'^$',  ## ignore commits with empty messages
+    r'^$',  # ignore commits with empty messages
     r'^Bump version: .*',
 ]
 
-
-## ``section_regexps`` is a list of 2-tuples associating a string label and a
-## list of regexp
-##
-## Commit messages will be classified in sections thanks to this. Section
-## titles are the label, and a commit is classified under this section if any
-## of the regexps associated is matching.
-##
-## Please note that ``section_regexps`` will only classify commits and won't
-## make any changes to the contents. So you'll probably want to go check
-## ``subject_process`` (or ``body_process``) to do some changes to the subject,
-## whenever you are tweaking this variable.
-##
 section_regexps = [
-    ('New', [
-        r'^[fF]eature.*$'
+    ("New", [
+        r"^[fF]eature.*$",
     ]),
-    ('Fix', [
-        r'^[bB]ugfix.*$',
-        r'^[fF]ix.*$',
-        r'^[hH]otfix.*$',
+    ("Fix", [
+        r"^[bB]ugfix.*$",
+        r"^[fF]ix.*$",
+        r"^[hH]otfix.*$",
     ]),
-    ('Other', None), ## Match all lines
+    ("Other", None),  # Match all remaining
 ]
 
+# Drop commit bodies from changelog (keep only titles)
+body_process = ReSub(r".*", "") | strip
 
-## ``body_process`` is a callable
-##
-## This callable will be given the original body and result will
-## be used in the changelog.
-##
-## Available constructs are:
-##
-##   - any python callable that take one txt argument and return txt argument.
-##
-##   - ReSub(pattern, replacement): will apply regexp substitution.
-##
-##   - Indent(chars="  "): will indent the text with the prefix
-##     Please remember that template engines gets also to modify the text and
-##     will usually indent themselves the text if needed.
-##
-##   - Wrap(regexp=r"\n\n"): re-wrap text in separate paragraph to fill 80-Columns
-##
-##   - noop: do nothing
-##
-##   - ucfirst: ensure the first letter is uppercase.
-##     (usually used in the ``subject_process`` pipeline)
-##
-##   - final_dot: ensure text finishes with a dot
-##     (usually used in the ``subject_process`` pipeline)
-##
-##   - strip: remove any spaces before or after the content of the string
-##
-##   - SetIfEmpty(msg="No commit message."): will set the text to
-##     whatever given ``msg`` if the current text is empty.
-##
-## Additionally, you can `pipe` the provided filters, for instance:
-#body_process = Wrap(regexp=r'\n(?=\w+\s*:)') | Indent(chars="  ")
-#body_process = Wrap(regexp=r'\n(?=\w+\s*:)')
-#body_process = noop
-#body_process = ReSub(r'((^|\n)[A-Z]\w+(-\w+)*: .*(\n\s+.*)*)+$', r'') | strip
-body_process = ReSub(r'.*', '') | strip
-
-
-## ``subject_process`` is a callable
-##
-## This callable will be given the original subject and result will
-## be used in the changelog.
-##
-## Available constructs are those listed in ``body_process`` doc.
-#subject_process = (strip |
-#    ReSub(r'^([cC]hg|[fF]ix|[nN]ew)\s*:\s*((dev|use?r|pkg|test|doc)\s*:\s*)?([^\n@]*)(@[a-z]+\s+)*$', r'\4') |
-#    SetIfEmpty("No commit message.") | ucfirst | final_dot)
 subject_process = ReSub(
-    r'^(.*)(\ ?\(\#([0-9]+)\))$',
-    r'\1 (`#\3 <https://github.com/bioio-devs/bioio/pull/\3>`_)'
+    r"^(.*)(\ ?\(\#([0-9]+)\))$",
+    r"\1 (`#\3 <https://github.com/bioio-devs/bioio/pull/\3>`_)",
 )
-#subject_process = ReSub(r'.*', '')
-
-
-## ``tag_filter_regexp`` is a regexp
-##
-## Tags that will be used for the changelog must match this regexp.
-##
-tag_filter_regexp = r'^v[0-9]+\.[0-9]+(\.[0-9]+)?$'
 
+tag_filter_regexp = r"^v[0-9]+\.[0-9]+(\.[0-9]+)?$"
 
-## ``unreleased_version_label`` is a string or a callable that outputs a string
-##
-## This label will be used as the changelog Title of the last set of changes
-## between last valid tag and HEAD if any.
+# Label for changes since last tag on main
 unreleased_version_label = "(unreleased)"
 
-
-## ``output_engine`` is a callable
-##
-## This will change the output format of the generated changelog file
-##
-## Available choices are:
-##
-##   - rest_py
-##
-##        Legacy pure python engine, outputs ReSTructured text.
-##        This is the default.
-##
-##   - mustache(<template_name>)
-##
-##        Template name could be any of the available templates in
-##        ``templates/mustache/*.tpl``.
-##        Requires python package ``pystache``.
-##        Examples:
-##           - mustache("markdown")
-##           - mustache("restructuredtext")
-##
-##   - makotemplate(<template_name>)
-##
-##        Template name could be any of the available templates in
-##        ``templates/mako/*.tpl``.
-##        Requires python package ``mako``.
-##        Examples:
-##           - makotemplate("restructuredtext")
-##
 output_engine = rest_py
-#output_engine = mustache("restructuredtext")
-#output_engine = mustache("markdown")
-#output_engine = makotemplate("restructuredtext")
-
 
-## ``include_merge`` is a boolean
-##
-## This option tells git-log whether to include merge commits in the log.
-## The default is to include them.
+# Don’t include merge commits
 include_merge = False
 
-
-## ``log_encoding`` is a string identifier
-##
-## This option tells gitchangelog what encoding is outputed by ``git log``.
-## The default is to be clever about it: it checks ``git config`` for
-## ``i18n.logOutputEncoding``, and if not found will default to git's own
-## default: ``utf-8``.
-#log_encoding = 'utf-8'
-
-
-## ``publish`` is a callable
-##
-## Sets what ``gitchangelog`` should do with the output generated by
-## the output engine. ``publish`` is a callable taking one argument
-## that is an interator on lines from the output engine.
-##
-## Some helper callable are provided:
-##
-## Available choices are:
-##
-##   - stdout
-##
-##        Outputs directly to standard output
-##        (This is the default)
-##
-##   - FileInsertAtFirstRegexMatch(file, pattern, idx=lamda m: m.start())
-##
-##        Creates a callable that will parse given file for the given
-##        regex pattern and will insert the output in the file.
-##        ``idx`` is a callable that receive the matching object and
-##        must return a integer index point where to insert the
-##        the output in the file. Default is to return the position of
-##        the start of the matched string.
-##
-##   - FileRegexSubst(file, pattern, replace, flags)
-##
-##        Apply a replace inplace in the given file. Your regex pattern must
-##        take care of everything and might be more complex. Check the README
-##        for a complete copy-pastable example.
-##
-#publish = stdout
-OUTPUT_FILE = "docs/CHANGELOG.rst"
-INSERT_POINT_REGEX = r'''(?isxu)
-^
-(
-  \s*Changelog\s*(\n|\r\n|\r)        ## ``Changelog`` line
-  ==+\s*(\n|\r\n|\r){2}              ## ``=========`` rest underline
-)
-
-(                     ## Match all between changelog and release rev
-    (
-      (?!
-         (?<=(\n|\r))                ## look back for newline
-         %(rev)s                     ## revision
-         \s+
-         \([0-9]+-[0-9]{2}-[0-9]{2}\)(\n|\r\n|\r)   ## date
-           --+(\n|\r\n|\r)                          ## ``---`` underline
-      )
-      .
-    )*
-)
-
-(?P<rev>%(rev)s)
-''' % {'rev': r"v[0-9]+\.[0-9]+(\.[0-9]+)?"}
-
-revs = [
-    Caret(FileFirstRegexMatch(OUTPUT_FILE, INSERT_POINT_REGEX)),
-    "HEAD"
-]
-
-publish = FileRegexSubst(OUTPUT_FILE, INSERT_POINT_REGEX, r"\1\o\g<rev>")
-
-
-## ``revs`` is a list of callable or a list of string
-##
-## callable will be called to resolve as strings and allow dynamical
-## computation of these. The result will be used as revisions for
-## gitchangelog (as if directly stated on the command line). This allows
-## to filter exaclty which commits will be read by gitchangelog.
-##
-## To get a full documentation on the format of these strings, please
-## refer to the ``git rev-list`` arguments. There are many examples.
-##
-## Using callables is especially useful, for instance, if you
-## are using gitchangelog to generate incrementally your changelog.
-##
-## Some helpers are provided, you can use them::
-##
-##   - FileFirstRegexMatch(file, pattern): will return a callable that will
-##     return the first string match for the given pattern in the given file.
-##     If you use named sub-patterns in your regex pattern, it'll output only
-##     the string matching the regex pattern named "rev".
-##
-##   - Caret(rev): will return the rev prefixed by a "^", which is a
-##     way to remove the given revision and all its ancestor.
-##
-## Please note that if you provide a rev-list on the command line, it'll
-## replace this value (which will then be ignored).
-##
-## If empty, then ``gitchangelog`` will act as it had to generate a full
-## changelog.
-##
-## The default is to use all commits to make the changelog.
-#revs = ["^1.0.3", ]
-
-# revs = [
-#     Caret(
-#         FileFirstRegexMatch(
-#             "docs/CHANGELOG.rst",
-#             r"(?P<rev>v[0-9]+\.[0-9]+(\.[0-9]+)?)\s+\([0-9]+-[0-9]{2}-[0-9]{2}\)\n--+\n")),
-#     "HEAD"
-# ]
-
+publish = stdout
 revs = []

.github/workflows/docs.yml

@@ -34,7 +34,6 @@ jobs:
           pip install .[docs]
       - name: Generate Docs
         run: |
-          gitchangelog
           just generate-docs
           touch docs/_build/.nojekyll
 

Justfile

@@ -42,6 +42,7 @@ build:
 generate-docs:
 	rm -f docs/bioio*.rst
 	rm -f docs/modules.rst
+	gitchangelog > docs/CHANGELOG.rst
 	sphinx-apidoc -o docs bioio **/tests
 	python -msphinx "docs" "docs/_build"
 

docs/index.md

@@ -0,0 +1,42 @@
+# Welcome to bioio's documentation!
+
+```{toctree}
+:hidden:
+:maxdepth: 1
+:caption: Contents:
+
+Overview <OVERVIEW>
+Installation <INSTALLATION>
+Full API Reference <api_reference>
+Developer Resources <developer_resources>
+Changelog <CHANGELOG>
+AICSImageIO Migration <MIGRATION>
+```
+
+---
+
+# Overview
+
+```{include} OVERVIEW.md
+:relative-docs: .
+:relative-images:
+```
+
+---
+
+# Specific Doc Pages
+
+```{autosummary}
+:toctree:
+:caption: Important Classes:
+
+bioio.BioImage
+```
+
+---
+
+# Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search