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Merge pull request #16 from bioio-devs/feature/upgrade-docs
Upgrade docs
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‎.gitchangelog.rc

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

‎.github/workflows/docs.yml

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pip install .[docs]
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- name: Generate Docs
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run: |
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gitchangelog
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just generate-docs
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touch docs/_build/.nojekyll
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- name: Publish Docs

‎README.md

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# bioio
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# BioIO
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[![Build Status](https://github.com/bioio-devs/bioio/actions/workflows/ci.yml/badge.svg)](https://github.com/bioio-devs/bioio/actions)
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[![Documentation](https://github.com/bioio-devs/bioio/actions/workflows/docs.yml/badge.svg)](https://bioio-devs.github.io/bioio)
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[![PyPI version](https://badge.fury.io/py/bioio.svg)](https://badge.fury.io/py/bioio)
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[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
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[![Python 3.9+](https://img.shields.io/badge/python-3.9,3.10,3.11-blue.svg)](https://www.python.org/downloads/release/python-390/)
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Image reading, metadata management, and image writing for Microscopy images in Python
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Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python
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---
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## Installation
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**Stable Release:** `pip install bioio`<br>
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**Development Head:** `pip install git+https://github.com/bioio-devs/bioio.git`
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## Quickstart
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```python
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from bioio import example
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## Documentation
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print(example.str_len("hello")) # prints 5
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```
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[See the full documentation on our GitHub pages site](https://bioio-devs.github.io/bioio/OVERVIEW.html)
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## Documentation
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## Example Usage (see full documentation for more examples)
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For full package documentation please visit [bioio-devs.github.io/bioio](https://bioio-devs.github.io/bioio).
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Install bioio alongside OME TIFF and OME ZARR plug-ins with pip (this example won't use the OME ZARR plug-in):
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## Development
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`pip install bioio bioio-ome-tiff bioio-ome-zarr`
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See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.
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```python
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from bioio import BioImage
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# Get a BioImage object
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img = BioImage("my_file.tiff") # selects the first scene found
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img.data # returns 5D TCZYX numpy array
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img.xarray_data # returns 5D TCZYX xarray data array backed by numpy
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img.dims # returns a Dimensions object
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img.dims.order # returns string "TCZYX"
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img.dims.X # returns size of X dimension
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img.shape # returns tuple of dimension sizes in TCZYX order
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img.get_image_data("CZYX", T=0) # returns 4D CZYX numpy array
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# Get the id of the current operating scene
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img.current_scene
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# Get a list valid scene ids
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img.scenes
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# Change scene using name
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img.set_scene("Image:1")
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# Or by scene index
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img.set_scene(1)
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# Use the same operations on a different scene
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# ...
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```
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**BSD License**
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## Issues
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[_Click here to view all open issues in bioio-devs organization at once_](https://github.com/search?q=user%3Abioio-devs+is%3Aissue+is%3Aopen&type=issues&ref=advsearch)

‎bioio/writers/timeseries_writer.py

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"""
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A writer for timeseries Greyscale, RGB, or RGBA image data.
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Primarily directed at formats: "gif", "mp4", "mkv", etc.
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Notes
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-----
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To use this writer, install with: `pip install aicsimageio[base-imageio]`.
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"""
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_TIMEPOINT_DIMENSIONS = [
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a non-time dimension. For example, creating a timeseries image where each frame
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is a Z-plane from a source volumetric image as seen below.
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>>> image = AICSImageIO("some_z_stack.ome.tiff")
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>>> image = BioImage("some_z_stack.ome.tiff")
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... TimeseriesWriter.save(
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... data=image.get_image_data("ZYX", T=0, C=0),
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... uri="some_z_stack.mp4",

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