Merge pull request #16 from bioio-devs/feature/upgrade-docs

Upgrade docs

.gitchangelog.rc

@@ -0,0 +1,293 @@
+# -*- 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'^$',  ## ignore commits with empty messages
+    r'^Bump version: .*',
+]
+
+
+## ``section_regexps`` is a list of 2-tuples associating a string label and a
+## list of regexp
+##
+## Commit messages will be classified in sections thanks to this. Section
+## titles are the label, and a commit is classified under this section if any
+## of the regexps associated is matching.
+##
+## Please note that ``section_regexps`` will only classify commits and won't
+## make any changes to the contents. So you'll probably want to go check
+## ``subject_process`` (or ``body_process``) to do some changes to the subject,
+## whenever you are tweaking this variable.
+##
+section_regexps = [
+    ('New', [
+        r'^[fF]eature.*$'
+    ]),
+    ('Fix', [
+        r'^[bB]ugfix.*$',
+        r'^[fF]ix.*$',
+        r'^[hH]otfix.*$',
+    ]),
+    ('Other', None), ## Match all lines
+]
+
+
+## ``body_process`` is a callable
+##
+## This callable will be given the original body and result will
+## be used in the changelog.
+##
+## Available constructs are:
+##
+##   - any python callable that take one txt argument and return txt argument.
+##
+##   - ReSub(pattern, replacement): will apply regexp substitution.
+##
+##   - Indent(chars="  "): will indent the text with the prefix
+##     Please remember that template engines gets also to modify the text and
+##     will usually indent themselves the text if needed.
+##
+##   - Wrap(regexp=r"\n\n"): re-wrap text in separate paragraph to fill 80-Columns
+##
+##   - noop: do nothing
+##
+##   - ucfirst: ensure the first letter is uppercase.
+##     (usually used in the ``subject_process`` pipeline)
+##
+##   - final_dot: ensure text finishes with a dot
+##     (usually used in the ``subject_process`` pipeline)
+##
+##   - strip: remove any spaces before or after the content of the string
+##
+##   - SetIfEmpty(msg="No commit message."): will set the text to
+##     whatever given ``msg`` if the current text is empty.
+##
+## Additionally, you can `pipe` the provided filters, for instance:
+#body_process = Wrap(regexp=r'\n(?=\w+\s*:)') | Indent(chars="  ")
+#body_process = Wrap(regexp=r'\n(?=\w+\s*:)')
+#body_process = noop
+#body_process = ReSub(r'((^|\n)[A-Z]\w+(-\w+)*: .*(\n\s+.*)*)+$', 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'^(.*)(\ ?\(\#([0-9]+)\))$',
+    r'\1 (`#\3 <https://github.com/bioio-devs/bioio/pull/\3>`_)'
+)
+#subject_process = ReSub(r'.*', '')
+
+
+## ``tag_filter_regexp`` is a regexp
+##
+## Tags that will be used for the changelog must match this regexp.
+##
+tag_filter_regexp = r'^v[0-9]+\.[0-9]+(\.[0-9]+)?$'
+
+
+## ``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.
+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.
+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"
+# ]
+
+revs = []

.github/workflows/docs.yml

@@ -24,6 +24,7 @@ jobs:
           pip install .[docs]
       - name: Generate Docs
         run: |
+          gitchangelog
           just generate-docs
           touch docs/_build/.nojekyll
       - name: Publish Docs

README.md

@@ -1,33 +1,52 @@
-# bioio
+# BioIO
 
 [![Build Status](https://github.com/bioio-devs/bioio/actions/workflows/ci.yml/badge.svg)](https://github.com/bioio-devs/bioio/actions)
 [![Documentation](https://github.com/bioio-devs/bioio/actions/workflows/docs.yml/badge.svg)](https://bioio-devs.github.io/bioio)
 [![PyPI version](https://badge.fury.io/py/bioio.svg)](https://badge.fury.io/py/bioio)
+[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+[![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/)
 
-
-Image reading, metadata management, and image writing for Microscopy images in Python
+Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python
 
 ---
 
-## Installation
-
-**Stable Release:** `pip install bioio`<br>
-**Development Head:** `pip install git+https://github.com/bioio-devs/bioio.git`
-
-## Quickstart
-
-```python
-from bioio import example
+## Documentation
 
-print(example.str_len("hello"))  # prints 5
-```
+[See the full documentation on our GitHub pages site](https://bioio-devs.github.io/bioio/OVERVIEW.html)
 
-## Documentation
+## Example Usage (see full documentation for more examples)
 
-For full package documentation please visit [bioio-devs.github.io/bioio](https://bioio-devs.github.io/bioio).
+Install bioio alongside OME TIFF and OME ZARR plug-ins with pip (this example won't use the OME ZARR plug-in):
 
-## Development
+`pip install bioio bioio-ome-tiff bioio-ome-zarr`
 
-See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.
+```python
+from bioio import BioImage
+
+# Get a BioImage object
+img = BioImage("my_file.tiff")  # selects the first scene found
+img.data  # returns 5D TCZYX numpy array
+img.xarray_data  # returns 5D TCZYX xarray data array backed by numpy
+img.dims  # returns a Dimensions object
+img.dims.order  # returns string "TCZYX"
+img.dims.X  # returns size of X dimension
+img.shape  # returns tuple of dimension sizes in TCZYX order
+img.get_image_data("CZYX", T=0)  # returns 4D CZYX numpy array
+
+# Get the id of the current operating scene
+img.current_scene
+
+# Get a list valid scene ids
+img.scenes
+
+# Change scene using name
+img.set_scene("Image:1")
+# Or by scene index
+img.set_scene(1)
+
+# Use the same operations on a different scene
+# ...
+```
 
-**BSD License**
+## Issues
+[_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

@@ -19,10 +19,6 @@ class TimeseriesWriter(Writer):
     """
     A writer for timeseries Greyscale, RGB, or RGBA image data.
     Primarily directed at formats: "gif", "mp4", "mkv", etc.
-
-    Notes
-    -----
-    To use this writer, install with: `pip install aicsimageio[base-imageio]`.
     """
 
     _TIMEPOINT_DIMENSIONS = [
@@ -124,7 +120,7 @@ def save(
         a non-time dimension. For example, creating a timeseries image where each frame
         is a Z-plane from a source volumetric image as seen below.
 
-        >>> image = AICSImageIO("some_z_stack.ome.tiff")
+        >>> image = BioImage("some_z_stack.ome.tiff")
         ... TimeseriesWriter.save(
         ...     data=image.get_image_data("ZYX", T=0, C=0),
         ...     uri="some_z_stack.mp4",