Merge pull request #13 from sbslee/1.8.0-dev

1.8.0 dev

Author: sbslee

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+   version: 3.7
+   install:
+   - requirements: docs/requirements.txt

CHANGELOG.md

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+Changelog
+*********
+
+1.8.0 (2021-05-09)
+------------------
+
+* Updated docstring.
+* Moved the official documentation from Wiki page to Read the Docs.
+
+1.7.0 (2021-04-05)
+------------------
+
+- Added a new command called ``count-reads`` which counts the number of sequence reads from FASTQ.
+- Updated the ``summarize`` command.
+- Updated the following methods:
+
+    - ``taxa_abundance_box_plot()``
+    - ``taxa_abundance_bar_plot()``
+    - ``distance_matrix_plot()``
+    - ``ordinate()``
+    - ``barplot()``
+
+- See :issue:`10` for more details.
+
+1.6.0 (2021-03-08)
+------------------
+
+- Added a new method called ``pname()`` which returns a prettified taxon name.
+- Added a new method called ``num2sig()`` which converts a p-value to significance annotation.
+- Added a new method called ``wilcoxon()`` which performs the Wilcoxon Signed-rank test between two paired groups for a given taxon.
+- Added a new method called ``mannwhitneyu()`` which performs the Mann–Whitney U test between two groups for a given taxon.
+- There have been major changes to the ``heatmap()`` method. First, it now supports two grouping variables instead of just one (e.g. ``hue1`` and ``hue2``). Second, it supports the centered log-ratio (CLR) transformation as a normalization option (in addition to ``log10``). Third, it now has ``kwargs`` that are passed to the ``seaborn.clustermap()`` method (e.g. ``xticklabels=False``). Fourth, the bug giving the ``FloatingPointError: NaN dissimilarity value.`` error when sample-filtered metadata is provided and the ``metric='correlation'`` argument is used has been fixed. Fifth, the bug giving an error when one of the metadata columns has only zeros has been fixed.
+- In addition to ``heatmap()``, the following methods have been updated:
+
+    - ``addpairs()``
+    - ``alpha_diversity_plot()``
+
+- Updated the ``summarize`` command.
+- Updated the ``prepare-lefse`` command to output more informative taxa name than just underscores (e.g. ``__`` and ``g__``).
+- See :issue:`8` for more details.
+
+1.5.0 (2021-02-03)
+------------------
+
+- Starting this version, Dokdo is packaged with ``setuptools``.
+- There have been major changes to Dokdo CLI.
+- Added a new plotting method called ``regplot()``.
+- Added a new command called ``prepare-lefse``.
+- The ``merge_metadata`` command has been deprecated.
+- Updated the following methods:
+
+    - ``_artist()``
+    - ``alpha_diversity_plot()``
+    - ``beta_3d_plot()``
+    - ``beta_parallel_plot()``
+    - ``barplot()``
+    - ``ordinate()``
+    - ``taxa_abundance_bar_plot()``
+    - ``taxa_abundance_box_plot()``
+    - ``heatmap()``
+
+- Updated the ``make_manifest`` command.
+- See :issue:`6` for more details.
+
+1.4.0 (2021-01-09)
+------------------
+
+- Added a new command called ``summarize``.
+- Added a new plotting method called ``heatmap()``.
+- Updated the following commands:
+
+    - ``make_manifest``
+    - ``add_metadata``
+    - ``collapse``
+
+* Updated the following methods:
+
+    - ``_artist()``
+    - ``alpha_rarefaction_plot()``
+    - ``taxa_abundance_bar_plot()``
+    - ``taxa_abundance_box_plot()``
+
+- See :issue:`4` for more details.
+
+1.3.0 (2020-12-23)
+------------------
+
+- Updated the ``ordinate()`` method so that the user can now choose to:
+
+    - skip rarefying,
+    - provide custom sampling depth for rarefying,
+    - provide ``qiime2.Artifact`` as input instead of file path, and
+    - output ``PCoAResults % Properties('biplot')`` as well as ``PCoAResults``.
+
+- Added new plotting methods:
+
+    - ``beta_scree_plot()``
+    - ``beta_parallel_plot()``
+    - ``addbiplot()``
+    - ``barplot()``
+
+- See :issue:`2` for more details.
+
+1.2.0 (2020-12-08)
+------------------
+
+- The ``tax2seq`` command has been deprecated.
+- Updated the ``_artist()`` method to set the font size of title, labels, etc.
+- Added the ``s`` argument to the ``ancom_volcano_plot()`` method for setting marker size.
+- Updated the docstring.
+- See :issue:`1` for more details.
+
+1.1.0 (2020-11-23)
+------------------
+
+- Introduced the ``addpairs()`` method.
+- The ``beta_2d_plot_gallery()`` method has been deprecated.
+- Made some changes to the following methods:
+
+    - ``ordinate()``
+    - ``taxa_abundance_bar_plot()``
+    - ``taxa_abundance_box_plot()``
+    - ``_artist()``
+
+- Fixed some bugs.
+- Made keyword arguments for the ``_artist()`` method more explicit with ``artist_kwargs``.
+- Temporary files will be deleted automatically from now on.
+- Updated the docstring.
+- Plotting methods now accept Artifact and Visualization objects as input.
+
+1.0.0 (2020-11-09)
+------------------
+
+- Initial release.