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href=&amp;amp;amp;amp;amp;quot;https://git&amp;amp;amp;amp;quot;&amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;lt;a class=&amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;gt;hub.com/keiserlab/e3fp/commit/&amp;amp;amp;amp;amp;lt;a class=&amp;amp;amp;amp;amp;quot;double-link&amp;amp;amp;amp;amp;quot; href=&amp;amp;amp;amp;amp;quot;https://git&amp;amp;amp;amp;quot;&amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;lt;a class=&amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;gt;hub.com/keiserlab/e3fp/commit/2d20820c375367d27adacf51a064d7e4e3c097e6&amp;amp;amp;amp;quot;&amp;amp;amp;amp;gt;2d20820c3&amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;gt;&amp;amp;amp;amp;lt;a href=&amp;amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/2d20820c375367d27adacf51a064d7e4e3c097e6&amp;amp;amp;amp;quot;&amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;lt;a href=&amp;amp;amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/2d20820c375367d27adacf51a064d7e4e3c097e6&amp;amp;amp;amp;amp;quot;&amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;quot;&amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;amp;lt;a href=&amp;amp;amp;amp;amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/&amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;lt;a class=&amp;amp;amp;amp;amp;amp;quot;double-link&amp;amp;amp;amp;amp;amp;quot; 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* Convert README to RestructuredText

* Cleanup formatting

* Fix formatting of relative links

* Place code on its own line

* Fix indentation

* Add F1000 badge

* Rescale image

* Push URLs to bottom

This makes main text much cleaner

* Store version in __version__

* Add prompts to code blocks

* Add initial documentation

Add initial sphinx documentation.

* Switch theme to default

This enables ReadTheDocs own theme to be used

* Add another system path

* Remove excess sys paths

* Import e3fp after modding path

This is necessary for ReadTheDocs, when the path has not yet been set.

* Streamline README and link to documentation

* Don&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;t track build-related files

* Switch versions of napoleon

* Switch back to new napoleon and add autodoc

* Mock out modules with C code

* Special case ReadTheDocs setup

* Don&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;t check NumPy headers on RTD

* Require mock on RTD

* Mock rdkit submodules

* Mock more scipy submodules

* Mock more scipy submodules

* Add more status badges

* Add more to summary

* Use readme for long_description on pypi

* Gitignore coverage file

* Fix url

* Rewrap text

* Document license and contributions

* Don&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;t mock numpy and scipy

We now allow ReadTheDocs to access the global site-packages (and
numpy/scipy) while building, so mocking these modules is no longer
necessary.

* Remove redundant statement

* Correct instructions

* Push substitutions/references to global file

* Rewrap lines

* Use same formats as documentation

* Update badges

Remove unnecessary badges and clarify existing badges

* Use header for references

This looks better on Github, where rubric is just text.

* Add/fix substitutions

* Remove comment

* Use title reference

* Link scipy docs through inter sphinx

* Add caption for embedded file

* Use RTD theme if available

* Make examples directory

* Change header

* Add config file documentation

* Install coveralls with conda

Also wait to install until after installing test packages.

* Add punctuation to deprecation note

* Add analytics code

* Update paper reference

* Install E3FP on ReadtheDocs

In order to have automatically updated examples, we need a working
installation of E3FP on ReadtheDocs. Here we use conda support to
install all required dependencies. In the future, we will need an
expanded environment.yml file if we have any examples that require
additional packages.

* Add doctest extension

Doctest lets us verify all code snippets in docstrings and
documentation execute correctly, so that code is always up-to-date.
Relates #2.

* Ensure config examples produce exact outputs

* Update config documentation

* Don&amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;t wrap docstring snippets

doctest can’t parse wrapped commands.

* Update and correct fingerprint usage in docstring

Relates #2.

* Remove unnecessary ellipsis flag

By default, this flag is turned on for sphinx.ext.doctest

* Add warning for potential conda bug

* Test docstring code snippets with each commit

Relates #2

* Fix bold formatting

* Don&amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;t use dict in doctest snippet

Dicts are ordered differently for each version of Python, so it is
impossible for doctest to pass for all.

* Add cython dependency for readthedocs

This should enable compiling fast_soergel on RTD.

* Revert &amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;Add cython dependency for readthedocs&amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;

This reverts commit &amp;amp;amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;amp;amp;lt;a class=&amp;amp;amp;amp;amp;amp;amp;amp;quot;double-link&amp;amp;amp;amp;amp;amp;amp;amp;quot; href=&amp;amp;amp;amp;amp;amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/&amp;amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;amp;amp;lt;a class=&amp;amp;amp;amp;amp;amp;amp;quot;double-link&amp;amp;amp;amp;amp;amp;amp;quot; href=&amp;amp;amp;amp;amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/&amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;gt;&amp;amp;amp;amp;lt;a class=&amp;amp;amp;amp;quot;double-link&amp;amp;amp;amp;quot; href=&amp;amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/&amp;amp;lt;/a&amp;amp;gt;&amp;amp;lt;a class=&amp;amp;quot;double-link&amp;amp;quot; href=&amp;amp;quot;https://github.com/keiserlab/e3fp/commit/&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/keiserlab/e3fp/commit/7a9c18cdc18c005443b53bc2dd24bc41f5d4a381&quot;&gt;7a9c18cdc&lt;/a&gt;&amp;amp;quot;&amp;amp;gt;7a9c18cdc&amp;amp;lt;/a&amp;amp;gt;&amp;amp;amp;quot;&amp;amp;amp;gt;7a9c18cdc&amp;amp;amp;lt;/a&amp;amp;amp;gt;&amp;amp;amp;lt;a href=&amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/2d20820c375367d27adacf51a064d7e4e3c097e6&amp;amp;quot;&amp;amp;gt;&amp;amp;amp;amp;amp;quot;&amp;amp;amp;amp;amp;gt;7a9c18cdc&amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;quot;&amp;amp;amp;amp;amp;gt;7a9c18cdc&amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;gt;&amp;amp;amp;amp;amp;lt;a href=&amp;amp;amp;&lt;/a&gt;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/2d20820c375367d27adacf51a064d7e4e3c097&amp;amp;amp;lt;/a&amp;amp;amp;gt;e6&amp;amp;amp;quot;&amp;amp;amp;gt;.

* Use installed version for documentation, not source

* Revert &amp;amp;amp;amp;quot;Revert &amp;amp;amp;amp;quot;Add cython dependency for readthedocs&amp;amp;amp;amp;quot;&amp;amp;amp;amp;quot;

This reverts commit &amp;amp;amp;lt;/a&amp;amp;amp;gt;&amp;amp;amp;lt;a class=&amp;amp;amp;quot;double-link&amp;amp;amp;quot; href=&amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/&amp;amp;amp;lt;a class=&amp;amp;amp;quot;double-link&amp;amp;amp;quot; href=&amp;amp;amp;quot;https://github.com/keiserlab/e3fp/commit/&amp;lt;/a&amp;gt;&amp;lt;a class=&amp;quot;double-link&amp;quot; href=&amp;quot;https://github.com/keiserlab/e3fp/commit/&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/keiserlab/e3fp/commit/<a class="double-link" href="https://github.com/keiserlab/e3fp/commit/2f5b465e9620202e81d25d31bd11564170a29289">2f5b465e9</a>&quot;&gt;2f5b465e9&lt;/a&gt;&amp;quot;&amp;gt;2f5b465e9&amp;lt;/a&amp;gt;&amp;amp;quot;&amp;amp;gt;2f5b465e9&amp;amp;lt;/a&amp;amp;gt;&amp;amp;quot;&amp;amp;gt;2f5b465e9&amp;amp;lt;/a&amp;amp;gt;&amp;amp;lt;a href=&amp;amp;quot;https://github.com/keiserlab/e3fp/commit/2d20820c375367d27adacf51a064d7e4e3c097e6&amp;amp;quot;&amp;amp;gt;.

* Reorganize api doc source

* Build from local source except on RTD

* Update and reformat fprints docstrings

Relates #2.

* Use Napoleon for better docstring parsing

* Use &amp;amp;amp;quot;autolink&amp;amp;amp;quot; default role

By default “autolink” attempts to link to objects whenever possible,
providing cleaner docstrings.

* Use full type name for refs

* Add and reformat database documentation

Relates #2, #20, #12

* Use concat, not append

Append is deprecate</a>d

* Clean and reformat docstrings

Relates #2

* Make API hierarchy more human-readable

* Add rst file for each module

This should enable finer organization in the future.

* Add rst file for each module

* Add ellipses

‘type’ or ‘class’ used differently depending
on Python version

* Add import to snippet

* Use single backticks for Python objects

* Add more detail to refs

* Link out to Python 3

* Add docstrings to Python methods

* Use new database extension

* Clean up and reformat array metrics docstrings

Relates #2

* Add command-line outputs

* Add programoutput doc dependency

* Use syntax-highlighting for shell

* Add options to makefile

* Use image converter for SVG to PDF

* Add API doc for fingerprint util module

* Test config examples with doctest

* Don&amp;amp;#39;</a>t mock modules

Mocking is no longer necessary, since the ReadtheDocs build is using
the conda environment.

* Use more readable section refs and headers

* Ad</a>d pipeline documentation

* Add pipeline documentation

* Conform to PEP257

Ensure existing docstrings are formatted according to Python’s style
guides.

* Conform to PEP8

* Remove unused fingerprinting doc

* Remove unnecessary doctest commands

By default python-session blocks are detected and doctested without
being specified.

* Use non-planar example for conf gen

* Remove excess quotation mark

* Add documentation for fingerprints

* Add developer notes

* Remove unused docs

* Change section headings to standard

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