Memote

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* Enable test result and meta-data collection.
* Allow command line option and configuration of exclusive test cases and
modules skipping all others (``--exclusive test_biomass``).
* Allow command line option and configuration to skip test cases and
modules (``--skip test_model_id_presence``).
* Introduce a dummy configuration file for the report organization and test
scoring weights.
* Sort unconfigured tests into the card 'Misc. Tests' in the snapshot report.
* Handle skipped tests better in the snapshot report.
* Bundle the Angular report javascript libraries in the snapshot template
* Pass results into the report as JSON
* Fixed/ changed a lot of visuals on the angular report:
- Indent the rows of the parametrized test results
- Color the header text of the parametrized test results in pure black
- Remove the horizontal lines in the parametrized test results
- Display all results regardless of scored/ unscored inside of buttons to
force a uniform line height and a more consistent look
- Add logic to correctly display errored tests
- Give skipped and errored test results a distinct look
- Explicitly handle boolean results, and add boolean as an option for the
'type' attribute.
- Fix the raw data output in the textboxes so that they are formatted
python code.
* Allow command line option to enable the definition of a custom test directory
in combination with a corresponding config file.
* Extend test descriptions to make it more clear how a user can satisfy the
test conditions.
* Remove duplicate test for the presence of transport reactions.
* Implement a test for unbounded flux through reactions in the default
condition.
* Implement a test for detecting metabolites that can either be produced or
removed from the model when all system boundaries are closed.
* Implement a test for 'direct' metabolites, i.e. the detection of biomass
precursors that are not involved in any metabolic reactions; only in
exchange reactions, transporters and the biomass reaction itself.
* Implement a test that checks for a low ratio of transport reactions without
GPR relative to the total amount of transport reactions.
* Fix UnicodeDecodeError when memote tries to open the html template for the
snapshot report.

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* Improve the automated release pipeline. It now creates pumpkins.
* Provide a new decorator ``register_with`` that can be used in all
``test_for*`` modules and replaces the ``model_builder`` function.
* Temporarily change the links to readthedocs to point to latest instead of stable.
* Provide angular2 app for the snapshot report instead of the jinja template

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* Correctly account for reversibility when testing for dead-end and orphan
metabolites.

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* Fix a bunch of bugs:
- Remove false positive detection of Biocyc annotation
- Allow memote to identify CTP or GTP driven transport reactions
- Refactor how memote detects GAM in the biomass reaction
* Add tests to find deadend, orphan and disconnected metabolites.
* Extend and improve algorithm to find energy-generating cycles
* Remove the ``print`` statement from ``memote.support.annotation
.generate_component_annotation_miriam_match``.
* Fix the bug in the assertion output of ``memote.memote.suite.tests.test_basic
.test_gene_protein_reaction_rule_presence``.
* Split mass-charge-balance test into two separate tests for more clarity
* Fix a bug in ``memote.support.consistency_helpers.get_internals`` that did
not exclude the (by definition) imbalanced biomass reactions.

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* Fix documentation building and add auto-generation of docs.
* Make the command line output of pytest more verbose until the report is up to
speed.
* Temporarily skip ``test_find_stoichiometrically_balanced_cycles``
* Catch errors when testing for compartments and loops.

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* Push all branches with ``memote online``.