Next Release

0.5.0 (2018-01-16)

  • 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.

0.4.6 (2017-10-31)

  • 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

0.4.5 (2017-10-09)

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

0.4.4 (2017-09-26)

  • 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.

0.4.3 (2017-09-25)

  • 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.

0.4.2 (2017-08-22)

  • Push all branches with memote online.

0.4.1 (2017-08-22)

  • Fix JSON serialization of test results.

0.4.0 (2017-08-21)

  • Add a programmatic API in module memote.suite.api (#162).
  • Reorganize the structure and build process for auto-documenting memote (#172).
  • Add a new command memote online (#95, #153).
  • Add more basic tests.

0.3.6 (2017-08-15)

  • Improve GitHub support.
  • Update the readthedocs and gitter badge.
  • Add a function memote.show_versions() for easy dependency checking.

0.3.4 (2017-08-12)

  • Properly configure Travis deployment.

0.3.3 (2017-08-12)

  • Build tags.

0.3.2 (2017-08-12)

  • Enable automatic deployment to PyPi.

0.3.0 (2017-08-12)

  • Greatly extend the core test modules: * basic * consistency * biomass * annotation * syntax
  • Add an Angular-material based report with plotly.
  • Add documentation on readthedocs.io.
  • Make the first release on PyPi.

0.2.0 (2017-02-09)

  • Yet another package structure for supporting functions, their tests, and the model test suite.

0.1.0 (2017-01-30)

  • New package structure and start of joint development