HISTORY.rst

History

Next Release

0.8.6 (2018-09-13)

• Fix test titles and descriptions.

0.8.5 (2018-08-20)

• Unpin cobra dependency and set it to >0.13.3.
• Set ruamel.yaml to >=0.15 to keep up with cobra.

0.8.4 (2018-07-18)

• Handle various pytest verbosity options better.
• Improve memote new behavior.

0.8.3 (2018-07-16)

• memote run in a repository now immediately commits the result to the deployment branch.

0.8.2 (2018-07-16)

• Allow running of memote history from any branch.
• Let the history report only use commits where the model actually changed.
• Proofread and update all docstrings and comments inside the memote subfolder.
• Reworded all test titles to be a) shorter and b) as neutral as was sensibly possible.
• Reordered tests in the test-config.yaml such that results belonging to a category are grouped logically.
• Updated the documentation to include a newer flowchart, up-to-date getting started and custom test sections.
• Update code to account for breaking changes in the most recent version of cobrapy (0.13.0) and subsequently unpin cobrapy dependency (set to >=0.13.0).

0.8.1 (2018-06-27)

• Allow users to selective recompute the history of results.
• Skip commits in the history that did not change the model file.
• Change format_type on experimental tests from count to percent
• Fix typo in test_basic.py that lead to tests returning null which breaks the diff report frontend.
• Update the diff report to properly show errored and skipped tests
• Fix issues with asynchronicity on the diff report.
• Change format_type on experimental tests from count to percent
• Fix typo in test_basic.py that lead to tests returning null which breaks the diff report frontend.
• Update the diff report to properly show errored and skipped tests

0.8.0 (2018-06-22)

• Finalize testing comparing with experimental data (growth and esentiality).
• Temporarily disable test_find_inconsistent_min_stoichiometry.
• Update the nullspace function.
• Improve optlang compatibility.
• Add test find_medium_metabolites to detect and display all substrates capable of being taken up by model
• Display the score on History and Snapshot reports.
• Invert the colour coding.
• Display results as percentages.
• Add ability to generate a diff report which compares two or more models.
• Annotation of metabolite shortlist simplified.

0.7.6 (2018-05-28)

• Refactor internal API and JSON object creation.

0.7.5 (2018-05-25)

• Expose more of the internal API to the top level.
• Also, remember to carry a towel!

0.7.4 (2018-05-23)

• Add test find_duplicate_reactions to detect duplicate reactions in model
• Add dynamic upper and lower bounds. They are based on the most extreme bound values given in a model (if none exist -1000 and 1000 are chosen as defaults)
• Fix logic in find_bounds function in helpers.py

0.7.3 (2018-05-23)

• Make the report type variable a string in the index.html.

0.7.2 (2018-05-22)

• Distribute the missing tests.

0.7.1 (2018-05-16)

• Fix a problem with the report caused by previous refactoring.

0.7.0 (2018-05-15)

• Remove the pip dependency in show_versions.
• Update the CI to use stages and tox-travis.
• Modify some editor and other configuration.
• Expose testing of experimental essentiality and growth data in memote.
• Create a configuration system for media that is extensible to further experimental data types.
• Add test for identifying purely metabolic reactions with fixed constraints in models
• Add test for identifying transport reactions with fixed constraints in models
• Add test for identifying reversible oxygen-containing reactions in models
• Add division import from __future__ to test_biomass and test_consistency where it was missing.
• Add O2 to MetaNetX shortlist, allowing for easier identification
• Allow tests and test module to be skipped or run exclusively when creating a snapshot report.
• Fix some typos
• Add history report view and connect it to memote report history call.
• find_direct_metabolites detects and removes false positives.
• find_transport_reactions detects reactions using forumlae and annotations
• Add tests for detecting gene annotations (and verifying they are in MIRIAM style)
• Add unit tests for matrix.py in file test_for_matrix.py.
• Add tests find_metabolites_not_produced_with_open_bounds and find_metabolites_not_consumed_with_open_bounds
• Add test find_duplicate_metabolites_in_compartments to detect duplicate metabolites in identical compartments
• Cache heavily used support functions in helpers.py and consistency_helpers.py

0.6.2 (2018-03-12)

• Test summary only displays extended narrative summary describing test, and not one-line summary describing expected function behavior/output

• Fix the following bugs:

  • Fix type annotation on the test for Biomass Production in Complete Medium
  • Fix TypeError when running memote new which was associated with unicode and string formatting in py2.7
  • Sort existing test results from misc into the respective categories (by editing test_config.yml)
  • Move Matrix statistics category to unscored side into their own card
  • Add a tuple of (number of reactions, number of genes) to the data annotation of the metabolic coverage test.

• Add filter in report_data_service that changed the test result status to "error" when the data attribute is null, thus avoiding that the report interface breaks when trying to access data.
• Add test for identifying stoichiometrically balanced cycles in models
• Correct the arguments used for repositories such that memote run and memote history work as expected inside of a repository.

0.6.1 (2018-03-01)

• Emergency fix for distributing required JSON file.

0.6.0 (2018-02-27)

• Let Travis re-package the snapshot report with every release.

• Add new module to test for the presence of SBO term annotations.

• Add a test for Biomass production in complete medium.

• Clarify extend of mass- and charge-imbalance testing.

• Remove much of the boilerplate code of the report template as a preparation for the history and diff report.

• Fix bug with test_blocked_reactions

• Update the testData.json with data from the previous release

• Fix a small bug with the metrics of mass/charge unbalanced reactions.

• Correctly invert the found identifiers in wrong annotations and namespace consistency in order to report the correct results.

• Add a cross-reference shortlist using MetaNetX flatfiles

• Add a script that can be used to add more metabolites and then to re-generate the shortlist

• Add helper function find_met_in_model which looks up a query metabolite ID using the MNX namespace in the shortlist and:

  • If no compartment is provided, returns a list of all possible candidates metabolites.
  • If a compartment is provided, tries to return a list containing only ONE corresponding metabolite.

• Add helper function find_compartment_id_in_model to identify compartments using an internal shortlist of possible compartment names.

• Provide tests for each function

• Refactor code to use these functions specifically:

  • find_ngam
  • find_biomass_reaction
  • detect_energy_generating_cycles
  • find_exchange_rxns
  • find_demand_rxns
  • find_sink_rxns
  • gam_in_biomass
  • find_biomass_precursors

• Improve find_ngam in addition to agnostically looking for ATP hydrolysis reactions, the test now also looks for a range of possible "buzzwords" in the reaction NAME: ['maintenance', 'atpm', 'requirement', 'ngam', 'non-growth', 'associated']. One match suffices as a classification.

• Improve find_biomass_reaction to look for three attributes in a biomass reaction, one of which is sufficient to classify it as a biomass reaction:

  1. "Buzzwords" in the reaction ID: ['biomass', 'growth', 'bof']
  2. An annotation matching the SBO-Term SBO:0000630 specifically!
  3. Containing a metabolite matching the regex: ^biomass(_[a-zA-Z]+?)*?$ (case-insensitive)

• Add function bundle_biomass_components to identify whether a given biomass reaction is 'split' or 'lumped'. This function looks simply at the size of the biomass reaction. Based on a guess-timated cut-off the reaction is then classified. If it is 'lumped' it is returned without changes, if it is 'split' the reactions of any non-energy precursor metabolite are returned as well. This is based on the assumption that a 'split' biomass reaction has the following structure: a (1 gDW ash) + b (1 gDW phospholipids) + c (free fatty acids) + d (1 gDW carbs) + e (1 gDW protein) + f (1 gDW RNA) + g (1 gDW DNA) + h (vitamins/cofactors)-> 1 gDCW biomass. We're supposing that for each macromolecule precursor metabolite there is a single reaction defining its composition i.e. e = protein would have the reaction: alanine + asparagine + ... + valine --> e

• Add function, test and model test to identify missing essential precursors to the biomass reaction. The function is essential_precursors_not_in_biomass

• Record the score of individual test cases and sections in the result output.

• Correct the import of module 'annotation' with 'sbo' in test_sbo.py

• Refactor sink_react_list to sink_reactions for improved readability

• Allow test_sink_specific_sbo_presence to be skipped when no sink reactions are present with a metric of 1.0

• Fix a bug that compared the length of a float to generate a metric in test_basic.py and generated a TypeError.

• Fix a bug that prevented find_biomass_precursors in memote/support/biomass.py from functioning due to a malformed set

• In CONTRIBUTING.rst replace link to semantic commit guide by seesparkbox with link to guide by karma, due to error with sphinx linkcheck.

• Fix a bug that prevented find_biomass_precursors from correctly identifying atp and h2o metabolites in cobra model reactions

• Fix improperly labeled sbo terms for biomass production in biomass.py and test_for_helpers.py.

• Add matrix conditioning functions in matrix.py which are used for model stoichiometric matrix testing in test_matrix.py

• Add missing rank and nullspace_basis functions in consistency_helpers.py

• Fix issue with improper string/dict formatting in test_biomass.py tests

• Re-organize the architecture to read in external configurations and add custom tests.

• Add an argument --location which replaces --directory which can be used to set the directory or database where results should be stored.

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.
• Fix UnicodeDecodeError when memote tries to open the html template for the snapshot report.

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