Fmdtools

Latest version: v2.0.3

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2.0rc4

v2.0-rc-4 is mainly an update to documentation in preparation to the official v2.0 release.

Highlights include:
- Updated logo
- Improved organization of docs
- More resources for docs (figures/diagrams, etc)
- Removed minor bug in Result.get_values

Notes:

Release Notes - Resilience Analysis and Design - Version fmdtools 2.0-rc-4

<h2> Story
</h2>
<ul>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-241'>RAD-241</a>] - Release documentation update
</li>
</ul>

**Full Changelog**: https://github.com/nasa/fmdtools/compare/v2.0-rc-3...v2.0-rc-4

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<body link="467886" vlink="96607D">

Step | Description | Complete? | Comment
-- | -- | -- | --
1 | Sync appropriate branches into release branch | x |
1a | "Internal branches (e.g. main dev)" | x |
1b | "External branches (e.g. main)" | x |
2 | Run script run_all_tests.py and verify test results are appropriate | x |
2a | "Run full tests" | x |
2b | "Regenerate badge" | x |
3 | Update version numbers in appropriate files | x | updated to 2.0-rc-4
3a | "Check files conf.py LICENSE.py README.py Intro_to_fmdtools.md pyproject.toml" | x |
3b | "Run a repository-wide search for the version number" | x |
4 | Generate the documentation using "./make html" | x |
5 | Commit and tag branch with the appropriate version. | x |
5a | "git tag -a v2.x.x -m 'version 2.x.x'" | x |
6 | Sync to remotes | x |
6a | "Push release branch to github and internal remotes" | x |
6b | "Push docs using `git subtree push --prefix=_build/html public gh-pages`" | x |
7 | Create a release in GitHub | x |
7a | "incorporate a narrative summary of features and changes" | x |
7b | "incorporate the auto-generated bitbucket release notes." | x |
8 | "Update project plan" | x |
8a | "Include any changed dependencies" | x |
8b | "Include version in schedule" | x |
8c | "Identify and include additional changes/activities" | x |
9 | Update/check external CI resources as needed | x |
9a | "CodeFactor" | x |
10 | If release is 'stable' Upload to PyPI (see below | x |

</body>

</html>

2.0rc3

These updates cover basic adaptation of the rover model(s) and use cases, not counting the adaptation will need to be done for various papers.
- Notably, it re-adds the ability to sample from histories using the ParameterHistSample class.
- It also adapts a few of the notebooks for the RoverModel using this new class.
- It also cleans up a few bugs which have been identified so far.
- This version also comes with significant updates to documentation, to reflect upcoming release.

**Full Changelog**: https://github.com/nasa/fmdtools/compare/v2.0-rc-2...v2.0-rc-3

<h2> Links to Bugs/Stories
</h2>
<ul>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-389'>RAD-389</a>] - Final Version 2 Rover Adaptation and Bugfixes
</li>
</ul>

**Checklist**
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Step | Description | Complete? | Comment
-- | -- | -- | --
1 | Sync appropriate branches into release branch | x |
1a | "Internal branches (e.g. main dev)" | x |
1b | "External branches (e.g. main)" | x |
2 | Run script run_all_tests.py and verify test results are appropriate | x |
2a | "Run full tests" | x | All pass except skiped. Added RAD-401 for numpy warning
2b | "Regenerate badge" | x |
3 | Update version numbers in appropriate files | x | 2.0-rc-3
3a | "Check files conf.py LICENSE.py README.py Intro_to_fmdtools.md" | x |
3b | "Run a repository-wide search for the version number" | x | added pyproject.toml to list for next time
4 | Generate the documentation using "./make html" | x |
5 | Commit and tag branch with the appropriate version. | x |
5a | "git tag -a v2.x.x -m 'version 2.x.x'" | x |
6 | Sync to remotes | x |
6a | "Push release branch to github and internal remotes" | x |
6b | "Overwrite documentation on gh-pages and push to GitHub" | x |
7 | Create a release in GitHub | x |
7a | "incorporate a narrative summary of features and changes" | x |
7b | "incorporate the auto-generated bitbucket release notes." | x | Using github notes instead
8 | "Update project plan" | x |
8a | "Include any changed dependencies" | x |
8b | "Include version in schedule" | x |
8c | "Identify and include additional changes/activities" | x |
9 | Update/check external CI resources as needed | x | Some issues added but still rated A
9a | "CodeFactor" | x |
10 | If release is 'stable' Upload to PyPI (see below | N/A |

</body>

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2.0rc2

The 2.0-rc-2 release adds more polish to the fmdtools codebase prior to release. This progress point represents a final refinement on the codebase and features prior to our official release.

The main changes are:
- All blocks now require a defined __slots__ for new objects, encouraging speed and type-safety
- Results now save using numpy.save, removing an instance where the pickle module was (unsafely) being used to save and load results
- Bringing several research examples in the rover up to speed with the current developments in fmdtools
- Incorporation of a new taxiway model to demonstrate modelling of Systems of Systems
- A polishing of the documentation repository.

Release Notes - Resilience Analysis and Design - Version fmdtools 2.0-rc-2

<h2> Story
</h2>
<ul>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-224'>RAD-224</a>] - Adapt AST Sampling notebook/methodology
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-242'>RAD-242</a>] - Incorporate Taxiway model in examples
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-249'>RAD-249</a>] - Avoid and deprecate pickle for save/load
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-317'>RAD-317</a>] - Fix bug in multiplots - ticks should rotate even if no plot
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-337'>RAD-337</a>] - Enable better attribute safety in Flows, Blocks, etc
</li>
</ul>

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Release Checklist

<body link="0563C1" vlink="954F72">

Step | Description | Complete? | Comment
-- | -- | -- | --
1 | Sync appropriate branches into release branch | x |
1a | "Internal branches (e.g. main dev)" | x |
1b | "External branches (e.g. main)" | x |
2 | Run script run_all_tests.py and verify test results are appropriate | x |
2a | "Run full tests" | x | Errors added as bug:s =========================== short test summary info =========================== ERROR examples/rover/rover_mode_space.py - TypeError: 'NoneType' object is not callable ERROR examples/rover/optimization/ea_analysis.py - FileNotFoundError: [Errno 2] No such file or directory: 'results/rslt_ea.csv'
2b | "Regenerate badge" | x |
3 | Update version numbers in appropriate files | x |
3a | "Check files conf.py LICENSE.py README.py Intro_to_fmdtools.md" | x |
3b | "Run a repository-wide search for the version number" | x |
4 | Generate the documentation using "./make html" | x |
5 | Commit and tag branch with the appropriate version. | x |
5a | "git tag -a v2.x.x -m 'version 2.x.x'" | x |
6 | Sync to remotes | x |
6a | "Push release branch to github and internal remotes" | x |
6b | "Overwrite documentation on gh-pages and push to GitHub" | x |
7 | Create a release in GitHub | x |
7a | "incorporate a narrative summary of features and changes" | x |
7b | "incorporate the auto-generated bitbucket release notes." | x |
8 | "Update project plan" | x |
8a | "Include any changed dependencies" | x |
8b | "Include version in schedule" | x |
8c | "Identify and include additional changes/activities" | x |
9 | Update/check external CI resources as needed | x |
9a | "CodeFactor" | x | Grade went from A- to A!
10 | If release is 'stable' Upload to PyPI (see below | N/A |

</body>

</html>

2.0rc1

- Re-organization of define package into object, container, block, and architecture subpackages representing each type of simulation.
- Definition of new BaseObject, Container, and Architecture classes which are now used to define how simulation structures initialize attributes, create histories, return mutables, etc
- FxnBlock is now named Function in keeping with class name convention
- Model, ASG, Comparch repaced by FunctionArchitecture, ActionArchitecture, and ComponentArchitecture classes which all inherit from/specialize the base Architecture class
- Simulation histories now fully created at instantiation via the tracking argument rather than in propagate.
- Roles (i.e., init_c, init_p, init_flowname) now given explicit names corresponding to their type (i.e., container_c, container_p, flow_flowname)
- Basic adaptation of tests, examples, and documentation.
- Usage of "coverage" package in testing to give overall testing coverage report.

Auto-generated release notes

Release Notes - Resilience Analysis and Design - Version fmdtools 2.0-rc-1

<h2> Sub-task
</h2>
<ul>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-334'>RAD-334</a>] - Create sub-package for roles
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-335'>RAD-335</a>] - Decompose/Refactor Architectures
</li>
</ul>

<h2> Story
</h2>
<ul>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-233'>RAD-233</a>] - Refactor and Generalize Architectures (ASG, CompArch, Model)
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-319'>RAD-319</a>] - Add testing coverage to code testing reporting
</li>
</ul>

Release checklist
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Step | Description | Complete? | Comment
-- | -- | -- | --
1 | Sync appropriate branches into release branch | X |
1a | Internal branches (e.g. main dev) | X |
1b | External branches (e.g. main) | x |
2 | Run script run_all_tests.py and verify test results are appropriate | X |
2a | Run full tests | x | 11 failures, mainly in model reset (no longer used but kept for future) and rover model. Some errors also in rover model, AST sampling due to lack of packages. 76% coverage on inaugural run, weak spots identified in rover, pump examples.
2b | Regenerate badge | x |
3 | Update version numbers in appropriate files | x | Fmdtools 2.0-rc-1
3a | Check files conf.py LICENSE.py README.py Intro_to_fmdtools.md | x |
3b | Run a repository-wide search for the version number | x |
4 | Generate the documentation using “./make html” | x | Need to figure out what is going on with badge – adds extra tests to numerator and denominator. (the errors?)
5 | Commit and tag branch with the appropriate version. | x |
5a | git tag -a v2.x.x -m ‘version 2.x.x’ | x |
6 | Sync to remotes | x |
6a | Push release branch to github and internal remotes | x |
6b | Overwrite documentation on gh-pages and push to GitHub | x |
7 | Create a release in GitHub | X |
7a | incorporate a narrative summary of features and changes | X |
7b | incorporate the auto-generated bitbucket release notes. | x |
9 | Update/check external CI resources as needed | x |
9a | CodeFactor | x | 66 fixed issues, 27 new issues in the past month (173 total). Grade remains A-.
10 | If release is ‘stable’ Upload to PyPI (see below | | NA


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2.0beta3

**Overall Summary:**
This PR covers the reimplementation of fmdtools.sim.search.ProblemInterface as:
• ParameterSimProblem, a class for optimizing parameters over simulations
• FaultSimProblem, a class for optimizing fault times
• DisturbanceSimProblem, a class for optimizing disturbances in the context of a simulation
• SimpleProblem, a class for setting up external function calls in an optimization
• ProblemArchitecture, a class for connecting different problems in an overall optimization architecture
It also covers adaptation of examples and tests to fit this:
• Pump optimization
• Drone/multirotor optimization
• Tank optimization
• New exampes/tests in the docstrings
Also in this PR are some bugfixes for the new version of recordclass (0.21).

**Commit Narrative:**
• Developing ParameterSearch class
o ParameterSearch will be used to search ParameterDomains over sims
o Add ability to pass variable mappings to ParameterDomains so you can search/sample discrete parameters more easily
• Adding tests/docs to ParameterProblem
o ExampleParameter, ExampleState, ExampleFxnBlocks defined in respective modules for testing purposes
o Tests added to ParameterProblem showcasing input/output callables
• Adding ParameterProblem to Search
o ParameterProblem added to search
o Some consolidation of drone scripts
• Adding tests for Drone to example
o Basic search tests added for Drone
o Variables now nan at initialization (instead of 0.0)
• Adding single-fault and disturbance optimization classes
-DisturbanceProblem, SingleFaultProblem now available for optimizaiton
o Tests of both in docs + drone model
o Fixed bug in Block copying--no longer requires new flows
o Single/JointFault scenario generation moved to respective scenario classes form sample.
• Developing SimpleProblem
o SimpleProblem added to search for callables which will be input to a ProblemArchitecture for the Drone (and others)
• More initial work on ProblemArchitecture
• Update search_testing.py
• More prototyping of ProblemArchitechture
• Adding way to connect/update variables in ProblemArchitectechture
• Further work on Problem Architecture
o Creating test problemarch to use in doctest
o Made it so that Problem tests can be imported from the module (and into ProblemArch)
• Creating initial docstrings for ProblemArchitecture
• Adding preliminary tests to ProblemArchitecture
o doctests now used for some problemarchitecture functions
• More development of ProblemArchitecture
o ProblemArch now mirrors objectives/constraints at arch level
o ProblemArch now creates callables for objectives/constraints at arch level
o ProblemArch now checks/updates consistency of upstream/downstream sims
• Incorporating ParameterArchitecture in search
o Added tests, examples, and docstrings to ParameterArchitecture.
o ParameterArchitecture moved from search_testing to search.
• Reformat DynamicInterface
DynamicInterface now follows programming style
• Adapting Drone Optimization
o drone_opt_rural now has problems defined
o adding better support for nested variables--now properly sets args
• More drone optimization adaptation
o Full optimization architecture implemented on drone arch
o Added ability to not include nominal result in fault scenario optimization
• Update recordclass requirement
o Recordclass to be used now 0.21.1, updated docs and modules to reflect this
• Adding optimization problem timing, history
o iter_hist now records the problem iterations
o time_execution can now be used to time the amount of time a problem takes to sim/update
o some adaptation of common and history to support iteration histories
• Adding ability to use history values as objectives/constraints
• Drone optimization example now working/up-to-date
o Adapted multirotor optimization notebook and consolidated codes from opt_drone_rural and search_testing into it
o propagate now has a fault_sample_from method which auto-generates a SampleApproach from arguments/nominal
o some polishing of search methods--now make it so showprogress=false by default, can work with multiple returns
o fixed various bugs in the drone model, coords, rand
• Adapting pump optimization
o bugfixing so that states etc copy instead of use defaults
o halfway done on pump optimization notebook
o some fixes to pump_stochastic.py
• Finishing Pump Optimization
o Optimization notebook for pump finished
o 'expected cost' changed to 'expected_cost' everywhere
• Finished adapting tank optimization example
o Tank optimization notebook completed. This notebook incorporates all functions from tank_opt.py
o Fixed bugs in tank optimization model
o Fixed bugs in search--objective connectors now work as desired
o closes [RAD-328](https://babelfish.arc.nasa.gov/jira/browse/RAD-328)

**Checklist**

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Step | Description | Complete? | Comment
-- | -- | -- | --
1 | Sync appropriate branches into release branch | x | Nothing new
1a | Internal branches (e.g. main dev) | x |
1b | External branches (e.g. main) | x |
2 | Run script run_all_tests.py and verify test results are appropriate | x | Flagged two notebooks to fix: multirotor demonstration and tank optimization. Other notebooks should also be fixed in the next few efforts.
2a | Run full tests | x | 10 failures, 4 warnings, 15 errors, 226 passed. Significant number of tests added in this cycle. Failures mainly reflect unimplemented examples
2b | Regenerate badge | x |
3 | Update version numbers in appropriate files | x |
3a | Check files conf.py LICENSE.py README.py Intro_to_fmdtools.md | x |
3b | Run a repository-wide search for the version number | x |
4 | Generate the documentation using “./make html” | x | Generated, some formatting errors found and flagged to be fixed.
5 | Commit and tag branch with the appropriate version. | X |
5a | git tag -a v2.x.x -m ‘version 2.x.x’ | x |
6 | Sync to remotes | x |
6a | Push release branch to github and internal remotes | x |
6b | Overwrite documentation on gh-pages and push to GitHub | x |
7 | Create a release in GitHub | x |
7a | incorporate a narrative summary of features and changes | x |
7b | incorporate the auto-generated bitbucket release notes. | x |
9 | Update/check external CI resources as needed | x |
9a | CodeFactor | x |
10 | If release is ‘stable’ Upload to PyPI (see below | |


</body>

</html>

2.0beta2

Summary

This second beta milestone for the `fmdtools-2.0` development cycle has focused on the refactoring of fault and parameter sampling functionality, along with the `analyze` module as a whole. Notably, this refactoring has **increased our codefactor score from C+ to B+**, mainly from the refactoring of major trouble spots like fmdtools.sim.approach and fmdtools.analyze.plot. Throughout this process, we also have added **57 new tests**, bringing us to 266 from 209.

Details
* Replacement of approach module (NominalApproach and SampleApproach) with analyze.phases and sim.sample modules with the following classes:
* FaultDomain for specifying types of fault modes to sample from
* FaultSample for sampling these modes (Generating FaultScenarios)
* PhaseMap for (and phases module) for representing phases of operation from the model history for fault sampling
* SampleApproach for joining multiple faultsamples over multiple FaultDomains
* ParameterDomain for defining variables to sample from parameters
* ParameterSample for sampling parameters from a parameterdomain (generating ParameterScenarios)
* Adaptation of propagate methods to align with these new names/classes. e.g., propagate.nominal_approach is now propagate.parameter_sample, etc.
* Replacement of tabulate/plot methods with classes that perform the same role
* FMEA taking the role of fmea()
* Comparison taking the role of nominal_factor_comparison, nested_factor, comparison, etc
* NominalEnvelope taking the role of plot.nominal_vals_xd
* Refactoring analyze functionality to follow an object-oriented (rather than module-oriented) convention:
* show module methods now a part of their respective classes (Geom, Coords, etc)
* plot_dyn_order now a part of Model
* plot_trajectories and plot_hist now a part of History
* plot_metric now a part of Result, History
* Creation of a analyze.common module for remaining base plot, analysis functionality
* Removal of show, plot modules
* Adaptation of presently-working examples and tests.

Auto-generated release notes:

<h2> Sub-task
</h2>
<ul>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-96'>RAD-96</a>] - Refactor SampleApproach
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-255'>RAD-255</a>] - Adapt SampleApproach Use-cases in Rover Example
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-259'>RAD-259</a>] - Enable exploration of sub-parameters in NominalApproach
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-268'>RAD-268</a>] - Update Propagate methods
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-272'>RAD-272</a>] - Fix complexity in plot module
</li>
</ul>

<h2> Epic
</h2>
<ul>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-70'>RAD-70</a>] - Create function, flow, patterns/attributes for next generation of the Stereo Model
</li>
</ul>

<h2> Story
</h2>
<ul>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-258'>RAD-258</a>] - Fix/update tabulate module and less-used plot methods
</li>
<li>[<a href='https://babelfish.arc.nasa.gov/jira/browse/RAD-260'>RAD-260</a>] - Refactor approach classes
</li>
</ul>

Release checklist

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<body lang=EN-US style='tab-interval:.5in;word-wrap:break-word'>


Step | Description | Complete? | Comment
-- | -- | -- | --
1 | Sync appropriate branches into release branch | X |
1a | Internal branches (e.g. main dev) | X |
1b | External branches (e.g. main) | X | No external changes
2 | Run script run_all_tests.py and verify test results are appropriate | X | 10 failures, 2 warnings, 22 errors. 3 issues resolved since last release. Failures are almost wholly in search tests and known (not yet adapted) examples
2a | Run full tests | X |
2b | Regenerate badge | X |
3 | Update version numbers in appropriate files | X |
3a | Check files conf.py LICENSE.py README.py Intro_to_fmdtools.md | X |
3b | Run a repository-wide search for the version number | X |
4 | Generate the documentation using “./make html” | X | Updated docs and figures where needed. Some descriptions flagged to be updated in the future.
5 | Commit and tag branch with the appropriate version. | X | V2.0-beta2
5a | git tag -a v2.x.x -m ‘version 2.x.x’ | X |
6 | Sync to remotes | X |
6a | Push release branch to github and internal remotes | X |
6b | Overwrite documentation on gh-pages and push to GitHub | X |
7 | Create a release in GitHub | X |
7a | incorporate a narrative summary of features and changes | X |
7b | incorporate the auto-generated bitbucket release notes. | X |
9 | Update/check external CI resources as needed | X |
9a | CodeFactor | X | Update brought us from C+ to B+
10 | If release is ‘stable’ Upload to PyPI (see below | |


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