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Metadata fbc3 group #988

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782b645
added annotation class
Hemant27031999 Jun 4, 2020
9709974
made some modifications
Hemant27031999 Jun 4, 2020
a7af772
made the complete metadata package
Hemant27031999 Jun 9, 2020
a191413
modified meta_data classes
Hemant27031999 Jun 10, 2020
4ea5b3e
modified classes to look exactly like dictionaries and lists
Hemant27031999 Jun 11, 2020
7795ea6
modified imports and incorporated SBO term in metadata
Hemant27031999 Jun 11, 2020
02345bb
made the classed to inherit from MutableSequence and MutableMapping
Hemant27031999 Jun 13, 2020
4c6c1ca
adding backward compatibility
Hemant27031999 Jun 15, 2020
ff72c55
added instance
Hemant27031999 Jun 15, 2020
989ffe4
work on annotation structure
matthiaskoenig Jun 15, 2020
a4eb840
adding json example
matthiaskoenig Jun 15, 2020
cf38e02
fixed instance2
Hemant27031999 Jun 15, 2020
7d490a4
work on cvterms
matthiaskoenig Jun 15, 2020
024c980
made backward compatible
Hemant27031999 Jun 18, 2020
ff440fb
code review metadata
matthiaskoenig Jun 18, 2020
e4ad484
cleaned the metadata class by putting code in respective classes
Hemant27031999 Jun 21, 2020
2508ac3
new annotation format supported for SBML to cobra model
Hemant27031999 Jun 23, 2020
d5fc54c
added io for json and other formats
Hemant27031999 Jun 24, 2020
c9e904b
added tests for new annotation format
Hemant27031999 Jun 25, 2020
a6e2f8a
updated history
matthiaskoenig Jun 25, 2020
23f9699
fixing broken tests
Hemant27031999 Jun 28, 2020
2f55bbf
commented a few methods
Hemant27031999 Jun 28, 2020
5aae1b0
added equal method inisde metadata classes
Hemant27031999 Jun 29, 2020
d467a14
modified directories paths
Hemant27031999 Jun 30, 2020
e4cc72b
fixed imports and tox tests
Hemant27031999 Jun 30, 2020
32a81da
solved the problem of annotation copy
Hemant27031999 Jul 1, 2020
a07ccaf
new notes format
Hemant27031999 Jul 2, 2020
f69a55c
code refactoring
matthiaskoenig Jul 2, 2020
e4ab40b
modified history, keyvaluepair and notes
Hemant27031999 Jul 4, 2020
8dc96cf
modified tests and imports
Hemant27031999 Jul 5, 2020
a3685d4
modified cvterm class
Hemant27031999 Jul 6, 2020
991123b
small fixes
matthiaskoenig Jul 9, 2020
70b33db
refactored a few names
Hemant27031999 Jul 12, 2020
0e20a91
modified notes documentation
Hemant27031999 Jul 15, 2020
eeee56a
added user defined constraint class
Hemant27031999 Jul 16, 2020
f93723b
example test cases
matthiaskoenig Jul 16, 2020
efcf064
added tests for UserDefinedConstraints
Hemant27031999 Jul 23, 2020
3039344
modified tests
Hemant27031999 Jul 23, 2020
d5dedc9
small modifications
Hemant27031999 Jul 26, 2020
f839755
moved cobra directory to src directory
Hemant27031999 Jul 26, 2020
9704a4b
solved conflicts
Hemant27031999 Jul 26, 2020
211bf48
fixed some tests
Hemant27031999 Jul 26, 2020
1dba21e
fixed conflicts and tests
Hemant27031999 Jul 26, 2020
90c156f
fixed tests
Hemant27031999 Jul 27, 2020
91177cd
added support of group to JSON
Hemant27031999 Jul 27, 2020
1fc7ab2
added support for optional ids in UserDefinedConstraint class
Hemant27031999 Jul 28, 2020
de2398d
added test for json validation function
Hemant27031999 Jul 30, 2020
54809ad
added json schema import requirement
Hemant27031999 Jul 30, 2020
c758bc5
added helper function for UserDefinedConstraint
Hemant27031999 Jul 30, 2020
5c5e2c2
added validate function for json models
Hemant27031999 Jul 30, 2020
0884f4a
added ast tree for parsing constraint expression
Hemant27031999 Aug 5, 2020
0f93cdd
modified json validation function
Hemant27031999 Aug 6, 2020
3da58be
removed python 2 support
Hemant27031999 Aug 6, 2020
8ec5ef2
modified ids in json
Hemant27031999 Aug 6, 2020
d2d8ee9
code refactoring
matthiaskoenig Aug 6, 2020
14a68f5
reformatted code to python 3
Hemant27031999 Aug 9, 2020
80fdcaa
added datetime validation for py3.6
Hemant27031999 Aug 15, 2020
06cb989
modified dict.py
Hemant27031999 Aug 15, 2020
c10f3fa
modified xfail
Hemant27031999 Aug 15, 2020
1747a7b
removed .idea files
Hemant27031999 Aug 15, 2020
14a1415
removed .idea
Hemant27031999 Aug 15, 2020
ba2990c
merged with devel
Hemant27031999 Aug 16, 2020
b04b81a
removed idea
Hemant27031999 Aug 16, 2020
6bae4c0
modified notes string passing
Hemant27031999 Aug 21, 2020
66dd463
modified notes return type
Hemant27031999 Aug 26, 2020
479c2b2
adding dependency for json validation
matthiaskoenig Aug 26, 2020
543d1f8
added .idea files
matthiaskoenig Aug 26, 2020
65e48f1
merged latest devel
matthiaskoenig Aug 26, 2020
564a51a
refactored and cleanup of history
matthiaskoenig Aug 26, 2020
a6aefc5
Intermediate refactoring, breaking changes
matthiaskoenig Aug 26, 2020
42f4838
refactored keyvaluepairs
matthiaskoenig Aug 26, 2020
b3e26cc
cleanup of datetimes
matthiaskoenig Aug 26, 2020
ca9ef48
cleanup metadata
matthiaskoenig Aug 26, 2020
093f799
cleanup dict methods
matthiaskoenig Aug 26, 2020
b5f7516
added to_dict for CVTerm and fixed models
Hemant27031999 Aug 27, 2020
c8b850a
added metadata.ipynb
Hemant27031999 Aug 27, 2020
67d3af1
fixed imports
Hemant27031999 Aug 27, 2020
b951dbd
Merge branch 'devel' into metadata_fbc3_group
Hemant27031999 Aug 27, 2020
e5b3fba
smaller fix to_dict usage
matthiaskoenig Aug 27, 2020
8b2d6dc
modified to_dict for cvterms
Hemant27031999 Aug 28, 2020
010bb44
separated UserDefinedConstraint
Hemant27031999 Aug 28, 2020
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46 changes: 0 additions & 46 deletions .coveragerc

This file was deleted.

20 changes: 20 additions & 0 deletions .editorconfig
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# Editor Configuration (http://editorconfig.org)
root = true

[*]
charset = utf-8
indent_style = space
indent_size = 4
end_of_line = lf
insert_final_newline = true
trim_trailing_whitespace = true
max_line_length = 88

[*.{json,yml}]
indent_size = 2

[*.{md,rst}]
trim_trailing_whitespace = false

[Makefile]
indent_style = tab
139 changes: 139 additions & 0 deletions .github/CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, religion, or sexual identity
and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our
community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the
overall community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or
advances of any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email
address, without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.

## Scope

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at
[[email protected]](mailto:[email protected]).
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
reporter of any incident.

The current team handling Code of Conduct incidents consists of:

* [Maureen Carey](mailto:[email protected])
* [Svetlana Kutuzova](mailto:[email protected])
* [Greg Medlock](mailto:[email protected])

If your issue is with one or more of these members of the team, please do not write
to [email protected] but contact the remaining members individually.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series
of actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or
permanent ban.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within
the community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.0, available at
https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.

Community Impact Guidelines were inspired by [Mozilla's code of conduct
enforcement ladder](https://github.com/mozilla/diversity).

[homepage]: https://www.contributor-covenant.org

For answers to common questions about this code of conduct, see the FAQ at
https://www.contributor-covenant.org/faq. Translations are available at
https://www.contributor-covenant.org/translations.

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