vinisalazar / BioProv / 88

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Merge v0.1.12 (#18)

### v0.1.12
* Patching errors for JSON IO [x]
    * Create File, Program, Run deserializers [x]
* Implement path replacing methods for multi-user support [x]

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* Encapsulate BioProvDocument constructor actions into functions.

* Bump version number

* Add serializer_filter options to remove keys from serializer out

* Reformatting with Black after update

* Fixing Program.found error by adding another check to Program._getoutput()

* Adding envs on Project JSON reader

* Creating instance of EnvProv on Project JSON reader

* Added error handling for SeqFile loading

* Improve pretty printing of commands

* Improve Env constructor in Project deserializer

* Update CHANGELOG

* Bump version number

* Clearing notebook state

* Refactoring hashes with hashlib.
    - Added utils.dict_to_sha1() function
    - Removed EnvProv.env_set attribute
    - Refactored tests

* Remove unused import

* Add file_to_sha1() function

* Add sha1 attribute to File class

* Improve EnvProv JSON deserializer

* Refactor tests. Testing BioProvDocument with add_attributes=True

* Update CHANGELOG

* Improve pretty printing of commands.

* Improve default parameters of bioprov.programs.prodigal PresetProgram

* Update introduction tutorial

* Add serializer_filter method to File class

* Improve EnvProv namespace constructor

* Update introduction tutorial

* Update changelog

* Bump version number

* Add assertion to PresetProgram tests

Now tests use assertions based on the flags of the serialized program,
instead of only testing if the class can be initiated.

* Update changelog

* Fix test_Run datetime problem. Tests are more stable

* Update changelog

* Add env attribute to Run. Improve command printing

* Attribute Runs to Environments and Environments with users

* Fix test warning for literal comparison

* Improve Namespace organization for provn output

* Impr... (continued)

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