Merge v0.1.20

[vinisalazar]

v0.1.20

• Debug graphical DOT output [x]
• Add Muscle PresetProgram [x]
• Add MAFFT PresetProgram [x]
• Add Kallisto PresetProgram [x]
• Add extra_flags attribute to PresetProgram [x]
• Refactor EnvProv class as Environment [x]
• Allow creation of users and envs to be optional [x]
• Create environments only when there's an associated activity [x]
• Create Sample dunder enter and dunder exit methods [x]
• Fixing wasDerivedFrom bug when sample and file have same names [x]
• Fix extra Environments bug [x]