Improve user interface #117
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vedran-kasalica
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Hi @eladrion, this is the PR I was talking about, please feel free to leave any comments or questions. Thanks! |
src/main/java/nl/uu/cs/ape/models/sltlxStruc/SLTLxVariable.java
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src/main/java/nl/uu/cs/ape/models/templateFormulas/SLTLxTemplateFormula.java
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Hi @vedran-kasalica , I took a brief look on the PR, see my comments above. Best, Mario |
Thank you Mario, I had a quick look and you left quite detailed and relevant comments! I will come back to them later this week |
…used repo was renamed
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The writer is instantiated in this method, appendToFile (base case) and appendToFile (CNFClause case) identically. Just an idea: If you implement a function which opens the file (if it exists and excepts otherwise) and writes a list of strings in append mode to the file, you could reuse that function and restrict the current functions to checking whether the encoding/content is non-null. Also, the current functions would have to provide a list of strings to the new function.
This PR refactors parts of the codebase, improving the
bio.toolsAPI, which is now exposed at the CLI level. Users can generate APE annotations directly frombio.tools. Additionally, it introduces two new constraint templates that proved useful in generating workflows within the Workflomics project. Finally, I simplified the GitHub templates to lower the threshold for creating PRs and Issues.Key updates:
bio.toolsAPIbio.toolsAPI at the CLI levelOn a technical side, the constraint templates are explicitly encoded in CNF, unlike parsed SLTLx formulas. The plan is to start using logical constructs when defining the templates as well, but I didn't get a chance to do that yet. For the reference, the logical constructs were introduced with v2.0.