Create a new scanner module and move functions from crawl module there

Summary

Refactoring of the crawler and scanner:

• I basically split the crawler into two parts:
  • Scanner module that walks through the file system and other structure elements and collects all the information into record types.
  • The crawler module (crawl.py) does everything else which needs a CaosDB interaction.

The main steps in refactoring were:

• Extraction of the functions related only to the scanning process.
• Slight renaming and consistency checks.
• Adapting all the tests to the new structure.

Left TODO:

• Fixing the integration tests

Focus

The best procedure for the review probably is to go through the individual commits. I tried to keep them as fine-grained as possible. Fixing the tests actually was very repetitive, because the API was changed slightly.

There is one thing that might be solved not completely ideal:

• Setting of the runid and the crawled_directory attributes. These are member variables that were previously set by functions now contained in the independent scanner module. This might need some cross-checking with @henrik who probably introduced these variables for logging.

Test Environment

Unittests

I did not run the integration tests manually, but this is probably done by the pipeline.

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CHANGELOG.md

@@ -26,6 +26,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - JSONFileConverter, YAMLFileConverter and MarkdownFileConverter now inherit from
   SimpleFileConverter. Behavior is unchanged, except that the MarkdownFileConverter now raises a
   ConverterValidationError when the YAML header cannot be read instead of silently not matching.
+- Refactoring of the crawl.py module: Now there is a separate scanner module handling the
+  collecting of information that is independent of CaosDB itself.
 
 ### Deprecated ###
 
@@ -44,7+46,7 @@
 ### Security ###
 
 ### Documentation ###
 
 ## [0.3.0] - 2022-01-30 ##
 (Florian Spreckelsen)