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Draft: remove all content for review (DO NOT MERGE!)

Open Draft: remove all content for review (DO NOT MERGE!)
review_milestone_2 into main
1 unresolved thread
Open Alex Kanitz requested to merge review_milestone_2 into main
1 unresolved thread

This branch and merge request is for reviewing your code and code structure. It is only for the purpose of reviewing and should never be merged! Note that any changes made to the repo by you after creation of this merge request are not considered for this review. Please also note that we will not review code style here (we will use automatic tools for that in a future session), but rather we will keep feedback high level at this point. Please address any issues raised (if you haven't already addressed them on your own in the meantime).

Next to the in-line and general code comments we will give during the review sessions (done by me and Mihaela), we keep track of the status of the more formal requirements (i.e., not the actual code) with respect to repository setup, packaging and documentation in the following checklist. Please complete any pieces that remain after the "List checked by reviewers" was set to "Yes" by us (indicating that we are done checking your repo against the checklist). To address these, please check the relevant notebooks and homeworks for more info.

List checked by reviewers

  • Yes
  • No

Version control

  • Repo configured correctly: repo public; default branch protected against pushes; fast-forward merges; encourage squash commits; delete source branch by default
  • License available in file LICENSE without any file extension
  • .gitignore available and includes common Python artifacts; no such artifacts (e.g., from building/packaging) are under version control
  • Files organized as expected, with at least one and not more than three directories, all in lower case; one directory containing all the tool/app code and named after the app (required), one directory tests containing all test-related content (required if tests or test files are available), and one directory named img or images, containing the screenshots from exercise 1 (fine if omitted or deleted at this point); all other files (LICENSE, README.md, .gitignore, setup.py, etc.) in repository root directory

Packaging

  • setup.py available
  • CLI executable available
  • CLI arguments available
  • Tool can be successfully installed with pip install .
  • CLI executable can be successfully executed with -h option

Documentation

  • README.md has at least a synopsis, usage and installation instructions and contact information (can use zavolab-biozentrum@unibas.ch if you don't want to put your own); other sections, as outlined in the course materials, welcome
  • Google-style docstrings available for all modules, classes, functions, methods
  • Type hints provided at least for all functions & methods
Edited by Hugo Madge Leon

Merge request reports

Approval is optional
Merge blocked: 3 checks failed
Merge request must not be draft.
Merge conflicts must be resolved.
Merge request must be rebased, because a fast-forward merge is not possible.

Merge details

  • The source branch is 47 commits behind the target branch.
  • 1 commit will be added to main.
  • Source branch will be deleted.

Activity

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  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
    Alex Kanitz @kanitz started a thread on the diff
    • frag_package/fragmentation_v2.py deleted 100644 → 0
    11 ident_pattern = re.compile('>(\S+)')
    12 seq_pattern = re.compile('^(\S+)$')
    13
    14 genes = {}
    15 for line in lines:
    16 if ident_pattern.search(line):
    17 seq_id = (ident_pattern.search(line)).group(1)
    18 elif seq_id in genes.keys():
    19 genes[seq_id] += (seq_pattern.search(line)).group(1)
    20 else:
    21 genes[seq_id] = (seq_pattern.search(line)).group(1)
    22 return genes
    23
    24 def fragmentation(fasta_file, counts_file, mean_length, std):
    25 fasta = fasta_process(fasta_file)
    26 seq_counts = pd.read_csv(counts_file, names = ["seqID", "count"])
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
  • Alex Kanitz
    Alex Kanitz @kanitz
    Author Owner

    Overall good work. Please address the algorithmic issues and also please provide a setup.py file and command-line tool so that we can easily run the tool :smile:

    @zavolan: can you please have a look at the two comments where I tagged you? On file frag_package/main.py

  • Alex Kanitz requested review from @zavolan

    requested review from @zavolan

  • Tanya Santosh Nandan assigned to @t.nandan

    assigned to @t.nandan

  • Tanya Santosh Nandan unassigned @t.nandan

    unassigned @t.nandan

  • Hugo Madge Leon marked the checklist item Files organized as expected, with at least one and not more than three directories, all in lower case; one directory containing all the tool/app code and named after the app (required), one directory tests containing all test-related content (required if tests or test files are available), and one directory named img or images, containing the screenshots from exercise 1 (fine if omitted or deleted at this point); all other files (LICENSE, README.md, .gitignore, setup.py, etc.) in repository root directory as completed

    marked the checklist item Files organized as expected, with at least one and not more than three directories, all in lower case; one directory containing all the tool/app code and named after the app (required), one directory tests containing all test-related content (required if tests or test files are available), and one directory named img or images, containing the screenshots from exercise 1 (fine if omitted or deleted at this point); all other files (LICENSE, README.md, .gitignore, setup.py, etc.) in repository root directory as completed

  • Hugo Madge Leon mentioned in issue #10 (closed)

    mentioned in issue #10 (closed)

  • Hugo Madge Leon marked the checklist item Repo configured correctly: repo public; default branch protected against pushes; fast-forward merges; encourage squash commits; delete source branch by default as completed

    marked the checklist item Repo configured correctly: repo public; default branch protected against pushes; fast-forward merges; encourage squash commits; delete source branch by default as completed

  • Hugo Madge Leon marked the checklist item Google-style docstrings available for all modules, classes, functions, methods as completed

    marked the checklist item Google-style docstrings available for all modules, classes, functions, methods as completed

  • Hugo Madge Leon marked the checklist item Type hints provided at least for all functions & methods as completed

    marked the checklist item Type hints provided at least for all functions & methods as completed

  • Hugo Madge Leon marked the checklist item CLI arguments available as completed

    marked the checklist item CLI arguments available as completed

  • Hugo Madge Leon marked the checklist item CLI executable available as completed

    marked the checklist item CLI executable available as completed

  • Hugo Madge Leon marked the checklist item Tool can be successfully installed with pip install . as completed

    marked the checklist item Tool can be successfully installed with pip install . as completed

  • Hugo Madge Leon marked the checklist item CLI executable can be successfully executed with -h option as completed

    marked the checklist item CLI executable can be successfully executed with -h option as completed

  • Hugo Madge Leon marked the checklist item README.md has at least a synopsis, usage and installation instructions and contact information (can use zavolab-biozentrum@unibas.ch if you don't want to put your own); other sections, as outlined in the course materials, welcome as completed

    marked the checklist item README.md has at least a synopsis, usage and installation instructions and contact information (can use zavolab-biozentrum@unibas.ch if you don't want to put your own); other sections, as outlined in the course materials, welcome as completed

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