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Merge v0.1.19 #36

Merged
merged 29 commits into from Nov 10, 2020
Merged

Merge v0.1.19 #36

merged 29 commits into from Nov 10, 2020

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vinisalazar
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v0.1.19

  • Debug API endpoint (Add support for ProvStore API #23) [x]
  • Implement logging [x]
    • Implement Workflow logging [x]
  • Debug Workflow Steps [x]
  • Remove workflow main methods [x]
    • Workflows must now be called only from the CLI [x]
  • Implement post-workflow actions [x]
    • Update db [x]
    • Upload to ProvStore [x]
    • Write PROVN [x]
    • Write PDF [x]
  • Add Sample.auto_update_db() methods [x]
  • Remove logger call when updating Project in database [x]

jvfe and others added 29 commits November 8, 2020 16:59
@jvfe
Fix issues in the blast presets
869158c 
Fixes some dumb mistakes introduced in my last PR due to me not looking
very carefully. Docstring now says the right thing and removes a
duplicated test.
@vinisalazar
Merge pull request #35 from jvfe/minor_blast_fixes
3c347b9 
Fix issues in the blast presets
@vinisalazar
Bump version number
eb15591
@vinisalazar
Update CHANGELOG.md
e098976
@vinisalazar
Fix API endpoint bug
ce12dbe
@vinisalazar
Improving coverage statements
d07e8a4
@vinisalazar
Optimize imports
2187606
@vinisalazar
Update CHANGELOG.md
1b63b9b
@vinisalazar
Refactoring print statements to logging
f217e5d
@vinisalazar
Log from both stdout and file
385176d
@vinisalazar
Add default logger to utils (create_logger() function) and src.config…
fb08b5a 
… module
@vinisalazar
Refactor log statements to use the default logger
b2506b4
@vinisalazar
Refactoring workflows
bbc4581
@vinisalazar
Remove parser_help() call when KeyError during workflow
8407752
@vinisalazar
Modify PresetProgram add_param and run behaviour
8f1de55
@vinisalazar
Improving Workflow.run_steps() behaviour
86ca436
@vinisalazar
Update CHANGELOG
d8f87fe
@vinisalazar
Remove Workflow main methods. Must call workflows only from the CLI.
214ac4e
@vinisalazar
Improve default logger handlers
3e3f950
@vinisalazar
Return Run instance on run method
36f8fc0
@vinisalazar
Remove Workflow main method
aafa52c
@vinisalazar
Modify pytest.raises call to accept new CLI behaviour
12c9f3b
@vinisalazar
Improve docstring
7d01a0d
@vinisalazar
Add log files to .gitignore
d955912
@vinisalazar
Move logger logic to main module. Add auto_update_db methods to Sample.
6f6b2a9
@vinisalazar
Debug upload_to_provstore methods. Improve tests.
0b44d14
@vinisalazar
Fix Sample.to_series() method
2c33f6b
@vinisalazar
Add log tests to workflow test module.
0bdaf96
@vinisalazar
Add try/except block in BioProvDocument._iter_samples to prevent erro…
111c0db 
…rs when initiating Projects with no Samples
@vinisalazar vinisalazar merged commit bf4fca7 into master Nov 10, 2020
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@vinisalazar @jvfe