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Parquet_integration #122

Merged
merged 153 commits into from
Sep 17, 2020
Merged

Parquet_integration #122

merged 153 commits into from
Sep 17, 2020

Commits on Dec 16, 2019

  1. [WIP] Integrated Parquet Engine Option, started with test modifications

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Commits on Jan 2, 2020

  1. Included Parquet-Writer in ingest.py : In this version, the writer is… 

    … opened and closed only once per compartment, in the higher-level function seed(). ToDo: 1. Write lower-level second version, 2. Design and run tests.
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Commits on Jan 3, 2020

  1. Added 'database_engine' section to the config files, incl. tests.

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Commits on Jan 6, 2020

  1. Added Parquet Option to config files. Corrected argument list of into().

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  2. Fixed SyntaxError: positional argument follows keyword argument

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  3. debuggig: removed comments from config.ini, removed splitext() when r… 

    …eading out of config file (in seed() from ingest.py)
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  4. debugged: changed argument list of getWriter()

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Commits on Jan 7, 2020

  1. corrected 4 bugs: 1)completed argument list when calling getWriters()… 

    …. 2) Corrected writer path using .join() in getWriters(). 3) Corrected construction of the local variable TablePaths, with which getWriters is called. It is now a string list, not a list of lists. 4)Capitalization of the string value of the name variable, i.e. images is now capitalized when called as name, which was the default case for the compartments.
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Commits on Jan 16, 2020

  1. Started integration of schema-checking

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Commits on Jan 18, 2020

  1. -

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Commits on Jan 22, 2020

  1. Added sampling and conversion functions

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  2. Merge pull request #1 from diskontinuum/convert_schemata 

    Convert schemata
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Commits on Feb 8, 2020

  1. Does not contain changes from colab notebook.

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Commits on Feb 10, 2020

  1. Added original ingest.py and deleted old partial code. All new code i… 

    …s in ingest_parquet.py.
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  2. fixed imports and naming bugs

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  3. Added option to ignore object.csv

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Commits on Feb 11, 2020

  1. renamed WIP folder

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Commits on Feb 14, 2020

  1. deleted deprecated ingest.py. The new version is named ingest_parquet… 

    ….py, the original file is named ingest_old.px
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Commits on Feb 19, 2020

  1. removed additional test folder, updated test_ingest.py, renamed inges… 

    …t.py-versions
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  2. updated install requirement 'pyarrow' in setup.py

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Commits on Feb 24, 2020

  1. added 'pyarrow>=0.16.1' to requirements.txt

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  2. removed pyarrow from install_requires in setup.py

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  3. comma

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  4. quotation marks

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  5. reduced requirements pyarrow>=0.16.1 to pyarrow>=0.16.0

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  6. added numpy to requirements.txt

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  7. renaming of ingest files to check if tests work on original files in … 

    …this branch
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  8. Added original test_ingest.py code

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  9. changed function argument name in munge.py. Reading the config file (… 

    …by calling utils.read_config(filename) was moved s.t. the path is passed, not the loaded file.
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  10. new separate folders for new layout of config file (cytominer_databas… 

    …e/config_incl_parquet), deleted new entries in original config files folder (cytominer_database/config), commented on the config loading function pkg_resources.resource_filename() .
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Commits on Feb 27, 2020

  1. changed config_file arguments to config_path for function calls of cy… 

    …tominer_database.munge.munge in all testing functions. Now all old tests run with ORIGINAL ingest.py code. Next step: take modified testing files and pass them on ingest_parquet.py
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  2. added new options to the default config.ini. Old tests pass.

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  3. modified the local config.ini files in all test folders. All original… 

    … tests pass.
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Commits on Feb 28, 2020

  1. Changed entries in config.ini files to default value 'sample' and sta… 

    …rted debugging.
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Commits on Apr 28, 2020

  1. Refatored. ToDo: Finish original tests, add new tests, clean up and d… 

    …ocument.
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  2. Original tests pass with given config files. ToDo: Test with differen… 

    …t config files (SQLite option, different sample ratio, fixed schema). Clean up and document. Add new tests.
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  3. deleted test duplicates

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  4. Added a documentation for the configuration file config.ini to rhe re… 

    …adme.
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  5. updated readme.

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  6. updated readme.

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  7. updated readme.

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  8. updated readme.

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  9. updated readme.

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  10. updated readme.

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  11. updated readme.

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  12. updated readme.

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  13. updated readme.

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  14. updated readme.

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  15. updated readme.

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  16. updated readme.

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  17. updated readme.

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  18. updated readme.

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  19. updated readme.

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  20. updated readme.

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Commits on May 4, 2020

  1. Merged load_df(). Debugged. Passes all tests. ToDo: Further unificati… 

    …on, get rid of debugging code and print statements.
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Commits on May 5, 2020

  1. Massive refactoring and clean-up. Merged engine-options. Tests pass.

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Commits on May 7, 2020

  1. Added docstrings. Deleted old comments.

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  2. Further code cleanse

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Commits on May 8, 2020

  1. added crucial assertions to write.py. ToDo: build pytest analogon.

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  2. removed unnecessary assignments in main script

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  3. added one missing assignment

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  4. Update README.rst

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  5. Update README.rst

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  6. Updated documentation in main script

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  7. Merge branch 'colab_updates' of github.com:diskontinuum/cytominer-dat… 

    …abase into colab_updates
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  8. Finalized docstring comments in main script, including general explan… 

    …ations of the methodology used in the new Parquet option.
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Commits on May 18, 2020

  1. change all type-converting functions (definitions and calls) to not r… 

    …eturn the dataframe, but to modify the actual object, as passedby reference as function arguments. Started to refactor open_writers() in tableSchema.py.
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Commits on May 19, 2020

  1. merging the tableSchema functions

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Commits on May 26, 2020

  1. simplified and unified the generation of reference files dictionary

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  2. removed redundant list unpacking

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Commits on May 27, 2020

  1. More expclicit name retrieval

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  2. Tests pass : corrected string capitalization error

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  3. Update cytominer_database/ingest_incl_parquet.py 

    redundant import

Co-authored-by: Greg Way <[email protected]>
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  4. Update README.rst 

    Co-authored-by: Greg Way <[email protected]>
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  5. Update cytominer_database/load.py 

    Co-authored-by: Greg Way <[email protected]>
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  6. comments removed from read_config()

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  7. Merge branch 'colab_updates' of github.com:diskontinuum/cytominer-dat… 

    …abase into colab_updates
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  8. various PR suggestions

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  9. renamed get_table_paths_from_directory_list() to directory_list_to_pa… 

    …th_dictionary()
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  10. renamed get_unique_reference_dirs() to get_path_dictionary

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  11. renamed return arguments ref_dirs and ref_dir to sampled_path_diction… 

    …ary and path_dictionary respectively
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Commits on May 31, 2020

  1. Update cytominer_database/config/config_cellpainting.ini 

    Co-authored-by: Greg Way <[email protected]>
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  2. Changed default sampling fractions from 1 to 0.3 in the config files.

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  3. Update cytominer_database/config/config_htqc.ini 

    Co-authored-by: Greg Way <[email protected]>
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  4. Update cytominer_database/ingest.py 

    Co-authored-by: Greg Way <[email protected]>
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  5. Update cytominer_database/ingest.py 

    Co-authored-by: Greg Way <[email protected]>
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  6. deleted old code

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  7. deleted space

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  8. removed docstring prose

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  9. isolated warning-block

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  10. isolated warning-block

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  11. warning box .rst

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  12. Added .html version of README.rst. Warning box is displayed correctly.

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  13. strong emphasis instead of warning box

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  14. added .vscode json files to .gitignore

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Commits on Jun 24, 2020

  1. Update .gitignore 

    Co-authored-by: Greg Way <[email protected]>
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  2. vscode cleanup

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  3. Update README.rst 

    Co-authored-by: Greg Way <[email protected]>
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  4. Update cytominer_database/config/config_default.ini 

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  5. Update cytominer_database/ingest.py 

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  6. Update cytominer_database/write.py 

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Commits on Jul 1, 2020

  1. Update cytominer_database/ingest.py 

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  2. rm unused imports

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  3. smaller import: os -> os.path

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  4. decreased or removed os imports

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  5. narrowed remaining os imports where possible

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  6. Update cytominer_database/ingest.py 

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  7. removed comments

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  8. Merge branch 'colab_updates' of github.com:diskontinuum/cytominer-dat… 

    …abase into colab_updates
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  9. Removed unnecessary comments

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  10. Added raise ValueError to type_conver_dataframe(), for the case in wh… 

    …ich the config.ini file does not contain the correct entry
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  11. Moved and renamed constant list of column names that should not be co… 

    …nverted
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  12. Added UserWarning in case no values were converted

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  13. missing bracket error

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  14. Added further ValueErrors and UserWarnings (in case of conversion err… 

    …ors or missing conversions).
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  15. ran BLACK formatting tool over all files

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  16. removed python 2

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  17. replaced tricky list comprehension

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  18. replaced the f-string with .format()

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  19. removed print()-statements

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  20. removed remaining print()-statements from chaotic tableSchema.py

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  21. f-strings for the original ingest()

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  22. fixed prefixing of column labels in both ingest() and load() (no list… 

    … comprehension)
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  23. Update README.rst 

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  24. Update README.rst 

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  25. Update README.rst 

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  26. Update README.rst 

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  27. Update README.rst 

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  28. Update README.rst 

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  29. Update README.rst 

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Commits on Jul 2, 2020

  1. bracket

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  2. Merge branch 'colab_updates' of github.com:diskontinuum/cytominer-dat… 

    …abase into colab_updates
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Commits on Jul 24, 2020

  1. added author 'Frances Hubis' and updated year

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  2. added author 'Frances Hubis' and git link to CONTRIBUTORS.md

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  3. renamed module ingest_incl_parquet.py to ingest_parquet.py . Changed … 

    …imports and tests accordingly.
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  4. added a 'parquet' flag option

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  5. removed old-named ingest_incl_parquet.py

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  6. changed command structure. Now the flag '--parquet' will trigger the … 

    …parquet backend. The default (no flag) is SQLite.
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  7. updated README.md to contain the click command instruction for the 'p… 

    …arquet' option.
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  8. removed deprecated filename

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Commits on Jul 26, 2020

  1. removed 'parquet' flag - command tests pass again

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  2. included new command flag '--variable_engine/--no-variable_engine' in… 

    … a separate, new command module and included all corresponding tests for the command (including default, explicit sqlite and explicit parquet) on all test data. All tests pass.
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  3. renamed new code version 'ingest_parquet.py'/'test_ingest_parquet.py'… 

    … to'ingest_variable_engine.py'/'test_ingest_variable_engine.py'
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  4. prettified code with black

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Commits on Jul 28, 2020

  1. reversed accidental erasure

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  2. reversed ordering

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  3. -

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  4. Merge branch 'master' into colab_updates

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Commits on Jul 29, 2020

  1. Update CONTRIBUTORS.md 

    Co-authored-by: Greg Way <[email protected]>
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  2. Update cytominer_database/commands/command_ingest_variable_engine.py 

    Co-authored-by: Greg Way <[email protected]>
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  3. Added Hubis to copyright list and ran black again.

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  4. Addressed incomplete doctring in ingest.seed()

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Commits on Sep 17, 2020

  1. Update cytominer_database/ingest.py

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