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New release 0 3 8 #53

Merged
merged 193 commits into from
Feb 7, 2024
Merged

New release 0 3 8 #53

merged 193 commits into from
Feb 7, 2024

Commits on Aug 29, 2023

  1. Reposition examples example after returns

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  2. Expand example so that it builds up from scratch

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Commits on Aug 31, 2023

  1. Update documentation_test.yml 

    test build docs/archive to be able to see how dev version looks with doc changes
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  2. Update example to format code in doc

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  3. code format lines past 1 in docs

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Commits on Sep 1, 2023

  1. finish doc example for map functions. Consider combining into one fun… 

    …ction instead of 2/3 in the future.
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  2. Add link to demos within doc

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  3. Attempt to add references to pandas docs

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  4. connecting other docs worked well, add a bunch more

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  5. Started adding doc examples to location module

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Commits on Sep 6, 2023

  1. Finished adding doc examples where appropriate

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Commits on Sep 8, 2023

  1. Added examples to this module

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  2. minor doc edits

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  3. Started adding examples to basis - still need basis_from_methodSpec, … 

    …update_result _basis and basis_qa_flag.
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Commits on Sep 10, 2023

  1. Added doc examples

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  2. When basis is set df isn't being replaced by the result

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  3. Added doc examples for the functions that are fully implemented (not … 

    …check_precision(), methods_check(), wet_dry_checks(), or wet_dry_drop())
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  4. Drop from todo - datetime no longer pops old values in latest version… 

    … of dataretrieval. Generally trying to keep everything from original table.
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Commits on Sep 11, 2023

  1. Added examples for all domains functions (except accepted_methods as … 

    …that isn't fully imploemented yet)
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  2. Initial doc additions

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  3. Added examples for remaining functions. Note several had implementati… 

    …on problems preventing examples from being added (e.g.,) or from working as expected (e.g., DO concentration not fully implemented), mass_to_moles works for tests but throws a dimensionalityError)
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Commits on Sep 12, 2023

  1. Move docs up from init to class. Added example to df_checks()

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  2. Made several methods internal (these are only used within class)

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  3. Drop method char_val(), this helper function was only used once, had … 

    …the same name as a common var, and was easily replaced with two lines of code.
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  4. Added example to class

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  5. Update test.yml 

    Add docs branch to tests
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  6. Update calls to internal methods. Eliminated _unit_mask() since it wa… 

    …s only used in one place.
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  7. Merge branch 'add-doc-examples' of https://github.com/USEPA/harmonize-wq 

     into add-doc-examples
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  8. linter

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  9. Added check_units() example

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  10. unit_col was originally included to allow user to specify a different… 

    … unit column, but if they are they should assigned it on the object rather than every time they want to run methods on it. infer_units was made internal because it is currently only used in method check_units().
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  11. No reason to remove old basis from MethodSpecificationName

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  12. Fix doc typos

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  13. Added check_basis() examples

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  14. Move creation of basis column up (if it doesn't exist)

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  15. Added doc examples for four methods

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Commits on Sep 13, 2023

  1. Changed replace_in_col() from a function to an internal method.

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  2. Added examples to docs

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  3. Internal method def over indented

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  4. Gets df from self now

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  5. Complete example for replace_unit_by_str

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  6. BREAKING CHANGE: replace_unit_by_str() now replace_unit_str() so it i… 

    …s clearer that all instances of str within unit are replaced, whereas replace_unit_by_dict() replaces the entire unit one for one.
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  7. Compleated doc example for replace_unit_by_dict()

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  8. Complete exmaple for handle_dimensions() method

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  9. Move dimenions_handling from function to internal method, this allows… 

    … units to come from self (function was only used by handle_dimensions method).
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  10. No longer need to pass self.units (internal method now)

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  11. hndle_dimensions -> dimension_fixes, as this method returns lists to … 

    …help handle them but doesn't make changes directly
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  12. Example for moles_convert method

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  13. Add examples for convert_unit_series, add_qa_flag, and unit_qa_flag f… 

    …unctions.
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  14. unit_qa_flag -> _unit_qa_flag (4 ->2 args, and this is just an intern… 

    …al helper to construct a common flag)
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  15. Added example for units_dimension()

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  16. In doc examples, import just DataFrame from pandas (saves 7 char per … 

    …line and is more consistent)
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  17. Moved class into it's own module. This is a major structural change

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  18. Attempt to fix circular import

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Commits on Sep 14, 2023

  1. Added examples for main functions using tests data and added see also… 

    … for notebook demos
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  2. Merge from tests_builds to test full suite of win builds.

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  3. Refresh of demos from demo_refresh branch

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  4. From frac_dict_TADA branch: Added speciation conversion factors, thes… 

    …e are very close to moles based conversions (inverse?).
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  5. merge from frac_dict_TADA branch: Add functions to pull in harmonizat… 

    …ion table from TADA. Check against domain values for sample fraction to revert case.
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  6. merge from frac_dict_TADA branch: Working on implementing sample frac… 

    …tion updates from TADA table. Current implementation doesn't make any changes. Once changes are detected they need to be assigned QA flags. Better to switch order if possible.
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  7. Update test.yml 

    Run tests on combined branch for release
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  8. Resolve break from frac_dict_TADA

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  9. Merge branch 'new_release_0-3-8' of https://github.com/USEPA/harmoniz… 

    …e-wq into new_release_0-3-8
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  10. Merge pull request #44 from USEPA/main 

    Update requirements.txt
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  11. Reduced GOM demo to the one thats most manageable - where a user chos… 

    …es an estuarie from the list.
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  12. Re-ran all simple demos with most up to date data and branch code

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  13. Re-ran all detailed demos with latest data and branch code

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  14. Merge branch 'new_release_0-3-8' of https://github.com/USEPA/harmoniz… 

    …e-wq into new_release_0-3-8
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  15. Add new module to api index

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  16. Use coerce name for python types to link to python docs (e.g., str no… 

    …t 'string')
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  17. Add '.' for attributes (numpy PEP484)

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  18. Reduce class desc to one line

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  19. Do test docs build on push to this branch

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  20. Add sphinxcontrib-spelling as part of docs build (not yet deploy). Te… 

    …sting locally.
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  21. Somehow missed these unwritten doc strings

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  22. if there isn't a _static dir leave it blank to avoid warning.

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  23. Fix rst errors

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  24. fix rst errors

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  25. Attempt to resolve some doc test warnings

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  26. docs had trouble interpreting as python3

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  27. Make title for page indexing

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  28. Fix :: vs : issues (and some pandas imports I missed)

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  29. identify as line of code or Q_ will confuse docs

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  30. line of code, sorry sphinx

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  31. Simplify pint Q_ type so it'll link to their class doc

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Commits on Sep 15, 2023

  1. Attempt to resolve doctest errors (mostly missing imports)

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  2. Round two of trying to resolve doctest errors

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  3. Fixed <BLANKLINE> results

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  4. doctests (should resolve some of the 43/329)

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Commits on Sep 28, 2023

  1. Update docstrings based on pydocstyle.

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  2. Spelling in rst files.

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  3. First round of spellings to ignore.

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  4. First round of dostring spelling updates.

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Commits on Sep 29, 2023

  1. Second round of spelling corrections

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  2. Finished with spelling corrections for now, most of these were actual… 

    …ly formating/syntax. Worked out that references to other package docs have to be special character quotes (` not ')
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Commits on Sep 30, 2023

  1. Internal docs review1 (R. Ennis)

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  2. Internal docs review1 (R. Ennis). Additional comments: When the docum… 

    …ent was knit, you used to get a warning indicating the YAML title and the vignette title were different. I changed it them to match and there is no warning. Might be better to leave the title as just the package name since you have a description of what the package does, how to install, etc and not just the Pensacola Bay specific example.
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  3. Fromatting to fix doc warnings/errors from last commit

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  4. Resolve new doc warnings/spelling that resulted from review fixes.

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Commits on Jan 17, 2024

  1. Create test_r 

    init commit for tests r demo
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  2. Update and rename test_r to test_r.yaml 

    First attempt to add R install to existing test
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  3. Update test_r.yaml 

    Run manually
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  4. Update test_r.yaml 

    Trigger on push
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  5. Update test_r.yaml 

    Test running it
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  6. Update test_r.yaml 

    try using shell to run as R
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  7. Update test_r.yaml 

    Dedent shell
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  8. Update test_r.yaml 

    lib isn't loaded, reference where import is
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Commits on Jan 26, 2024

  1. Init Commit JOSS paper

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Commits on Jan 29, 2024

  1. Got DO conversions w/ non-standard pressure/temperature functional an… 

    …d passing tests.
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  2. Updates to docs to get doctests passing (the easy fixes)

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Commits on Jan 30, 2024

  1. Update documentation_test.yml 

    Try building doctest as part of doc build test
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  2. Update documentation_test.yml 

    Be specific about python version
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  3. CI doctest and local readout don't always match (...). Changing this … 

    …to pass CI, this is also what IDE shows.
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  4. Updates to doc results shown

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  5. 'PSU' has to be defined locally for the demo and internally in the mo… 

    …dule for the wrapper.
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  6. SPU_to_density() result as str. NTU -> 'Nephelometric_Turbidity_Units'

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  7. Quantity for context needs to be defined by multiplier not string. (q… 

    …1 = 1 * ureg('g'), not q2 = pint.Quantity('1 g'), even though q1==q2)
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  8. Hoping the missing emptyline was at fault

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  9. Try with expected error

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  10. Compleated moles_convert() example.

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  11. Sort added columns to ensure consistent order. Not sure how to do tha… 

    …t for column sorder in table, may need to reduce example read in
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  12. Change ureg name in dict

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  13. whitespace

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  14. line in example needed to be run (>>>)

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  15. ignore spacing

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  16. Needed to skip a line...

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Commits on Jan 31, 2024

  1. Reduce detects being collected (suspect query errors w/ so many resul… 

    …ting in inconsistent result)
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  2. Need to show expected result (also illustrates the point when rows in… 

    …creases)
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  3. Try adding notebooks using nbsphinx

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  4. Confirmed it is 100 not 101 columns

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  5. Move notebooks to make it easier for the docs index to find them

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  6. Update documentation_test.yml 

    Try installing pandoc as a step...
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  7. Update documentation_test.yml 

    Try without with...
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Commits on Feb 1, 2024

  1. Update documentation_test.yml 

    Trying to get pandoc installed
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  2. Add caption (heading) for nb tutorials

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  3. try r-lib workflow

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  4. Fix typo in index

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  5. formatting to try to get tutorial section

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  6. Try adding link/reference to nb outside docs

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  7. Skip doctest while working on build/conf

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  8. Add nbsphinx_link

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  9. Notebook name needs to be consistent throughout

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  10. Move notebooks folder to within docs/source

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  11. Update heading to use in docs TOC

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  12. Try two in nblink json?

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  13. Adding all the example notebooks

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  14. Moved Tampa demos back to demos dir

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  15. Update headings

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  16. Fixed notebooks linked in json files

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  17. Fix heading size to get TOC right

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Commits on Feb 2, 2024

  1. Try moving install section into index

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  2. Continue to rearrange getting started to index

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  3. Pull farther down from rst

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  4. Remove missing from toc (otherwise it doesn't populate any)

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  5. Fix rst whitespace

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  6. Move notebooks to their own rst

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  7. Landing page edits

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  8. Move text

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  9. Self reference?

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  10. Move notebooks back into index

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  11. Edit TOC

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  12. whitespace

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  13. Drop header

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  14. Add requirements dev version

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  15. two packages (typo)

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  16. Merge pull request #48 from USEPA/main 

    Update to main
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  17. Merge pull request #49 from USEPA/reticulate_demo_test 

    Reticulate demo test
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  18. Switching to f strings

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  19. Update when tests run

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  20. Drop bacteria_reg (not being used anywhere and doesn't really do anyt… 

    …hing...)
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  21. Support py3.8-3.11

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Commits on Feb 5, 2024

  1. pylint

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  2. harmonize_generic() -> harmonize()

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  3. Updated fraction() to simplify it (only need to run on present sample… 

    … fractions), implemented getting it from tada, default to running it on nitrogen that way.
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  4. Fix up docs for Fraction

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  5. get consistent result order (see #51)

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  6. Fix minor change/typo in docs

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  7. set() doesn't maintain char_vals order, added sort to keep it consist… 

    …ent (see #51)
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  8. update doc example expected result

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  9. fix typo

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Commits on Feb 6, 2024

  1. Add tests to increase viz coverage

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  2. Add backward test

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  3. Re-run to update inputs

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  4. Update - run 2/6/2024 results

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  5. run update results 2/6/2024

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  6. run update results 2/6/2024

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  7. run update results 2/6/2024

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Commits on Feb 7, 2024

  1. Refresh data results 2/6/2024

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  2. Refresh data results 2/6/2024

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  3. shp -> geojson

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  4. Update version for new release

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  5. Update data results for 2/6/2024

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  6. Update branches to run on

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