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JDFTx IO module #4078

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JDFTx IO module #4078

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Commits on Sep 19, 2024

  1. copy-paste of existing work done on atomate2 fork

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  2. Calling it a night, logging changes (all pre-commit edits)

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Commits on Sep 20, 2024

  1. Explicitly defining class properties from downstream class objects on… 

    … top of __getattr__ magic method so it is more clear to the user what variables are accessible from a jdftxoutfile object (and other downstream class objects)
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  2. Removing unused content

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  3. Undoing partial move of utility function to utils - this needs to be … 

    …done 100% to work properly without circular imports, but the size of this repo causes refactor symbol movement to take literally minutes, so keeping the structure like so for now
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Commits on Sep 23, 2024

  1. (Likely) last commit before pull request, mostly bug fixes in infile … 

    …stuff + JDFTXInfile item setting safety nets, additional testing for infile, and more informative README
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  2. Update README.MD 

    Problems on readme line breaks

Signed-off-by: benrich37 <[email protected]>
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  3. Update README.MD 

    Problems on README

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  4. Update README.MD 

    Problems on README

Signed-off-by: benrich37 <[email protected]>
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  5. Update README.MD 

    Problems on README

Signed-off-by: benrich37 <[email protected]>
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  6. Update README.MD 

    Signed-off-by: benrich37 <[email protected]>
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  7. Update README.MD 

    Signed-off-by: benrich37 <[email protected]>
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  8. Update README.MD 

    Updated README for JDFTX io branch

Signed-off-by: benrich37 <[email protected]>
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  9. Moving example files to designated pymatgen example file directory, r… 

    …emoving empty test modules
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  10. Merge branch 'master' of https://github.com/benrich37/pymatgen

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  11. Removed hurtful comments towards pre-commit

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  12. Authorship for major modules + pre-commit edits on README

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  13. Authorship

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Commits on Sep 24, 2024

  1. coverage data

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  2. Create main.yml for codecov workflow 

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  3. updated gitignore

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  4. Merge branch 'master' of https://github.com/benrich37/pymatgen

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  5. Updated .gitignore

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  6. add codecov workflow

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  7. Update codecov.yml 

    Added pyproject.toml to workflow dependencies

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  8. removed old main yaml

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  9. Merge branch 'master' of https://github.com/benrich37/pymatgen

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  10. updating gitignore

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  11. unwanted files

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  12. Expanding test coverage + correct some return type annotations

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  13. Notes and function fix

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  14. Changing which should be None or not, correct incorrect return types … 

    …and allowing some variables to remain None
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  15. Changing which should be None or not, correct incorrect return types … 

    …and allowing some variables to remain None
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  16. Changing which should be None or not, correct incorrect return types … 

    …and allowing some variables to remain None
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  17. Updating for greater coverage - currently 88%

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  18. Removing accidentally added workflow

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  19. pre-commit auto-fixes

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Commits on Sep 25, 2024

  1. Expanding coverage for generic_tags

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  2. Expanding coverage for generic_tags

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  3. Expanding coverage for jdftxoutfileslice

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  4. Wrong error raise approach

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  5. Expanding coverage for generic_tags and commenting out unused/unreach… 

    …able code
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  6. Merge pull request #1 from benrich37/input_cov 

    Input cov
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  7. Merge branch 'materialsproject:master' into master

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  8. Additional coverage along with changes I cannot keep track of - in re… 

    …trospect I think defining __setitem__ explicitly was a misstep and should've been a public set_tag method, but changing it breaks a lot of tests so that is now a whole task. I think enough new code has been written here that my coverage may actually drop
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  9. replacing read/write methods of multiformattag with dummy error-raisi… 

    …ng methods since they are never reached by the current code design.
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  10. new coverage

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  11. Adding fix for incorrect site label initialization of JDFTXInfile

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  12. Merge pull request #2 from benrich37/input_cov 

    Minor tweaks
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Commits on Sep 26, 2024

  1. Forgot to make eigstats optional!

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  2. Thank you @Soge for identifying lack of eigstats should not break cal… 

    …culation
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  3. Thank you @Soge for identifying lack of eigstats should not break cal… 

    …culation
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  4. File added to make new_files dir exist

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  5. Merge pull request #3 from benrich37/new_files_dir 

    One-line change - added file to occupy new_files directory in the io files for jdftx
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  6. Merge remote-tracking branch 'origin' into input_cov

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  7. get_Start_lines error handling test

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  8. removed empty case scenario for find_first_range_key that didn't seem… 

    … to match intended purpose
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  9. tests for find_first_range_key

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  10. Removing unreachable warning

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  11. joutstructures_start_idx test and no-find case fix

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  12. Moving all utility functions to the utils module

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  13. Moving all utility functions to the utils module

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  14. Moving all utility functions to the utils module

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  15. Moving all utility functions and classes to the utils module

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  16. Moved all utility functions and classes to the utils module.

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  17. Moving util tests to test_utils

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Commits on Sep 27, 2024

  1. Removing unused helper modules

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Commits on Sep 28, 2024

  1. Reducing clutter for code review

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  2. Reducing clutter

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  3. Removing TODO from README

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Commits on Sep 29, 2024

  1. Reorganization of testing + starting the broader "JDFTxOutput" class

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  2. Merge branch 'materialsproject:master' into master

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  3. Merge remote-tracking branch 'origin' into input_cov

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  4. Generalizing the 1/2 layer AttributeError to a pytest fixture

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  5. de-clutter

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  6. Commenting out new content before master merge

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  7. Merge pull request #4 from benrich37/input_cov 

    Organization merge
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Commits on Oct 1, 2024

  1. Adding jdftx out file typos to codespell ignore words list

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  2. Merge remote-tracking branch 'origin' into input_cov

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  3. Merge pull request #5 from benrich37/input_cov 

    Adding codespell exceptions to pyproject.toml
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Commits on Oct 2, 2024

  1. Merge branch 'materialsproject:master' into master

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  2. Moving module information into __init__.py

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  3. Addressing redundancy of contents of "data.py" to data you can refere… 

    …nce from the Element class. Improving clarity in module docustrings for JEiter
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  4. Removing valence electron dictionary

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  5. Removing commented out method

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  6. Merge pull request #6 from benrich37/review_edits 

    Review edits
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Commits on Oct 3, 2024

  1. Adding edit to the "valence" property as described in review comment … 

    …+ update to existing code so that pre-commit will let me commit
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  2. Merge branch 'materialsproject:master' into period_table_edits

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  3. Merge remote-tracking branch 'origin' into period_table_edits

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  4. Merge branch 'period_table_edits' of https://github.com/benrich37/pym… 

    …atgen into period_table_edits
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  5. Merge branch 'materialsproject:master' into master

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Commits on Oct 4, 2024

  1. Merge branch 'materialsproject:master' into master

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  2. Adding imports to jdftx module's __init__ so I can start using this p… 

    …ymatgen fork as a dependency (anticipating the class objects not being kept in individual submodules for very long)
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  3. Merge pull request #7 from benrich37/flexible_imports 

    Adding imports to jdftx module's __init__ so I can start using this p…
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Commits on Oct 14, 2024

  1. Merge branch 'materialsproject:master' into master

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Commits on Oct 21, 2024

  1. Merge branch 'master' into master

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  2. Merge branch 'materialsproject:master' into master

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Commits on Oct 22, 2024

  1. Merge branch 'materialsproject:master' into master

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  2. Merge remote-tracking branch 'origin' into period_table_edits

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  3. Replacing "get_Atom_valence_electrons" function with newly added "Val… 

    …ences" method in pmg Element class
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  4. Merge pull request #8 from benrich37/period_table_edits 

    Periodic table edits
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  5. Changing naming of JEiter(s) to JElStep(s), adding dataclass inheritance

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  6. removing unused file

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  7. Merge pull request #9 from benrich37/jeiters_rename 

    Jeiters rename
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Commits on Oct 23, 2024

  1. Fix for Species class's valence(s) property

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  2. Merge pull request #10 from benrich37/period_table_edits 

    Fix for Species class's valence(s) property
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  3. Merge branch 'materialsproject:master' into master

    @benrich37
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  4. Changing JMinSettings class to just have a "params" variable to avoid… 

    … conflict with unexpected minimization keywords
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  5. Fix for __getattr__ on jdftxoutfileslice not being able to access pro… 

    …perties
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  6. Merge pull request #11 from benrich37/period_table_edits 

    JDFTXOutfileSlice __getattr__ fix
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  7. Adding testing of out file that previously threw an error

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  8. Merge pull request #12 from benrich37/period_table_edits 

    JMinSettings edge case fix
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Commits on Oct 24, 2024

  1. Merge branch 'materialsproject:master' into master

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Commits on Oct 25, 2024

  1. Merge branch 'materialsproject:master' into master

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Commits on Oct 28, 2024

  1. Merge branch 'materialsproject:master' into master

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Commits on Oct 30, 2024

  1. Merge branch 'materialsproject:master' into master

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Commits on Oct 31, 2024

  1. Adding more informative docustrings for JDFTXOutfile and low-priority… 

    … todo's
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  2. Merge pull request #13 from benrich37/docustrings 

    Adding more informative docustrings for JDFTXOutfile and low-priority…
    @benrich37
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  3. Removing commented out code 

    Co-authored-by: Matthew Horton <[email protected]>
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  4. Removing commented out code

    @benrich37
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  5. Removing unused test files in wrong directory

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  6. removing commented out code, clarifying language

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  7. Merge pull request #14 from benrich37/liveshare 

    Liveshare edits
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  8. test to assert that joustructure's can be created and store data inde… 

    …pendently
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  9. outfile for Etot etype and testing instance var behavior for JOutStru… 

    …cture
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  10. Merge pull request #15 from benrich37/classvar_fix 

    etype fix
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Commits on Nov 1, 2024

  1. Changing naming convention of step number (previously "niter") to "ns… 

    …tep" to avoid confusing with an iterable object
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  2. Changing naming convention of step number (previously "niter") to "ns… 

    …tep" to avoid confusing with an iterable object
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  3. Backing up changes - need to make a deep change on how JOutStructure … 

    …is constructed
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  4. Merge pull request #16 from benrich37/classvar_fix 

    Changes backup
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  5. Letting more values be None

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  6. Letting more values be None

    @benrich37
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  7. removing commented out code block

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  8. Disabling block of pseudopotentials not of GBRV or SG15 (relevant dat… 

    …a will just be left as None) + redoing rename of niter to nstep (why was this reverted?)
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Commits on Nov 2, 2024

  1. Debugging new behavior and untested old behavior

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  2. Merge branch 'master' into relax_req_vars 

    Signed-off-by: benrich37 <[email protected]>
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  3. Merge pull request #17 from benrich37/relax_req_vars 

    Relax req vars
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  4. pre-commit auto-fixes

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  5. removing commented out code, renaming "iter_type" to "step_type"

    @benrich37
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  6. should be lower-case e

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  7. remove completed todo

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  8. Filling in missing information in docustrings

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Commits on Nov 4, 2024

  1. Adding language to docustrings to provide context to attributes

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  2. Completing incomplete refactoring (renaming backup variables to be pr… 

    …ivate) + removing commented out code
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  3. removing commented out code

    @benrich37
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  4. Moving "get_pseudo_read_section_bounds" utility function to jdftxoutf… 

    …ileslice as its only foreseeable utility is in its initializing a jdftxoutfileslice object
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  5. Moving "is_<logtype>_start_line" utility functions to joutstructure a… 

    …s its only foreseeable utility is in its initializing a joutstructure object. "is_lowdin_start_line" not included due to usage in other class initializations. Moving "get_joutstructures_start_idx" and "get_joutstructure_step_bounds" to joutructures module.
    @benrich37
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  6. Removing "data" module as it is no longer used

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Commits on Nov 5, 2024

  1. Making changes to stringify/repr behavior for IO module objects to ca… 

    …ll pprint and to extend repr to incorporate properties for JDFTXOutfileSlice (but not for deeper objects). This behavior is far from good, but is at least better than it was. This can be fixed later once the usage for stringify is more clear
    @benrich37
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  2. Moving JDFTXInfile and JDFTXOutfile to inputs and outputs module, res… 

    …pectively
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  3. Removing commented out testing

    @benrich37
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  4. Updated module docustring

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  5. Modified docustrings

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  6. Merge pull request #18 from benrich37/cleanup 

    Cleanup
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  7. Removing unused modules and commented out code. Adding options for fl… 

    …uid kinetic functionals
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Commits on Nov 6, 2024

  1. Modifying comments, removing empty "sets" module for now

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  2. Tagging @mkhorton in files ready to be reviewed

    @benrich37
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  3. Removing empty jdftxoutput module

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  4. Tagging @mkhorton on files ready to review + adding context to some d… 

    …ocustrings
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  5. Tagging @mkhorton on files ready to review

    @benrich37
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  6. Merge pull request #19 from benrich37/cleanup 

    Cleanup
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Commits on Nov 11, 2024

  1. Adding an explicit pytest module for testing built-in representation … 

    …functions on IO module objects (currently only tests to make sure the built-in functions don't raise errors)
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  2. Removing overwrite of "dir" for JDFTXOutfile

    @benrich37
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  3. Removing commented out testing

    @benrich37
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  4. Merge pull request #20 from benrich37/cleanup 

    Cleanup
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Commits on Nov 12, 2024

  1. Merge branch 'materialsproject:master' into master

    @benrich37
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Commits on Nov 13, 2024

  1. First type check syntax fix for linux workstation

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  2. Second type check syntax fix for linux workstation

    @benrich37
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  3. Third type check syntax fix for linux workstation

    @benrich37
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  4. Removing commented out code

    @benrich37
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  5. Merge pull request #21 from benrich37/cleanup 

    Not currently understood pre-commit bug fix
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  6. Merge branch 'materialsproject:master' into master

    @benrich37
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  7. Moving project .gitignore exceptions added for files generated by cod… 

    …ecov to personal .gitignore
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  8. Merge pull request #22 from benrich37/cleanup 

    Moving project .gitignore exceptions added for files generated by cod…
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  9. Adding problem out file which does not inherit initial lattice correc… 

    …tly and test to satisify
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  10. Merge branch 'materialsproject:master' into master

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Commits on Nov 14, 2024

  1. Adding problem out file which does not inherit initial lattice correc… 

    …tly and test to satisify
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  2. Merge pull request #23 from benrich37/cleanup 

    Cleanup
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  3. Added "initial_structure" keyword arguments to allow for default Stru… 

    …cture metadata to be passed to subsequent JOutStructure objects when intializing a JOutStructures object
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  4. Merge pull request #24 from benrich37/jstruc_init 

    Added "initial_structure" keyword arguments to allow for default Stru…
    @benrich37
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  5. Moving question from comment to discussion post

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  6. Merge pull request #25 from benrich37/jstruc_init 

    Moving question from comment to discussion post
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