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CliCon #1

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Commits on Aug 1, 2014

  1. minor edits to README

    Willie Boag committed Aug 1, 2014
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  2. Minor edits in install.sh

    Willie Boag committed Aug 1, 2014
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  3. Minor edits in install.sh

    Willie Boag committed Aug 1, 2014
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  4. Added pip install for nose

    Willie Boag committed Aug 1, 2014
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  5. Added pip install for nose

    Willie Boag committed Aug 1, 2014
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  6. Forgot to mention install.sh must be run with 'source', not 'bash'

    Willie Boag committed Aug 1, 2014
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  7. Forgot to mention install.sh must be run with 'source', not 'bash'

    Willie Boag committed Aug 1, 2014
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  8. typo in README

    Willie Boag committed Aug 1, 2014
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  9. typo in README

    Willie Boag committed Aug 1, 2014
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Commits on Aug 5, 2014

  1. adjust model.py to use crfsuite's SWIG wrapper

    Willie Boag committed Aug 5, 2014
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  2. adjust model.py to use crfsuite's SWIG wrapper

    Willie Boag committed Aug 5, 2014
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  3. Merge branch 'master' into machine-learning 

    Conflicts:
	clicon/model.py
    Willie Boag committed Aug 5, 2014
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  4. Merge branch 'master' into machine-learning 

    Conflicts:
	clicon/model.py
    Willie Boag committed Aug 5, 2014
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  5. get rid of self.type

    Willie Boag committed Aug 5, 2014
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  6. get rid of self.type

    Willie Boag committed Aug 5, 2014
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Commits on Aug 10, 2014

  1. Fold CRF back using python-crfsuite (with model file workaround)

    Willie Boag committed Aug 10, 2014
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  2. Fold CRF back using python-crfsuite (with model file workaround)

    Willie Boag committed Aug 10, 2014
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  3. Add CRF installation to install.sh

    Willie Boag committed Aug 10, 2014
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  4. Add CRF installation to install.sh

    Willie Boag committed Aug 10, 2014
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  5. modify install.sh to use machine-learning branch (until merged back t… 

    …o master)
    Willie Boag committed Aug 10, 2014
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  6. modify install.sh to use machine-learning branch (until merged back t… 

    …o master)
    Willie Boag committed Aug 10, 2014
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Commits on Aug 12, 2014

  1. Update README.rst

    @arumshisky
    arumshisky committed Aug 12, 2014
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  2. Update README.rst

    @arumshisky
    arumshisky committed Aug 12, 2014
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  3. Set crf to use default parameters

    Willie Boag committed Aug 12, 2014
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  4. Set crf to use default parameters

    Willie Boag committed Aug 12, 2014
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Commits on Aug 13, 2014

  1. Added sanity checks for first pass predictions

    Willie Boag committed Aug 13, 2014
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  2. Added sanity checks for first pass predictions

    Willie Boag committed Aug 13, 2014
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  3. Modified install script so it doesn't git clone the project

    Willie Boag committed Aug 13, 2014
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  4. Modified install script so it doesn't git clone the project

    Willie Boag committed Aug 13, 2014
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Commits on Aug 16, 2014

  1. Merge branch 'command-line-interface' of https://github.com/mitmedg/C… 

    …liCon
    @kwaco
    kwaco committed Aug 16, 2014
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  2. Merge branch 'command-line-interface' of https://github.com/mitmedg/C… 

    …liCon
    @kwaco
    kwaco committed Aug 16, 2014
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  3. merging scripting and cli

    @kwaco
    kwaco committed Aug 16, 2014
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  4. merging scripting and cli

    @kwaco
    kwaco committed Aug 16, 2014
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  5. Reorganized features_dir module

    Willie Boag committed Aug 16, 2014
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  6. Reorganized features_dir module

    Willie Boag committed Aug 16, 2014
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  7. Changed features/ to features_dir/

    Willie Boag committed Aug 16, 2014
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  8. Changed features/ to features_dir/

    Willie Boag committed Aug 16, 2014
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  9. Extend returned values (for easier testing of first pass results)

    Willie Boag committed Aug 16, 2014
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  10. Extend returned values (for easier testing of first pass results)

    Willie Boag committed Aug 16, 2014
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  11. Extend for first pass development

    Willie Boag committed Aug 16, 2014
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  12. Extend for first pass development

    Willie Boag committed Aug 16, 2014
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  13. Added crf back into first pass

    Willie Boag committed Aug 16, 2014
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  14. Added crf back into first pass

    Willie Boag committed Aug 16, 2014
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  15. Merging machine-learning branch

    Willie Boag committed Aug 16, 2014
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  16. Merging machine-learning branch

    Willie Boag committed Aug 16, 2014
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  17. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Aug 16, 2014
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  18. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Aug 16, 2014
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Commits on Aug 21, 2014

  1. Added a few examples to readme

    Willie Boag committed Aug 21, 2014
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  2. Added a few examples to readme

    Willie Boag committed Aug 21, 2014
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  3. updating readme with examples

    Willie Boag committed Aug 21, 2014
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  4. updating readme with examples

    Willie Boag committed Aug 21, 2014
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  5. Add usage examples to readme & extend support for xml format

    Willie Boag committed Aug 21, 2014
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  6. Add usage examples to readme & extend support for xml format

    Willie Boag committed Aug 21, 2014
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  7. Update README.rst

    @wboag
    wboag committed Aug 21, 2014
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  8. Update README.rst

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    wboag committed Aug 21, 2014
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  9. Update README.rst

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    arumshisky committed Aug 21, 2014
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  10. Update README.rst

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  11. Update README.rst

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  12. Update README.rst

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  13. Update README.rst

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  14. Update README.rst

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    arumshisky committed Aug 21, 2014
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  15. Update README.rst

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    arumshisky committed Aug 21, 2014
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  16. Update README.rst

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  17. Update README.rst

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  18. Update README.rst

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  19. Update README.rst

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  20. Update README.rst

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  21. Update README.rst

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  22. Update README.rst

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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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  30. Update README.rst

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  31. Update README.rst

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  32. Update README.rst

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  33. Update README.rst

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  34. Update README.rst

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  35. Update README.rst

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  36. Update README.rst

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  37. Update README.rst

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  38. Update README.rst

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  39. Update README.rst

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  40. Update README.rst

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  41. Update README.rst

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  42. Update README.rst

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  43. Update README.rst

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  44. Update README.rst

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  45. Update README.rst

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  46. Update README.rst

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  47. Update README.rst

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  48. Update README.rst

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  49. Update README.rst

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  50. Update README.rst

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Commits on Aug 22, 2014

  1. Added CLICON_DIR stuff and package check into install.sh

    Willie Boag committed Aug 22, 2014
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  2. Added CLICON_DIR stuff and package check into install.sh

    Willie Boag committed Aug 22, 2014
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  3. Update README.rst

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  4. Update README.rst

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  5. Update README.rst

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  6. Update README.rst

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Commits on Aug 26, 2014

  1. Add cli flag to enabled/disable CRF (default is enable)

    Willie Boag committed Aug 26, 2014
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  2. Add cli flag to enabled/disable CRF (default is enable)

    Willie Boag committed Aug 26, 2014
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  3. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Aug 26, 2014
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  4. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Aug 26, 2014
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  5. Update README.rst

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  6. Update README.rst

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  7. Update README.rst

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  8. Update README.rst

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Commits on Aug 27, 2014

  1. Modified install.sh to skip compilation of existing libraries

    Willie Boag committed Aug 27, 2014
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  2. Modified install.sh to skip compilation of existing libraries

    Willie Boag committed Aug 27, 2014
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  3. Update README.rst

    Willie Boag committed Aug 27, 2014
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  4. Update README.rst

    Willie Boag committed Aug 27, 2014
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  5. merge readme

    Willie Boag committed Aug 27, 2014
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  6. merge readme

    Willie Boag committed Aug 27, 2014
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  7. Add demo script of usage example for running system

    Willie Boag committed Aug 27, 2014
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  8. Add demo script of usage example for running system

    Willie Boag committed Aug 27, 2014
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  9. replace depricated ImmutableSet with frozenset

    Willie Boag committed Aug 27, 2014
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  10. replace depricated ImmutableSet with frozenset

    Willie Boag committed Aug 27, 2014
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  11. Replace depricated ImmutableSet with frozenset

    Willie Boag committed Aug 27, 2014
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  12. Replace depricated ImmutableSet with frozenset

    Willie Boag committed Aug 27, 2014
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  13. Update README.rst

    @wboag
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  14. Update README.rst

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  15. Update README.rst

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  16. Update README.rst

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Commits on Aug 29, 2014

  1. Removing broken badge images from README.rst.

    @tnaumann
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  2. Removing broken badge images from README.rst.

    @tnaumann
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  3. Adding Apache license. 

    Closes #1.
    @tnaumann
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  4. Adding Apache license. 

    Closes #1.
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  5. Updating development team. 

    Closes #5.
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  6. Updating development team. 

    Closes #5.
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  7. Removing features section from README.rst 

    Closes #4.
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  8. Removing features section from README.rst 

    Closes #4.
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Commits on Aug 30, 2014

  1. Create COPYRIGHT file 

    Closes #1.
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  2. Create COPYRIGHT file 

    Closes #1.
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  3. Updating OSX dependencies. 

    Closes #2
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  4. Updating OSX dependencies. 

    Closes #2
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  5. Removing cookiecutter installation/usage. 

    Since both sections are documented in the README.rst, this led to
redundancies in the document generation. Closes #7.
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  6. Removing cookiecutter installation/usage. 

    Since both sections are documented in the README.rst, this led to
redundancies in the document generation. Closes #7.
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  7. Update README.rst

    @arumshisky
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  8. Update README.rst

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  9. Update README to have include proper license. 

    Existing template stated BSD, changed to Apache v2.0 license.
    @tnaumann
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  10. Update README to have include proper license. 

    Existing template stated BSD, changed to Apache v2.0 license.
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Commits on Aug 31, 2014

  1. Update README.rst

    @wboag
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  2. Update README.rst

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Commits on Sep 1, 2014

  1. i2b2 eval update

    @kwaco
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  2. i2b2 eval update

    @kwaco
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  3. user friendly installation messages and log

    Willie Boag committed Sep 1, 2014
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  4. user friendly installation messages and log

    Willie Boag committed Sep 1, 2014
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  5. Safe guard against duplicate entries in concept file

    Willie Boag committed Sep 1, 2014
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  6. Safe guard against duplicate entries in concept file

    Willie Boag committed Sep 1, 2014
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  7. cache genia features

    Willie Boag committed Sep 1, 2014
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  8. cache genia features

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  9. Merge branch 'master' of https://github.com/mitmedg/CliCon 

    Conflicts:
	clicon/evaluate.py
    Willie Boag committed Sep 1, 2014
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  10. Merge branch 'master' of https://github.com/mitmedg/CliCon 

    Conflicts:
	clicon/evaluate.py
    Willie Boag committed Sep 1, 2014
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  11. update install.sh

    Willie Boag committed Sep 1, 2014
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  12. update install.sh

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Commits on Sep 2, 2014

  1. update install.sh

    Willie Boag committed Sep 2, 2014
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  2. update install.sh

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  3. update install.sh

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  4. update install.sh

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  5. update install.sh

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  6. update install.sh

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  7. Update install.sh

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  8. Update install.sh

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  9. update install.sh

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  10. update install.sh

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  11. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Sep 2, 2014
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  12. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Sep 2, 2014
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  13. Update install.sh

    @wboag
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  14. Update install.sh

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  15. Update install.sh

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  16. Update install.sh

    @wboag
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  17. add genia cache

    Willie Boag committed Sep 2, 2014
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  18. add genia cache

    Willie Boag committed Sep 2, 2014
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  19. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Sep 2, 2014
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  20. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Sep 2, 2014
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  21. go back to new eval script

    Willie Boag committed Sep 2, 2014
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  22. go back to new eval script

    Willie Boag committed Sep 2, 2014
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  23. Escape command inside string

    @wboag
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  24. Escape command inside string

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Commits on Sep 3, 2014

  1. Strip non-printable characters from text

    Willie Boag committed Sep 3, 2014
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  2. Strip non-printable characters from text

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  3. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Sep 3, 2014
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  4. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Sep 3, 2014
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Commits on Sep 24, 2014

  1. Update SQLookup.py

    Kevin Wacome committed Sep 24, 2014
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  2. Update SQLookup.py

    Kevin Wacome committed Sep 24, 2014
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Commits on Oct 6, 2014

  1. Update demos & calls using clicon script

    Willie Boag committed Oct 6, 2014
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  2. Update demos & calls using clicon script

    Willie Boag committed Oct 6, 2014
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  3. move all data format logic into Note and add author descriptions

    Willie Boag committed Oct 6, 2014
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  4. move all data format logic into Note and add author descriptions

    Willie Boag committed Oct 6, 2014
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  5. Add trie for UMLS lookups (not fully done yet)

    Willie Boag committed Oct 6, 2014
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  6. Add trie for UMLS lookups (not fully done yet)

    Willie Boag committed Oct 6, 2014
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  7. Bugfixes in features directory

    Willie Boag committed Oct 6, 2014
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  8. Bugfixes in features directory

    Willie Boag committed Oct 6, 2014
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  9. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Oct 6, 2014
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  10. Merge branch 'master' of https://github.com/mitmedg/CliCon

    Willie Boag committed Oct 6, 2014
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  11. Add support for semeval reader

    Willie Boag committed Oct 6, 2014
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  12. Add support for semeval reader

    Willie Boag committed Oct 6, 2014
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Commits on Oct 8, 2014

  1. Update note.py

    Kevin Wacome committed Oct 8, 2014
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  2. Update note.py

    Kevin Wacome committed Oct 8, 2014
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Commits on Oct 22, 2014

  1. semeval reader

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  2. semeval reader

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Commits on Oct 28, 2014

  1. A little work for UMLS trie stuff

    @wboag
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  2. A little work for UMLS trie stuff

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Commits on Nov 4, 2014

  1. Merge branch 'master' into character_offsets 

    Conflicts:
	clicon/note.py
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  2. Merge branch 'master' into character_offsets 

    Conflicts:
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Commits on Nov 5, 2014

  1. Update README.rst

    @arumshisky
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  2. Update README.rst

    @arumshisky
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  3. Update README.rst

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  4. Update README.rst

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  5. Update README.rst

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  6. Update README.rst

    @arumshisky
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  7. Update README.rst

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  8. Update README.rst

    @arumshisky
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  9. fixed off-by-one error in writer

    @wboag
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  10. fixed off-by-one error in writer

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  11. Merge branch 'master' of https://github.com/mitmedg/CliCon

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  12. Merge branch 'master' of https://github.com/mitmedg/CliCon

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Commits on Nov 6, 2014

  1. reorganized structure to localize all machine learning code

    @wboag
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  2. reorganized structure to localize all machine learning code

    @wboag
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  3. removing statistics.py

    @wboag
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  4. removing statistics.py

    @wboag
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  5. removing runall.py

    @wboag
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  6. removing runall.py

    @wboag
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  7. removing libml.py

    @wboag
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  8. removing libml.py

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Commits on Nov 10, 2014

  1. Restructured notes representation for extendability

    @wboag
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  2. Restructured notes representation for extendability

    @wboag
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Commits on Nov 11, 2014

  1. rearranging features_dir organization for consistency

    @wboag
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  2. rearranging features_dir organization for consistency

    @wboag
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  3. fixed index error in note_i2b2

    @wboag
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  4. fixed index error in note_i2b2

    @wboag
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  5. renamed SQLookup to interface_umls

    @wboag
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  6. renamed SQLookup to interface_umls

    @wboag
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  7. renamed umls to interpret_umls

    @wboag
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  8. renamed umls to interpret_umls

    @wboag
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  9. Fixed should-never-get-here bug to work even if reached

    @wboag
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  10. Fixed should-never-get-here bug to work even if reached

    @wboag
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  11. Added getText selector to notes

    @wboag
    wboag committed Nov 11, 2014
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  12. Added getText selector to notes

    @wboag
    wboag committed Nov 11, 2014
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Commits on Nov 13, 2014

  1. Repair write methods for notes

    @wboag
    wboag committed Nov 13, 2014
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  2. Repair write methods for notes

    @wboag
    wboag committed Nov 13, 2014
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  3. took out some files

    @wboag
    wboag committed Nov 13, 2014
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Commits on Nov 18, 2014

  1. Merge branch 'master' of https://github.com/mitmedg/CliCon

    @wboag
    wboag committed Nov 18, 2014
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Commits on Jan 28, 2015

  1. fixed issue with note in master

    @kwaco
    kwaco committed Jan 28, 2015
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Commits on Feb 28, 2015

  1. Replacing project with relocation notice. 

    - Removing all project files.
- Adding README which will display relocation notice.
    @tnaumann
    tnaumann committed Feb 28, 2015
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  2. Replacing project with relocation notice. 

    - Removing all project files.
- Adding README which will display relocation notice.
    @tnaumann
    tnaumann committed Feb 28, 2015
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