…s example config file for testing interactive tiebreaker with sequential multi-seat enabled; adds commented command in build.gradle for executing CLI arguments.

More cert fixes

# Conflicts:
#	src/main/java/network/brightspots/rcv/TabulatorSession.java

add residual surplus to overall summary JSON

add a test for the generatePermutation tie-breaking option

…dom tie-break option

# Conflicts:
#	src/main/java/network/brightspots/rcv/Main.java
#	src/test/resources/network/brightspots/rcv/test_data/2013_minneapolis_mayor/2013_minneapolis_mayor_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2013_minneapolis_mayor_scale/2013_minneapolis_mayor_scale_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2013_minneapolis_park/2013_minneapolis_park_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2013_minneapolis_park_bottoms_up/2013_minneapolis_park_bottoms_up_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2013_minneapolis_park_hare/2013_minneapolis_park_hare_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2013_minneapolis_park_sequential/2013_minneapolis_park_sequential_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2015_portland_mayor/2015_portland_mayor_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2015_portland_mayor_codes/2015_portland_mayor_codes_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2017_minneapolis_mayor/2017_minneapolis_mayor_config.json
#	src/test/resources/network/brightspots/rcv/test_data/2018_maine_governor_primary/2018_maine_governor_primary_config.json
#	src/test/resources/network/brightspots/rcv/test_data/continue_tabulation_test/continue_tabulation_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/duplicate_test/duplicate_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/excluded_test/excluded_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/minimum_threshold_test/minimum_threshold_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/minneapolis_multi_seat_threshold/minneapolis_multi_seat_threshold_config.json
#	src/test/resources/network/brightspots/rcv/test_data/missing_precinct_example/missing_precinct_example_config.json
#	src/test/resources/network/brightspots/rcv/test_data/precinct_example/precinct_example_config.json
#	src/test/resources/network/brightspots/rcv/test_data/sample_interactive_tiebreak/sample_interactive_tiebreak_config.json
#	src/test/resources/network/brightspots/rcv/test_data/sample_interactive_tiebreak/sample_interactive_tiebreak_sequential_config.json
#	src/test/resources/network/brightspots/rcv/test_data/skip_to_next_test/skip_to_next_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_0_skipped_first_choice/test_set_0_skipped_first_choice_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_1_exhaust_at_overvote/test_set_1_exhaust_at_overvote_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_2_overvote_skip_to_next/test_set_2_overvote_skip_to_next_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_3_skipped_choice_exhaust/test_set_3_skipped_choice_exhaust_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_4_skipped_choice_next/test_set_4_skipped_choice_next_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_5_two_skipped_choice_exhaust/test_set_5_two_skipped_choice_exhaust_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_6_duplicate_exhaust/test_set_6_duplicate_exhaust_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_7_duplicate_skip_to_next/test_set_7_duplicate_skip_to_next_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_allow_only_one_winner_per_round/test_set_allow_only_one_winner_per_round_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_multi_winner_fractional_threshold/test_set_multi_winner_fractional_threshold_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_multi_winner_whole_threshold/test_set_multi_winner_whole_threshold_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_treat_blank_as_undeclared_write_in/test_set_treat_blank_as_undeclared_write_in_config.json
#	src/test/resources/network/brightspots/rcv/test_data/tiebreak_generate_permutation_test/tiebreak_generate_permutation_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/tiebreak_previous_round_counts_then_random_test/tiebreak_previous_round_counts_then_random_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/tiebreak_seed_test/tiebreak_seed_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/tiebreak_use_permutation_in_config_test/tiebreak_use_permutation_in_config_test_config.json

* test for Dominion csv conversion routine #415

* 2 more tests for cvr conversion

* updates for Dominion conversion tests: PR #425

* fix for PR #425

Co-authored-by: jonmoldover <jonmoldover@gmail.com>

…rsion updates (fixes #426). (#435)

* Dominion conversion output files now output to same directory as input files and include timestamp in filename (#408).

* Updates Dominion tests to account for new filename schema; Dominion test files are now cleaned up automatically; fixes bug with fileCompare not closing readers.

* All delete operations in `TabulatorTests` now handle exceptions with useful error messages if they fail.

* read and write precinct portion + precinct

* edits for precinct portion PR#433

* Update src/main/java/network/brightspots/rcv/DominionCvrReader.java

Co-Authored-By: HEdingfield <HEdingfield@users.noreply.github.com>

* Update src/main/java/network/brightspots/rcv/DominionCvrReader.java

Co-Authored-By: HEdingfield <HEdingfield@users.noreply.github.com>

Co-authored-by: HEdingfield <HEdingfield@users.noreply.github.com>

* add UWI test files

* add an additional test to validate my fix of #397

* use a better name for the first test

…andidatesRemain (#441)

* make batch elimination work properly with singleSeatContinueUntilTwoCandidatesRemain

* cleaned up wording

### New features:
* Added support for converting Dominion JSON CVRs to generic .csv format (including precinct portions) (#404, #406, #407, #408, #415, #439)
* Added multiSeatBottomsUpPercentageThreshold option (#403)
* Added CLI option to convert Dominion CVR to generic .csv (#408)
* New GUI menu and conversion options (can now convert to CDF and convert Dominion to generic via the GUI) (#408, #421)
* Added Dominion Alaska CVR to sample_input folder

### Bug fixes:
* Batch elimination now works properly with singleSeatContinueUntilTwoCandidatesRemain (#396)
* In a multi-seat contest, if someone wins in the first round, we now automatically eliminate undeclared write-ins before we eliminate any other candidates; previously, we treated UWIs like a normal candidate, which meant we potentially eliminated other candidates with lower tallies first (#397)
* If UWI exceeds the winning threshold in the initial count, we no longer mistakenly elect this candidate (#398)

### Backend updates:
* Updated dependencies to latest version: JDK, JavaFX, Checkstyle google_checks.xml, Checkstyle plugin, org.openjfx.javafxplugin, org.beryx.jlink, org.apache.commons:commons-csv, org.apache.poi:poi-ooxml, com.fasterxml.jackson.core:jackson-*
* Added special code to test configs to obviate the need to update the version with each increment (#426)
* Updated tests and improved test coverage
* Copyright update (#414)
* Code cleanup

* add contest id to config

* add xml parsing module

* First cut at Hart CVR reader + test assets.

* cleanup paths and add expected results

* add full cvr data

* refactor contestId from Integer to String

* add school board test

* fix xml parsing

* logging

* re-add accidentally removed import

* cleanup for PR#548

* updates for PR #458

* updates for PR #458

* test other file reading options

* more cleanup for PR #458

* more cleanup for PR #458

* Fixes tests not working in Windows due to mangled UTF-8 BOM marker.

* Handles potential NPE if chosen directory contains no files.

Co-authored-by: HEdingfield <hylton@groupagree.com>

* Updates to latest version:
    * Gradle 6.5.1
    * JDK 14.0.1
    * JavaFX 14.0.1
    * Checkstyle google_checks.xml 8.34
    * Checkstyle plugin 8.34
    * org.openjfx.javafxplugin 0.0.9
    * org.beryx.jlink 2.20.0
    * com.fasterxml.jackson.core:jackson-* 2.11.1
    * org.junit.jupiter.junit-jupiter-* 5.6.2
* Gets tests working with Gradle 6.5.1 (fixes #283)
* Updates `APP_VERSION` to temporary value 1.2.0_alpha
* Addresses Checkstyle warnings
* Fixes versions in Hart tests

* make contestId a real config field

* update .txt

* Changes "Provider" field for CVR source to be required, bases it on an enum of valid values, and changes it to a ChoiceBox at the start of the "CVR Files" tab in the GUI  (progress on #460 and #461).
* Adds log message to help identify which CVR source validation errors pertain to.
* Gets rid of `SimpleObjectProperty` warnings during compile (fixes #280).

* Provider ComboBox now dynamically enables and disables fields and buttons when different providers are selected. (Progress on #461... actually progress on GUI phase 2!)
* Enables `DirectoryChooser` for Hart so it now functions through the GUI. (Fixes #460)
* Validation improved to fail if `firstVoteColumnIndex`, `firstVoteRowIndex`, `idColumnIndex`, `precinctColumnIndex` are defined for CVRs from non-ES&S providers.
* Removes superfluous logging.

* direct Dominion tabulation

* enable specifying a Dominion CVR source path in the UI

* output generic CSV and add test coverage

* remove extra log line

* filter out CVRs from other contests during the loading

…#474)

* First cut at Clear Ballot rcv reader
Add Kansas Dem Primary regression test
Add Clear Ballot reference files
#400

* updates for PR #475

* updates for PR #475

* updates for PR #475

* Splits Output tab into new Contest Info and Output tabs.
* Redesigns GUI CVR Files tab, adds Clear button, and changes Add button so it only clears the file path to make it easier to manually enter multiple sources that share fields.
* Improves visual presentation of Candidate tab; adds Clear button and adds checkBoxCandidateExcluded when adding a candidate.
* Reorganizes presentation of rules in "Winning Rules" and "Voter Error Rules" tabs.
* Winner Election Mode and Tiebreak Mode now start undefined with all relevant fields disabled; choosing specific modes enables applicable fields.
* Changes Winner Election Modes and Tiebreak Modes to be more user-friendly, including necessary migration logic to update older config files.
* Adds `continueUntilTwoCandidatesRemain` boolean (fixes #481).
* Expands footprint of GUI window to 1200x1000.
* Implements bordered boxes.

* update test files

* remove conversion feature from code

* update test configs

* remove unnecessary check

* test

* update winner election mode logic

* comments

* final comments

* plumbing for xml cdf reading

* add contestId to json and xml CDF parse logic
update unisyn cvr test to use the full (but still incorrect) cvr data.  This test is expected to fail.
add candidate parsing code to xml CDF parser

* dont parse Candidate data from CDF at runtime - this enforces the same constraints on validation as all other file types.  The un-used candidate parsing code is left in for implementing future helper functions which will automatically populate config files.

* Handle ContestSelections in XML correctly

* add NIST example 2 (seems to be correctly formed)

* fill out CDF XML class definitions needed for tabulation

* add some helpers

* cleanup pre-processing code

* add more class fields around contest selections
fix ranking parsing
add example Unisyn contests

* handle write-ins

* get first 2 Unisyn regression tests working :)

* fix first NIST CDF XML test

* cleanup test names

* parse GpUnit from CVRs

* remove un-used assets

* updates for PR #504

* updated data from Unisyn with GpUnit (precinct) parsing validated

* add more Unisyn regression tests
tests share a single cvr input file

* tabulate all elections - in practice we should not see more than one

* updates for PR #504

* updates for PR #504

* Converts `overvoteRule` from a `ChoiceBox` to an array of `RadioButton`s; changes `overvoteRule` string display in config files and adds migration logic.
* Disables `decimalPlacesForVoteArithmetic` and `nonIntegerWinningThreshold` except when `winnerElectionMode` is "Multi-winner allow only one winner per round" or "Multi-winner allow multiple winners per round" (fixes #500).
* Adds suggested values for `overvoteLabel`, `undervoteLabel`, and ES&S column and row indices as requested by @chughes297 (overriding what was in the original GUI mock-ups).
* Clarifies language to address confusing UX in `passesBasicCvrSourceValidation()` for CVR-specific errors.

* plumbing for xml cdf reading

* add contestId to json and xml CDF parse logic
update unisyn cvr test to use the full (but still incorrect) cvr data.  This test is expected to fail.
add candidate parsing code to xml CDF parser

* dont parse Candidate data from CDF at runtime - this enforces the same constraints on validation as all other file types.  The un-used candidate parsing code is left in for implementing future helper functions which will automatically populate config files.

* Handle ContestSelections in XML correctly

* add NIST example 2 (seems to be correctly formed)

* fill out CDF XML class definitions needed for tabulation

* add some helpers

* cleanup pre-processing code

* add more class fields around contest selections
fix ranking parsing
add example Unisyn contests

* handle write-ins

* get first 2 Unisyn regression tests working :)

* fix first NIST CDF XML test

* cleanup test names

* parse GpUnit from CVRs

* remove un-used assets

* updates for PR #504

* updated data from Unisyn with GpUnit (precinct) parsing validated

* add more Unisyn regression tests
tests share a single cvr input file

* tabulate all elections - in practice we should not see more than one

* updates for PR #504

* better logging

* first cut at fixing JSON CDF reader:
- all static election objects are parsed at beginning of cvr processing
- during processing contest selections are linked to candidate objects
- candidates are stored in config - not pulled from CDF file
- fixed NIST test set 0 config and CDF json to match the NIST 1500-103 UML
- verified tabulation results are correct for Nist test set 0 test

* update ResultsWriter CVR generation code to create Candidate objects and link to them from ContestSelection objects.
verified updated NIST test 0 cvr output

* updates for PR #504

* fix typo

* update test asset with contest name

* better handling for cdf reader parse errors

* update all CDF json assets

* Updates to CDF parsing logic:
Candidate validation and CandidateId validation are done while parsing CVRs (not during static parsing)
xml parser throws unrecognizedCandidatesException (instead of just CVRParserException)
Add json getCvrContest helper
json parser logic upgrades:
 handle writeIns in both places
 check for rank in both places
 check for HasIndication
 check for IsAllocable
 synthesize cvrId

* cleanup for PR #506

* updates for PR #505

* Throw if undeclared write-in is found but label has not been defined.

* create new class

* helpful errors in CLI; don't allow newer version in config than in app

* make fields per-source

* comments

* Jon's changes

* fix almost all tests

* fix Dominion tests

…vel (#518)

* update validation and documentation for 4 fields that moved to CVR level

* Fixes broken tests and a couple of typos.

Co-authored-by: HEdingfield <hylton@groupagree.com>

* use camelCase for enum values in configs and update migration logic accordingly
* disable editing of CVR source rows in GUI table

* Updates checkstyle from 8.34 to 8.36.2, and google_checks.xml.
* Creates and implements separate `checkstyle-suppressions.xml` file to suppress Checkstyle warnings that don't make sense for our project (fixes #489).
* Addresses relevant Checkstyle warnings (fixes #490).
* Addresses IntelliJ warnings.
* Pixel-pushing for Linux (get thicc, boi)
* Changes all logging to use new `fine()`, `info()`, `warning()`, and `severe()` methods.
* Gets rid of now-unused `onEditCommit` functions for the CVR Files and Candidates tables.
* Makes util classes `final`, with private constructors to prevent instantiation.
* Renames `TieBreakMode`, `tieBreakMode`, `TieBreak`, and `tieBreak` to `TiebreakMode`, `tiebreakMode`, `Tiebreak`, and `tiebreak`, respectively. This word has now lost all meaning.
* Removes unnecessary usages of `.toString()`.
* Standardizes exceptions as `exception` instead of `e` to comply with VVSG requirement on variable names (5.2.5 paragraph c) that only index loops are allowed to have single-character variable names.
* Fixes broken test.
* Minor fixes to hints.
* Get rid of the Devilish Double Spaces after periods.

* fix README

* CDF JSON: throw if a CandidateObject can't be found during parsing.

* Cleanup CDF class (type) names as output from ResultsWriter.

* fix label

* Handle missing precinct data for older Dominion data sets #533
* Add test data with missing precinct data for older Dominion data sets #533

* Fix for #536 - allow multiple CDF files
Add regression test with multiple CDF files

# Conflicts:
#	.idea/misc.xml
#	README.md
#	build.gradle
#	config/checkstyle/google_checks.xml
#	config_file_documentation.txt
#	src/main/java/network/brightspots/rcv/CastVoteRecord.java
#	src/main/java/network/brightspots/rcv/CommonDataFormatReader.java
#	src/main/java/network/brightspots/rcv/ContestConfig.java
#	src/main/java/network/brightspots/rcv/DominionCvrReader.java
#	src/main/java/network/brightspots/rcv/FileUtils.java
#	src/main/java/network/brightspots/rcv/GuiConfigController.java
#	src/main/java/network/brightspots/rcv/Logger.java
#	src/main/java/network/brightspots/rcv/Main.java
#	src/main/java/network/brightspots/rcv/ResultsWriter.java
#	src/main/java/network/brightspots/rcv/StreamingCvrReader.java
#	src/main/java/network/brightspots/rcv/Tabulator.java
#	src/main/java/network/brightspots/rcv/TabulatorSession.java
#	src/main/java/network/brightspots/rcv/Tiebreak.java
#	src/main/resources/network/brightspots/rcv/GuiConfigLayout.fxml
#	src/test/java/network/brightspots/rcv/TabulatorTests.java
#	src/test/resources/network/brightspots/rcv/test_data/2013_minneapolis_mayor_scale/2013_minneapolis_mayor_scale_config.json
#	src/test/resources/network/brightspots/rcv/test_data/continue_until_two_with_batch_elimination_test/continue_until_two_with_batch_elimination_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/multi_seat_bottoms_up_with_threshold/multi_seat_bottoms_up_with_threshold_config.json
#	src/test/resources/network/brightspots/rcv/test_data/multi_seat_uwi_test/multi_seat_uwi_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/multi_seat_uwi_test/multi_seat_uwi_test_expected_summary.json
#	src/test/resources/network/brightspots/rcv/test_data/precinct_example/precinct_example_config.json
#	src/test/resources/network/brightspots/rcv/test_data/skip_to_next_test/skip_to_next_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_1_exhaust_at_overvote/test_set_1_exhaust_at_overvote_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_2_overvote_skip_to_next/test_set_2_overvote_skip_to_next_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_3_skipped_choice_exhaust/test_set_3_skipped_choice_exhaust_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_4_skipped_choice_next/test_set_4_skipped_choice_next_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_6_duplicate_exhaust/test_set_6_duplicate_exhaust_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_multi_winner_fractional_threshold/test_set_multi_winner_fractional_threshold_config.json
#	src/test/resources/network/brightspots/rcv/test_data/test_set_multi_winner_whole_threshold/test_set_multi_winner_whole_threshold_config.json
#	src/test/resources/network/brightspots/rcv/test_data/uwi_cannot_win_test/uwi_cannot_win_test_config.json
#	src/test/resources/network/brightspots/rcv/test_data/uwi_cannot_win_test/uwi_cannot_win_test_expected_summary.json

…it '15f077983ccc5d370bd815e926798ef993758613'

git-subtree-dir: src/test/resources/network/brightspots/rcv/test_data
git-subtree-mainline: 31c2ec8
git-subtree-split: 15f0779