Starting Sphinx Docs #56

jiffyclub · 2015-06-01T18:31:57Z

Has basically a landing page and installation instructions.

[ci skip]

Starting Sphinx Docs

* code changes to add joint tour utilities in cdap * add joint tour frequency composition component * post process jtfc result to tours * update joint tour participation * update #inmtf to tm2 specs * allow alternative id > 127 * set up testing infrastructure * cdap test script * cdap configs * set up testing infrastructure * joint tour test script * joint tour configs * set up testing infrastructure * nm tour frequency test script * nm tour frequency configs * add jtfc alt table dictionary to yaml * update jtfc yaml * jtfc move coef values to coef.csv * jtfc update preprocessor * add jtfc alt table dictionary to yaml * nmtf consolidate all -999 to one coef * code changes to fix bug in parking location choice model * Revert "code changes to fix bug in parking location choice model" This reverts commit 5a38ebb. * parking location choice bug fix * move coefficients to csv file * restore the original mandatory channels * restore the original mandatory channels * RSG Phase 7 Development (#49) * school escorting initial commit * bundles created * added pure escort tours after non_mand_sched * created escorting tours & trips * integrated escort tours and trips * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * downstream model integration * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * initial commit of flexible tour/trip ids * pycodestyle * black formatting * Bump version: 1.0.4 → 1.1.0 * adding frequency alternatives configs required for test system * added additional unit tests * added setup function for test configs dir * formatting * handling missing alts files in examples * error catching around extension probs * passing tests * still passing tests around missing config files * accounting for missing mtf spec in marin example * nm tour scheduling passing * updating stop freq in tours table * added check for mand tour overlap with pe tours * num chauffeurs and escortees * fixed defaults not getting used if file missing * merging canonical ids from flexible id work * setting escorting tour and trip ids * remove unneeded nmtf settings file * black formatting * excluding escort trips from trip scheduling * fixing bug where mand tours not getting assigned correct id * adding school_escorting to mp model list * Added mwcog small area * missed one edit * adding school escort tour flavors as own category * reformatting * updating timetable windows with pure escort tours * additional logging * Update README.MD * call as module * github actions tests * adding non-mand destination changes * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * fixing bad tdd merge * repair test multiple zones for github actions * publish develop docs * fix docbuild env * merging tdd alts to all tours * adding ride share threshold to unvailability for pure escort time overlap * cleanup * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * mins per time bin * black formatting * black formatting * fixing reindex import bug * fixing missed import * replacing trips test table * inserting default setting if no models in config for tests * publish docs to branch name * adding setup function to tests to set configs_dir injectable * documentation * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * fixed origin bug and missing outbound trip to work * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * proper cleanup when trips that get removed if schedule failed * changed failed trip scheduling option for example * updating regress table * blacken * extending nmtf and stop frequency to demonstrate flexible ids * param on rtol * fix sandag_2 test files * fix test file names * allowing multiple escort tours in the same period * sandag 3-zone example fix * fixing expression for missing escort participants sandag 3_zone * cleanup * blacken * Update trip_destination.py applying valid primary origin default value * Update trip_destination.py blacken * fixing bug for inbound destination for second escortee * blacken * Disaggregate Accessibilities (#5) * initial commit with basic working proto pop gen * fixed bad dependency range * fixed vary_on method to vary all with mapped fields after * added check if already dataframe * added dataframe check if the table passed is already a dataframe * working proto pop gen. still debugging mandatory work/school model * check all table is df * workplace runs, next testing school * began setting up to get all logsums, not just chosen ones * restructured to run as either one-off or model step * revert to last merge. Removed dataframe check in iterate, no longer needed to modify this file * extracted logsums, need to inject into pipeline or save output? * working standalone or step model * extractable accessibilities for fixed and nonmandatory * extractable accessibilities for fixed and nonmandatory * cleanup and add documentation * resolved duplicates of old 'example' folders * model uses write_tables functionality * disaggregate accessibility runs as model step or standalone. Runs as subprocess * working model test. table initialization not yet working * added logsum short circuit to get logsums and avoid drawing unneccesary samples * working model plus major cleanup * working model plus major cleanup * override sample size * fixed trace output files * skip_choice default to False * fixed empty logsums bug * cleanup redundent parameters * fixed list index instead of set * coordinated model run files * added default skip to false * added multiprocessing line * began setup for multiprocessing * fixed sampling problem. Pipeline for multi processing, NOT WORKING YET * deleted run file, not needed anymore * update release instructions * auto-build docs on release * remind to update switcher * need checkout * added helper functions for handling suffix args * to enable multiprocessing, overhauled pipeline method to include proto_ tables rather than overwriting main tables * working multiprocess, but requires debugging. fails on other models * working multiprocess, but requires debugging. fails on other models * cleanup of mp table registering * fixed tracing and slicing issue * removed old 'run' model * setup example 2 zones * minimum working 2 zone * multizone basic working * fixed buggy settings * multiprocessing working, but empty final tables * fixed blank output bug and cleaned up settings to use verbose table names (not just 'disaggregate_accessibility') * cleanup run scripts a bit * fixed missing base path for full run * fixed missing path * fixed typo * fixed 1 per taz sampling * fixing person merge bug and filtering workers * fixed duplicate tours! * updated settings for initialize disagg * removed obsolete file * cleaned up file and moved initialize to tables/... * added find nearest node function * added initialize disaggregate_accessibility to initialize_households * moved initialize steps to 'tables/disaggregate_accessibility' * updated settings to include initialize disaggregate accessibilities as part of initialize_households * moved initialize disagg accessibilities to tables. Created working merge step using naive bayes and 'hard' join * add mp back in * PEP formatting revisions * fixed logsums merge on households instead of persons * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * fixed missing column pipeline error * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * updated dependencies * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * update sampling script * 'blacken' * fixed replacement sample bug * updated documentation * more flexible scenario testing * blacken Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> * Shadow Pricing Enhancements (#7) * updated scripts to include simulation-based shadow pricing * blacken * Updated shadow_pricing.yaml for mtc example * code cleanup * more cleanup * documentation and passing tests * passing tests * passing tests * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * fixing pandas future warning * blacken * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * always updating choices * testing removal of lognormal for hh vot * putting hh vot back in * updating to match sharrow test versions * raw person table for buffer instead of injectable * adding segmentation, output by iteration, and external worker removal * formatting & documentation Co-authored-by: aletzdy <[email protected]> * updating mtc_extended test files * no sp for non-work or school, better logging, weighting options * sample TAZ only if available MAZ when shadow pricing * adding missed weight column option * cleaning up comments Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> * set up testing infrastructure (#40) Co-authored-by: Lisa Zorn <[email protected]> * BayDAG auto ownership configs and test (#41) * set up testing infrastructure * auto ownership test script * auto ownership configs * ao move coef values to coef.csv Co-authored-by: Lisa Zorn <[email protected]> * blacken * more formatting * blacken * blacken * blacken * BayDAG parking location choice configs and test (#45) * code changes to fix bug in parking location choice model * parking location choice configs * Revert "code changes to fix bug in parking location choice model" This reverts commit 5a38ebb. * parking location choice bug fix * parking location choice config updates move coefficients to csv file and activitysim variable naming consistency * parking location choice summary Co-authored-by: Lisa Zorn <[email protected]> * blacken * cdap bug fixes * adding sklearn to dependencies * Update activitysim-dev.yml fixing bad reference to scikit-learn * Update activitysim-test.yml fixing bad reference to scikit-learn * Update setup.cfg fixing bad reference to scikit-learn * Memory Bug Fix * working with 2k no sp * optimize nearest zone determination * Changed data type of participant_id in candidates in joint_tour_participation_candidates() to unsigned 64-bit integer to prevent overflow * better comments * fix overflow in jtp participant id * blacken * forcing participation * Trip Scheduling (#51) * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * Bump version: 1.0.4 → 1.1.0 * Added mwcog small area * missed one edit * reformatting * Update README.MD * call as module * github actions tests * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * repair test multiple zones for github actions * publish develop docs * fix docbuild env * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * publish docs to branch name * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * param on rtol * fix sandag_2 test files * fix test file names * added pre-processor option to trip scheduling * trip scheduling relative mode initial commit * moved everything to mwcog example * adding output analysis notebook * adding additional segmentation * testing and documentation * blacken * not assuming scheduling mode is set * fixing merge trip scheduling * still fixing merge * reverting regression trips * fixing bad merge and updating test Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * Trip Scheduling Bug & Trip Mode Choice Annotate (#55) * other sp methods price updates * Trip Scheduling into Resident Debug (#54) * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * Bump version: 1.0.4 → 1.1.0 * Added mwcog small area * missed one edit * reformatting * Update README.MD * call as module * github actions tests * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * repair test multiple zones for github actions * publish develop docs * fix docbuild env * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * publish docs to branch name * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * param on rtol * fix sandag_2 test files * fix test file names * added pre-processor option to trip scheduling * trip scheduling relative mode initial commit * moved everything to mwcog example * adding output analysis notebook * adding additional segmentation * testing and documentation * blacken * not assuming scheduling mode is set * fixing merge trip scheduling * still fixing merge * reverting regression trips * fixing bad merge and updating test Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * adding annotate to trip mode choice * no earliest change if previous trip fail Co-authored-by: David Hensle <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * adding locals_dict to annotate * chooser cols in final trips table * BayDAG merge with ActivitySim v1.2 (#56) * fixed logsums merge on households instead of persons * code cleanup * more cleanup * documentation and passing tests * passing tests * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * passing tests * ext cli arg * memory sidecar * restart if resume_after checkpoint is missing * no pandas 1.5 yet * stop the sidecar * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * minor repairs * skip when household_income is None * fixed missing column pipeline error * fixing pandas future warning * blacken * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * updated dependencies * always updating choices * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * testing removal of lognormal for hh vot * putting hh vot back in * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * updating to match sharrow test versions * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * raw person table for buffer instead of injectable * add mp test for prototype_mtc_extended * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * Update random.py * Updated test environment to reflect changes in pandas * Removed random random seed generation from placeholder_sandage 1-zone test configuration to get example to pass automated test * update sampling script * 'blacken' * fixed replacement sample bug * adding segmentation, output by iteration, and external worker removal * updated documentation * more flexible scenario testing * blacken * Added test_random_seed.py * blacken test_random_seed.py * Moved random seed generation testing out of prototype_mtc folder and edited core_tests.yaml to call it * Corrected name of check_outputs() * Added print statements to debug script * Blacken test_random_seed.py * keep alternative attributes in parking location * move coeff values to coeff csv * Added pipe character to call that tests the random generator * Added explicit call for pytest to run test_random_seed.py * Added print statement at start of script for debugging * Replaced single quotes with double quotes in print statement * reformat with Black * Moved random seed test into activitysim folder * Edited core_tests.yml to reflect change in location of random seed test * Renamed tests folder to test to reflect call in core-tests.yml * formatting & documentation * Added test_random_seed function for PyTest to read * Fixed defition of seeds list and removed print statements * updating github test env * responding to review comments * Added line to create output folder as that's not being committed * create_rng_configs() now copies entire example configs directory instead of just settings.yaml * Added try except statement when creating the output directory in case it already exists * additional logging, random seed option, landuse sample weight column * ensuring TAZ is not selected if no available MAZ * adding logic to skip external location choice models * Applied suggested changes * Removed activitysim\test\random_seed\configs directory to reduce confusion * Moved random seed test directory to folder that had already existed * temporarily constrain pandas #608 * work around psutil runtimeerror * temp constrain pandas * add mwcog full example * review responses * revisions per Sijia's comments, except for the proto-table-template implementation, still working. * added template pop option * blacken * set back to create_tables to pass test against old tables * updated proto-pop test data * resolved bad test data issue * warn don't fail on duplicate skims * include sharrow in mwcog example * cleanup * zarr digital encoding for mwcog * include reference in psrc mini * fow window ids to int64 because windows * handle expected warnings * unpin dependencies * columns cannot be a set * unpin pandas * columns cannot be a set * numeric_only args in groupby.sum * docs: correct the unit of `chunk_size`. * change 'arry' to more readable 'sizearray' * repair tests * catch FileNotFound * add check that land use is zero-based when using sharrow * better docs on skims in shared memory * better docstrings for skimdataset * remove old code * remove junk * add logging for recoding * optimize nearest zone determination * consistent multiprocessing results * blacken * updating regression trips * adding sandag 2-zone test * blacken * fix merge error * allow pandas 1.5 again * sharrow compatibility with #606 * remove outdated code in comments * note on tracing limitation * allow repeating key cols * fix decoding in MP output * escortee modes match chauf modes * updating regression tests * fixing bad var name in inbound expressions * add note about `condense_parameters` * change default condense_parameters to False * Update .gitignore Co-authored-by: Sijia Wang <[email protected]> * ignore caches * remove special install instructions * remove sharrow_skip's * Revert "remove sharrow_skip's" This reverts commit 6b52af2. * add note about why sharrow_skip is activated * Update school_escorting.yaml * Update config.py * arc trip destination spec skim correction * update regression trips * require sharrow 2.5 * fix mtc_ext for sharrow * fix test consistent with escort mode alignments * allow sharrow skipping * remove stray indent * delete expression values after sharrow testing to make debugging easier * require sharrow 2.5.2 * recode only once * testing repairs * note about why sharrow_skip * fork mtc_extended testing on shadow pricing and sharrow * note on sharrow_skip * size term scaling only for full run * reordering * multiprocessing hangs! * never scale size terms for disagg * tally pending persons * tests cleanup * fix error with orca * let pipeline tables be dropped * check on available MAZs, comment cleanup * work zone to -1 if wfh, removed unneeded extensions * fix tests for sandag 2zone * ignore deprecation warning in tests not clear why this started being a problem suddenly in only the xborder-MP model * add scikit-learn to formal dependencies * docs update for installer * fixing black to 22.12.0 * missed merge conflicts * fixing merge issues in prototype_semcog * fixing prototype_arc merge * fixing placeholder_sandag merge issues * blacken * fixing mwcog merge issues * skims not found during estimation test --------- Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeff Newman <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Joe Flood <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: amarin <[email protected]> * do not require all alts in data file * int8 to int16 lost in v1.2 merge --------- Co-authored-by: Lisa Zorn <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: Ashish Kulshrestha <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: JoeJimFlood <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: amarin <[email protected]>

* keep black 2022 style for now * typo in link * note about pre-package installer in quick start * add model_settings to estimator.write_coefficients * BayDAG Contributions (#657) * code changes to add joint tour utilities in cdap * add joint tour frequency composition component * post process jtfc result to tours * update joint tour participation * update #inmtf to tm2 specs * allow alternative id > 127 * set up testing infrastructure * cdap test script * cdap configs * set up testing infrastructure * joint tour test script * joint tour configs * set up testing infrastructure * nm tour frequency test script * nm tour frequency configs * add jtfc alt table dictionary to yaml * update jtfc yaml * jtfc move coef values to coef.csv * jtfc update preprocessor * add jtfc alt table dictionary to yaml * nmtf consolidate all -999 to one coef * code changes to fix bug in parking location choice model * Revert "code changes to fix bug in parking location choice model" This reverts commit 5a38ebb. * parking location choice bug fix * move coefficients to csv file * restore the original mandatory channels * restore the original mandatory channels * RSG Phase 7 Development (#49) * school escorting initial commit * bundles created * added pure escort tours after non_mand_sched * created escorting tours & trips * integrated escort tours and trips * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * downstream model integration * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * initial commit of flexible tour/trip ids * pycodestyle * black formatting * Bump version: 1.0.4 → 1.1.0 * adding frequency alternatives configs required for test system * added additional unit tests * added setup function for test configs dir * formatting * handling missing alts files in examples * error catching around extension probs * passing tests * still passing tests around missing config files * accounting for missing mtf spec in marin example * nm tour scheduling passing * updating stop freq in tours table * added check for mand tour overlap with pe tours * num chauffeurs and escortees * fixed defaults not getting used if file missing * merging canonical ids from flexible id work * setting escorting tour and trip ids * remove unneeded nmtf settings file * black formatting * excluding escort trips from trip scheduling * fixing bug where mand tours not getting assigned correct id * adding school_escorting to mp model list * Added mwcog small area * missed one edit * adding school escort tour flavors as own category * reformatting * updating timetable windows with pure escort tours * additional logging * Update README.MD * call as module * github actions tests * adding non-mand destination changes * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * fixing bad tdd merge * repair test multiple zones for github actions * publish develop docs * fix docbuild env * merging tdd alts to all tours * adding ride share threshold to unvailability for pure escort time overlap * cleanup * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * mins per time bin * black formatting * black formatting * fixing reindex import bug * fixing missed import * replacing trips test table * inserting default setting if no models in config for tests * publish docs to branch name * adding setup function to tests to set configs_dir injectable * documentation * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * fixed origin bug and missing outbound trip to work * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * proper cleanup when trips that get removed if schedule failed * changed failed trip scheduling option for example * updating regress table * blacken * extending nmtf and stop frequency to demonstrate flexible ids * param on rtol * fix sandag_2 test files * fix test file names * allowing multiple escort tours in the same period * sandag 3-zone example fix * fixing expression for missing escort participants sandag 3_zone * cleanup * blacken * Update trip_destination.py applying valid primary origin default value * Update trip_destination.py blacken * fixing bug for inbound destination for second escortee * blacken * Disaggregate Accessibilities (#5) * initial commit with basic working proto pop gen * fixed bad dependency range * fixed vary_on method to vary all with mapped fields after * added check if already dataframe * added dataframe check if the table passed is already a dataframe * working proto pop gen. still debugging mandatory work/school model * check all table is df * workplace runs, next testing school * began setting up to get all logsums, not just chosen ones * restructured to run as either one-off or model step * revert to last merge. Removed dataframe check in iterate, no longer needed to modify this file * extracted logsums, need to inject into pipeline or save output? * working standalone or step model * extractable accessibilities for fixed and nonmandatory * extractable accessibilities for fixed and nonmandatory * cleanup and add documentation * resolved duplicates of old 'example' folders * model uses write_tables functionality * disaggregate accessibility runs as model step or standalone. Runs as subprocess * working model test. table initialization not yet working * added logsum short circuit to get logsums and avoid drawing unneccesary samples * working model plus major cleanup * working model plus major cleanup * override sample size * fixed trace output files * skip_choice default to False * fixed empty logsums bug * cleanup redundent parameters * fixed list index instead of set * coordinated model run files * added default skip to false * added multiprocessing line * began setup for multiprocessing * fixed sampling problem. Pipeline for multi processing, NOT WORKING YET * deleted run file, not needed anymore * update release instructions * auto-build docs on release * remind to update switcher * need checkout * added helper functions for handling suffix args * to enable multiprocessing, overhauled pipeline method to include proto_ tables rather than overwriting main tables * working multiprocess, but requires debugging. fails on other models * working multiprocess, but requires debugging. fails on other models * cleanup of mp table registering * fixed tracing and slicing issue * removed old 'run' model * setup example 2 zones * minimum working 2 zone * multizone basic working * fixed buggy settings * multiprocessing working, but empty final tables * fixed blank output bug and cleaned up settings to use verbose table names (not just 'disaggregate_accessibility') * cleanup run scripts a bit * fixed missing base path for full run * fixed missing path * fixed typo * fixed 1 per taz sampling * fixing person merge bug and filtering workers * fixed duplicate tours! * updated settings for initialize disagg * removed obsolete file * cleaned up file and moved initialize to tables/... * added find nearest node function * added initialize disaggregate_accessibility to initialize_households * moved initialize steps to 'tables/disaggregate_accessibility' * updated settings to include initialize disaggregate accessibilities as part of initialize_households * moved initialize disagg accessibilities to tables. Created working merge step using naive bayes and 'hard' join * add mp back in * PEP formatting revisions * fixed logsums merge on households instead of persons * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * fixed missing column pipeline error * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * updated dependencies * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * update sampling script * 'blacken' * fixed replacement sample bug * updated documentation * more flexible scenario testing * blacken Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> * Shadow Pricing Enhancements (#7) * updated scripts to include simulation-based shadow pricing * blacken * Updated shadow_pricing.yaml for mtc example * code cleanup * more cleanup * documentation and passing tests * passing tests * passing tests * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * fixing pandas future warning * blacken * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * always updating choices * testing removal of lognormal for hh vot * putting hh vot back in * updating to match sharrow test versions * raw person table for buffer instead of injectable * adding segmentation, output by iteration, and external worker removal * formatting & documentation Co-authored-by: aletzdy <[email protected]> * updating mtc_extended test files * no sp for non-work or school, better logging, weighting options * sample TAZ only if available MAZ when shadow pricing * adding missed weight column option * cleaning up comments Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> * set up testing infrastructure (#40) Co-authored-by: Lisa Zorn <[email protected]> * BayDAG auto ownership configs and test (#41) * set up testing infrastructure * auto ownership test script * auto ownership configs * ao move coef values to coef.csv Co-authored-by: Lisa Zorn <[email protected]> * blacken * more formatting * blacken * blacken * blacken * BayDAG parking location choice configs and test (#45) * code changes to fix bug in parking location choice model * parking location choice configs * Revert "code changes to fix bug in parking location choice model" This reverts commit 5a38ebb. * parking location choice bug fix * parking location choice config updates move coefficients to csv file and activitysim variable naming consistency * parking location choice summary Co-authored-by: Lisa Zorn <[email protected]> * blacken * cdap bug fixes * adding sklearn to dependencies * Update activitysim-dev.yml fixing bad reference to scikit-learn * Update activitysim-test.yml fixing bad reference to scikit-learn * Update setup.cfg fixing bad reference to scikit-learn * Memory Bug Fix * working with 2k no sp * optimize nearest zone determination * Changed data type of participant_id in candidates in joint_tour_participation_candidates() to unsigned 64-bit integer to prevent overflow * better comments * fix overflow in jtp participant id * blacken * forcing participation * Trip Scheduling (#51) * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * Bump version: 1.0.4 → 1.1.0 * Added mwcog small area * missed one edit * reformatting * Update README.MD * call as module * github actions tests * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * repair test multiple zones for github actions * publish develop docs * fix docbuild env * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * publish docs to branch name * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * param on rtol * fix sandag_2 test files * fix test file names * added pre-processor option to trip scheduling * trip scheduling relative mode initial commit * moved everything to mwcog example * adding output analysis notebook * adding additional segmentation * testing and documentation * blacken * not assuming scheduling mode is set * fixing merge trip scheduling * still fixing merge * reverting regression trips * fixing bad merge and updating test Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * Trip Scheduling Bug & Trip Mode Choice Annotate (#55) * other sp methods price updates * Trip Scheduling into Resident Debug (#54) * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * Bump version: 1.0.4 → 1.1.0 * Added mwcog small area * missed one edit * reformatting * Update README.MD * call as module * github actions tests * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * repair test multiple zones for github actions * publish develop docs * fix docbuild env * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * publish docs to branch name * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * param on rtol * fix sandag_2 test files * fix test file names * added pre-processor option to trip scheduling * trip scheduling relative mode initial commit * moved everything to mwcog example * adding output analysis notebook * adding additional segmentation * testing and documentation * blacken * not assuming scheduling mode is set * fixing merge trip scheduling * still fixing merge * reverting regression trips * fixing bad merge and updating test Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * adding annotate to trip mode choice * no earliest change if previous trip fail Co-authored-by: David Hensle <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * adding locals_dict to annotate * chooser cols in final trips table * BayDAG merge with ActivitySim v1.2 (#56) * fixed logsums merge on households instead of persons * code cleanup * more cleanup * documentation and passing tests * passing tests * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * passing tests * ext cli arg * memory sidecar * restart if resume_after checkpoint is missing * no pandas 1.5 yet * stop the sidecar * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * minor repairs * skip when household_income is None * fixed missing column pipeline error * fixing pandas future warning * blacken * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * updated dependencies * always updating choices * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * testing removal of lognormal for hh vot * putting hh vot back in * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * updating to match sharrow test versions * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * raw person table for buffer instead of injectable * add mp test for prototype_mtc_extended * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * Update random.py * Updated test environment to reflect changes in pandas * Removed random random seed generation from placeholder_sandage 1-zone test configuration to get example to pass automated test * update sampling script * 'blacken' * fixed replacement sample bug * adding segmentation, output by iteration, and external worker removal * updated documentation * more flexible scenario testing * blacken * Added test_random_seed.py * blacken test_random_seed.py * Moved random seed generation testing out of prototype_mtc folder and edited core_tests.yaml to call it * Corrected name of check_outputs() * Added print statements to debug script * Blacken test_random_seed.py * keep alternative attributes in parking location * move coeff values to coeff csv * Added pipe character to call that tests the random generator * Added explicit call for pytest to run test_random_seed.py * Added print statement at start of script for debugging * Replaced single quotes with double quotes in print statement * reformat with Black * Moved random seed test into activitysim folder * Edited core_tests.yml to reflect change in location of random seed test * Renamed tests folder to test to reflect call in core-tests.yml * formatting & documentation * Added test_random_seed function for PyTest to read * Fixed defition of seeds list and removed print statements * updating github test env * responding to review comments * Added line to create output folder as that's not being committed * create_rng_configs() now copies entire example configs directory instead of just settings.yaml * Added try except statement when creating the output directory in case it already exists * additional logging, random seed option, landuse sample weight column * ensuring TAZ is not selected if no available MAZ * adding logic to skip external location choice models * Applied suggested changes * Removed activitysim\test\random_seed\configs directory to reduce confusion * Moved random seed test directory to folder that had already existed * temporarily constrain pandas #608 * work around psutil runtimeerror * temp constrain pandas * add mwcog full example * review responses * revisions per Sijia's comments, except for the proto-table-template implementation, still working. * added template pop option * blacken * set back to create_tables to pass test against old tables * updated proto-pop test data * resolved bad test data issue * warn don't fail on duplicate skims * include sharrow in mwcog example * cleanup * zarr digital encoding for mwcog * include reference in psrc mini * fow window ids to int64 because windows * handle expected warnings * unpin dependencies * columns cannot be a set * unpin pandas * columns cannot be a set * numeric_only args in groupby.sum * docs: correct the unit of `chunk_size`. * change 'arry' to more readable 'sizearray' * repair tests * catch FileNotFound * add check that land use is zero-based when using sharrow * better docs on skims in shared memory * better docstrings for skimdataset * remove old code * remove junk * add logging for recoding * optimize nearest zone determination * consistent multiprocessing results * blacken * updating regression trips * adding sandag 2-zone test * blacken * fix merge error * allow pandas 1.5 again * sharrow compatibility with #606 * remove outdated code in comments * note on tracing limitation * allow repeating key cols * fix decoding in MP output * escortee modes match chauf modes * updating regression tests * fixing bad var name in inbound expressions * add note about `condense_parameters` * change default condense_parameters to False * Update .gitignore Co-authored-by: Sijia Wang <[email protected]> * ignore caches * remove special install instructions * remove sharrow_skip's * Revert "remove sharrow_skip's" This reverts commit 6b52af2. * add note about why sharrow_skip is activated * Update school_escorting.yaml * Update config.py * arc trip destination spec skim correction * update regression trips * require sharrow 2.5 * fix mtc_ext for sharrow * fix test consistent with escort mode alignments * allow sharrow skipping * remove stray indent * delete expression values after sharrow testing to make debugging easier * require sharrow 2.5.2 * recode only once * testing repairs * note about why sharrow_skip * fork mtc_extended testing on shadow pricing and sharrow * note on sharrow_skip * size term scaling only for full run * reordering * multiprocessing hangs! * never scale size terms for disagg * tally pending persons * tests cleanup * fix error with orca * let pipeline tables be dropped * check on available MAZs, comment cleanup * work zone to -1 if wfh, removed unneeded extensions * fix tests for sandag 2zone * ignore deprecation warning in tests not clear why this started being a problem suddenly in only the xborder-MP model * add scikit-learn to formal dependencies * docs update for installer * fixing black to 22.12.0 * missed merge conflicts * fixing merge issues in prototype_semcog * fixing prototype_arc merge * fixing placeholder_sandag merge issues * blacken * fixing mwcog merge issues * skims not found during estimation test --------- Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeff Newman <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Joe Flood <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: amarin <[email protected]> * do not require all alts in data file * int8 to int16 lost in v1.2 merge --------- Co-authored-by: Lisa Zorn <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: Ashish Kulshrestha <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: JoeJimFlood <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: amarin <[email protected]> * docs: apply a minor correction to user guides (#659) * Trip scheduling logic (#660) * trip scheduling logic_version * in testing ignore the warning we just added * cannot use logic_version 1 with relative scheduling * Pin Dependencies (#665) * pinderella * pandas in setup.cfg deps --------- Co-authored-by: Bo Wen <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: Lisa Zorn <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: Ashish Kulshrestha <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: JoeJimFlood <[email protected]> Co-authored-by: amarin <[email protected]>

* BayDAG Contributions (ActivitySim#657) * code changes to add joint tour utilities in cdap * add joint tour frequency composition component * post process jtfc result to tours * update joint tour participation * update #inmtf to tm2 specs * allow alternative id > 127 * set up testing infrastructure * cdap test script * cdap configs * set up testing infrastructure * joint tour test script * joint tour configs * set up testing infrastructure * nm tour frequency test script * nm tour frequency configs * add jtfc alt table dictionary to yaml * update jtfc yaml * jtfc move coef values to coef.csv * jtfc update preprocessor * add jtfc alt table dictionary to yaml * nmtf consolidate all -999 to one coef * code changes to fix bug in parking location choice model * Revert "code changes to fix bug in parking location choice model" This reverts commit 5a38ebb. * parking location choice bug fix * move coefficients to csv file * restore the original mandatory channels * restore the original mandatory channels * RSG Phase 7 Development (ActivitySim#49) * school escorting initial commit * bundles created * added pure escort tours after non_mand_sched * created escorting tours & trips * integrated escort tours and trips * Differentiate examples between quality and validity of example models (ActivitySim#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (ActivitySim#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * downstream model integration * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * initial commit of flexible tour/trip ids * pycodestyle * black formatting * Bump version: 1.0.4 → 1.1.0 * adding frequency alternatives configs required for test system * added additional unit tests * added setup function for test configs dir * formatting * handling missing alts files in examples * error catching around extension probs * passing tests * still passing tests around missing config files * accounting for missing mtf spec in marin example * nm tour scheduling passing * updating stop freq in tours table * added check for mand tour overlap with pe tours * num chauffeurs and escortees * fixed defaults not getting used if file missing * merging canonical ids from flexible id work * setting escorting tour and trip ids * remove unneeded nmtf settings file * black formatting * excluding escort trips from trip scheduling * fixing bug where mand tours not getting assigned correct id * adding school_escorting to mp model list * Added mwcog small area * missed one edit * adding school escort tour flavors as own category * reformatting * updating timetable windows with pure escort tours * additional logging * Update README.MD * call as module * github actions tests * adding non-mand destination changes * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * fixing bad tdd merge * repair test multiple zones for github actions * publish develop docs * fix docbuild env * merging tdd alts to all tours * adding ride share threshold to unvailability for pure escort time overlap * cleanup * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * mins per time bin * black formatting * black formatting * fixing reindex import bug * fixing missed import * replacing trips test table * inserting default setting if no models in config for tests * publish docs to branch name * adding setup function to tests to set configs_dir injectable * documentation * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * fixed origin bug and missing outbound trip to work * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * proper cleanup when trips that get removed if schedule failed * changed failed trip scheduling option for example * updating regress table * blacken * extending nmtf and stop frequency to demonstrate flexible ids * param on rtol * fix sandag_2 test files * fix test file names * allowing multiple escort tours in the same period * sandag 3-zone example fix * fixing expression for missing escort participants sandag 3_zone * cleanup * blacken * Update trip_destination.py applying valid primary origin default value * Update trip_destination.py blacken * fixing bug for inbound destination for second escortee * blacken * Disaggregate Accessibilities (#5) * initial commit with basic working proto pop gen * fixed bad dependency range * fixed vary_on method to vary all with mapped fields after * added check if already dataframe * added dataframe check if the table passed is already a dataframe * working proto pop gen. still debugging mandatory work/school model * check all table is df * workplace runs, next testing school * began setting up to get all logsums, not just chosen ones * restructured to run as either one-off or model step * revert to last merge. Removed dataframe check in iterate, no longer needed to modify this file * extracted logsums, need to inject into pipeline or save output? * working standalone or step model * extractable accessibilities for fixed and nonmandatory * extractable accessibilities for fixed and nonmandatory * cleanup and add documentation * resolved duplicates of old 'example' folders * model uses write_tables functionality * disaggregate accessibility runs as model step or standalone. Runs as subprocess * working model test. table initialization not yet working * added logsum short circuit to get logsums and avoid drawing unneccesary samples * working model plus major cleanup * working model plus major cleanup * override sample size * fixed trace output files * skip_choice default to False * fixed empty logsums bug * cleanup redundent parameters * fixed list index instead of set * coordinated model run files * added default skip to false * added multiprocessing line * began setup for multiprocessing * fixed sampling problem. Pipeline for multi processing, NOT WORKING YET * deleted run file, not needed anymore * update release instructions * auto-build docs on release * remind to update switcher * need checkout * added helper functions for handling suffix args * to enable multiprocessing, overhauled pipeline method to include proto_ tables rather than overwriting main tables * working multiprocess, but requires debugging. fails on other models * working multiprocess, but requires debugging. fails on other models * cleanup of mp table registering * fixed tracing and slicing issue * removed old 'run' model * setup example 2 zones * minimum working 2 zone * multizone basic working * fixed buggy settings * multiprocessing working, but empty final tables * fixed blank output bug and cleaned up settings to use verbose table names (not just 'disaggregate_accessibility') * cleanup run scripts a bit * fixed missing base path for full run * fixed missing path * fixed typo * fixed 1 per taz sampling * fixing person merge bug and filtering workers * fixed duplicate tours! * updated settings for initialize disagg * removed obsolete file * cleaned up file and moved initialize to tables/... * added find nearest node function * added initialize disaggregate_accessibility to initialize_households * moved initialize steps to 'tables/disaggregate_accessibility' * updated settings to include initialize disaggregate accessibilities as part of initialize_households * moved initialize disagg accessibilities to tables. Created working merge step using naive bayes and 'hard' join * add mp back in * PEP formatting revisions * fixed logsums merge on households instead of persons * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * fixed missing column pipeline error * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * updated dependencies * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * update sampling script * 'blacken' * fixed replacement sample bug * updated documentation * more flexible scenario testing * blacken Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> * Shadow Pricing Enhancements (#7) * updated scripts to include simulation-based shadow pricing * blacken * Updated shadow_pricing.yaml for mtc example * code cleanup * more cleanup * documentation and passing tests * passing tests * passing tests * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * fixing pandas future warning * blacken * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * always updating choices * testing removal of lognormal for hh vot * putting hh vot back in * updating to match sharrow test versions * raw person table for buffer instead of injectable * adding segmentation, output by iteration, and external worker removal * formatting & documentation Co-authored-by: aletzdy <[email protected]> * updating mtc_extended test files * no sp for non-work or school, better logging, weighting options * sample TAZ only if available MAZ when shadow pricing * adding missed weight column option * cleaning up comments Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> * set up testing infrastructure (ActivitySim#40) Co-authored-by: Lisa Zorn <[email protected]> * BayDAG auto ownership configs and test (ActivitySim#41) * set up testing infrastructure * auto ownership test script * auto ownership configs * ao move coef values to coef.csv Co-authored-by: Lisa Zorn <[email protected]> * blacken * more formatting * blacken * blacken * blacken * BayDAG parking location choice configs and test (ActivitySim#45) * code changes to fix bug in parking location choice model * parking location choice configs * Revert "code changes to fix bug in parking location choice model" This reverts commit 5a38ebb. * parking location choice bug fix * parking location choice config updates move coefficients to csv file and activitysim variable naming consistency * parking location choice summary Co-authored-by: Lisa Zorn <[email protected]> * blacken * cdap bug fixes * adding sklearn to dependencies * Update activitysim-dev.yml fixing bad reference to scikit-learn * Update activitysim-test.yml fixing bad reference to scikit-learn * Update setup.cfg fixing bad reference to scikit-learn * Memory Bug Fix * working with 2k no sp * optimize nearest zone determination * Changed data type of participant_id in candidates in joint_tour_participation_candidates() to unsigned 64-bit integer to prevent overflow * better comments * fix overflow in jtp participant id * blacken * forcing participation * Trip Scheduling (ActivitySim#51) * Differentiate examples between quality and validity of example models (ActivitySim#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (ActivitySim#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * Bump version: 1.0.4 → 1.1.0 * Added mwcog small area * missed one edit * reformatting * Update README.MD * call as module * github actions tests * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * repair test multiple zones for github actions * publish develop docs * fix docbuild env * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * publish docs to branch name * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * param on rtol * fix sandag_2 test files * fix test file names * added pre-processor option to trip scheduling * trip scheduling relative mode initial commit * moved everything to mwcog example * adding output analysis notebook * adding additional segmentation * testing and documentation * blacken * not assuming scheduling mode is set * fixing merge trip scheduling * still fixing merge * reverting regression trips * fixing bad merge and updating test Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * Trip Scheduling Bug & Trip Mode Choice Annotate (ActivitySim#55) * other sp methods price updates * Trip Scheduling into Resident Debug (ActivitySim#54) * Differentiate examples between quality and validity of example models (ActivitySim#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (ActivitySim#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * Bump version: 1.0.4 → 1.1.0 * Added mwcog small area * missed one edit * reformatting * Update README.MD * call as module * github actions tests * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * repair test multiple zones for github actions * publish develop docs * fix docbuild env * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * publish docs to branch name * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * param on rtol * fix sandag_2 test files * fix test file names * added pre-processor option to trip scheduling * trip scheduling relative mode initial commit * moved everything to mwcog example * adding output analysis notebook * adding additional segmentation * testing and documentation * blacken * not assuming scheduling mode is set * fixing merge trip scheduling * still fixing merge * reverting regression trips * fixing bad merge and updating test Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * adding annotate to trip mode choice * no earliest change if previous trip fail Co-authored-by: David Hensle <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * adding locals_dict to annotate * chooser cols in final trips table * BayDAG merge with ActivitySim v1.2 (ActivitySim#56) * fixed logsums merge on households instead of persons * code cleanup * more cleanup * documentation and passing tests * passing tests * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * passing tests * ext cli arg * memory sidecar * restart if resume_after checkpoint is missing * no pandas 1.5 yet * stop the sidecar * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * minor repairs * skip when household_income is None * fixed missing column pipeline error * fixing pandas future warning * blacken * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * updated dependencies * always updating choices * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * testing removal of lognormal for hh vot * putting hh vot back in * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * updating to match sharrow test versions * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * raw person table for buffer instead of injectable * add mp test for prototype_mtc_extended * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * Update random.py * Updated test environment to reflect changes in pandas * Removed random random seed generation from placeholder_sandage 1-zone test configuration to get example to pass automated test * update sampling script * 'blacken' * fixed replacement sample bug * adding segmentation, output by iteration, and external worker removal * updated documentation * more flexible scenario testing * blacken * Added test_random_seed.py * blacken test_random_seed.py * Moved random seed generation testing out of prototype_mtc folder and edited core_tests.yaml to call it * Corrected name of check_outputs() * Added print statements to debug script * Blacken test_random_seed.py * keep alternative attributes in parking location * move coeff values to coeff csv * Added pipe character to call that tests the random generator * Added explicit call for pytest to run test_random_seed.py * Added print statement at start of script for debugging * Replaced single quotes with double quotes in print statement * reformat with Black * Moved random seed test into activitysim folder * Edited core_tests.yml to reflect change in location of random seed test * Renamed tests folder to test to reflect call in core-tests.yml * formatting & documentation * Added test_random_seed function for PyTest to read * Fixed defition of seeds list and removed print statements * updating github test env * responding to review comments * Added line to create output folder as that's not being committed * create_rng_configs() now copies entire example configs directory instead of just settings.yaml * Added try except statement when creating the output directory in case it already exists * additional logging, random seed option, landuse sample weight column * ensuring TAZ is not selected if no available MAZ * adding logic to skip external location choice models * Applied suggested changes * Removed activitysim\test\random_seed\configs directory to reduce confusion * Moved random seed test directory to folder that had already existed * temporarily constrain pandas ActivitySim#608 * work around psutil runtimeerror * temp constrain pandas * add mwcog full example * review responses * revisions per Sijia's comments, except for the proto-table-template implementation, still working. * added template pop option * blacken * set back to create_tables to pass test against old tables * updated proto-pop test data * resolved bad test data issue * warn don't fail on duplicate skims * include sharrow in mwcog example * cleanup * zarr digital encoding for mwcog * include reference in psrc mini * fow window ids to int64 because windows * handle expected warnings * unpin dependencies * columns cannot be a set * unpin pandas * columns cannot be a set * numeric_only args in groupby.sum * docs: correct the unit of `chunk_size`. * change 'arry' to more readable 'sizearray' * repair tests * catch FileNotFound * add check that land use is zero-based when using sharrow * better docs on skims in shared memory * better docstrings for skimdataset * remove old code * remove junk * add logging for recoding * optimize nearest zone determination * consistent multiprocessing results * blacken * updating regression trips * adding sandag 2-zone test * blacken * fix merge error * allow pandas 1.5 again * sharrow compatibility with ActivitySim#606 * remove outdated code in comments * note on tracing limitation * allow repeating key cols * fix decoding in MP output * escortee modes match chauf modes * updating regression tests * fixing bad var name in inbound expressions * add note about `condense_parameters` * change default condense_parameters to False * Update .gitignore Co-authored-by: Sijia Wang <[email protected]> * ignore caches * remove special install instructions * remove sharrow_skip's * Revert "remove sharrow_skip's" This reverts commit 6b52af2. * add note about why sharrow_skip is activated * Update school_escorting.yaml * Update config.py * arc trip destination spec skim correction * update regression trips * require sharrow 2.5 * fix mtc_ext for sharrow * fix test consistent with escort mode alignments * allow sharrow skipping * remove stray indent * delete expression values after sharrow testing to make debugging easier * require sharrow 2.5.2 * recode only once * testing repairs * note about why sharrow_skip * fork mtc_extended testing on shadow pricing and sharrow * note on sharrow_skip * size term scaling only for full run * reordering * multiprocessing hangs! * never scale size terms for disagg * tally pending persons * tests cleanup * fix error with orca * let pipeline tables be dropped * check on available MAZs, comment cleanup * work zone to -1 if wfh, removed unneeded extensions * fix tests for sandag 2zone * ignore deprecation warning in tests not clear why this started being a problem suddenly in only the xborder-MP model * add scikit-learn to formal dependencies * docs update for installer * fixing black to 22.12.0 * missed merge conflicts * fixing merge issues in prototype_semcog * fixing prototype_arc merge * fixing placeholder_sandag merge issues * blacken * fixing mwcog merge issues * skims not found during estimation test --------- Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeff Newman <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Joe Flood <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: amarin <[email protected]> * do not require all alts in data file * int8 to int16 lost in v1.2 merge --------- Co-authored-by: Lisa Zorn <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: Ashish Kulshrestha <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: JoeJimFlood <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: amarin <[email protected]> * docs: apply a minor correction to user guides (ActivitySim#659) * Trip scheduling logic (ActivitySim#660) * trip scheduling logic_version * in testing ignore the warning we just added * cannot use logic_version 1 with relative scheduling * Pin Dependencies (ActivitySim#665) * pinderella * pandas in setup.cfg deps * Updated SEMCOG Example (ActivitySim#603) * initial example_semcog commit * documentation * single process passing but not multiprocess * testing infrastructure * blacken * formatting * implemented stable sample for university extensions * adding ignored output folder * removed squared term and re-estimated * updating test env * calibrated configs * fixing bad merge * updated configs * reading in extension folder * updated shadowpricing yaml file * updated test regress * Revert "updated test regress" This reverts commit 8d5af7d. * updated regress test table * updated test regress table * updated cropped land use and skim * updated shadow pricing method * updated network_los to read segmented skims if needed * updated example_manifest.yaml * fixing conflicts * making fixes per review comments * push mistake! * Revert "making fixes per review comments" This reverts commit c05c7f3. * Revert "Revert "making fixes per review comments"" This reverts commit d83019a. * added back accidentally untracked output folder + updated regress table * misc small fixes --------- Co-authored-by: Ali Etezady <[email protected]> * syncronize (ActivitySim#680) issue templates into develop --------- Co-authored-by: Lisa Zorn <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: Ashish Kulshrestha <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: JoeJimFlood <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: amarin <[email protected]>

* initial commit * Input checker runs, but log file is written incompletely * updated input checker to write out full log file * blacked input_checker.py * data model integration initial commit * initial pandera commit * initial cleanup * tested on full mtc sample with landuse and skim check * lu types in enums & input cleanup * initial commit of both pydantic & pandera * formatting * Getting into sync with ActivitySim/develop (#8) * BayDAG Contributions (#657) * code changes to add joint tour utilities in cdap * add joint tour frequency composition component * post process jtfc result to tours * update joint tour participation * update #inmtf to tm2 specs * allow alternative id > 127 * set up testing infrastructure * cdap test script * cdap configs * set up testing infrastructure * joint tour test script * joint tour configs * set up testing infrastructure * nm tour frequency test script * nm tour frequency configs * add jtfc alt table dictionary to yaml * update jtfc yaml * jtfc move coef values to coef.csv * jtfc update preprocessor * add jtfc alt table dictionary to yaml * nmtf consolidate all -999 to one coef * code changes to fix bug in parking location choice model * Revert "code changes to fix bug in parking location choice model" This reverts commit 5a38ebb. * parking location choice bug fix * move coefficients to csv file * restore the original mandatory channels * restore the original mandatory channels * RSG Phase 7 Development (#49) * school escorting initial commit * bundles created * added pure escort tours after non_mand_sched * created escorting tours & trips * integrated escort tours and trips * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * downstream model integration * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * initial commit of flexible tour/trip ids * pycodestyle * black formatting * Bump version: 1.0.4 → 1.1.0 * adding frequency alternatives configs required for test system * added additional unit tests * added setup function for test configs dir * formatting * handling missing alts files in examples * error catching around extension probs * passing tests * still passing tests around missing config files * accounting for missing mtf spec in marin example * nm tour scheduling passing * updating stop freq in tours table * added check for mand tour overlap with pe tours * num chauffeurs and escortees * fixed defaults not getting used if file missing * merging canonical ids from flexible id work * setting escorting tour and trip ids * remove unneeded nmtf settings file * black formatting * excluding escort trips from trip scheduling * fixing bug where mand tours not getting assigned correct id * adding school_escorting to mp model list * Added mwcog small area * missed one edit * adding school escort tour flavors as own category * reformatting * updating timetable windows with pure escort tours * additional logging * Update README.MD * call as module * github actions tests * adding non-mand destination changes * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * fixing bad tdd merge * repair test multiple zones for github actions * publish develop docs * fix docbuild env * merging tdd alts to all tours * adding ride share threshold to unvailability for pure escort time overlap * cleanup * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * mins per time bin * black formatting * black formatting * fixing reindex import bug * fixing missed import * replacing trips test table * inserting default setting if no models in config for tests * publish docs to branch name * adding setup function to tests to set configs_dir injectable * documentation * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * fixed origin bug and missing outbound trip to work * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * proper cleanup when trips that get removed if schedule failed * changed failed trip scheduling option for example * updating regress table * blacken * extending nmtf and stop frequency to demonstrate flexible ids * param on rtol * fix sandag_2 test files * fix test file names * allowing multiple escort tours in the same period * sandag 3-zone example fix * fixing expression for missing escort participants sandag 3_zone * cleanup * blacken * Update trip_destination.py applying valid primary origin default value * Update trip_destination.py blacken * fixing bug for inbound destination for second escortee * blacken * Disaggregate Accessibilities (#5) * initial commit with basic working proto pop gen * fixed bad dependency range * fixed vary_on method to vary all with mapped fields after * added check if already dataframe * added dataframe check if the table passed is already a dataframe * working proto pop gen. still debugging mandatory work/school model * check all table is df * workplace runs, next testing school * began setting up to get all logsums, not just chosen ones * restructured to run as either one-off or model step * revert to last merge. Removed dataframe check in iterate, no longer needed to modify this file * extracted logsums, need to inject into pipeline or save output? * working standalone or step model * extractable accessibilities for fixed and nonmandatory * extractable accessibilities for fixed and nonmandatory * cleanup and add documentation * resolved duplicates of old 'example' folders * model uses write_tables functionality * disaggregate accessibility runs as model step or standalone. Runs as subprocess * working model test. table initialization not yet working * added logsum short circuit to get logsums and avoid drawing unneccesary samples * working model plus major cleanup * working model plus major cleanup * override sample size * fixed trace output files * skip_choice default to False * fixed empty logsums bug * cleanup redundent parameters * fixed list index instead of set * coordinated model run files * added default skip to false * added multiprocessing line * began setup for multiprocessing * fixed sampling problem. Pipeline for multi processing, NOT WORKING YET * deleted run file, not needed anymore * update release instructions * auto-build docs on release * remind to update switcher * need checkout * added helper functions for handling suffix args * to enable multiprocessing, overhauled pipeline method to include proto_ tables rather than overwriting main tables * working multiprocess, but requires debugging. fails on other models * working multiprocess, but requires debugging. fails on other models * cleanup of mp table registering * fixed tracing and slicing issue * removed old 'run' model * setup example 2 zones * minimum working 2 zone * multizone basic working * fixed buggy settings * multiprocessing working, but empty final tables * fixed blank output bug and cleaned up settings to use verbose table names (not just 'disaggregate_accessibility') * cleanup run scripts a bit * fixed missing base path for full run * fixed missing path * fixed typo * fixed 1 per taz sampling * fixing person merge bug and filtering workers * fixed duplicate tours! * updated settings for initialize disagg * removed obsolete file * cleaned up file and moved initialize to tables/... * added find nearest node function * added initialize disaggregate_accessibility to initialize_households * moved initialize steps to 'tables/disaggregate_accessibility' * updated settings to include initialize disaggregate accessibilities as part of initialize_households * moved initialize disagg accessibilities to tables. Created working merge step using naive bayes and 'hard' join * add mp back in * PEP formatting revisions * fixed logsums merge on households instead of persons * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * fixed missing column pipeline error * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * updated dependencies * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * update sampling script * 'blacken' * fixed replacement sample bug * updated documentation * more flexible scenario testing * blacken Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> * Shadow Pricing Enhancements (#7) * updated scripts to include simulation-based shadow pricing * blacken * Updated shadow_pricing.yaml for mtc example * code cleanup * more cleanup * documentation and passing tests * passing tests * passing tests * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * fixing pandas future warning * blacken * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * always updating choices * testing removal of lognormal for hh vot * putting hh vot back in * updating to match sharrow test versions * raw person table for buffer instead of injectable * adding segmentation, output by iteration, and external worker removal * formatting & documentation Co-authored-by: aletzdy <[email protected]> * updating mtc_extended test files * no sp for non-work or school, better logging, weighting options * sample TAZ only if available MAZ when shadow pricing * adding missed weight column option * cleaning up comments Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> * set up testing infrastructure (#40) Co-authored-by: Lisa Zorn <[email protected]> * BayDAG auto ownership configs and test (#41) * set up testing infrastructure * auto ownership test script * auto ownership configs * ao move coef values to coef.csv Co-authored-by: Lisa Zorn <[email protected]> * blacken * more formatting * blacken * blacken * blacken * BayDAG parking location choice configs and test (#45) * code changes to fix bug in parking location choice model * parking location choice configs * Revert "code changes to fix bug in parking location choice model" This reverts commit 5a38ebb. * parking location choice bug fix * parking location choice config updates move coefficients to csv file and activitysim variable naming consistency * parking location choice summary Co-authored-by: Lisa Zorn <[email protected]> * blacken * cdap bug fixes * adding sklearn to dependencies * Update activitysim-dev.yml fixing bad reference to scikit-learn * Update activitysim-test.yml fixing bad reference to scikit-learn * Update setup.cfg fixing bad reference to scikit-learn * Memory Bug Fix * working with 2k no sp * optimize nearest zone determination * Changed data type of participant_id in candidates in joint_tour_participation_candidates() to unsigned 64-bit integer to prevent overflow * better comments * fix overflow in jtp participant id * blacken * forcing participation * Trip Scheduling (#51) * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * Bump version: 1.0.4 → 1.1.0 * Added mwcog small area * missed one edit * reformatting * Update README.MD * call as module * github actions tests * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * repair test multiple zones for github actions * publish develop docs * fix docbuild env * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * publish docs to branch name * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * param on rtol * fix sandag_2 test files * fix test file names * added pre-processor option to trip scheduling * trip scheduling relative mode initial commit * moved everything to mwcog example * adding output analysis notebook * adding additional segmentation * testing and documentation * blacken * not assuming scheduling mode is set * fixing merge trip scheduling * still fixing merge * reverting regression trips * fixing bad merge and updating test Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * Trip Scheduling Bug & Trip Mode Choice Annotate (#55) * other sp methods price updates * Trip Scheduling into Resident Debug (#54) * Differentiate examples between quality and validity of example models (#571) * change examples that are no longer tied to an agency to fictional place names * change name of full example also * add back missing output dir * restore test output dir also * more empty dirs that got lost * clean up docs * example_mtc -> prototype_mtc * Prototype MTC extended * add all the ignored files * add test output dirs * remove superfluous example_test * prototype_sf * prototype_arc * prototype_marin * move dirs * psrc * semcog * sandag_xborder * placeholder_sandag * placeholder_multiple_zone * no more coveralls * repair docs * clean up example names * black and isort (#578) * black and isort * stop emitting output dir it fails later tests * trace files in nested directories because windows * swap files for xborder model * repair ARC MP * print checksum even when not used * add hashes for sandag_xborder_full * fix dtype in university hack * fix persons to match tours * repair ARC * Bump version: 1.0.4 → 1.1.0 * Added mwcog small area * missed one edit * reformatting * Update README.MD * call as module * github actions tests * pre commit hooks * pyproject toml * limit numpy * docs for mamba instead of conda * ignore generated files * add nbmake to test env * fix dupe line * repair test multiple zones for github actions * publish develop docs * fix docbuild env * Update .travis.yml * fixed testing files * fixed testing files (again) * fixed test script again * publish docs to branch name * updated testing scripts (note shorter travis script for now) * fixed slash (windows vs. linux testing issue) * added output folders * updated travis script to run all tests, should pass * docs cleaning * docs re-style * rebuild * dynamic versioning docs * version switcher * blacken * fix switcher url * fix conf * switcher update * master to main * deployment actions * actions * build wheel * fix for testpypi * blacken * manual switcher * branch docs service [makedocs] * syntax [makedocs] * travis depends * checkout v3, fix versioning in docs * only build develop docs once * failsafe version * documentation repairs * python-simplified-semver * front cards * end testing w travis * add mwcog test to gh-actions * add mwcog to docs * point to data not copy it * sort dependencies * req sh 2.2.4 * account for variance across platforms in trip dest est * copy bike skims for sandag test * param on rtol * fix sandag_2 test files * fix test file names * added pre-processor option to trip scheduling * trip scheduling relative mode initial commit * moved everything to mwcog example * adding output analysis notebook * adding additional segmentation * testing and documentation * blacken * not assuming scheduling mode is set * fixing merge trip scheduling * still fixing merge * reverting regression trips * fixing bad merge and updating test Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * adding annotate to trip mode choice * no earliest change if previous trip fail Co-authored-by: David Hensle <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> * adding locals_dict to annotate * chooser cols in final trips table * BayDAG merge with ActivitySim v1.2 (#56) * fixed logsums merge on households instead of persons * code cleanup * more cleanup * documentation and passing tests * passing tests * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * passing tests * ext cli arg * memory sidecar * restart if resume_after checkpoint is missing * no pandas 1.5 yet * stop the sidecar * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * minor repairs * skip when household_income is None * fixed missing column pipeline error * fixing pandas future warning * blacken * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * updated dependencies * always updating choices * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * testing removal of lognormal for hh vot * putting hh vot back in * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * updating to match sharrow test versions * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * raw person table for buffer instead of injectable * add mp test for prototype_mtc_extended * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * Update random.py * Updated test environment to reflect changes in pandas * Removed random random seed generation from placeholder_sandage 1-zone test configuration to get example to pass automated test * update sampling script * 'blacken' * fixed replacement sample bug * adding segmentation, output by iteration, and external worker removal * updated documentation * more flexible scenario testing * blacken * Added test_random_seed.py * blacken test_random_seed.py * Moved random seed generation testing out of prototype_mtc folder and edited core_tests.yaml to call it * Corrected name of check_outputs() * Added print statements to debug script * Blacken test_random_seed.py * keep alternative attributes in parking location * move coeff values to coeff csv * Added pipe character to call that tests the random generator * Added explicit call for pytest to run test_random_seed.py * Added print statement at start of script for debugging * Replaced single quotes with double quotes in print statement * reformat with Black * Moved random seed test into activitysim folder * Edited core_tests.yml to reflect change in location of random seed test * Renamed tests folder to test to reflect call in core-tests.yml * formatting & documentation * Added test_random_seed function for PyTest to read * Fixed defition of seeds list and removed print statements * updating github test env * responding to review comments * Added line to create output folder as that's not being committed * create_rng_configs() now copies entire example configs directory instead of just settings.yaml * Added try except statement when creating the output directory in case it already exists * additional logging, random seed option, landuse sample weight column * ensuring TAZ is not selected if no available MAZ * adding logic to skip external location choice models * Applied suggested changes * Removed activitysim\test\random_seed\configs directory to reduce confusion * Moved random seed test directory to folder that had already existed * temporarily constrain pandas #608 * work around psutil runtimeerror * temp constrain pandas * add mwcog full example * review responses * revisions per Sijia's comments, except for the proto-table-template implementation, still working. * added template pop option * blacken * set back to create_tables to pass test against old tables * updated proto-pop test data * resolved bad test data issue * warn don't fail on duplicate skims * include sharrow in mwcog example * cleanup * zarr digital encoding for mwcog * include reference in psrc mini * fow window ids to int64 because windows * handle expected warnings * unpin dependencies * columns cannot be a set * unpin pandas * columns cannot be a set * numeric_only args in groupby.sum * docs: correct the unit of `chunk_size`. * change 'arry' to more readable 'sizearray' * repair tests * catch FileNotFound * add check that land use is zero-based when using sharrow * better docs on skims in shared memory * better docstrings for skimdataset * remove old code * remove junk * add logging for recoding * optimize nearest zone determination * consistent multiprocessing results * blacken * updating regression trips * adding sandag 2-zone test * blacken * fix merge error * allow pandas 1.5 again * sharrow compatibility with #606 * remove outdated code in comments * note on tracing limitation * allow repeating key cols * fix decoding in MP output * escortee modes match chauf modes * updating regression tests * fixing bad var name in inbound expressions * add note about `condense_parameters` * change default condense_parameters to False * Update .gitignore Co-authored-by: Sijia Wang <[email protected]> * ignore caches * remove special install instructions * remove sharrow_skip's * Revert "remove sharrow_skip's" This reverts commit 6b52af2. * add note about why sharrow_skip is activated * Update school_escorting.yaml * Update config.py * arc trip destination spec skim correction * update regression trips * require sharrow 2.5 * fix mtc_ext for sharrow * fix test consistent with escort mode alignments * allow sharrow skipping * remove stray indent * delete expression values after sharrow testing to make debugging easier * require sharrow 2.5.2 * recode only once * testing repairs * note about why sharrow_skip * fork mtc_extended testing on shadow pricing and sharrow * note on sharrow_skip * size term scaling only for full run * reordering * multiprocessing hangs! * never scale size terms for disagg * tally pending persons * tests cleanup * fix error with orca * let pipeline tables be dropped * check on available MAZs, comment cleanup * work zone to -1 if wfh, removed unneeded extensions * fix tests for sandag 2zone * ignore deprecation warning in tests not clear why this started being a problem suddenly in only the xborder-MP model * add scikit-learn to formal dependencies * docs update for installer * fixing black to 22.12.0 * missed merge conflicts * fixing merge issues in prototype_semcog * fixing prototype_arc merge * fixing placeholder_sandag merge issues * blacken * fixing mwcog merge issues * skims not found during estimation test --------- Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeff Newman <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Joe Flood <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: amarin <[email protected]> * do not require all alts in data file * int8 to int16 lost in v1.2 merge --------- Co-authored-by: Lisa Zorn <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: Ashish Kulshrestha <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: JoeJimFlood <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: amarin <[email protected]> * docs: apply a minor correction to user guides (#659) * Trip scheduling logic (#660) * trip scheduling logic_version * in testing ignore the warning we just added * cannot use logic_version 1 with relative scheduling * Pin Dependencies (#665) * pinderella * pandas in setup.cfg deps * Updated SEMCOG Example (#603) * initial example_semcog commit * documentation * single process passing but not multiprocess * testing infrastructure * blacken * formatting * implemented stable sample for university extensions * adding ignored output folder * removed squared term and re-estimated * updating test env * calibrated configs * fixing bad merge * updated configs * reading in extension folder * updated shadowpricing yaml file * updated test regress * Revert "updated test regress" This reverts commit 8d5af7d. * updated regress test table * updated test regress table * updated cropped land use and skim * updated shadow pricing method * updated network_los to read segmented skims if needed * updated example_manifest.yaml * fixing conflicts * making fixes per review comments * push mistake! * Revert "making fixes per review comments" This reverts commit c05c7f3. * Revert "Revert "making fixes per review comments"" This reverts commit d83019a. * added back accidentally untracked output folder + updated regress table * misc small fixes --------- Co-authored-by: Ali Etezady <[email protected]> * syncronize (#680) issue templates into develop --------- Co-authored-by: Lisa Zorn <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: Ashish Kulshrestha <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: JoeJimFlood <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: amarin <[email protected]> * added documentation * no input checker to test develop merge * testing state object in input checker * adding pandera to dependencies * getting settings in sync * data_model_dir, checker logging, network data * allowing None for trace and resume_after settings * documentation * blacken * data_model dir added to test * cleanup * multiple errors & warnings * clarified warning msgs, fixed error counts * added auxiliary logging to input_checker * Added more descriptive input checker test names * Added info-level input checker logging * in-line documentation cleanup * test_input_checker initial commit (not passing) * Clean up input checker log message styles * Add MTC example input checks, cleanup * reformat code with black * Fixed pytest fixture scope issue * change networklinks path to platform-agnostic path * add input checker to mtc extended test * Input checker bugfixes, added SEMCOG example - Updated pytables dependency version to fix deprecation warnings - Added flexible resolve for external input checker file paths (can be absolute paths or paths relative to one of the data directories) - Added data_model directory to prototype_mtc_example files - Added input_checker config yamls to SEMCOG example - Added sample network data to SEMCOG example * Add SEMCOG input check files * Formatting previous commit * Add missing file handling to input checker * Blackening previous commit * Added input checking relative to calling dir * cleanup and documentation * Input checker path bugfix, MTC reversion * suspend buggy test Suspend test per ActivitySim issue #781 * fix progressive test * fix external url * drop extra file * remove extra imports * remove vscode file * pydantic not implemented comments --------- Co-authored-by: Ali Etezady <[email protected]> Co-authored-by: Lisa Zorn <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: Ashish Kulshrestha <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Andrew Rohne <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: David Hensle <[email protected]> Co-authored-by: JoeJimFlood <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: amarin <[email protected]> Co-authored-by: Will <[email protected]> Co-authored-by: Jeff Newman <[email protected]>

* fixed logsums merge on households instead of persons * code cleanup * more cleanup * documentation and passing tests * passing tests * fixed _accessibility suffix * fixed conflict with persons_merged * updated yaml to use simpler join method * PEP formatting fixes * refreshed example folder from develop * added missing line at end of file * black fixes * black fixes to disaggregate accessibility changes * passing tests * ext cli arg * memory sidecar * restart if resume_after checkpoint is missing * no pandas 1.5 yet * stop the sidecar * updated doc on shadow pricing * 2nd Update model doc on shadow pricing * more doc update on shadow pricing * minor repairs * skip when household_income is None * fixed missing column pipeline error * fixing pandas future warning * blacken * merged disagg accessibilities into mtc_extended and added doc section * ran black on disaggregate_accessibility.py * bug in trying to access shadow price settings when not running shadow pricing * limiting pandas version * updated dependencies * always updating choices * removing sklearn imports * blacken * add if none catch * fixed None suffix default * moved order of get_table(persons_merged) to avoid pulling prematurely in xborder * testing removal of lognormal for hh vot * putting hh vot back in * tested and cleaned up rng channels * setup injectable suffixes to allow add_size_table as model step not just function * removed accessibility output from test * re blacken py scripts * updating to match sharrow test versions * fixed tracing typo * added variable index name suffix to pass optionally * pipeline housekeeping to cleanup any tables, traceables, or channels that were touched during disagg * added multiprocess testing * blacken updates * updated test scripts to include MP, problem with vehicle model in mp (even without disagg acc?) * added improved origin sampling, resolved issue with merging with sample <100%. Need to address random seed for origins * added sci-kit learn to test depends * fixed person merging error causing pytest fail, uses inject method to ensure consistency * cleanup comments * fixed pytest to include accessibility table in regress * setup for mp test, but needs debugging * 'blacken' * 'blacken' * cleanup example folder * fixed pipeline NoneType bug for disagg accessibility table * raw person table for buffer instead of injectable * add mp test for prototype_mtc_extended * fixed pytest fail on mp, due to exept:True on mp_simulate * 'blacken' * added weighted k-means method * created run script for multiple sampling scenarios * blacken changes * blacken * fixed copy script * blacken sampling script * fixed n_zone when integer * fixed typo * Update random.py * Updated test environment to reflect changes in pandas * Removed random random seed generation from placeholder_sandage 1-zone test configuration to get example to pass automated test * update sampling script * 'blacken' * fixed replacement sample bug * adding segmentation, output by iteration, and external worker removal * updated documentation * more flexible scenario testing * blacken * Added test_random_seed.py * blacken test_random_seed.py * Moved random seed generation testing out of prototype_mtc folder and edited core_tests.yaml to call it * Corrected name of check_outputs() * Added print statements to debug script * Blacken test_random_seed.py * keep alternative attributes in parking location * move coeff values to coeff csv * Added pipe character to call that tests the random generator * Added explicit call for pytest to run test_random_seed.py * Added print statement at start of script for debugging * Replaced single quotes with double quotes in print statement * reformat with Black * Moved random seed test into activitysim folder * Edited core_tests.yml to reflect change in location of random seed test * Renamed tests folder to test to reflect call in core-tests.yml * formatting & documentation * Added test_random_seed function for PyTest to read * Fixed defition of seeds list and removed print statements * updating github test env * responding to review comments * Added line to create output folder as that's not being committed * create_rng_configs() now copies entire example configs directory instead of just settings.yaml * Added try except statement when creating the output directory in case it already exists * additional logging, random seed option, landuse sample weight column * ensuring TAZ is not selected if no available MAZ * adding logic to skip external location choice models * Applied suggested changes * Removed activitysim\test\random_seed\configs directory to reduce confusion * Moved random seed test directory to folder that had already existed * temporarily constrain pandas ActivitySim#608 * work around psutil runtimeerror * temp constrain pandas * add mwcog full example * review responses * revisions per Sijia's comments, except for the proto-table-template implementation, still working. * added template pop option * blacken * set back to create_tables to pass test against old tables * updated proto-pop test data * resolved bad test data issue * warn don't fail on duplicate skims * include sharrow in mwcog example * cleanup * zarr digital encoding for mwcog * include reference in psrc mini * fow window ids to int64 because windows * handle expected warnings * unpin dependencies * columns cannot be a set * unpin pandas * columns cannot be a set * numeric_only args in groupby.sum * docs: correct the unit of `chunk_size`. * change 'arry' to more readable 'sizearray' * repair tests * catch FileNotFound * add check that land use is zero-based when using sharrow * better docs on skims in shared memory * better docstrings for skimdataset * remove old code * remove junk * add logging for recoding * optimize nearest zone determination * consistent multiprocessing results * blacken * updating regression trips * adding sandag 2-zone test * blacken * fix merge error * allow pandas 1.5 again * sharrow compatibility with ActivitySim#606 * remove outdated code in comments * note on tracing limitation * allow repeating key cols * fix decoding in MP output * escortee modes match chauf modes * updating regression tests * fixing bad var name in inbound expressions * add note about `condense_parameters` * change default condense_parameters to False * Update .gitignore Co-authored-by: Sijia Wang <[email protected]> * ignore caches * remove special install instructions * remove sharrow_skip's * Revert "remove sharrow_skip's" This reverts commit 6b52af2. * add note about why sharrow_skip is activated * Update school_escorting.yaml * Update config.py * arc trip destination spec skim correction * update regression trips * require sharrow 2.5 * fix mtc_ext for sharrow * fix test consistent with escort mode alignments * allow sharrow skipping * remove stray indent * delete expression values after sharrow testing to make debugging easier * require sharrow 2.5.2 * recode only once * testing repairs * note about why sharrow_skip * fork mtc_extended testing on shadow pricing and sharrow * note on sharrow_skip * size term scaling only for full run * reordering * multiprocessing hangs! * never scale size terms for disagg * tally pending persons * tests cleanup * fix error with orca * let pipeline tables be dropped * check on available MAZs, comment cleanup * work zone to -1 if wfh, removed unneeded extensions * fix tests for sandag 2zone * ignore deprecation warning in tests not clear why this started being a problem suddenly in only the xborder-MP model * add scikit-learn to formal dependencies * docs update for installer * fixing black to 22.12.0 * missed merge conflicts * fixing merge issues in prototype_semcog * fixing prototype_arc merge * fixing placeholder_sandag merge issues * blacken * fixing mwcog merge issues * skims not found during estimation test --------- Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Jeff Newman <[email protected]> Co-authored-by: aletzdy <[email protected]> Co-authored-by: Jeffrey Newman <[email protected]> Co-authored-by: Nick Fournier <[email protected]> Co-authored-by: Joe Flood <[email protected]> Co-authored-by: Sijia Wang <[email protected]> Co-authored-by: amarin <[email protected]>

jiffyclub added 6 commits May 26, 2015 14:15

Starting ActivitySim sphinx docs

40c2cac

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Add numpydoc, sphinx-rtd-theme to sphinx config

21fe7b6

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Add intro the root doc page

7d40e8c

[ci skip]

Starting installation docs

a9d221e

[ci skip]

Finish installation docs

eeb38f8

[ci skip]

add script to automatically build docs on travis

00f308d

jiffyclub added a commit that referenced this pull request Jun 1, 2015

Merge pull request #56 from synthicity/sphinx-docs

c2ab75e

Starting Sphinx Docs

jiffyclub merged commit c2ab75e into master Jun 1, 2015

jiffyclub deleted the sphinx-docs branch June 1, 2015 21:04

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