.. _issues_list_05: Issues closed in the 0.5.0 development cycle ============================================ Issued closed in 0.5.0 ----------------------- GitHub stats for release 0.5.0 (07/02/2012/ - 08/14/2013/). We closed a total of 380 issues, 172 pull requests and 208 regular issues. This is the full list (generated with the script :file:`tools/github_stats.py`): This list is automatically generated, and may be incomplete: Pull Requests (172): * :ghpull:`1015`: DOC: Bump version. Remove done tasks. * :ghpull:`1010`: DOC/RLS: Update release notes workflow. Help Needed! * :ghpull:`1014`: DOC: nbgenerate does not like the comment at end of line. * :ghpull:`1012`: DOC: Add link to notebook and crosslink ref. Closes #924. * :ghpull:`997`: misc, tests, diagnostic * :ghpull:`1009`: MAINT: Add .mailmap file. * :ghpull:`817`: Add 3 new unit tests for arima_process * :ghpull:`1001`: BUG include_package_data for install closes #907 * :ghpull:`1005`: GITHUB: Contributing guidlines * :ghpull:`1007`: Cleanup docs for release * :ghpull:`1003`: BUG: Workaround for bug in sphinx 1.1.3. See #1002. * :ghpull:`1004`: DOC: Update maintainer notes with branching instructions. * :ghpull:`1000`: BUG: Support pandas 0.8.0. * :ghpull:`996`: BUG: Handle combo of pandas 0.8.0 and dateutils 1.5.0 * :ghpull:`995`: ENH: Print dateutil version. * :ghpull:`994`: ENH: Fail gracefully for version not found. * :ghpull:`993`: More conservative error catching in TimeSeriesModel * :ghpull:`992`: Misc fixes 12: adjustments to unit test * :ghpull:`985`: MAINT: Print versions script. * :ghpull:`986`: ENH: Prefer to_offset to get_offset. Closes #964. * :ghpull:`984`: COMPAT: Pandas 0.8.1 compatibility. Closes #983. * :ghpull:`982`: Misc fixes 11 * :ghpull:`978`: TST: generic mle pareto disable bsejac tests with estimated loc * :ghpull:`977`: BUG python 3.3 fix for numpy str TypeError, see #633 * :ghpull:`975`: Misc fixes 10 numdiff * :ghpull:`970`: BUG: array too long, raises exception with newer numpy closes #967 * :ghpull:`965`: Vincent summary2 rebased * :ghpull:`933`: Update and improve GenericlikelihoodModel and miscmodels * :ghpull:`950`: BUG/REF mcnemar fix exact pvalue, allow table as input * :ghpull:`951`: Pylint emplike formula genmod * :ghpull:`956`: Fix a docstring in KDEMultivariateConditional. * :ghpull:`949`: BUG fix lowess sort when nans closes #946 * :ghpull:`932`: ENH: support basinhopping solver in LikelihoodModel.fit() * :ghpull:`927`: DOC: clearer minimal example * :ghpull:`919`: Ols summary crash * :ghpull:`918`: Fixes10 emplike lowess * :ghpull:`909`: Bugs in GLM pvalues, more tests, pylint * :ghpull:`906`: ENH: No fmax with Windows SDK so define inline. * :ghpull:`905`: MAINT more fixes * :ghpull:`898`: Misc fixes 7 * :ghpull:`896`: Quantreg rebase2 * :ghpull:`895`: Fixes issue #832 * :ghpull:`893`: ENH: Remove unneeded restriction on low. Closes #867. * :ghpull:`894`: MAINT: Remove broken function. Keep deprecation. Closes #781. * :ghpull:`856`: Carljv improved lowess rebased2 * :ghpull:`884`: Pyflakes cleanup * :ghpull:`887`: BUG: Fix kde caching * :ghpull:`883`: Fixed pyflakes issue in discrete module * :ghpull:`882`: Update predstd.py * :ghpull:`871`: Update of sandbox doc * :ghpull:`631`: WIP: Correlation positive semi definite * :ghpull:`857`: BLD: apt get dependencies from Neurodebian, whitespace cleanup * :ghpull:`855`: AnaMP issue 783 mixture rvs tests rebased * :ghpull:`854`: Enrico multinear rebased * :ghpull:`849`: Tyler tukeyhsd rebased * :ghpull:`848`: BLD TravisCI use python-dateutil package * :ghpull:`784`: Misc07 cleanup multipletesting and proportions * :ghpull:`841`: ENH: Add load function to main API. Closes #840. * :ghpull:`820`: Ensure that tuples are not considered as data, not as data containers * :ghpull:`822`: DOC: Update for Cython changes. * :ghpull:`765`: Fix build issues * :ghpull:`800`: Automatically generate output from notebooks * :ghpull:`802`: BUG: Use two- not one-sided t-test in t_test. Closes #740. * :ghpull:`806`: ENH: Import formula.api in statsmodels.api namespace. * :ghpull:`803`: ENH: Fix arima error message for bad start_params * :ghpull:`801`: DOC: Fix ANOVA section titles * :ghpull:`795`: Negative Binomial Rebased * :ghpull:`787`: Origintests * :ghpull:`794`: ENH: Allow pandas-in/pandas-out in tsa.filters * :ghpull:`791`: Github stats for release notes * :ghpull:`779`: added np.asarray call to durbin_watson in stattools * :ghpull:`772`: Anova docs * :ghpull:`776`: BUG: Fix dates_from_range with length. Closes #775. * :ghpull:`774`: BUG: Attach prediction start date in AR. Closes #773. * :ghpull:`767`: MAINT: Remove use of deprecated from examples and docs. * :ghpull:`762`: ENH: Add new residuals to wrapper * :ghpull:`754`: Fix arima predict * :ghpull:`760`: ENH: Adjust for k_trend in information criteria. Closes #324. * :ghpull:`761`: ENH: Fixes and tests sign_test. Closes #642. * :ghpull:`759`: Fix 236 * :ghpull:`758`: DOC: Update VAR docs. Closes #537. * :ghpull:`752`: Discrete cleanup * :ghpull:`750`: VAR with 1d array * :ghpull:`748`: Remove reference to new_t_test and new_f_test. * :ghpull:`739`: DOC: Remove outdated note in docstring * :ghpull:`732`: BLD: Check for patsy dependency at build time + docs * :ghpull:`731`: Handle wrapped * :ghpull:`730`: Fix opt fulloutput * :ghpull:`729`: Get rid of warnings in docs build * :ghpull:`698`: update url for hsb2 dataset * :ghpull:`727`: DOC: Fix indent and add missing params to linear models. Closes #709. * :ghpull:`726`: CLN: Remove unused method. Closes #694 * :ghpull:`725`: BUG: Should call anova_single. Closes #702. * :ghpull:`723`: Rootfinding for Power * :ghpull:`722`: Handle pandas.Series with names in make_lags * :ghpull:`714`: Fix 712 * :ghpull:`668`: Allow for any pandas frequency to be used in TimeSeriesModel. * :ghpull:`711`: Misc06 - bug fixes * :ghpull:`708`: BUG: Fix one regressor case for conf_int. Closes #706. * :ghpull:`700`: Bugs rebased * :ghpull:`680`: BUG: Swap arguments in fftconvolve for scipy >= 0.12.0 * :ghpull:`640`: Misc fixes 05 * :ghpull:`663`: a typo in runs.py doc string for mcnemar test * :ghpull:`652`: WIP: fixing pyflakes / pep8, trying to improve readability * :ghpull:`619`: DOC: intro to formulas * :ghpull:`648`: BF: Make RLM stick to Huber's description * :ghpull:`649`: Bug Fix * :ghpull:`637`: Pyflakes cleanup * :ghpull:`634`: VAR DOC typo * :ghpull:`623`: Slowtests * :ghpull:`621`: MAINT: in setup.py, only catch ImportError for pandas. * :ghpull:`590`: Cleanup test output * :ghpull:`591`: Interrater agreement and reliability measures * :ghpull:`618`: Docs fix the main warnings and errors during sphinx build * :ghpull:`610`: nonparametric examples and some fixes * :ghpull:`578`: Fix 577 * :ghpull:`575`: MNT: Remove deprecated scikits namespace * :ghpull:`499`: WIP: Handle constant * :ghpull:`567`: Remove deprecated * :ghpull:`571`: Dataset docs * :ghpull:`561`: Grab rdatasets * :ghpull:`570`: DOC: Fixed links to Rdatasets * :ghpull:`524`: DOC: Clean up discrete model documentation. * :ghpull:`506`: ENH: Re-use effects if model fit with QR * :ghpull:`556`: WIP: L1 doc fix * :ghpull:`564`: TST: Use native integer to avoid issues in dtype asserts * :ghpull:`543`: Travis CI using M.Brett nipy hack * :ghpull:`558`: Plot cleanup * :ghpull:`541`: Replace pandas DataMatrix with DataFrame * :ghpull:`534`: Stata test fixes * :ghpull:`532`: Compat 323 * :ghpull:`531`: DOC: Add ECDF to distributions docs * :ghpull:`526`: ENH: Add class to write Stata binary dta files * :ghpull:`521`: DOC: Add abline plot to docs * :ghpull:`518`: Small fixes: interaction_plot * :ghpull:`508`: ENH: Avoid taking cholesky decomposition of diagonal matrix * :ghpull:`509`: DOC: Add ARIMA to docs * :ghpull:`510`: DOC: realdpi is disposable personal income. Closes #394. * :ghpull:`507`: ENH: Protect numdifftools import. Closes #45 * :ghpull:`504`: Fix weights * :ghpull:`498`: DOC: Add patys requirement to install docs * :ghpull:`491`: Make _data a public attribute. * :ghpull:`494`: DOC: Fix pandas links * :ghpull:`492`: added intersphinx for pandas * :ghpull:`422`: Handle missing data * :ghpull:`485`: ENH: Improve error message for pandas objects without dates in index * :ghpull:`428`: Remove other data * :ghpull:`483`: Arima predict bug * :ghpull:`482`: TST: Do array-array comparison when using numpy.testing * :ghpull:`471`: Formula rename df -> data * :ghpull:`473`: Vincent docs tweak rebased * :ghpull:`468`: Docs 050 * :ghpull:`462`: El aft rebased * :ghpull:`461`: TST: numpy 1.5.1 compatibility * :ghpull:`460`: Emplike desc reg rebase * :ghpull:`410`: Discrete model marginal effects * :ghpull:`417`: Numdiff cleanup * :ghpull:`398`: Improved plot_corr and plot_corr_grid functions. * :ghpull:`401`: BUG: Finish refactoring margeff for dummy. Closes #399. * :ghpull:`400`: MAINT: remove lowess.py, which was kept in 0.4.x for backwards compatibi... * :ghpull:`371`: BF+TEST: fixes, checks and tests for isestimable * :ghpull:`351`: ENH: Copy diagonal before write for upcoming numpy changes * :ghpull:`384`: REF: Move mixture_rvs out of sandbox. * :ghpull:`368`: ENH: Add polished version of acf/pacf plots with confidence intervals * :ghpull:`378`: Infer freq * :ghpull:`374`: ENH: Add Fair's extramarital affair dataset. From tobit-model branch. * :ghpull:`358`: ENH: Add method to OLSResults for outlier detection * :ghpull:`369`: ENH: allow predict to pass through patsy for transforms * :ghpull:`352`: Formula integration rebased * :ghpull:`360`: REF: Deprecate order in fit and move to ARMA init * :ghpull:`366`: Version fixes * :ghpull:`359`: DOC: Fix sphinx warnings Issues (208): * :ghissue:`1036`: Series no longer inherits from ndarray * :ghissue:`1038`: DataFrame with integer names not handled in ARIMA * :ghissue:`1028`: Test fail with windows and Anaconda - Low priority * :ghissue:`676`: acorr_breush_godfrey undefined nlags * :ghissue:`922`: lowess returns inconsistent with option * :ghissue:`425`: no bse in robust with norm=TrimmedMean * :ghissue:`1025`: add_constant incorrectly detects constant column * :ghissue:`533`: py3 compatibility ``pandas.read_csv(urlopen(...))`` * :ghissue:`662`: doc: install instruction: explicit about removing scikits.statsmodels * :ghissue:`910`: test failure Ubuntu TestARMLEConstant.test_dynamic_predict * :ghissue:`80`: t_model: f_test, t_test don't work * :ghissue:`432`: GenericLikelihoodModel change default for score and hessian * :ghissue:`454`: BUG/ENH: HuberScale instance is not used, allow user defined scale estimator * :ghissue:`98`: check connection or connect summary to variable names in wrappers * :ghissue:`418`: BUG: MNLogit loglikeobs, jac * :ghissue:`1017`: nosetests warnings * :ghissue:`924`: DOCS link in notebooks to notebook for download * :ghissue:`1011`: power ttest endless loop possible * :ghissue:`907`: BLD data_files for stats.libqsturng * :ghissue:`328`: consider moving example scripts into IPython notebooks * :ghissue:`1002`: Docs won't build with Sphinx 1.1.3 * :ghissue:`69`: Make methods like compare_ftest work with wrappers * :ghissue:`503`: summary_old in RegressionResults * :ghissue:`991`: TST precision of normal_power * :ghissue:`945`: Installing statsmodels from github? * :ghissue:`964`: Prefer to_offset not get_offset in tsa stuff * :ghissue:`983`: bug: pandas 0.8.1 incompatibility * :ghissue:`899`: build_ext inplace doesn't cythonize * :ghissue:`923`: location of initialization code * :ghissue:`980`: auto lag selection in S_hac_simple * :ghissue:`968`: genericMLE Ubuntu test failure * :ghissue:`633`: python 3.3 compatibility * :ghissue:`728`: test failure for solve_power with fsolve * :ghissue:`971`: numdiff test cases * :ghissue:`976`: VAR Model does not work in 1D * :ghissue:`972`: numdiff: epsilon has no minimum value * :ghissue:`967`: lowes test failure Ubuntu * :ghissue:`948`: nonparametric tests: mcnemar, cochranq unit test * :ghissue:`963`: BUG in runstest_2sample * :ghissue:`946`: Issue with lowess() smoother in statsmodels * :ghissue:`868`: k_vars > nobs * :ghissue:`917`: emplike emplikeAFT stray dimensions * :ghissue:`264`: version comparisons need to be made more robust (may be just use LooseVersion) * :ghissue:`674`: failure in test_foreign, pandas testing * :ghissue:`828`: GLMResults inconsistent distribution in pvalues * :ghissue:`908`: RLM missing test for tvalues, pvalues * :ghissue:`463`: formulas missing in docs * :ghissue:`256`: discrete Nbin has zero test coverage * :ghissue:`831`: test errors running bdist * :ghissue:`733`: Docs: interrater cohens_kappa is missing * :ghissue:`897`: lowess failure - sometimes * :ghissue:`902`: test failure tsa.filters precision too high * :ghissue:`901`: test failure stata_writer_pandas, newer versions of pandas * :ghissue:`900`: ARIMA.__new__ errors on python 3.3 * :ghissue:`832`: notebook errors * :ghissue:`867`: Baxter King has unneeded limit on value for low? * :ghissue:`781`: discreteResults margeff method not tests, obsolete * :ghissue:`870`: discrete unit tests duplicates * :ghissue:`630`: problems in regression plots * :ghissue:`885`: Caching behavior for KDEUnivariate icdf * :ghissue:`869`: sm.tsa.ARMA(..., order=(p,q)) gives "__init__() got an unexpected keyword argument 'order'" error * :ghissue:`783`: statsmodels\distributions\mixture_rvs.py no unit tests * :ghissue:`824`: Multicomparison w/Pandas Series * :ghissue:`789`: presentation of multiple comparison results * :ghissue:`764`: BUG: multipletests incorrect reject for Holm-Sidak * :ghissue:`766`: multipletests - status and tests of 2step FDR procedures * :ghissue:`763`: Bug: multipletests raises exception with empty array * :ghissue:`840`: sm.load should be in the main API namespace * :ghissue:`830`: invalid version number * :ghissue:`821`: Fail gracefully when extensions are not built * :ghissue:`204`: Cython extensions built twice? * :ghissue:`689`: tutorial notebooks * :ghissue:`740`: why does t_test return one-sided p-value * :ghissue:`804`: What goes in statsmodels.formula.api? * :ghissue:`675`: Improve error message for ARMA SVD convergence failure. * :ghissue:`15`: arma singular matrix * :ghissue:`559`: Add Rdatasets to optional dependencies list * :ghissue:`796`: Prediction Standard Errors * :ghissue:`793`: filters are not pandas aware * :ghissue:`785`: Negative R-squared * :ghissue:`777`: OLS residuals returned as Pandas series when endog and exog are Pandas series * :ghissue:`770`: Add ANOVA to docs * :ghissue:`775`: Bug in dates_from_range * :ghissue:`773`: AR model pvalues error with Pandas * :ghissue:`768`: multipletests: numerical problems at threshold * :ghissue:`355`: add draw if interactive to plotting functions * :ghissue:`625`: Exog is not correctly handled in ARIMA predict * :ghissue:`626`: ARIMA summary does not print exogenous variable coefficients * :ghissue:`657`: order (0,1) breaks ARMA forecast * :ghissue:`736`: ARIMA predict problem for ARMA model * :ghissue:`324`: ic in ARResults, aic, bic, hqic, fpe inconsistent definition? * :ghissue:`642`: sign_test check * :ghissue:`236`: AR start_params broken * :ghissue:`235`: tests hang on Windows * :ghissue:`156`: matplotlib deprecated legend ? var plots * :ghissue:`331`: Remove stale tests * :ghissue:`592`: test failures in datetools * :ghissue:`537`: Var Models * :ghissue:`755`: Unable to access AR fit parameters when model is estimated with pandas.DataFrame * :ghissue:`670`: discrete: numerically useless clipping * :ghissue:`515`: MNLogit residuals raise a TypeError * :ghissue:`225`: discrete models only define deviance residuals * :ghissue:`594`: remove skiptest in TestProbitCG * :ghissue:`681`: Dimension Error in discrete_model.py When Running test_dummy_* * :ghissue:`744`: DOC: new_f_test * :ghissue:`549`: Ship released patsy source in statsmodels * :ghissue:`588`: patsy is a hard dependency? * :ghissue:`716`: Tests missing for functions if pandas is used * :ghissue:`715`: statmodels regression plots not working with pandas datatypes * :ghissue:`450`: BUG: full_output in optimizers Likelihood model * :ghissue:`709`: DOCstrings linear models don't have missing params * :ghissue:`370`: BUG weightstats has wrong cov * :ghissue:`694`: DiscreteMargins duplicate method * :ghissue:`702`: bug, pylint stats.anova * :ghissue:`423`: Handling of constant across models * :ghissue:`456`: BUG: ARMA date handling incompatibility with recent pandas * :ghissue:`514`: NaNs in Multinomial * :ghissue:`405`: Check for existing old version of scikits.statsmodels? * :ghissue:`586`: Segmentation fault with OLS * :ghissue:`721`: Unable to run AR on named time series objects * :ghissue:`125`: caching pinv_wexog broke iterative fit - GLSAR * :ghissue:`712`: TSA bug with frequency inference * :ghissue:`319`: Timeseries Frequencies * :ghissue:`707`: .summary with alpha ignores parsed value * :ghissue:`673`: nonparametric: bug in _kernel_base * :ghissue:`710`: test_power failures * :ghissue:`706`: .conf_int() fails on linear regression without intercept * :ghissue:`679`: Test Baxter King band-pass filter fails with scipy 0.12 beta1 * :ghissue:`552`: influence outliers breaks when regressing on constant * :ghissue:`639`: test folders not on python path * :ghissue:`565`: omni_normtest doesn't propagate the axis argument * :ghissue:`563`: error in doc generation for AR.fit * :ghissue:`109`: TestProbitCG failure on Ubuntu * :ghissue:`661`: from scipy import comb fails on the latest scipy 0.11.0 * :ghissue:`413`: DOC: example_discrete.py missing from 0.5 documentation * :ghissue:`644`: FIX: factor plot + examples broken * :ghissue:`645`: STY: pep8 violations in many examples * :ghissue:`173`: doc sphinx warnings * :ghissue:`601`: bspline.py dependency on old scipy.stats.models * :ghissue:`103`: ecdf and step function conventions * :ghissue:`18`: Newey-West sandwich covariance is missing * :ghissue:`279`: cov_nw_panel not tests, example broken * :ghissue:`150`: precision in test_discrete.TestPoissonNewton.test_jac ? * :ghissue:`480`: rescale loglike for optimization * :ghissue:`627`: Travis-CI support for scipy * :ghissue:`622`: mark tests as slow in emplike * :ghissue:`589`: OLS F-statistic error * :ghissue:`572`: statsmodels/tools/data.py Stuck looking for la.py * :ghissue:`580`: test errors in graphics * :ghissue:`577`: PatsyData detection buglet * :ghissue:`470`: remove deprecated features * :ghissue:`573`: lazy imports are (possibly) very slow * :ghissue:`438`: New results instances are not in online documentation * :ghissue:`542`: Regression plots fail when Series objects passed to sm.OLS * :ghissue:`239`: release 0.4.x * :ghissue:`530`: l1 docs issues * :ghissue:`539`: test for statwriter (failure) * :ghissue:`490`: Travis CI on PRs * :ghissue:`252`: doc: distributions.rst refers to sandbox only * :ghissue:`85`: release 0.4 * :ghissue:`65`: MLE fit of AR model has no tests * :ghissue:`522`: ``test`` doesn't propagate arguments to nose * :ghissue:`517`: missing array conversion or shape in linear model * :ghissue:`523`: test failure with ubuntu decimals too large * :ghissue:`520`: web site documentation, source not updated * :ghissue:`488`: Avoid cholesky decomposition of diagonal matrices in linear regression models * :ghissue:`394`: Definition in macrodata NOTE * :ghissue:`45`: numdifftools dependency * :ghissue:`501`: WLS/GLS post estimation results * :ghissue:`500`: WLS fails if weights is a pandas.Series * :ghissue:`27`: add hasconstant indicator for R-squared and df calculations * :ghissue:`497`: DOC: add patsy? * :ghissue:`495`: ENH: add footer SimpleTable * :ghissue:`402`: model._data -> model.data? * :ghissue:`477`: VAR NaN Bug * :ghissue:`421`: Enhancment: Handle Missing Data * :ghissue:`489`: Expose model._data as model.data * :ghissue:`315`: tsa models assume pandas object indices are dates * :ghissue:`440`: arima predict is broken for steps > q and q != 1 * :ghissue:`458`: TST BUG? comparing pandas and array in tests, formula * :ghissue:`464`: from_formula signature * :ghissue:`245`: examples in docs: make nicer * :ghissue:`466`: broken example, pandas * :ghissue:`57`: Unhelpful error from bad exog matrix in model.py * :ghissue:`271`: ARMA.geterrors requires model to be fit * :ghissue:`350`: Writing to array returned np.diag * :ghissue:`354`: example_rst does not copy unchanged files over * :ghissue:`467`: Install issues with Pandas * :ghissue:`444`: ARMA example on stable release website not working * :ghissue:`377`: marginal effects count and discrete adjustments * :ghissue:`426`: "svd" method not supported for OLS.fit() * :ghissue:`409`: Move numdiff out of the sandbox * :ghissue:`416`: Switch to complex-step Hessian for AR(I)MA * :ghissue:`415`: bug in kalman_loglike_complex * :ghissue:`397`: plot_corr axis text labeling not working (with fix) * :ghissue:`399`: discrete errors due to incorrect in-place operation * :ghissue:`389`: VAR test_normality is broken with KeyError * :ghissue:`388`: Add tsaplots to graphics.api as graphics.tsa * :ghissue:`387`: predict date wasn't getting set with start = None * :ghissue:`386`: p-values not returned from acf * :ghissue:`385`: Allow AR.select_order to work without model being fit * :ghissue:`383`: Move mixture_rvs out of sandbox. * :ghissue:`248`: ARMA breaks with a 1d exog * :ghissue:`273`: When to give order for AR/AR(I)MA * :ghissue:`363`: examples folder -> tutorials folder * :ghissue:`346`: docs in sitepackages * :ghissue:`353`: PACF docs raise a sphinx warning * :ghissue:`348`: python 3.2.3 test failure zip_longest