lifelines 0.28.0__tar.gz → 0.29.0__tar.gz

{lifelines-0.28.0/lifelines.egg-info → lifelines-0.29.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lifelines
-Version: 0.28.0
+Version: 0.29.0
 Summary: Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regression
 Home-page: https://github.com/CamDavidsonPilon/lifelines
 Author: Cameron Davidson-Pilon
@@ -17,8 +17,8 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy<2.0,>=1.14.0
-Requires-Dist: scipy>=1.2.0
-Requires-Dist: pandas>=1.2.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: pandas>=2.1
 Requires-Dist: matplotlib>=3.0
 Requires-Dist: autograd>=1.5
 Requires-Dist: autograd-gamma>=0.3
@@ -50,8 +50,8 @@ If you are new to survival analysis, wondering why it is useful, or are interest
 
 ## Contact
  - Start a conversation in our [Discussions room](https://github.com/CamDavidsonPilon/lifelines/discussions).
- - Some users have posted common questions at [stats.stackexchange.com](https://stats.stackexchange.com/search?tab=votes&q=%22lifelines%22%20is%3aquestion)
- - creating an issue in the [Github repository](https://github.com/camdavidsonpilon/lifelines).
+ - Some users have posted common questions at [stats.stackexchange.com](https://stats.stackexchange.com/search?tab=votes&q=%22lifelines%22%20is%3aquestion).
+ - Creating an issue in the [Github repository](https://github.com/camdavidsonpilon/lifelines).
 
 ## Development
 

{lifelines-0.28.0 → lifelines-0.29.0}/README.md

@@ -24,8 +24,8 @@ If you are new to survival analysis, wondering why it is useful, or are interest
 
 ## Contact
  - Start a conversation in our [Discussions room](https://github.com/CamDavidsonPilon/lifelines/discussions).
- - Some users have posted common questions at [stats.stackexchange.com](https://stats.stackexchange.com/search?tab=votes&q=%22lifelines%22%20is%3aquestion)
- - creating an issue in the [Github repository](https://github.com/camdavidsonpilon/lifelines).
+ - Some users have posted common questions at [stats.stackexchange.com](https://stats.stackexchange.com/search?tab=votes&q=%22lifelines%22%20is%3aquestion).
+ - Creating an issue in the [Github repository](https://github.com/camdavidsonpilon/lifelines).
 
 ## Development
 

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/datasets/__init__.py

@@ -54,7 +54,7 @@ def load_multicenter_aids_cohort_study(**kwargs):
     """
     Originally in [1]::
 
-        Siz: (78, 4)
+        Size: (78, 4)
 
         AIDSY: date of AIDS diagnosis
         W: years from AIDS diagnosis to study entry

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/fitters/__init__.py

@@ -18,7 +18,7 @@ from autograd.misc import flatten
 import autograd.numpy as anp
 
 from scipy.optimize import minimize, root_scalar
-from scipy.integrate import trapz
+from scipy.integrate import trapezoid
 from scipy import stats
 
 import pandas as pd
@@ -573,7 +573,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
 
             # convergence successful.
             # I still need to check for ~np.isnan(minimizing_results.x).any() since minimize will happily
-            # return nans even when criteria is satisified.
+            # return nans even when criteria is satisfied.
             if minimizing_results and minimizing_results.success and ~np.isnan(minimizing_results.x).any():
                 sol = utils._to_1d_array(minimizing_results.x)
                 # pylint: disable=no-value-for-parameter
@@ -876,7 +876,7 @@ class ParametricUnivariateFitter(UnivariateFitter):
           length n, the end of the period the subject experienced the event in. If the value is equal to the corresponding value in lower_bound, then
           the individual's event was observed (not censored).
         event_observed: numpy array or pd.Series, optional
-          length n, if left optional, infer from ``lower_bound`` and ``upper_cound`` (if lower_bound==upper_bound then event observed, if lower_bound < upper_bound, then event censored)
+          length n, if left optional, infer from ``lower_bound`` and ``upper_bound`` (if lower_bound==upper_bound then event observed, if lower_bound < upper_bound, then event censored)
         timeline: list, optional
             return the estimate at the values in timeline (positively increasing)
         label: string, optional
@@ -1925,7 +1925,7 @@ class ParametricRegressionFitter(RegressionFitter):
     def _fit_model(
         self, likelihood, Ts, Xs, E, weights, entries, fit_options, show_progress=False, user_supplied_initial_point=None
     ):
-        inital_points_as_arrays, unflatten_array_to_dict = self._prepare_initial_points(
+        initial_points_as_arrays, unflatten_array_to_dict = self._prepare_initial_points(
             user_supplied_initial_point, Ts, E, entries, weights, Xs
         )
 
@@ -1939,7 +1939,7 @@ class ParametricRegressionFitter(RegressionFitter):
 
         minimum_ll = np.inf
         minimum_results = None
-        for _initial_point in inital_points_as_arrays:
+        for _initial_point in initial_points_as_arrays:
 
             if _initial_point.shape[0] != Xs.columns.size:
                 raise ValueError("initial_point is not the correct shape.")
@@ -2507,7 +2507,7 @@ class ParametricRegressionFitter(RegressionFitter):
         warnings.warn("""Approximating the expected value using trapezoid rule.\n""", exceptions.ApproximationWarning)
         subjects = utils._get_index(X)
         v = self.predict_survival_function(X, conditional_after=conditional_after)[subjects]
-        return pd.Series(trapz(v.values.T, v.index), index=subjects).squeeze()
+        return pd.Series(trapezoid(v.values.T, v.index), index=subjects).squeeze()
 
     @property
     def median_survival_time_(self):

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/fitters/aalen_additive_fitter.py

@@ -6,7 +6,7 @@ import time
 import numpy as np
 import pandas as pd
 from numpy.linalg import LinAlgError
-from scipy.integrate import trapz
+from scipy.integrate import trapezoid
 
 from lifelines.fitters import RegressionFitter
 from lifelines.utils.printer import Printer
@@ -396,7 +396,7 @@ It's important to know that the naive variance estimates of the coefficients are
         """
         index = _get_index(X)
         t = self._index
-        return pd.Series(trapz(self.predict_survival_function(X)[index].values.T, t), index=index)
+        return pd.Series(trapezoid(self.predict_survival_function(X)[index].values.T, t), index=index)
 
     def _compute_confidence_intervals(self):
         ci = 100 * (1 - self.alpha)

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/fitters/cox_time_varying_fitter.py

@@ -801,7 +801,7 @@ See https://stats.stackexchange.com/questions/11109/how-to-deal-with-perfect-sep
             hazards = self.predict_partial_hazard(tv_data).values
 
         unique_death_times = np.unique(stop[events.values])
-        baseline_hazard_ = pd.DataFrame(np.zeros_like(unique_death_times), index=unique_death_times, columns=["baseline hazard"])
+        baseline_hazard_ = pd.DataFrame(np.zeros_like(unique_death_times).astype(float), index=unique_death_times, columns=["baseline hazard"])
 
         for t in unique_death_times:
             ix = (start.values < t) & (t <= stop.values)

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/fitters/coxph_fitter.py

@@ -9,7 +9,7 @@ import time
 from numpy import dot, einsum, log, exp, zeros, arange, multiply, ndarray
 import numpy as np
 from scipy.linalg import solve as spsolve, LinAlgError, norm, inv
-from scipy.integrate import trapz
+from scipy.integrate import trapezoid
 from scipy import stats
 from pandas import DataFrame, Series, Index
 import pandas as pd
@@ -2514,7 +2514,7 @@ See https://stats.stackexchange.com/q/11109/11867 for more.\n",
         """
         subjects = utils._get_index(X)
         v = self.predict_survival_function(X, conditional_after=conditional_after)[subjects]
-        return pd.Series(trapz(v.values.T, v.index), index=subjects)
+        return pd.Series(trapezoid(v.values.T, v.index), index=subjects)
 
     def _compute_baseline_hazard(self, partial_hazards: DataFrame, name: Any) -> pd.DataFrame:
         # https://stats.stackexchange.com/questions/46532/cox-baseline-hazard
@@ -3223,7 +3223,7 @@ class ParametricPiecewiseBaselinePHFitter(ParametricCoxModelFitter, Proportional
 
             for stratum, stratified_X in df.groupby(self.strata):
                 log_lambdas_ = anp.array(
-                    [0] + [self.params_[self._strata_labeler(stratum, i)][0] for i in range(2, self.n_breakpoints + 2)]
+                    [0] + [self.params_.loc[self._strata_labeler(stratum, i)].iloc[0] for i in range(2, self.n_breakpoints + 2)]
                 )
                 lambdas_ = np.exp(log_lambdas_)
 
@@ -3237,7 +3237,9 @@ class ParametricPiecewiseBaselinePHFitter(ParametricCoxModelFitter, Proportional
             return cumulative_hazard
 
         else:
-            log_lambdas_ = np.array([0] + [self.params_[param][0] for param in self._fitted_parameter_names if param != "beta_"])
+            log_lambdas_ = np.array(
+                [0] + [self.params_.loc[param].iloc[0] for param in self._fitted_parameter_names if param != "beta_"]
+            )
             lambdas_ = np.exp(log_lambdas_)
 
             Xs = self.regressors.transform_df(df)

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/fitters/mixins.py

@@ -110,7 +110,7 @@ class ProportionalHazardMixin:
         axes = []
 
         for variable in self.params_.index.intersection(columns or self.params_.index):
-            minumum_observed_p_value = test_results.summary.loc[variable, "p"].min()
+            minimum_observed_p_value = test_results.summary.loc[variable, "p"].min()
 
             # plot is done (regardless of test result) whenever `show_plots = True`
             if show_plots:
@@ -154,7 +154,7 @@ class ProportionalHazardMixin:
                 plt.tight_layout()
                 plt.subplots_adjust(top=0.90)
 
-            if np.round(minumum_observed_p_value, 2) > p_value_threshold:
+            if np.round(minimum_observed_p_value, 2) > p_value_threshold:
                 continue
 
             counter += 1
@@ -182,7 +182,7 @@ class ProportionalHazardMixin:
             print()
             print(
                 "%d. Variable '%s' failed the non-proportional test: p-value is %s."
-                % (counter, variable, format_p_value(4)(minumum_observed_p_value)),
+                % (counter, variable, format_p_value(4)(minimum_observed_p_value)),
                 end="\n\n",
             )
 

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/fitters/nelson_aalen_fitter.py

@@ -200,7 +200,7 @@ class NelsonAalenFitter(UnivariateFitter):
         Parameters
         -----------
         bandwidth: float
-            the bandwith used in the Epanechnikov kernel.
+            the bandwidth used in the Epanechnikov kernel.
 
         Returns
         -------

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/fitters/npmle.py

@@ -291,7 +291,7 @@ def reconstruct_survival_function(
 
     # First backfill at events between known observations
     # Second fill all events _outside_ known obs with running_sum
-    return full_dataframe.combine_first(df).bfill().fillna(running_sum).clip(lower=0.0)
+    return full_dataframe.combine_first(df).astype(float).bfill().fillna(running_sum).clip(lower=0.0)
 
 
 def npmle_compute_confidence_intervals(left, right, mle_, alpha=0.05, samples=1000):

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/fitters/piecewise_exponential_regression_fitter.py

@@ -66,7 +66,7 @@ class PiecewiseExponentialRegressionFitter(ParametricRegressionFitter):
         coef_penalty = 0
         if self.penalizer > 0:
             for i in range(params_stacked.shape[1]):
-                if not self._cols_to_not_penalize[i]:
+                if not self._cols_to_not_penalize.iloc[i]:
                     coef_penalty = coef_penalty + (params_stacked[:, i]).var()
 
         return neg_ll + self.penalizer * coef_penalty

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/generate_datasets.py

@@ -5,7 +5,7 @@ import pandas as pd
 
 from scipy import stats
 from scipy.optimize import newton
-from scipy.integrate import cumtrapz
+from scipy.integrate import cumulative_trapezoid
 
 random = np.random
 
@@ -172,7 +172,7 @@ def constant_coefficients(d, timelines, constant=True, independent=0):
     timelines: the observational times
     constant: True for constant coefficients
     independent: the number of coffients to set to 0 (covariate is ind of survival), or
-      a list of covariates to make indepent.
+      a list of covariates to make independent.
 
     returns a matrix (t,d+1) of coefficients
     """
@@ -187,7 +187,7 @@ def time_varying_coefficients(d, timelines, constant=False, independent=0, randg
     timelines: the observational times
     constant: True for constant coefficients
     independent: the number of coffients to set to 0 (covariate is ind of survival), or
-      a list of covariates to make indepent.
+      a list of covariates to make independent.
     randgen: how scalar coefficients (betas) are sampled.
 
     returns a matrix (t,d+1) of coefficients
@@ -221,7 +221,7 @@ def generate_hazard_rates(n, d, timelines, constant=False, independent=0, n_bina
       n: the number of instances
       d: the number of covariates
       lifelines: the observational times
-      constant: make the coeffients constant (not time dependent)
+      constant: make the coefficients constant (not time dependent)
       n_binary: the number of binary covariates
       model: from ["aalen", "cox"]
 
@@ -253,7 +253,7 @@ def generate_random_lifetimes(hazard_rates, timelines, size=1, censor=None):
       timelines: (t,) the observation times
       size: the number to return, per hardard rate
       censor: If True, adds uniform censoring between timelines.max() and  0
-              If a postive number, censors all events above that value.
+              If a positive number, censors all events above that value.
               If (n,) np.array >=0 , censor elementwise.
 
 
@@ -308,7 +308,7 @@ def cumulative_integral(fx, x):
     fx: (n,d) numpy array, what you want to integral of
     x: (n,) numpy array, location to integrate over.
     """
-    return cumtrapz(fx.T, x, initial=0).T
+    return cumulative_trapezoid(fx.T, x, initial=0).T
 
 
 def construct_survival_curves(hazard_rates, timelines):

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/tests/test_estimation.py

@@ -2008,7 +2008,7 @@ class TestRegressionFitters:
     def test_fit_will_accept_object_dtype_as_event_col(self, regression_models_sans_strata_model, rossi):
         # issue #638
         rossi["arrest"] = rossi["arrest"].astype(object)
-        rossi["arrest"].iloc[0] = None
+        rossi.loc[0, "arrest"] = None
 
         assert rossi["arrest"].dtype == object
         rossi = rossi.dropna()
@@ -2953,7 +2953,7 @@ class TestCoxPHFitter_SemiParametric:
         assert_frame_equal(cph.baseline_cumulative_hazard_, cph_scaled.baseline_cumulative_hazard_)
 
 
-class TestCoxPHFitterPeices:
+class TestCoxPHFitterPieces:
     @pytest.fixture
     def cph(self):
         return CoxPHFitter(baseline_estimation_method="piecewise", breakpoints=[25])
@@ -3108,7 +3108,7 @@ class TestCoxPHFitter:
         cph.fit(df, "T", formula="C(cat)")
         assert cph.summary.shape[0] == 2
 
-    def test_trival_entry_col(self, rossi):
+    def test_trivial_entry_col(self, rossi):
         cph_without_entry_summary = CoxPHFitter().fit(rossi, "week", "arrest").summary
         cphs_without_entry_summary = (
             CoxPHFitter(baseline_estimation_method="spline", n_baseline_knots=2).fit(rossi, "week", "arrest").summary
@@ -3125,7 +3125,7 @@ class TestCoxPHFitter:
         assert_frame_equal(cph_without_entry_summary, cph_with_entry_summary)
         assert_frame_equal(cphs_without_entry_summary, cphs_with_entry_summary)
 
-    def test_trival_entry_col_with_strata(self, rossi):
+    def test_trivial_entry_col_with_strata(self, rossi):
         cph_without_entry_summary = CoxPHFitter().fit(rossi, "week", "arrest", strata=["fin"]).summary
 
         rossi["entry"] = 0
@@ -3466,7 +3466,7 @@ class TestCoxPHFitter:
         cph.fit(rossi, "week", "arrest")
         cph.check_assumptions(rossi)
 
-    def test_check_assumptions_thows_if_raise_on_fail_enalbed(self, cph, rossi):
+    def test_check_assumptions_throws_if_raise_on_fail_enabled(self, cph, rossi):
         cph.fit(rossi, "week", "arrest")
         with pytest.raises(ProportionalHazardAssumptionError):
             cph.check_assumptions(rossi, p_value_threshold=0.05, raise_on_fail=True)
@@ -4169,7 +4169,7 @@ log-likelihood ratio test = 33.27 on 7 df
         expected = pd.Series({"var": 0.643})
         assert_series_equal(cph.summary["se(coef)"], expected, atol=0.01, check_names=False)
 
-    def test_robust_errors_with_less_trival_weights_is_the_same_as_R(self, regression_dataset):
+    def test_robust_errors_with_less_trivial_weights_is_the_same_as_R(self, regression_dataset):
         """
         df <- data.frame(
             "var1" = c(0.209325, 0.693919, 0.443804, 0.065636, 0.386294),
@@ -4343,7 +4343,7 @@ log-likelihood ratio test = 33.27 on 7 df
             expected = 0.05
             assert abs(cph.log_likelihood_ratio_test().test_statistic - expected) < 0.01
 
-    def test_trival_float_weights_with_no_ties_is_the_same_as_R(self, regression_dataset):
+    def test_trivial_float_weights_with_no_ties_is_the_same_as_R(self, regression_dataset):
         """
         df <- data.frame(
             "var1" = c(0.209325, 0.693919, 0.443804, 0.065636, 0.386294),
@@ -4374,7 +4374,7 @@ log-likelihood ratio test = 33.27 on 7 df
             expected_ll = -1.142397
             assert abs(cph.log_likelihood_ - expected_ll) < 0.001
 
-    def test_less_trival_float_weights_with_no_ties_is_the_same_as_R(self, regression_dataset):
+    def test_less_trivial_float_weights_with_no_ties_is_the_same_as_R(self, regression_dataset):
         """
         df <- data.frame(
             "var1" = c(0.209325, 0.693919, 0.443804, 0.065636, 0.386294),
@@ -4402,7 +4402,7 @@ log-likelihood ratio test = 33.27 on 7 df
             expected = pd.Series({"var1": 6.690, "var2": 1.614})
             assert_series_equal(cph.summary["se(coef)"], expected, atol=0.01, check_names=False)
 
-    def test_non_trival_float_weights_with_no_ties_is_the_same_as_R(self, regression_dataset):
+    def test_non_trivial_float_weights_with_no_ties_is_the_same_as_R(self, regression_dataset):
         """
         df <- read.csv('.../lifelines/datasets/regression.csv')
         coxph(formula=Surv(T, E) ~ var1 + var2, data=df, weights=var3)
@@ -5588,7 +5588,7 @@ log-likelihood ratio test = 15.11 on 4 df
         ctv.fit(heart, id_col="id", event_col="event", strata=["transplant"], initial_point=0.1 * np.ones(3))
         npt.assert_allclose(ctv.log_likelihood_ratio_test().test_statistic, 15.68, atol=0.01)
 
-    def test_fitter_is_okay_with_trival_df(self, ctv):
+    def test_fitter_is_okay_with_trivial_df(self, ctv):
         # after all the necessary columns are removed, does this fitter still work with a trivial df?
         df = pd.DataFrame.from_records(
             [

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/tests/test_plotting.py

@@ -360,12 +360,12 @@ class TestPlotting:
         self.plt.show(block=block)
         return
 
-    def test_naf_plot_cumulative_hazard_bandwith_1(self, block):
+    def test_naf_plot_cumulative_hazard_bandwidth_1(self, block):
         data1 = np.random.exponential(5, size=(2000, 1)) ** 2
         naf = NelsonAalenFitter()
         naf.fit(data1)
         naf.plot_hazard(bandwidth=5.0, iloc=slice(0, 1700))
-        self.plt.title("test_naf_plot_cumulative_hazard_bandwith_1")
+        self.plt.title("test_naf_plot_cumulative_hazard_bandwidth_1")
         self.plt.show(block=block)
         return
 

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/tests/utils/test_utils.py

@@ -347,7 +347,7 @@ def test_survival_table_from_events_at_risk_column():
         1.0,
     ]
     df = utils.survival_table_from_events(df["T"], df["E"])
-    assert list(df["at_risk"][1:]) == expected  # skip the first event as that is the birth time, 0.
+    assert list(df["at_risk"].loc[1:]) == expected  # skip the first event as that is the birth time, 0.
 
 
 def test_survival_table_to_events_casts_to_float():

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/utils/__init__.py

@@ -11,7 +11,7 @@ import warnings
 from numpy import ndarray
 import numpy as np
 
-from scipy.integrate import quad, trapz
+from scipy.integrate import quad, trapezoid
 from scipy.linalg import solve
 from scipy import stats
 
@@ -266,7 +266,7 @@ def _expected_value_of_survival_up_to_t(model_or_survival_function, t: float = n
         )
         sf = model_or_survival_function.loc[:t]
         sf = pd.concat((sf, pd.DataFrame([1], index=[0], columns=sf.columns))).sort_index()
-        return trapz(y=sf.values[:, 0], x=sf.index)
+        return trapezoid(y=sf.values[:, 0], x=sf.index)
     elif isinstance(model_or_survival_function, lifelines.fitters.UnivariateFitter):
         # lifelines model
         model = model_or_survival_function
@@ -313,7 +313,7 @@ def _expected_value_of_survival_squared_up_to_t(
         sf = model_or_survival_function.loc[:t]
         sf = pd.concat((sf, pd.DataFrame([1], index=[0], columns=sf.columns))).sort_index()
         sf_tau = sf * sf.index.values[:, None]
-        return 2 * trapz(y=sf_tau.values[:, 0], x=sf_tau.index)
+        return 2 * trapezoid(y=sf_tau.values[:, 0], x=sf_tau.index)
     elif isinstance(model_or_survival_function, lifelines.fitters.UnivariateFitter):
         # lifelines model
         model = model_or_survival_function
@@ -556,7 +556,7 @@ def _group_event_table_by_intervals(event_table, intervals) -> pd.DataFrame:
 
         intervals = np.arange(0, event_max + bin_width, bin_width)
 
-    event_table = event_table.groupby(pd.cut(event_table["event_at"], intervals, include_lowest=True)).agg(
+    event_table = event_table.groupby(pd.cut(event_table["event_at"], intervals, include_lowest=True), observed=False).agg(
         {"removed": ["sum"], "observed": ["sum"], "censored": ["sum"], "at_risk": ["max"]}
     )
     # convert columns from multiindex
@@ -648,7 +648,7 @@ def datetimes_to_durations(
         the units of time to use.  See Pandas 'freq'. Default 'D' for days.
     dayfirst: bool, optional (default=False)
         see Pandas `to_datetime`
-    na_values : list, optional
+    na_values : list[str], optional
         list of values to recognize as NA/NaN. Ex: ['', 'NaT']
     format:
         see Pandas `to_datetime`
@@ -679,7 +679,7 @@ def datetimes_to_durations(
     start_times = pd.Series(start_times).copy()
     end_times = pd.Series(end_times).copy()
 
-    C = ~(pd.isnull(end_times).values | end_times.isin(na_values or [""]))
+    C = ~(pd.isnull(end_times).values | end_times.astype(str).isin(na_values or [""]))
     end_times[~C] = fill_date_
     start_times_ = pd.to_datetime(start_times, dayfirst=dayfirst, format=format)
     end_times_ = pd.to_datetime(end_times, dayfirst=dayfirst, errors="coerce", format=format)
@@ -1464,7 +1464,7 @@ def add_covariate_to_timeline(
     cv = cv.sort_values([id_col, duration_col])
     cvs = cv.pipe(remove_redundant_rows).pipe(transform_cv_to_long_format).groupby(id_col, sort=True)
 
-    long_form_df = long_form_df.groupby(id_col, group_keys=False, sort=True).apply(expand, cvs=cvs)
+    long_form_df = long_form_df.groupby(id_col, group_keys=False, sort=True)[long_form_df.columns].apply(expand, cvs=cvs)
     return long_form_df.reset_index(drop=True)
 
 
@@ -1506,7 +1506,7 @@ def covariates_from_event_matrix(df, id_col) -> pd.DataFrame:
     """
     df = df.set_index(id_col)
     df = df.fillna(np.inf)
-    df = df.stack(dropna=False).reset_index()
+    df = df.stack(future_stack=True).reset_index()
     df.columns = [id_col, "event", "duration"]
     df["_counter"] = 1
     return (

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines/version.py

@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 from __future__ import unicode_literals
 
-__version__ = "0.28.0"
+__version__ = "0.29.0"

{lifelines-0.28.0 → lifelines-0.29.0/lifelines.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lifelines
-Version: 0.28.0
+Version: 0.29.0
 Summary: Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regression
 Home-page: https://github.com/CamDavidsonPilon/lifelines
 Author: Cameron Davidson-Pilon
@@ -17,8 +17,8 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy<2.0,>=1.14.0
-Requires-Dist: scipy>=1.2.0
-Requires-Dist: pandas>=1.2.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: pandas>=2.1
 Requires-Dist: matplotlib>=3.0
 Requires-Dist: autograd>=1.5
 Requires-Dist: autograd-gamma>=0.3
@@ -50,8 +50,8 @@ If you are new to survival analysis, wondering why it is useful, or are interest
 
 ## Contact
  - Start a conversation in our [Discussions room](https://github.com/CamDavidsonPilon/lifelines/discussions).
- - Some users have posted common questions at [stats.stackexchange.com](https://stats.stackexchange.com/search?tab=votes&q=%22lifelines%22%20is%3aquestion)
- - creating an issue in the [Github repository](https://github.com/camdavidsonpilon/lifelines).
+ - Some users have posted common questions at [stats.stackexchange.com](https://stats.stackexchange.com/search?tab=votes&q=%22lifelines%22%20is%3aquestion).
+ - Creating an issue in the [Github repository](https://github.com/camdavidsonpilon/lifelines).
 
 ## Development
 

{lifelines-0.28.0 → lifelines-0.29.0}/lifelines.egg-info/requires.txt

@@ -1,6 +1,6 @@
 numpy<2.0,>=1.14.0
-scipy>=1.2.0
-pandas>=1.2.0
+scipy>=1.7.0
+pandas>=2.1
 matplotlib>=3.0
 autograd>=1.5
 autograd-gamma>=0.3

{lifelines-0.28.0 → lifelines-0.29.0}/reqs/base-requirements.txt

@@ -1,6 +1,6 @@
 numpy>=1.14.0,<2.0
-scipy>=1.2.0
-pandas>=1.2.0
+scipy>=1.7.0
+pandas>=2.1
 matplotlib>=3.0
 autograd>=1.5
 autograd-gamma>=0.3

{lifelines-0.28.0 → lifelines-0.29.0}/reqs/dev-requirements.txt

@@ -15,8 +15,8 @@ black
 dill>=0.3.6
 statsmodels
 flaky
-scikit-learn>=0.22.0
 Jinja2
+joblib
 
 # ex: `py.test` in the docs/ folder. See conftest.py in docs/ first
 sybil