networked, stochastic SIRD epidemiological model with Bayesian parameter estimation and policy scenario comparison tools
Home Page: https://www.adaptivecontrol.org/
License: MIT License
![dependabot[bot] avatar](https://avatars.githubusercontent.com/in/29110?v=4 "dependabot[bot]")
supertype: new Model class
ModelUnit -> SIRModel
Model -> NetworkedModel, whose constructor takes arguments of type (new) Model
add SEIRModel and ARIMAModel classes
We need a more comprehensive unit testing suite as the functionality has matured.
currently using R0 rather than R_estimated
openjournals/joss-reviews#3464 | Related #117.
I am running a few lint tools e.g., pylint and pyflakes to locate errors in the module. This is related to #117 that also used studies folder. Since that may not be part of final release (#117 (comment)), this run restricts itself to the core files.
I am working on my fork and send a PR soon that will fix these issues if possible.
In this run, I am using poetry to manage the dependencies. Managing dependencies in Python has been less than ideal (poetry helps but the author need not add this to their DevOps).
The most critical among these should be fixed.
pylint$ poetry run pylint -E epimargin
[dilawars@chutki epimargin (poetry)]$ poetry run pylint -E epimargin
************* Module epimargin.policy
epimargin/policy.py:205:15: E1101: Instance of 'VaccinationPolicy' has no 'daily_doses' member (no-member)
************* Module epimargin.estimators
epimargin/estimators.py:25:18: E1101: Method 'params' has no 'join' member (no-member)
************* Module epimargin.plots
epimargin/plots.py:62:0: E0102: function already defined line 14 (function-redefined)
epimargin/plots.py:194:0: E0102: function already defined line 14 (function-redefined)
************* Module epimargin.etl.covid19india
epimargin/etl/covid19india.py:348:22: E1101: Instance of 'TextFileReader' has no 'set_index' member (no-member)
************* Module epimargin.etl.devdatalab
epimargin/etl/devdatalab.py:28:57: E1101: Instance of 'TextFileReader' has no 'O_StateCensus2011' member (no-member)
************* Module epimargin.etl.csse
epimargin/etl/csse.py:27:8: E1101: Instance of 'TextFileReader' has no 'assign' member (no-member)
************* Module epimargin.etl
epimargin/etl/__init__.py:2:11: E0604: Invalid object 'download_data' in __all__, must contain only strings (invalid-all-object)
[dilawars@chutki epimargin (poetry)]$\
mypy[dilawars@chutki epimargin (poetry)]$ poetry run mypy --ignore-missing-imports epimargin
epimargin/etl/commons.py:2: error: Library stubs not installed for "requests" (or incompatible with Python 3.9)
epimargin/etl/commons.py:2: note: Hint: "python3 -m pip install types-requests"
epimargin/etl/commons.py:2: note: (or run "mypy --install-types" to install all missing stub packages)
epimargin/etl/commons.py:2: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
epimargin/etl/__init__.py:2: error: Type of __all__ must be "Sequence[str]", not "List[Callable[[Path, str, str], Any]]"
epimargin/etl/devdatalab.py:14: error: Function "numpy.array" is not valid as a type
epimargin/etl/devdatalab.py:14: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/etl/devdatalab.py:16: error: Value of type np.array? is not indexable
epimargin/models.py:127: error: "int" has no attribute "copy"
epimargin/models.py:175: error: "int" has no attribute "copy"
epimargin/models.py:250: error: "int" has no attribute "shape"
epimargin/models.py:279: error: Need type annotation for "dV" (hint: "dV: List[<type>] = ...")
epimargin/models.py:283: error: Function "numpy.array" is not valid as a type
epimargin/models.py:283: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/models.py:283: error: Signature of "parallel_forward_epi_step" incompatible with supertype "SIR"
epimargin/models.py:448: error: Incompatible types in assignment (expression has type "bool", variable has type "str")
epimargin/models.py:455: error: Incompatible return value type (got "List[Union[_T, int]]", expected "Union[Dict[str, Sequence[float]], Sequence[float]]")
epimargin/models.py:456: error: Incompatible return value type (got "Dict[str, List[Union[_T, int]]]", expected "Union[Dict[str, Sequence[float]], Sequence[float]]")
epimargin/policy.py:19: error: "SIR" has no attribute "set_parameters"
epimargin/policy.py:36: error: Argument 1 to "len" has incompatible type "SIR"; expected "Sized"
epimargin/policy.py:37: error: "SIR" has no attribute "set_parameters"
epimargin/policy.py:43: error: Need type annotation for "Gs" (hint: "Gs: Set[<type>] = ...")
epimargin/policy.py:43: error: Need type annotation for "Ys" (hint: "Ys: Set[<type>] = ...")
epimargin/policy.py:43: error: Need type annotation for "Os" (hint: "Os: Set[<type>] = ...")
epimargin/policy.py:43: error: Need type annotation for "Rs" (hint: "Rs: Set[<type>] = ...")
epimargin/policy.py:46: error: Need type annotation for "unit"
epimargin/policy.py:46: error: Argument 1 to "enumerate" has incompatible type "SIR"; expected "Iterable[<nothing>]"
epimargin/policy.py:79: error: Value of type "SIR" is not indexable
epimargin/policy.py:88: error: Too many arguments for "run" of "SIR"
epimargin/policy.py:91: error: "SIR" has no attribute "gantt"
epimargin/policy.py:96: error: Argument 1 to "len" has incompatible type "SIR"; expected "Sized"
epimargin/policy.py:97: error: "SIR" has no attribute "set_parameters"
epimargin/policy.py:103: error: Need type annotation for "Gs" (hint: "Gs: Set[<type>] = ...")
epimargin/policy.py:103: error: Need type annotation for "Ys" (hint: "Ys: Set[<type>] = ...")
epimargin/policy.py:103: error: Need type annotation for "Os" (hint: "Os: Set[<type>] = ...")
epimargin/policy.py:103: error: Need type annotation for "Rs" (hint: "Rs: Set[<type>] = ...")
epimargin/policy.py:106: error: Need type annotation for "unit"
epimargin/policy.py:106: error: Argument 1 to "enumerate" has incompatible type "SIR"; expected "Iterable[<nothing>]"
epimargin/policy.py:142: error: Value of type "SIR" is not indexable
epimargin/policy.py:151: error: Too many arguments for "run" of "SIR"
epimargin/policy.py:154: error: "SIR" has no attribute "gantt"
epimargin/policy.py:174: error: Value of type "SIR" is not indexable
epimargin/policy.py:176: error: Argument 1 to "len" has incompatible type "SIR"; expected "Sized"
epimargin/policy.py:180: error: Value of type "SIR" is not indexable
epimargin/policy.py:181: error: Too many arguments for "run" of "SIR"
epimargin/policy.py:183: error: Value of type "SIR" is not indexable
epimargin/policy.py:194: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:194: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:201: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:201: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:205: error: "VaccinationPolicy" has no attribute "daily_doses"
epimargin/policy.py:209: error: np.array? has no attribute "sum"
epimargin/policy.py:211: error: np.array? has no attribute "sum"
epimargin/policy.py:215: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:215: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:221: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:221: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:221: error: Signature of "distribute_doses" incompatible with supertype "VaccinationPolicy"
epimargin/policy.py:223: error: Incompatible return value type (got "Tuple[ndarray, ndarray, ndarray]", expected "Tuple[np.array?]")
epimargin/policy.py:223: error: np.array? has no attribute "shape"
epimargin/policy.py:225: error: No overload variant of "__setitem__" of "list" matches argument types "int", "float"
epimargin/policy.py:225: note: Possible overload variants:
epimargin/policy.py:225: note: def __setitem__(self, SupportsIndex, int) -> None
epimargin/policy.py:225: note: def __setitem__(self, slice, Iterable[int]) -> None
epimargin/policy.py:229: error: "int" has no attribute "mean"
epimargin/policy.py:231: error: Incompatible return value type (got "Tuple[Any, Any, Any]", expected "Tuple[np.array?]")
epimargin/policy.py:238: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:238: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:248: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:248: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:248: error: Signature of "distribute_doses" incompatible with supertype "VaccinationPolicy"
epimargin/policy.py:250: error: Incompatible return value type (got "Tuple[None, None, None]", expected "Tuple[np.array?]")
epimargin/policy.py:253: error: No overload variant of "__setitem__" of "list" matches argument types "int", "float"
epimargin/policy.py:253: note: Possible overload variants:
epimargin/policy.py:253: note: def __setitem__(self, SupportsIndex, int) -> None
epimargin/policy.py:253: note: def __setitem__(self, slice, Iterable[int]) -> None
epimargin/policy.py:256: error: np.array? has no attribute "shape"
epimargin/policy.py:257: error: Value of type np.array? is not indexable
epimargin/policy.py:259: error: Value of type np.array? is not indexable
epimargin/policy.py:260: error: Value of type np.array? is not indexable
epimargin/policy.py:260: error: Unsupported target for indexed assignment (np.array?)
epimargin/policy.py:263: error: Value of type np.array? is not indexable
epimargin/policy.py:264: error: Value of type np.array? is not indexable
epimargin/policy.py:265: error: Unsupported target for indexed assignment (np.array?)
epimargin/policy.py:267: error: Unsupported operand types for + ("None" and "int")
epimargin/policy.py:267: note: Left operand is of type "Optional[int]"
epimargin/policy.py:268: error: Value of type np.array? is not indexable
epimargin/policy.py:268: error: Unsupported target for indexed assignment (np.array?)
epimargin/policy.py:268: error: Unsupported operand types for + ("None" and "int")
epimargin/policy.py:268: note: Left operand is of type "Optional[int]"
epimargin/policy.py:271: error: Incompatible return value type (got "Tuple[ndarray, Any, Any]", expected "Tuple[np.array?]")
epimargin/policy.py:274: error: "int" has no attribute "mean"
epimargin/plots.py:308: error: "SIR" has no attribute "units"
epimargin/plots.py:322: error: "SIR" has no attribute "aggregate"
epimargin/plots.py:380: error: "SIR" has no attribute "aggregate"
epimargin/plots.py:387: error: Need type annotation for "ranges"
epimargin/plots.py:401: error: Incompatible types in assignment (expression has type "List[Any]", variable has type "int")
epimargin/plots.py:405: error: Incompatible types in assignment (expression has type "List[int]", variable has type "int")
epimargin/plots.py:422: error: Value of type "int" is not indexable
epimargin/plots.py:547: error: "Callable[[Any, Any, Any, Any, Any, Any, Any, Any], Any]" has no attribute "horizontal"
epimargin/plots.py:548: error: "Callable[[Any, Any, Any, Any, Any, Any, Any, Any], Any]" has no attribute "vertical"
Found 82 errors in 6 files (checked 13 source files)intLine 151 in 7170f5f
S, I and D are int here: clip wont work. Are these self.S etc that are list[int]?
Similary .copy(), .astype(), .clip() is called on int in a few places.
int is being treated as SequenceLine 250 in 7170f5f
doesn't make sense since S0 is int in argument.
openjournals/joss-reviews#3464
https://pypi.org/project/zipp/#history does not have zip==4.1.0 as specified in the requirements.txt file. I am on debian buster with python3.7.
Here is a summary of pip install -r requirements.txt.
Collecting xlrd==1.2.0
Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
ERROR: Could not find a version that satisfies the requirement zipp==4.1.0 (from versions: 0.1.0, 0.2.0, 0.2.1, 0.3.0, 0.3.1, 0.3.2, 0.3.3, 0.4.0, 0.5.0, 0.5.1, 0.5.2, 0.6.0, 1.0.0, 1.1.0, 1.1.1, 1.2.0, 2.0.0, 2.0.1, 2.1.0, 2.2.0, 2.2.1, 3.0.0, 3.1.0, 3.2.0, 3.3.0, 3.3.1, 3.3.2, 3.4.0, 3.4.1, 3.4.2, 3.5.0)
ERROR: No matching distribution found for zipp==4.1.0
Line 304 in 7170f5f
If model is a SIR type then it is missing .units (this function expects .units). Is it NetworkedSIR or other specialization (I don't see inheritance though)? If it is then t = has issues because model.Rt doesn't exist. I guess t= can be moved inside the loop?
Also in the for loop in this function, model is reused that may case mypy typer checker to fail (not essential).
Similarly plot_curves probably expects models: Sequence[NetworkedSIR] rather than model: Sequence[SIR]?
openjournals/joss-reviews#3464
Permission issues at the very first run.
After pip3 install epimargin on a Linux box. I ran the following snippets in python console.
from itertools import cycle
import epimargin.plots as plt
import numpy as np
import pandas as pd
from epimargin.utils import setup
(data, figs) = setup() # creates convenient directories
plt.set_theme("minimal")I hit by permission issues when application tried to create default directory. Is is necessary to use /usr/bin/ to save data. In line 44 below, may be root can be set to someplace in user's $HOME?
<ipython-input-1-710a13386d8f> in <module>
6 from epimargin.utils import setup
7
----> 8 (data, figs) = setup() # creates convenient directories
9 plt.set_theme("minimal")
~/Work/FORKES/epimargin/epimargin/utils.py in setup(**kwargs)
42 logging.basicConfig(**kwargs)
43 logging.getLogger('flat_table').addFilter(lambda _: 0)
---> 44 return (mkdir(root / "data"), mkdir(root / "figs"))
45
46 def fillna(array):
~/Work/FORKES/epimargin/epimargin/utils.py in mkdir(p, exist_ok)
30
31 def mkdir(p: Path, exist_ok: bool = True) -> Path:
---> 32 p.mkdir(exist_ok = exist_ok)
33 return p
34
/usr/lib/python3.9/pathlib.py in mkdir(self, mode, parents, exist_ok)
1311 """
1312 try:
-> 1313 self._accessor.mkdir(self, mode)
1314 except FileNotFoundError:
1315 if not parents or self.parent == self:
PermissionError: [Errno 13] Permission denied: '/usr/bin/data'On Linux and OSX, https://github.com/COVID-IWG/epimargin /blob/1a8094ae8173a9f09f2efc5b872ac56d67a86c6f/epimargin/utils.py#L18 most likely to return /usr/bin since argv0 is /usr/bin/python3.
Another solution is to check if the cwd() is writable by the user. If not, default to a user-writable directory in user's $HOME? If not, the application needs to be run as root or sudo user which is not advisable.
openjournals/joss-reviews#3464
Various lint errors. Undefined variables have been used in few scripts. These need to be cleaned up or removed.
[centos@ip-172-26-6-166 epimargin (joss_lint_errors)]$ flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
./studies/adaptive-policy-evaluation/policy_analysis.py:47:82: F821 undefined name 'add_lag_cols'
metro_state_policy_df = metro_state_policy_df.groupby(['metro-state']).apply(add_lag_cols, ['RR_pred'])
^
./studies/empirical-reporting-delay/delay_curve.py:129:55: F821 undefined name 'slope_labels'
plt.scatter(x = next(i for i in range(len(slopes)) if slope_labels[i] == "TT"), y = slopes["TT"], c='r', label = "national")
^
./studies/empirical-reporting-delay/delay_curve.py:142:13: F821 undefined name 'ts'
confirmed = ts.Hospitalized.copy()
^
./studies/empirical-reporting-delay/delay_curve.py:161:12: F821 undefined name 'ts'
mh_raw = ts.loc["Maharashtra"].Hospitalized
^
./studies/empirical-reporting-delay/delay_curve.py:162:25: F821 undefined name 'ts'
mh_notch = notch_filter(ts.loc["Maharashtra"].Hospitalized)
^
./studies/empirical-reporting-delay/delay_curve.py:163:25: F821 undefined name 'ts'
mh_adj = delay_adjust(ts.loc["Maharashtra"].Hospitalized, state_dist.loc["Maharashtra"])
^
./studies/empirical-reporting-delay/delay_curve.py:184:24: F821 undefined name 'ts'
notched = notch_filter(ts.loc["India"].Hospitalized)
^
./studies/empirical-reporting-delay/delay_curve.py:205:13: F821 undefined name 'ts'
raw = ts.loc[state].Hospitalized
^
./studies/india_districts/max_rt_choro.py:20:13: F821 undefined name 'label_fn'
label = label_fn(row)
^
./studies/india_districts/max_rt_choro.py:21:34: F821 undefined name 'Rt_c'
a1 = ax.annotate(s=f"{label}{Rt_c}", xy=list(row["pt"].coords)[0], ha = "center", fontfamily = note_font["family"], color="white", **label_kwargs)
^
./studies/india_districts/max_rt_choro.py:21:100: F821 undefined name 'note_font'
a1 = ax.annotate(s=f"{label}{Rt_c}", xy=list(row["pt"].coords)[0], ha = "center", fontfamily = note_font["family"], color="white", **label_kwargs)
^
./studies/india_districts/max_rt_choro.py:21:138: F821 undefined name 'label_kwargs'
a1 = ax.annotate(s=f"{label}{Rt_c}", xy=list(row["pt"].coords)[0], ha = "center", fontfamily = note_font["family"], color="white", **label_kwargs)
^
./studies/india_districts/max_rt_choro.py:22:26: F821 undefined name 'Stroke'
a1.set_path_effects([Stroke(linewidth = 2, foreground = "black"), Normal()])
^
./studies/india_districts/max_rt_choro.py:22:71: F821 undefined name 'Normal'
a1.set_path_effects([Stroke(linewidth = 2, foreground = "black"), Normal()])
^
./studies/india_districts/urban_aggregation.py:20:12: F821 undefined name 'data_path'
"v3": [data_path(i) for i in (1, 2)],
^
./studies/india_districts/urban_aggregation.py:21:12: F821 undefined name 'data_path'
"v4": [data_path(i) for i in (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)]
^
./studies/india_districts/urban_aggregation.py:25:5: F821 undefined name 'download_data'
download_data(data, target)
^
./studies/india_districts/urban_aggregation.py:27:6: F821 undefined name 'load_all_data'
df = load_all_data(
^
./studies/india_districts/urban_aggregation.py:40:6: F821 undefined name 'get_time_series'
ts = get_time_series(cases_UA, "detected_district").Hospitalized.unstack().fillna(0).cumsum(axis = 1)
^
./studies/india_districts/urban_aggregation.py:48:18: F821 undefined name 'get_time_series'
UA_ts["Delhi"] = get_time_series(df.query("detected_state == 'Delhi'")).Hospitalized.cumsum()
^
./studies/india_districts/sanity-checks/smoothing_checks.py:31:12: F821 undefined name 'cwd'
root = cwd()
^
./studies/india_districts/sanity-checks/smoothing_checks.py:59:79: F821 undefined name 'anomaly_dates'
plot_T_anomalies(dates, T_pred, T_CI_upper, T_CI_lower, new_cases_ts, anomaly_dates, anomalies, CI)
^
./studies/india_districts/sanity-checks/smoothing_checks.py:78:78: F821 undefined name 'box_filter'
) = analytical_MPVS(ts.Hospitalized, CI = CI, smoothing = lambda ts: box_filter(ts, n, None))
^
./studies/india_districts/sanity-checks/smoothing_checks.py:108:78: F821 undefined name 'box_filter'
) = analytical_MPVS(ts.Hospitalized, CI = CI, smoothing = lambda ts: box_filter(ts, n, s))
^
./studies/indonesia/idn_provinces.py:97:11: F821 undefined name 'Model'
IDN = Model.single_unit(name = province, population = priority_pops[province], I0 = T_pred[-1], RR0 = RR_pred[-1], upper_CI = T_CI_upper[-1], lower_CI = T_CI_lower[-1], mobility = 0, random_seed = 0)\
.run(prediction_period)
^
./studies/periodicity-analysis/periodicity.py:169:10: F821 undefined name 'signal'
b1, a1 = signal.iirnotch(f0, Q, fs)
^
./studies/periodicity-analysis/periodicity.py:170:10: F821 undefined name 'signal'
b2, a2 = signal.iirnotch(2*f0, 2*Q, fs)
^
./studies/periodicity-analysis/periodicity.py:183:11: F821 undefined name 'signal'
freq, h = signal.freqz(b, a, fs=fs)
^
./studies/realtime-epi-figs/delay_curve.py:56:50: F821 undefined name 'label_font'
plt.ylabel("percentage of cases\n", fontdict=label_font)
^
./studies/realtime-epi-figs/delay_curve.py:57:43: F821 undefined name 'label_font'
plt.xlabel("\ndelay (days)", fontdict=label_font)
^
./studies/realtime-epi-figs/delay_curve.py:116:55: F821 undefined name 'slope_labels'
plt.scatter(x = next(i for i in range(len(slopes)) if slope_labels[i] == "TT"), y = slopes["TT"], c='r', label = "national")
^
./studies/realtime-epi-figs/delay_curve.py:120:32: F821 undefined name 'label_font'
plt.xlabel("\nstate", fontdict=label_font)
^
./studies/realtime-epi-figs/delay_curve.py:121:38: F821 undefined name 'label_font'
plt.ylabel("coefficient\n", fontdict=label_font)
^
./studies/realtime-epi-figs/delay_curve.py:161:31: F821 undefined name 'label_font'
plt.xlabel("date\n", fontdict=label_font)
^
./studies/realtime-epi-figs/delay_curve.py:162:39: F821 undefined name 'label_font'
plt.ylabel("\nnumber cases", fontdict=label_font)
^
./studies/realtime-epi-figs/ica.py:22:1: F821 undefined name 'plt'
plt.plot(X_transformed[:, 1], X_transformed[:, 2])
^
./studies/realtime-epi-figs/ica.py:23:1: F821 undefined name 'plt'
plt.show()
^
./studies/realtime-epi-figs/ridge.py:86:6: F821 undefined name 'fig'
ax = fig.add_subplot(111, projection='3d')
^
./studies/vaccine_allocation/archive/agestruct.py:40:76: F821 undefined name 'dT'
self.dT = [(dT0 * prevalence_structure).astype(int)] if isinstance(dT, (int, float)) else dT
^
./studies/vaccine_allocation/archive/agestruct.py:40:107: F821 undefined name 'dT'
self.dT = [(dT0 * prevalence_structure).astype(int)] if isinstance(dT, (int, float)) else dT
^
./studies/vaccine_allocation/archive/agestruct.py:43:83: F821 undefined name 'dT'
self.S = [((population - I0) * age_structure).astype(int)] if isinstance(dT, (int, float)) else population
^
./studies/vaccine_allocation/archive/consumption_regression.py:1:19: F821 undefined name 'pd'
datareg_sep2020 = pd.read_stata(data/"datareg_sep2020.dta")\
.dropna()\
.drop(columns = ["_merge"])
^
./studies/vaccine_allocation/archive/consumption_regression.py:1:33: F821 undefined name 'data'
datareg_sep2020 = pd.read_stata(data/"datareg_sep2020.dta")\
.dropna()\
.drop(columns = ["_merge"])
^
43 F821 undefined name 'add_lag_cols'
43
Line 547 in 7170f5f
I don't understand it. mypy is also having trouble.
Effectively, we are assigning something to a Callable? Is it the expected behavior? Then how does assigning horizontal and vertical work here? I am not getting it.
Currently, SIR is parallelized by running separate models with different seeds, but AgeSIRVD instantiates a single model and advances a vector state through multivariate draws tied to a single seed.
todo:
[] Update SIR to match the latter.
[] Update plotting code and analysis functions to take in a single new SIR model rather than an array of models
yay
[centos@ip-172-26-6-166 karnataka (joss_lint_errors)]$ python3 age_rt.py
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
Traceback (most recent call last):
File "/home/centos/Work/FORKES/epimargin/studies/karnataka/age_rt.py", line 3, in <module>
from epimargin.estimators import analytical_MPVS
File "/home/centos/Work/FORKES/epimargin/epimargin/estimators.py", line 7, in <module>
import pymc3 as pm
File "/home/centos/.local/lib/python3.9/site-packages/pymc3-3.11.2-py3.9.egg/pymc3/__init__.py", line 34, in <module>
if not semver.match(theano.__version__, ">=1.1.2"):
AttributeError: module 'semver' has no attribute 'match'The package semver has deprecated/removed the match function (python-semver/python-semver#236).
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