Merge branch 'release/1.1.0'

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,52 @@
+on:
+  push:
+    branches:
+      - master
+
+name: Documentation
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "../.github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), "../.github/R-version")
+        shell: Rscript {0}
+        working-directory: ./R
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+
+      - name: Install dependencies
+        run: |
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary", quiet = TRUE)
+        shell: Rscript {0}
+        working-directory: ./R
+
+      - name: Install package
+        run: R CMD INSTALL .
+        working-directory: ./R
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+        working-directory: ./R

.travis.yml

@@ -2,10 +2,8 @@
 language: r
 r: release
 
-sudo: required
-
 os: linux
-dist: trusty
+dist: xenial
 
 branches:
   only:
@@ -32,22 +30,26 @@ addons:
     sources:
       - ubuntu-toolchain-r-test
     packages:
+      - git
       - gcc-7
       - g++-7
       - gfortran-7
       - libcurl4-openssl-dev
       - libxml2-dev
+      - libgit2-dev
+      - libharfbuzz-dev
+      - libfribidi-dev
 
-matrix:
+jobs:
   include:
   - name: 'Test R codes'
     env: TARGET='R'
-  - name: 'Test Python codes (Python 3.5)'
-    env: TARGET='Python' && PYTHON_VERSION=3.5
   - name: 'Test Python codes (Python 3.6)'
     env: TARGET='Python' && PYTHON_VERSION=3.6
   - name: 'Test Python codes (Python 3.7)'
     env: TARGET='Python' && PYTHON_VERSION=3.7
+  - name: 'Test Python codes (Python 3.8)'
+    env: TARGET='Python' && PYTHON_VERSION=3.8
 
 before_install:
   - export ROOTPATH=`pwd`

CONTRIBUTORS

@@ -9,12 +9,18 @@
 # Great thanks to our contributors!
 
 Ayoung Lee <aylee2008@naver.com>
+David Munoz Tord <david.munoztord@unige.ch>
 Dayeong Min <mindy2801@snu.ac.kr>
 Harhim Park <hrpark12@gmail.com>
+Heesun Park <heesunpark26@gmail.com>
 Jaeyeong Yang <jaeyeong.yang1125@gmail.com>
 Jeongbin Oh <ows0104@gmail.com>
 Jethro Lee <dlemfh96@gmail.com>
 Jiyoon Lee <nicole.lee2001@gmail.com>
 Junha Jang <andy627robo@naver.com>
+Lei Zhang <bnuzhanglei2008@gmail.com>
+Lili Zhang <lili.zhang27@mail.dcu.ie>
+Nathaniel Haines <haines.175@osu.edu>
+Woo-Young Ahn <wooyoung.ahn@gmail.com>
 Yoonseo Zoh <zohyos7@gmail.com>
 

Python/hbayesdm/__init__.py

@@ -1,5 +1,14 @@
+# -*- coding: utf-8 -*-
+try:
+    import importlib.metadata as importlib_metadata
+except ModuleNotFoundError:
+    import importlib_metadata
+
 import hbayesdm
 from hbayesdm.diagnostics import *
 
 __all__ = []
 __all__ += hbayesdm.diagnostics.__all__
+
+# Load version from the metadata
+__version__ = importlib_metadata.version(__name__)

Python/hbayesdm/base.py

@@ -1,19 +1,19 @@
+import multiprocessing
 import os
-from pathlib import Path
 import pickle
 import warnings
-import multiprocessing
 from abc import ABCMeta, abstractmethod
-from typing import Tuple, List, Sequence, Dict, Union, Callable, Any
 from collections import OrderedDict
+from pathlib import Path
+from typing import Any, Callable, Dict, List, Sequence, Tuple, Union
 
 import numpy as np
 import pandas as pd
 from scipy import stats
-from pystan import StanModel
-import matplotlib.pyplot as plt
-import arviz as az
 
+import arviz as az
+import matplotlib.pyplot as plt
+from pystan import StanModel
 from pystan import __version__ as _pystan_version
 
 __all__ = ['TaskModel']
@@ -246,7 +246,11 @@ def _handle_data_args(self, data) -> Tuple[pd.DataFrame, List]:
                 else:
                     filename = '%s_%s_exampleData.txt' % (
                         self.task_name, self.model_type)
+
                 example_data = PATH_EXTDATA / filename
+                if not example_data.exists():
+                    raise RuntimeError(
+                        'Example data for this task does not exist.')
                 raw_data = pd.read_csv(example_data, sep='\t')
             else:
                 if data.endswith('.csv'):

Python/hbayesdm/models/__init__.py

@@ -1,10 +1,13 @@
+from ._alt_delta import alt_delta
+from ._alt_gamma import alt_gamma
 from ._bandit2arm_delta import bandit2arm_delta
 from ._bandit4arm2_kalman_filter import bandit4arm2_kalman_filter
 from ._bandit4arm_2par_lapse import bandit4arm_2par_lapse
 from ._bandit4arm_4par import bandit4arm_4par
 from ._bandit4arm_lapse import bandit4arm_lapse
 from ._bandit4arm_lapse_decay import bandit4arm_lapse_decay
 from ._bandit4arm_singleA_lapse import bandit4arm_singleA_lapse
+from ._bart_ewmv import bart_ewmv
 from ._bart_par4 import bart_par4
 from ._cgt_cm import cgt_cm
 from ._choiceRT_ddm import choiceRT_ddm
@@ -34,11 +37,13 @@
 from ._prl_fictitious_woa import prl_fictitious_woa
 from ._prl_rp import prl_rp
 from ._prl_rp_multipleB import prl_rp_multipleB
+from ._pst_Q import pst_Q
 from ._pst_gainloss_Q import pst_gainloss_Q
 from ._ra_noLA import ra_noLA
 from ._ra_noRA import ra_noRA
 from ._ra_prospect import ra_prospect
 from ._rdt_happiness import rdt_happiness
+from ._task2AFC_sdt import task2AFC_sdt
 from ._ts_par4 import ts_par4
 from ._ts_par6 import ts_par6
 from ._ts_par7 import ts_par7
@@ -47,13 +52,16 @@
 from ._wcs_sql import wcs_sql
 
 __all__ = [
+    'alt_delta',
+    'alt_gamma',
     'bandit2arm_delta',
     'bandit4arm2_kalman_filter',
     'bandit4arm_2par_lapse',
     'bandit4arm_4par',
     'bandit4arm_lapse',
     'bandit4arm_lapse_decay',
     'bandit4arm_singleA_lapse',
+    'bart_ewmv',
     'bart_par4',
     'cgt_cm',
     'choiceRT_ddm',
@@ -83,11 +91,13 @@
     'prl_fictitious_woa',
     'prl_rp',
     'prl_rp_multipleB',
+    'pst_Q',
     'pst_gainloss_Q',
     'ra_noLA',
     'ra_noRA',
     'ra_prospect',
     'rdt_happiness',
+    'task2AFC_sdt',
     'ts_par4',
     'ts_par6',
     'ts_par7',