make release-tag: Merge branch 'master' into stable

Author: katxiao

.github/workflows/tests.yml

@@ -21,7 +21,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - if: matrix.os == 'windows-latest'
       name: Install dependencies - Windows
-      run: pip install 'torch>=1,<2' -f https://download.pytorch.org/whl/torch_stable.html
+      run: pip install 'torch>=1,<1.8' -f https://download.pytorch.org/whl/torch_stable.html
     - name: Install package
       run: pip install invoke .[dev]
     - name: invoke lint
@@ -58,7 +58,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - if: matrix.os == 'windows-latest'
       name: Install dependencies - Windows
-      run: pip install 'torch>=1,<2' -f https://download.pytorch.org/whl/torch_stable.html
+      run: pip install 'torch>=1,<1.8' -f https://download.pytorch.org/whl/torch_stable.html
     - name: Install package and dependencies
       run: pip install invoke .[test]
     - name: invoke pytest
@@ -105,7 +105,7 @@ jobs:
     - if: matrix.os == 'windows-latest'
       name: Install dependencies - Windows
       run: |
-        pip install 'torch>=1,<2' -f https://download.pytorch.org/whl/torch_stable.html
+        pip install 'torch>=1,<1.8' -f https://download.pytorch.org/whl/torch_stable.html
         choco install graphviz
     - name: Install package and dependencies
       run: pip install invoke jupyter .

conda/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "deepecho" %}
-{% set version = "version = '0.2.0'" %}
+{% set version = "version = '0.2.1.dev1'" %}
 
 package:
   name: "{{ name|lower }}"

deepecho/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = 'MIT Data To AI Lab'
 __email__ = 'dailabmit@gmail.com'
-__version__ = '0.2.0'
+__version__ = '0.2.1.dev1'
 __path__ = __import__('pkgutil').extend_path(__path__, __name__)
 
 from deepecho.demo import load_demo

deepecho/models/par.py

@@ -210,17 +210,23 @@ def _data_to_tensor(self, data):
 
                 elif props['type'] in ['continuous', 'timestamp']:
                     mu_idx, sigma_idx, missing_idx = props['indices']
-                    x[mu_idx] = 0.0 if (data[key][i] is None or props['std'] == 0) else (
-                        data[key][i] - props['mu']) / props['std']
+                    if pd.isnull(data[key][i]) or props['std'] == 0:
+                        x[mu_idx] = 0.0
+                    else:
+                        x[mu_idx] = (data[key][i] - props['mu']) / props['std']
+
                     x[sigma_idx] = 0.0
-                    x[missing_idx] = 1.0 if data[key][i] is None else 0.0
+                    x[missing_idx] = 1.0 if pd.isnull(data[key][i]) else 0.0
 
                 elif props['type'] in ['count']:
                     r_idx, p_idx, missing_idx = props['indices']
-                    x[r_idx] = 0.0 if (data[key][i] is None or props['range'] == 0) else (
-                        data[key][i] - props['min']) / props['range']
+                    if pd.isnull(data[key][i]) or props['range'] == 0:
+                        x[r_idx] = 0.0
+                    else:
+                        x[r_idx] = (data[key][i] - props['min']) / props['range']
+
                     x[p_idx] = 0.0
-                    x[missing_idx] = 1.0 if data[key][i] is None else 0.0
+                    x[missing_idx] = 1.0 if pd.isnull(data[key][i]) else 0.0
 
                 elif props['type'] in ['categorical', 'ordinal']:   # categorical
                     value = data[key][i]

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.2.1.dev1
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<candidate>\d+))?

setup.py

@@ -14,7 +14,7 @@
 install_requires = [
     'numpy>=1.18.0,<2',
     'pandas>=1.1,<1.1.5',
-    'torch>=1.4,<2',
+    'torch>=1.4,<1.8',
     'tqdm>=4.10,<5',
 ]
 
@@ -50,7 +50,7 @@
     'flake8-docstrings>=1.5.0,<2',
     'flake8-sfs>=0.0.3,<0.1',
     'isort>=4.3.4,<5',
-    'pylint>=2.5.3,<3',
+    'pylint>=2.5.3,<2.7.2',
 
     # fix style issues
     'autoflake>=1.1,<2',
@@ -99,6 +99,6 @@
     test_suite='tests',
     tests_require=tests_require,
     url='https://github.com/sdv-dev/DeepEcho',
-    version='0.2.0',
+    version='0.2.1.dev1',
     zip_safe=False,
 )

tests/integration/test_par.py

@@ -1,5 +1,7 @@
 import unittest
 
+import numpy as np
+
 from deepecho.models.par import PARModel
 
 
@@ -10,15 +12,15 @@ def test_basic(self):
             {
                 'context': [],
                 'data': [
-                    [0.0, 0.1, 0.2, 0.3, 0.4, 0.5],
+                    [0.0, np.nan, 0.2, 0.3, 0.4, 0.5],
                     [0.5, 0.4, 0.3, 0.2, 0.1, 0.0],
                 ]
             },
             {
                 'context': [],
                 'data': [
                     [0.0, 0.1, 0.2, 0.3, 0.4, 0.5],
-                    [0.5, 0.4, 0.3, 0.2, 0.1, 0.0],
+                    [0.5, 0.4, 0.3, 0.2, 0.1, np.nan],
                 ]
             }
         ]
@@ -35,14 +37,14 @@ def test_conditional(self):
                 'context': [0],
                 'data': [
                     [0.0, 0.1, 0.2, 0.3, 0.4, 0.5],
-                    [0.5, 0.4, 0.3, 0.2, 0.1, 0.0],
+                    [0.5, 0.4, 0.3, 0.2, np.nan, 0.0],
                 ]
             },
             {
                 'context': [1],
                 'data': [
                     [0.5, 0.4, 0.3, 0.2, 0.1, 0.0],
-                    [0.0, 0.1, 0.2, 0.3, 0.4, 0.5],
+                    [0.0, 0.1, np.nan, 0.3, 0.4, 0.5],
                 ]
             }
         ]
@@ -65,8 +67,8 @@ def test_mixed(self):
             {
                 'context': [1],
                 'data': [
-                    [0.5, 0.4, 0.3, 0.2, 0.1, 0.0],
-                    [0, 1, 0, 1, 0, 1],
+                    [0.5, np.nan, 0.3, 0.2, np.nan, 0.0],
+                    [0, 1, 0, 1, np.nan, 1],
                 ]
             }
         ]
@@ -82,7 +84,7 @@ def test_count(self):
             {
                 'context': [0.5],
                 'data': [
-                    [0, 5, 5, 3, 1, 1],
+                    [0, 5, 5, np.nan, 1, 1],
                     [0, 1, 2, 1, 0, 1],
                 ]
             },
@@ -114,7 +116,7 @@ def test_variable_length(self):
                 'context': [1],
                 'data': [
                     [1, 6, 6, 4, 2, 2],
-                    [0, 1, 0, 1, 0, 1],
+                    [np.nan, 1, 0, 1, 0, np.nan],
                 ]
             }
         ]