Merge pull request #180 from havakv/update-ci

Update python version

.github/workflows/publish_pypi.yml

@@ -12,7 +12,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v1
       with:
-        python-version: 3.7
+        python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/pythonpackage.yml

@@ -14,15 +14,15 @@ jobs:
       max-parallel: 4
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ['3.8', '3.9', '3.10']
         config:
-        - { os: ubuntu-latest, torch-version: "torch==1.5.0+cpu -f https://download.pytorch.org/whl/torch_stable.html"}
-        - { os: windows-latest, torch-version: "torch==1.5.0+cpu -f https://download.pytorch.org/whl/torch_stable.html"}
+        - { os: ubuntu-latest, torch-version: "torch --index-url https://download.pytorch.org/whl/cpu"}
+        - { os: windows-latest, torch-version: "torch"} 
         - { os: macOS-latest, torch-version: "torch"}
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

pycox/__init__.py

@@ -4,7 +4,7 @@
 
 __author__ = """Haavard Kvamme"""
 __email__ = 'haavard.kvamme@gmail.com'
-__version__ = '0.2.3'
+__version__ = '0.3.0'
 
 import pycox.datasets
 import pycox.evaluation

pycox/evaluation/eval_surv.py

@@ -33,7 +33,7 @@ def __init__(self, surv, durations, events, censor_surv=None, censor_durations=N
         self.censor_surv = censor_surv
         self.censor_durations = censor_durations
         self.steps = steps
-        assert pd.Series(self.index_surv).is_monotonic
+        assert pd.Series(self.index_surv).is_monotonic_increasing
 
     @property
     def censor_surv(self):

pycox/models/cox_time.py

@@ -94,7 +94,7 @@ def compute_expg_at_risk(ix, t):
                  [self.duration_col]
                  .loc[lambda x: x <= max_duration]
                  .drop_duplicates(keep='first'))
-        at_risk_sum = (pd.Series([compute_expg_at_risk(ix, t) for ix, t in times.iteritems()],
+        at_risk_sum = (pd.Series([compute_expg_at_risk(ix, t) for ix, t in times.items()],
                                  index=times.values)
                        .rename('at_risk_sum'))
         events = (df

pycox/models/data.py

@@ -15,7 +15,6 @@ def sample_alive_from_dates(dates, at_risk_dict, n_control=1):
     lengths = np.array([at_risk_dict[x].shape[0] for x in dates])  # Can be moved outside
     idx = (np.random.uniform(size=(n_control, dates.size)) * lengths).astype('int')
     samp = np.empty((dates.size, n_control), dtype=int)
-    samp.fill(np.nan)
 
     for it, time in enumerate(dates):
         samp[it, :] = at_risk_dict[time][idx[:, it]]
@@ -35,7 +34,7 @@ def make_at_risk_dict(durations):
     allidx = durations.index.values
     keys = durations.drop_duplicates(keep='first')
     at_risk_dict = dict()
-    for ix, t in keys.iteritems():
+    for ix, t in keys.items():
         at_risk_dict[t] = allidx[ix:]
     return at_risk_dict
 

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.3
+current_version = 0.3.0
 commit = True
 tag = False
 

setup.py

@@ -33,7 +33,7 @@
 
 setup(
     name='pycox',
-    version='0.2.3',
+    version='0.3.0',
     description="Survival analysis with PyTorch",
     long_description=long_description,
     long_description_content_type='text/markdown',
@@ -51,9 +51,6 @@
         'Intended Audience :: Developers',
         'License :: OSI Approved :: BSD License',
         'Natural Language :: English',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.6',
     ],
-    python_requires='>=3.6'
+    python_requires='>=3.8'
 )