update to Python 3.13 (#71)

* Update package, doc and workflow to use Python 3.13 as our official version

* Modernize type hints for Python 3.13 (list, dict, | operator)

* Modernize string formatting ('.format()' and '%') to f-strings

* fix lint errors

* Revert type hints to Python 3.9 compatible syntax

  Replace | operator with Union/Optional to support Python 3.9+.
  Keep modern list/dict syntax which works in Python 3.9+.

* remove unused import

* Fix Python 3.9 compatibility for generic type unions

Author: YeChen-IDM

.github/workflows/lint.yml

@@ -19,7 +19,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.13'
       - name: Install Python dependencies
         run: |
           python -m pip install .[lint]

.github/workflows/promote_package_to_production.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Setup python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.13'
       - name: Download package from staging
         env:
           PIP_EXTRA_INDEX_URL: https://${{ secrets.STAGING_ARTIFACTORY_USERNAME }}:${{ secrets.STAGING_ARTIFACTORY_PASSWORD }}@packages.idmod.org/api/pypi/idm-pypi-staging/simple/

.github/workflows/staging-build-package.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Setup python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.13'
       - name: Install dependencies
         run: |
           python -m pip install .[packaging]

README.md

@@ -4,6 +4,10 @@
 [![Lint](https://github.com/EMOD-Hub/emod-api/actions/workflows/lint.yml/badge.svg?branch=main)](https://github.com/EMOD-Hub/emod-api/actions/workflows/lint.yml)
 [![Test and deploy to staging](https://github.com/EMOD-Hub/emod-api/actions/workflows/test_and_publish_package_to_staging.yml/badge.svg?branch=main)](https://github.com/EMOD-Hub/emod-api/actions/workflows/test_and_publish_package_to_staging.yml)
 
+## Python Version
+
+Python 3.13 is the recommended and supported version.
+
 ## Documentation
 
 Documentation available at https://emod-hub.github.io/emod-api/.

docs/index.md

@@ -10,6 +10,12 @@ See the [idmtools documentation][idmtools] for a diagram of how each of the rela
 
 ## Installation
 
+### Python Version
+
+Python 3.13 is the recommended and supported version.
+
+### Installing the Package
+
 The emod-api package is currently available on a [Python package index server][idm_pypi] managed by the [Institute for Disease Modeling][idmod].
 
 ```

emod_api/campaign.py

@@ -164,7 +164,7 @@ def get_event(event, old=False):
         return_event = event_map[event]
     else:
         # get next entry in GP_EVENT_xxx
-        new_event_name = event if old else 'GP_EVENT_{:03d}'.format(len(event_map))
+        new_event_name = event if old else f'GP_EVENT_{len(event_map):03d}'
         event_map[event] = new_event_name
         return_event = event_map[event]
     return return_event

emod_api/channelreports/channels.py

@@ -5,7 +5,7 @@
 from datetime import datetime
 import json
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import Union
 import pandas as pd
 
 _CHANNELS = "Channels"
@@ -160,7 +160,7 @@ def num_time_steps(self, count: int) -> None:
         assert self._numTimeSteps > 0, "numTimeSteps must be > 0"
         return
 
-    def as_dictionary(self) -> Dict:
+    def as_dictionary(self) -> dict:
         # https://stackoverflow.com/questions/38987/how-do-i-merge-two-dictionaries-in-a-single-expression
         return {
             **{
@@ -179,7 +179,7 @@ def as_dictionary(self) -> Dict:
 
 class Channel(object):
 
-    def __init__(self, title: str, units: str, data: List) -> None:
+    def __init__(self, title: str, units: str, data: list) -> None:
         self._title = title
         self._units = units
         self._data = data
@@ -216,7 +216,7 @@ def __setitem__(self, key, value) -> None:
         self._data[key] = value
         return
 
-    def as_dictionary(self) -> Dict:
+    def as_dictionary(self) -> dict:
         return {self.title: {_UNITS: self.units, _DATA: list(self.data)}}
 
 
@@ -316,11 +316,11 @@ def num_channels(self) -> int:
         return len(self._channels)
 
     @property
-    def channel_names(self) -> List:
+    def channel_names(self) -> list:
         return sorted(self._channels)
 
     @property
-    def channels(self) -> Dict:
+    def channels(self) -> dict:
         """Channel objects keyed on channel name/title"""
         return self._channels
 
@@ -407,7 +407,7 @@ def validate_channel(_channel, _title, _header) -> None:
 
         return
 
-    def to_csv(self, filename: Union[str, Path], channel_names: List[str] = None, transpose: bool = False) -> None:
+    def to_csv(self, filename: Union[str, Path], channel_names: list[str] = None, transpose: bool = False) -> None:
 
         """
         Write each channel from the report to a row, CSV style, in the given file.

emod_api/channelreports/plot_prop_report.py

@@ -6,7 +6,6 @@
 from functools import reduce
 import json
 from pathlib import Path
-from typing import Dict, List
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -49,7 +48,7 @@ def main(args: argparse.Namespace):
     return
 
 
-def list_channels_and_ips(channel_keys: List[str]) -> None:
+def list_channels_and_ips(channel_keys: list[str]) -> None:
 
     """
     List the channels and properties found in a property report from the
@@ -79,7 +78,7 @@ def list_channels_and_ips(channel_keys: List[str]) -> None:
 
 
 def call_plot_traces(args: argparse.Namespace,
-                     trace_values: Dict[str, np.ndarray]) -> None:
+                     trace_values: dict[str, np.ndarray]) -> None:
 
     """
     Call the internal `plot_traces` function and, optionally, save the results to disk.

emod_api/channelreports/utils.py

@@ -4,7 +4,7 @@
 
 import json
 from pathlib import Path
-from typing import Dict, List, Optional, Union
+from typing import Union, Optional
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -27,8 +27,8 @@
 
 def property_report_to_csv(source_file: Union[str, Path],
                            csv_file: Union[str, Path],
-                           channels: Optional[List[str]] = None,
-                           groupby: Optional[List[str]] = None,
+                           channels: Optional[list[str]] = None,
+                           groupby: Optional[list[str]] = None,
                            transpose: bool = False) -> None:
 
     """
@@ -66,15 +66,15 @@ def property_report_to_csv(source_file: Union[str, Path],
     return
 
 
-def read_json_file(filename: Union[str, Path]) -> Dict:
+def read_json_file(filename: Union[str, Path]) -> dict:
 
     with Path(filename).open("r", encoding="utf-8") as file:
         json_data = json.load(file)
 
     return json_data
 
 
-def get_report_channels(json_data: Dict) -> Dict:
+def get_report_channels(json_data: dict) -> dict:
 
     try:
         channel_data = json_data['Channels']
@@ -112,7 +112,7 @@ def _validate_property_report_ips(groupby, channel_data) -> None:
     return
 
 
-def accumulate_channel_data(channels: List[str], verbose: bool, groupby: List[str], channel_data: Dict) -> Dict[str, np.ndarray]:
+def accumulate_channel_data(channels: list[str], verbose: bool, groupby: list[str], channel_data: dict) -> dict[str, np.ndarray]:
 
     """
     Extract selected channel(s) from property report data.
@@ -156,7 +156,7 @@ def accumulate_channel_data(channels: List[str], verbose: bool, groupby: List[st
     return trace_values
 
 
-def __get_trace_name(channel_title: str, key_value_pairs: List[str], groupby: List[str]) -> str:
+def __get_trace_name(channel_title: str, key_value_pairs: list[str], groupby: list[str]) -> str:
 
     """
     Return "canonical" trace name for a given channel, IP:value list, and groupby list.
@@ -197,7 +197,7 @@ def __get_trace_name(channel_title: str, key_value_pairs: List[str], groupby: Li
     return trace_name
 
 
-def save_to_csv(trace_values: Dict[str, np.ndarray],
+def save_to_csv(trace_values: dict[str, np.ndarray],
                 filename: Union[str, Path],
                 transpose: bool = False) -> None:
 
@@ -220,10 +220,10 @@ def save_to_csv(trace_values: Dict[str, np.ndarray],
     return
 
 
-def plot_traces(trace_values: Dict[str, np.ndarray],
-                norm_values: Optional[Union[int, np.ndarray]],
+def plot_traces(trace_values: dict[str, np.ndarray],
+                norm_values: Union[int, np.ndarray, None],
                 overlay: bool,
-                channels: List[str],
+                channels: list[str],
                 title: str,
                 legend: bool) -> plt.Figure:
 
@@ -291,7 +291,7 @@ def plot_traces(trace_values: Dict[str, np.ndarray],
     return figure
 
 
-def __index_for(trace_name: str, channels: List[str], trace_keys: List[str], normalize: bool, overlay: bool) -> int:
+def __index_for(trace_name: str, channels: list[str], trace_keys: list[str], normalize: bool, overlay: bool) -> int:
 
     if overlay:
         # all pools of the same channel overlaid
@@ -312,7 +312,7 @@ def __index_for(trace_name: str, channels: List[str], trace_keys: List[str], nor
     return index + 1
 
 
-def __title_for(trace_name: str, channels: List[str], overlay: bool):
+def __title_for(trace_name: str, channels: list[str], overlay: bool):
 
     # use channel name
     if overlay:

emod_api/config/default_from_schema_no_validation.py

@@ -2,11 +2,10 @@
 
 import json
 import os
+from typing import Union
 import warnings
 import emod_api.schema_to_class as s2c
 
-from typing import Union
-
 
 def _set_defaults_for_schema_group(dc_param,
                                    schema_section,