Merge pull request #11 from RTIInternational/pandas-2-bugfix

Use python 3.11 and pandas 2.1.1

README.md

@@ -14,7 +14,7 @@ See [docs/design.md](./docs/design.md) for a discussion of the package's design.
 
 To set up a Python development environment for `crcsim`:
 
-1. Create a Python virtual environment based on Python 3.6. (Currently, support is limited to Python 3.6, because that is the version installed on the RTI Cluster, which is where we expect to deploy and run the experiments.)
+1. Create a Python virtual environment based on Python 3.11.
 1. Activate the virtual environment.
 1. Install development dependencies with `pip install -r requirements.txt`.
 1. Install `crcsim` with `pip install -e .`. The `-e` option specifies "development" mode, meaning that any changes you make to the code are recognized immediately without having to reinstall the package.

crcsim/analysis.py

@@ -679,7 +679,7 @@ def summarize(self):
         stage_counts = clinical_detections.new_state.value_counts()
         stage_counts.index = stage_counts.index.str.replace("CLINICAL_", "").str.lower()
         onset_distrib = stage_counts / len(clinical_detections)
-        for stage, value in onset_distrib.iteritems():
+        for stage, value in onset_distrib.items():
             replication_output_row[f"crc_onset_proportion_{stage}"] = value
 
         # Among all individuals who died from CRC, mean time between the onset of CRC
@@ -779,7 +779,7 @@ def compute_status_arrays(self):
                     f"Unexpected: more than one death event for person {p}"
                 )
             else:
-                death_age = int(death.time)
+                death_age = int(death.time.iloc[0])
 
             alive = np.arange(max_age + 1)
             alive = np.where(alive > death_age, 0, 1)
@@ -906,11 +906,11 @@ def compute_status_arrays(self):
                         f"Unexpected: more than one clinical onset event for person {p}"
                     )
                 # Clinical onset overall
-                clinical_detection_age = int(clinical_detection.time)
+                clinical_detection_age = int(clinical_detection.time.iloc[0])
                 clinical_onset[clinical_detection_age] = 1
                 # Five-year survival overall
-                clinical_detection_age_decimal = float(clinical_detection.time)
-                death_age_decimal = float(death.time)
+                clinical_detection_age_decimal = float(clinical_detection.time.iloc[0])
+                death_age_decimal = float(death.time.iloc[0])
                 crc_onset_to_death = death_age_decimal - clinical_detection_age_decimal
                 if crc_onset_to_death > 5:
                     five_year_survival[clinical_detection_age] = 1

requirements.in

@@ -1,13 +1,13 @@
 # Requirements needed for installing and using the package. Include
 # everything necessary to satisfy setup.py's install_requires section.
 fire
-pandas
+pandas==2.1.1
 
 # Additional requirements needed for development.
-black==22.8.0
+black==23.1.0
 flake8==3.8.3
 isort==5.2.0
-mypy==0.812
+mypy==1.4.1
 pytest==5.4.3
 wheel==0.34.2
 pip-tools

requirements.txt

@@ -1,25 +1,25 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
 #
 #    pip-compile
 #
 appdirs==1.4.4
     # via virtualenv
 attrs==19.3.0
     # via pytest
-black==22.8.0
+black==23.1.0
     # via -r requirements.in
 cfgv==3.1.0
     # via pre-commit
 click==8.0.4
     # via
     #   black
     #   pip-tools
-dataclasses==0.8
-    # via black
 distlib==0.3.1
     # via virtualenv
+enum34==1.1.10
+    # via fire
 filelock==3.0.12
     # via virtualenv
 fire==0.3.1
@@ -28,37 +28,27 @@ flake8==3.8.3
     # via -r requirements.in
 identify==1.4.25
     # via pre-commit
-importlib-metadata==1.7.0
-    # via
-    #   click
-    #   flake8
-    #   pluggy
-    #   pre-commit
-    #   pytest
-    #   virtualenv
-importlib-resources==3.0.0
-    # via
-    #   pre-commit
-    #   virtualenv
 isort==5.2.0
     # via -r requirements.in
 mccabe==0.6.1
     # via flake8
 more-itertools==8.4.0
     # via pytest
-mypy-extensions==0.4.3
+mypy==1.4.1
+    # via -r requirements.in
+mypy-extensions==1.0.0
     # via
     #   black
     #   mypy
-mypy==0.812
-    # via -r requirements.in
 nodeenv==1.4.0
     # via pre-commit
-numpy==1.19.1
+numpy==1.26.3
     # via pandas
-packaging==20.4
-    # via pytest
-pandas==1.1.0
+packaging==23.2
+    # via
+    #   black
+    #   pytest
+pandas==2.1.1
     # via -r requirements.in
 pathspec==0.9.0
     # via black
@@ -76,11 +66,9 @@ pycodestyle==2.6.0
     # via flake8
 pyflakes==2.2.0
     # via flake8
-pyparsing==2.4.7
-    # via packaging
 pytest==5.4.3
     # via -r requirements.in
-python-dateutil==2.8.1
+python-dateutil==2.8.2
     # via pandas
 pytz==2020.1
     # via pandas
@@ -89,33 +77,22 @@ pyyaml==5.3.1
 six==1.15.0
     # via
     #   fire
-    #   packaging
     #   python-dateutil
     #   virtualenv
 termcolor==1.1.0
     # via fire
 toml==0.10.1
     # via pre-commit
-tomli==1.2.3
-    # via black
-typed-ast==1.4.3
-    # via
-    #   black
-    #   mypy
 typing-extensions==4.1.1
-    # via
-    #   black
-    #   mypy
+    # via mypy
+tzdata==2023.4
+    # via pandas
 virtualenv==20.0.28
     # via pre-commit
 wcwidth==0.2.5
     # via pytest
 wheel==0.34.2
     # via -r requirements.in
-zipp==3.1.0
-    # via
-    #   importlib-metadata
-    #   importlib-resources
 
 # The following packages are considered to be unsafe in a requirements file:
 # pip