Update dependencies (#72)

* WIP: updating dependencies

* Updated pip

* WIP: python versions

* WIP: changing py

* WIP: migrations

* WIP: deleting session

* WIP: removing migration

* WIP: app

* Adding pytest

* WIP: adding register

* Downgrading to python 3.9

* Adding importlib-metadata

* Updating requirements

* Updating requirements

* Updating fhirclient

* Adding tests

* Organizing

* Updating the docker to 3.11

* Returning to the latest versions

* WIP: date misformat after updating fhirclient

* Adding pytest-datadir

* Reverting and pinning fhirclient to support our existing date

* Downgrading fhirclient

* Fixing date

.github/workflows/test.yaml

@@ -6,7 +6,7 @@ on: [push]
 jobs:
   test:
     runs-on: ubuntu-latest
-    container: python:3.7
+    container: python:3.11
     # Service containers to run with `container-job`
     services:
       # Label used to access the service container

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.7
+FROM python:3.11
 
 WORKDIR /opt/app
 

isacc_messaging/models/isacc_fhirdate.py

@@ -36,4 +36,4 @@ def __repr__(self):
 
 
 DEEP_PAST = IsaccFHIRDate("1975-01-01T00:00:00Z")
-DEEP_FUTURE = IsaccFHIRDate("2025-01-01T00:00:00Z")
+DEEP_FUTURE = IsaccFHIRDate("2025-01-01T00:00:00Z")

requirements.dev.txt

@@ -1,25 +1,167 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
 #
-#    pip-compile
+#    pip-compile --extra=dev --output-file=requirements.dev.txt setup.cfg
 #
---requirement requirements.txt
-attrs==21.2.0             # via pytest
-importlib-metadata==4.8.1  # via pluggy, pytest
-iniconfig==1.1.1          # via pytest
-mirakuru==2.4.1           # via pytest-redis
-packaging==21.0           # via pytest
-pluggy==1.0.0             # via pytest
-port-for==0.6.1           # via pytest-redis
-psutil==5.8.0             # via mirakuru
-py==1.10.0                # via pytest
-pyparsing==2.4.7          # via packaging
-pytest-datadir==1.3.1     # via pytest-datadir
-pytest-mock==3.6.1        # via isacc_messaging (setup.py)
-pytest-redis==2.1.1       # via isacc_messaging (setup.py)
-pytest==6.2.5             # via pytest-mock, pytest-redis, isacc_messaging (setup.py)
-requests-mock==1.9.3      # via isacc_messaging (setup.py)
-toml==0.10.2              # via pytest
-typing-extensions==3.10.0.2  # via importlib-metadata
-zipp==3.5.0               # via importlib-metadata
+aiohappyeyeballs==2.4.0
+    # via aiohttp
+aiohttp==3.10.5
+    # via
+    #   aiohttp-retry
+    #   twilio
+aiohttp-retry==2.8.3
+    # via twilio
+aiosignal==1.3.1
+    # via aiohttp
+async-timeout==4.0.3
+    # via
+    #   aiohttp
+    #   redis
+attrs==24.2.0
+    # via
+    #   aiohttp
+    #   cattrs
+    #   requests-cache
+authlib==1.3.1
+    # via isacc_messaging (setup.cfg)
+blinker==1.8.2
+    # via flask
+cachelib==0.13.0
+    # via flask-session
+cattrs==23.2.3
+    # via requests-cache
+certifi==2024.7.4
+    # via requests
+cffi==1.17.0
+    # via cryptography
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via flask
+cryptography==43.0.0
+    # via
+    #   authlib
+    #   python-jose
+ecdsa==0.19.0
+    # via python-jose
+exceptiongroup==1.2.2
+    # via
+    #   cattrs
+    #   pytest
+fhirclient==4.1.0
+    # via isacc_messaging (setup.cfg)
+flask==3.0.3
+    # via
+    #   flask-cors
+    #   flask-session
+    #   isacc_messaging (setup.cfg)
+flask-cors==4.0.1
+    # via isacc_messaging (setup.cfg)
+flask-session==0.8.0
+    # via isacc_messaging (setup.cfg)
+frozenlist==1.4.1
+    # via
+    #   aiohttp
+    #   aiosignal
+gunicorn==23.0.0
+    # via isacc_messaging (setup.cfg)
+idna==3.7
+    # via
+    #   requests
+    #   yarl
+importlib-metadata==8.4.0
+    # via flask
+iniconfig==2.0.0
+    # via pytest
+itsdangerous==2.2.0
+    # via flask
+jinja2==3.1.4
+    # via flask
+markupsafe==2.1.5
+    # via
+    #   jinja2
+    #   werkzeug
+mirakuru==2.5.2
+    # via pytest-redis
+msgspec==0.18.6
+    # via flask-session
+multidict==6.0.5
+    # via
+    #   aiohttp
+    #   yarl
+packaging==24.1
+    # via
+    #   gunicorn
+    #   pytest
+platformdirs==4.2.2
+    # via requests-cache
+pluggy==1.5.0
+    # via pytest
+port-for==0.7.2
+    # via pytest-redis
+psutil==6.0.0
+    # via mirakuru
+pyasn1==0.6.0
+    # via
+    #   python-jose
+    #   rsa
+pycparser==2.22
+    # via cffi
+pyjwt==2.9.0
+    # via twilio
+pytest==8.3.2
+    # via
+    #   isacc_messaging (setup.cfg)
+    #   pytest-mock
+    #   pytest-redis
+pytest-mock==3.14.0
+    # via isacc_messaging (setup.cfg)
+pytest-redis==3.1.2
+    # via isacc_messaging (setup.cfg)
+pytest-datadir==1.3.1     
+    # via pytest-datadir
+python-jose[cryptography]==3.3.0
+    # via isacc_messaging (setup.cfg)
+python-json-logger==2.0.7
+    # via isacc_messaging (setup.cfg)
+redis==5.0.8
+    # via
+    #   isacc_messaging (setup.cfg)
+    #   pytest-redis
+requests==2.32.3
+    # via
+    #   fhirclient
+    #   isacc_messaging (setup.cfg)
+    #   requests-cache
+    #   requests-mock
+    #   twilio
+requests-cache==1.2.1
+    # via isacc_messaging (setup.cfg)
+requests-mock==1.12.1
+    # via isacc_messaging (setup.cfg)
+rsa==4.9
+    # via python-jose
+six==1.16.0
+    # via
+    #   ecdsa
+    #   url-normalize
+tomli==2.0.1
+    # via pytest
+twilio==9.2.3
+    # via isacc_messaging (setup.cfg)
+typing-extensions==4.12.2
+    # via cattrs
+url-normalize==1.4.3
+    # via requests-cache
+urllib3==2.2.2
+    # via
+    #   requests
+    #   requests-cache
+werkzeug==3.0.3
+    # via flask
+yarl==1.9.4
+    # via aiohttp
+zipp==3.20.0
+    # via importlib-metadata
+git+https://github.com/uwcirg/fhir-migrations

requirements.txt

@@ -1,43 +1,135 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
 #
-#    pip-compile --output-file=requirements.txt
+#    pip-compile --output-file=requirements.txt setup.cfg
 #
-authlib==0.14.3           # via isacc_messaging (setup.py)
-certifi==2021.5.30        # via requests
-cffi==1.14.1              # via cryptography
-charset-normalizer==2.0.6  # via requests
-click==8.0.1              # via flask
-cryptography==3.3.2         # via authlib, python-jose
-ecdsa==0.14.1             # via python-jose
-fhirclient==4.1.0         # via isacc_messaging (setup.py)
-flask==1.1.2              # via isacc_messaging (setup.py)
-gunicorn==20.1.0          # via isacc_messaging (setup.py)
-idna==3.2                 # via requests
-importlib-metadata==4.8.1  # via click
-itsdangerous==2.0.1       # via flask
-jinja2==3.0.1             # via flask
-markupsafe==2.0.1         # via jinja2
-pyasn1==0.4.8             # via python-jose, rsa
-pycparser==2.20           # via cffi
-python-jose[cryptography]==3.2.0  # via isacc_messaging (setup.py)
-python-json-logger==0.1.11  # via isacc_messaging (setup.py)
-redis==3.5.3              # via isacc_messaging (setup.py)
-requests-cache==0.6.4     # via isacc_messaging (setup.py)
-requests==2.26.0          # via requests-cache, isacc_messaging (setup.py)
-rsa==4.7                  # via python-jose
-six==1.16.0               # via ecdsa, flask-cors, url-normalize
-typing-extensions==3.10.0.2  # via importlib-metadata
-url-normalize==1.4.3      # via requests-cache
-urllib3==1.26.7           # via requests, requests-cache
-werkzeug==2.0.1           # via flask
-zipp==3.5.0               # via importlib-metadata
-twilio==7.14.1
+aiohappyeyeballs==2.4.0
+    # via aiohttp
+aiohttp==3.10.5
+    # via
+    #   aiohttp-retry
+    #   twilio
+aiohttp-retry==2.8.3
+    # via twilio
+aiosignal==1.3.1
+    # via aiohttp
+async-timeout==4.0.3
+    # via
+    #   aiohttp
+    #   redis
+attrs==24.2.0
+    # via
+    #   aiohttp
+    #   cattrs
+    #   requests-cache
+authlib==1.3.1
+    # via isacc_messaging (setup.cfg)
+blinker==1.8.2
+    # via flask
+cachelib==0.13.0
+    # via flask-session
+cattrs==23.2.3
+    # via requests-cache
+certifi==2024.7.4
+    # via requests
+cffi==1.17.0
+    # via cryptography
+charset-normalizer==3.3.2
+    # via requests
+click==8.1.7
+    # via flask
+cryptography==43.0.0
+    # via
+    #   authlib
+    #   python-jose
+ecdsa==0.19.0
+    # via python-jose
+exceptiongroup==1.2.2
+    # via cattrs
 fhirclient==4.1.0
-torch==1.13.0
-transformers==4.24.0
-scipy==1.7.3
-numpy==1.21.5
-pandas==1.3.5
+    # via isacc_messaging (setup.cfg)
+flask==3.0.3
+    # via
+    #   flask-cors
+    #   flask-session
+    #   isacc_messaging (setup.cfg)
+flask-cors==4.0.1
+    # via isacc_messaging (setup.cfg)
+flask-session==0.8.0
+    # via isacc_messaging (setup.cfg)
+frozenlist==1.4.1
+    # via
+    #   aiohttp
+    #   aiosignal
+gunicorn==23.0.0
+    # via isacc_messaging (setup.cfg)
+idna==3.7
+    # via
+    #   requests
+    #   yarl
+importlib-metadata==8.4.0
+    # via flask
+itsdangerous==2.2.0
+    # via flask
+jinja2==3.1.4
+    # via flask
+markupsafe==2.1.5
+    # via
+    #   jinja2
+    #   werkzeug
+msgspec==0.18.6
+    # via flask-session
+multidict==6.0.5
+    # via
+    #   aiohttp
+    #   yarl
+packaging==24.1
+    # via gunicorn
+platformdirs==4.2.2
+    # via requests-cache
+pyasn1==0.6.0
+    # via
+    #   python-jose
+    #   rsa
+pycparser==2.22
+    # via cffi
+pyjwt==2.9.0
+    # via twilio
+python-jose[cryptography]==3.3.0
+    # via isacc_messaging (setup.cfg)
+python-json-logger==2.0.7
+    # via isacc_messaging (setup.cfg)
+redis==5.0.8
+    # via isacc_messaging (setup.cfg)
+requests==2.32.3
+    # via
+    #   fhirclient
+    #   isacc_messaging (setup.cfg)
+    #   requests-cache
+    #   twilio
+requests-cache==1.2.1
+    # via isacc_messaging (setup.cfg)
+rsa==4.9
+    # via python-jose
+six==1.16.0
+    # via
+    #   ecdsa
+    #   url-normalize
+twilio==9.2.3
+    # via isacc_messaging (setup.cfg)
+typing-extensions==4.12.2
+    # via cattrs
+url-normalize==1.4.3
+    # via requests-cache
+urllib3==2.2.2
+    # via
+    #   requests
+    #   requests-cache
+werkzeug==3.0.3
+    # via flask
+yarl==1.9.4
+    # via aiohttp
+zipp==3.20.0
+    # via importlib-metadata
 git+https://github.com/uwcirg/fhir-migrations