diff --git a/pyproject.toml b/pyproject.toml index f7c9e891fd..fd29b80098 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,6 +35,7 @@ dependencies = [ "azure-storage-file-share", # For saving and loading simulation state "dill", + "sdv", ] description = "Thanzi la Onse Epidemiology Model" dynamic = ["version"] diff --git a/requirements/base.txt b/requirements/base.txt index 458aa584ea..ec9f6ddf30 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -34,6 +34,13 @@ azure-keyvault-secrets==4.7.0 # via azure-keyvault azure-storage-file-share==12.14.1 # via tlo (pyproject.toml) +boto3==1.41.0 + # via sdv +botocore==1.41.0 + # via + # boto3 + # s3transfer + # sdv certifi==2023.7.22 # via # msrest @@ -44,8 +51,14 @@ charset-normalizer==3.2.0 # via requests click==8.1.7 # via tlo (pyproject.toml) +cloudpickle==3.1.2 + # via sdv contourpy==1.1.1 # via matplotlib +copulas==0.12.3 + # via + # sdmetrics + # sdv cryptography==41.0.3 # via # adal @@ -54,18 +67,30 @@ cryptography==41.0.3 # azure-storage-file-share # msal # pyjwt +ctgan==0.11.1 + # via sdv cycler==0.11.0 # via matplotlib +deepecho==0.7.0 + # via sdv dill==0.3.8 # via tlo (pyproject.toml) et-xmlfile==1.1.0 # via openpyxl +faker==38.2.0 + # via rdt +filelock==3.20.0 + # via torch fonttools==4.42.1 # via matplotlib +fsspec==2025.10.0 + # via torch gitdb==4.0.10 # via gitpython gitpython==3.1.36 # via tlo (pyproject.toml) +graphviz==0.21 + # via sdv idna==3.4 # via requests isodate==0.6.1 @@ -75,10 +100,22 @@ isodate==0.6.1 # azure-keyvault-secrets # azure-storage-file-share # msrest +jinja2==3.1.6 + # via torch +jmespath==1.0.1 + # via + # boto3 + # botocore +joblib==1.5.2 + # via scikit-learn kiwisolver==1.4.5 # via matplotlib +markupsafe==3.0.3 + # via jinja2 matplotlib==3.7.3 # via tlo (pyproject.toml) +mpmath==1.3.0 + # via sympy msal==1.24.0 # via # azure-identity @@ -89,23 +126,49 @@ msrest==0.7.1 # via msrestazure msrestazure==0.6.4 # via azure-batch +narwhals==2.12.0 + # via plotly +networkx==3.5 + # via torch numpy==1.24.4 # via # contourpy + # copulas + # ctgan + # deepecho # matplotlib # pandas + # rdt + # scikit-learn # scipy + # sdmetrics + # sdv # tlo (pyproject.toml) oauthlib==3.2.2 # via requests-oauthlib openpyxl==3.1.0 # via tlo (pyproject.toml) packaging==23.1 - # via matplotlib + # via + # matplotlib + # plotly pandas==2.0.3 - # via tlo (pyproject.toml) + # via + # copulas + # ctgan + # deepecho + # rdt + # sdmetrics + # sdv + # tlo (pyproject.toml) pillow==10.0.1 # via matplotlib +platformdirs==4.5.0 + # via sdv +plotly==6.5.0 + # via + # copulas + # sdmetrics portalocker==2.8.2 # via msal-extensions pycparser==2.21 @@ -114,18 +177,25 @@ pyjwt[crypto]==2.8.0 # via # adal # msal - # pyjwt pyparsing==3.1.1 # via matplotlib pyshp==2.3.1 # via tlo (pyproject.toml) -python-dateutil==2.8.2 +python-dateutil==2.9.0.post0 # via # adal + # botocore # matplotlib # pandas + # rdt pytz==2023.3.post1 # via pandas +pyyaml==6.0.3 + # via sdv +rdt==1.18.2 + # via + # ctgan + # sdv requests==2.31.0 # via # adal @@ -135,7 +205,22 @@ requests==2.31.0 # requests-oauthlib requests-oauthlib==1.3.1 # via msrest +s3transfer==0.14.0 + # via boto3 +scikit-learn==1.7.2 + # via + # rdt + # sdmetrics scipy==1.10.1 + # via + # copulas + # rdt + # scikit-learn + # sdmetrics + # tlo (pyproject.toml) +sdmetrics==0.24.0 + # via sdv +sdv==1.24.1 # via tlo (pyproject.toml) six==1.16.0 # via @@ -147,6 +232,20 @@ smmap==5.0.1 # via gitdb squarify==0.4.3 # via tlo (pyproject.toml) +sympy==1.13.1 + # via torch +threadpoolctl==3.6.0 + # via scikit-learn +torch==2.5.1 + # via + # ctgan + # deepecho +tqdm==4.67.1 + # via + # ctgan + # deepecho + # sdmetrics + # sdv typing-extensions==4.8.0 # via # azure-core @@ -154,7 +253,12 @@ typing-extensions==4.8.0 # azure-keyvault-keys # azure-keyvault-secrets # azure-storage-file-share + # torch tzdata==2023.3 - # via pandas + # via + # faker + # pandas urllib3==2.0.4 - # via requests + # via + # botocore + # requests diff --git a/requirements/dev.txt b/requirements/dev.txt index 6c106e33cb..dffdab1e9a 100644 --- a/requirements/dev.txt +++ b/requirements/dev.txt @@ -2,24 +2,30 @@ # This file is autogenerated by pip-compile with Python 3.11 # by the following command: # -# pip-compile --extra=dev --output-file=requirements/dev.txt +# pip-compile --constraint=requirements/base.txt --extra=dev --output-file=requirements/dev.txt # adal==1.2.7 - # via msrestazure + # via + # -c requirements/base.txt + # msrestazure ansi2html==1.9.1 # via tlo (pyproject.toml) astroid==3.0.0 # via pylint azure-batch==14.0.0 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) azure-common==1.1.28 # via + # -c requirements/base.txt # azure-batch # azure-keyvault-certificates # azure-keyvault-keys # azure-keyvault-secrets azure-core==1.29.4 # via + # -c requirements/base.txt # azure-identity # azure-keyvault-certificates # azure-keyvault-keys @@ -27,79 +33,153 @@ azure-core==1.29.4 # azure-storage-file-share # msrest azure-identity==1.14.0 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) azure-keyvault==4.2.0 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) azure-keyvault-certificates==4.7.0 - # via azure-keyvault + # via + # -c requirements/base.txt + # azure-keyvault azure-keyvault-keys==4.8.0 - # via azure-keyvault + # via + # -c requirements/base.txt + # azure-keyvault azure-keyvault-secrets==4.7.0 - # via azure-keyvault + # via + # -c requirements/base.txt + # azure-keyvault azure-storage-file-share==12.14.1 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) +boto3==1.41.0 + # via + # -c requirements/base.txt + # sdv +botocore==1.41.0 + # via + # -c requirements/base.txt + # boto3 + # s3transfer + # sdv build==1.0.3 # via pip-tools cachetools==5.3.1 # via tox certifi==2023.7.22 # via + # -c requirements/base.txt # msrest # requests cffi==1.15.1 - # via cryptography + # via + # -c requirements/base.txt + # cryptography chardet==5.2.0 # via tox charset-normalizer==3.2.0 - # via requests + # via + # -c requirements/base.txt + # requests click==8.1.7 # via + # -c requirements/base.txt # pip-tools # tlo (pyproject.toml) +cloudpickle==3.1.2 + # via + # -c requirements/base.txt + # sdv colorama==0.4.6 # via tox contourpy==1.1.1 - # via matplotlib -coverage[toml]==7.3.1 # via - # coverage - # pytest-cov + # -c requirements/base.txt + # matplotlib +copulas==0.12.3 + # via + # -c requirements/base.txt + # sdmetrics + # sdv +coverage[toml]==7.3.1 + # via pytest-cov cryptography==41.0.3 # via + # -c requirements/base.txt # adal # azure-identity # azure-keyvault-keys # azure-storage-file-share # msal # pyjwt +ctgan==0.11.1 + # via + # -c requirements/base.txt + # sdv cycler==0.11.0 - # via matplotlib + # via + # -c requirements/base.txt + # matplotlib +deepecho==0.7.0 + # via + # -c requirements/base.txt + # sdv dill==0.3.8 # via + # -c requirements/base.txt # pylint # tlo (pyproject.toml) distlib==0.3.7 # via virtualenv et-xmlfile==1.1.0 - # via openpyxl + # via + # -c requirements/base.txt + # openpyxl execnet==2.0.2 # via pytest-xdist -filelock==3.12.4 +faker==38.2.0 + # via + # -c requirements/base.txt + # rdt +filelock==3.20.0 # via + # -c requirements/base.txt + # torch # tox # virtualenv fonttools==4.42.1 - # via matplotlib + # via + # -c requirements/base.txt + # matplotlib +fsspec==2025.10.0 + # via + # -c requirements/base.txt + # torch gitdb==4.0.10 - # via gitpython + # via + # -c requirements/base.txt + # gitpython gitpython==3.1.36 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) +graphviz==0.21 + # via + # -c requirements/base.txt + # sdv idna==3.4 - # via requests + # via + # -c requirements/base.txt + # requests iniconfig==2.0.0 # via pytest isodate==0.6.1 # via + # -c requirements/base.txt # azure-keyvault-certificates # azure-keyvault-keys # azure-keyvault-secrets @@ -109,78 +189,159 @@ isort==5.12.0 # via # pylint # tlo (pyproject.toml) +jinja2==3.1.6 + # via + # -c requirements/base.txt + # torch +jmespath==1.0.1 + # via + # -c requirements/base.txt + # boto3 + # botocore +joblib==1.5.2 + # via + # -c requirements/base.txt + # scikit-learn kiwisolver==1.4.5 - # via matplotlib + # via + # -c requirements/base.txt + # matplotlib +markupsafe==3.0.3 + # via + # -c requirements/base.txt + # jinja2 matplotlib==3.7.3 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) mccabe==0.7.0 # via pylint +mpmath==1.3.0 + # via + # -c requirements/base.txt + # sympy msal==1.24.0 # via + # -c requirements/base.txt # azure-identity # msal-extensions msal-extensions==1.0.0 - # via azure-identity + # via + # -c requirements/base.txt + # azure-identity msrest==0.7.1 - # via msrestazure + # via + # -c requirements/base.txt + # msrestazure msrestazure==0.6.4 - # via azure-batch + # via + # -c requirements/base.txt + # azure-batch +narwhals==2.12.0 + # via + # -c requirements/base.txt + # plotly +networkx==3.5 + # via + # -c requirements/base.txt + # torch numpy==1.24.4 # via + # -c requirements/base.txt # contourpy + # copulas + # ctgan + # deepecho # matplotlib # pandas + # rdt + # scikit-learn # scipy + # sdmetrics + # sdv # tlo (pyproject.toml) oauthlib==3.2.2 - # via requests-oauthlib + # via + # -c requirements/base.txt + # requests-oauthlib openpyxl==3.1.0 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) packaging==23.1 # via + # -c requirements/base.txt # build # matplotlib + # plotly # pyproject-api # pytest # tox pandas==2.0.3 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # copulas + # ctgan + # deepecho + # rdt + # sdmetrics + # sdv + # tlo (pyproject.toml) pillow==10.0.1 - # via matplotlib -pip-tools==7.3.0 + # via + # -c requirements/base.txt + # matplotlib +pip-tools==7.5.2 # via tlo (pyproject.toml) -platformdirs==3.10.0 +platformdirs==4.5.0 # via + # -c requirements/base.txt # pylint + # sdv # tox # virtualenv +plotly==6.5.0 + # via + # -c requirements/base.txt + # copulas + # sdmetrics pluggy==1.3.0 # via # pytest # tox portalocker==2.8.2 - # via msal-extensions + # via + # -c requirements/base.txt + # msal-extensions psutil==5.9.5 # via tlo (pyproject.toml) pycparser==2.21 - # via cffi + # via + # -c requirements/base.txt + # cffi pyinstrument==4.5.3 # via tlo (pyproject.toml) pyjwt[crypto]==2.8.0 # via + # -c requirements/base.txt # adal # msal - # pyjwt pylint==3.0.1 # via tlo (pyproject.toml) pyparsing==3.1.1 - # via matplotlib + # via + # -c requirements/base.txt + # matplotlib pyproject-api==1.6.1 # via tox pyproject-hooks==1.0.0 - # via build + # via + # build + # pip-tools pyshp==2.3.1 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) pytest==7.4.2 # via # pytest-cov @@ -190,52 +351,125 @@ pytest-cov==4.1.0 # via tlo (pyproject.toml) pytest-xdist==3.3.1 # via tlo (pyproject.toml) -python-dateutil==2.8.2 +python-dateutil==2.9.0.post0 # via + # -c requirements/base.txt # adal + # botocore # matplotlib # pandas + # rdt pytz==2023.3.post1 - # via pandas + # via + # -c requirements/base.txt + # pandas +pyyaml==6.0.3 + # via + # -c requirements/base.txt + # sdv +rdt==1.18.2 + # via + # -c requirements/base.txt + # ctgan + # sdv requests==2.31.0 # via + # -c requirements/base.txt # adal # azure-core # msal # msrest # requests-oauthlib requests-oauthlib==1.3.1 - # via msrest + # via + # -c requirements/base.txt + # msrest ruff==0.12.11 # via tlo (pyproject.toml) +s3transfer==0.14.0 + # via + # -c requirements/base.txt + # boto3 +scikit-learn==1.7.2 + # via + # -c requirements/base.txt + # rdt + # sdmetrics scipy==1.10.1 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # copulas + # rdt + # scikit-learn + # sdmetrics + # tlo (pyproject.toml) +sdmetrics==0.24.0 + # via + # -c requirements/base.txt + # sdv +sdv==1.24.1 + # via + # -c requirements/base.txt + # tlo (pyproject.toml) six==1.16.0 # via + # -c requirements/base.txt # azure-core # isodate # msrestazure # python-dateutil smmap==5.0.1 - # via gitdb + # via + # -c requirements/base.txt + # gitdb squarify==0.4.3 - # via tlo (pyproject.toml) + # via + # -c requirements/base.txt + # tlo (pyproject.toml) +sympy==1.13.1 + # via + # -c requirements/base.txt + # torch +threadpoolctl==3.6.0 + # via + # -c requirements/base.txt + # scikit-learn tomlkit==0.12.1 # via pylint +torch==2.5.1 + # via + # -c requirements/base.txt + # ctgan + # deepecho tox==4.11.3 # via tlo (pyproject.toml) +tqdm==4.67.1 + # via + # -c requirements/base.txt + # ctgan + # deepecho + # sdmetrics + # sdv typing-extensions==4.8.0 # via + # -c requirements/base.txt # azure-core # azure-keyvault-certificates # azure-keyvault-keys # azure-keyvault-secrets # azure-storage-file-share + # torch tzdata==2023.3 - # via pandas + # via + # -c requirements/base.txt + # faker + # pandas urllib3==2.0.4 - # via requests -virtualenv==20.24.5 + # via + # -c requirements/base.txt + # botocore + # requests +virtualenv==20.35.4 # via # tlo (pyproject.toml) # tox