Starting repo, added in pieces for flu data

reichlab · Aug 27, 2024 · b1acc80 · b1acc80
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diff --git a/README.md b/README.md
@@ -1,29 +1,8 @@
-# reichlab-python-template
+# jacques_flu
 
-[REPLACE WITH A DESCRIPTION OF YOUR PROJECT]
-
-A Python template for Reich Lab projects.
-
-This repo contains a Python package with minimal functionality. It serves as a starting point for new projects (it can be selected as the template when creating a new repo in the Reich Lab org).
-
-There as some opinionated choices here (explained below) which people should override as needed. The main goal is to have a consistent starting point to get up and running with a new Python code base.
-
-## Getting started
-
-[REMOVE THIS SECTION AFTER FOLLOWING THE INSTRUCTIONS BELOW]
-
-If you're using this repo as a template for a new project, make the following changes:
-
-1. Rename the `reichlab_python_template` directory (under `src`) to the name of your package (no hyphens!).
-
-2. Replace all instances of `reichlab-python-template` with the name of your repo/project.
-
-3. Replace all instances of `reichlab_python_template` with the name of your package (remember that Python module names cannot contain hyphens).
-
-4. Update [`pyproject.toml`](pyproject.toml). This file is required and will describe several aspects of your project. `pyproject.toml` replaces `setup.py` and is described in detail on [Python's packaging website](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/).
-
-5. Follow the _Setup for local development_ instructions below to ensure that everything works as expected.
+This project is an application of the just another conditional quantile estimator (Jacques) method to predict flu data.
 
+#NOTE: In order to run this package, you will have to copy the data-raw folder from https://github.com/reichlab/flusion into the src/jacques_flu directory.
 
 ## Installing and running the package (no development)
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
-name = "reichlab-python-template"
-description = "Python template for Reich Lab projects"
+name = "jacques_flu"
+description = "Using jacques to analyze flu data"
 license = {text = "MIT License"}
 readme = "README.md"
 requires-python = '>=3.10'
@@ -13,7 +13,19 @@ dynamic = ["version"]
 dependencies = [
     "structlog",
     "rich",
-    "toml"
+    "toml",
+    "pandas>=2.2.2",
+    "numpy>=1.26.1",
+    "tensorflow>=2.16.1,<3",
+    "tensorflow-probability==0.24.0",
+    "tf-keras>=2.16,<3",
+    "matplotlib >=3.5.1,<4",
+    "pymmwr",
+    "polars",
+    "pyarrow",
+    "timeseriesutils @ git+https://github.com/reichlab/timeseriesutils",
+    "jacques @ git+https://github.com/reichlab/jacques#egg=BWRedits", # referencing my branch for local work
+    'data-pipeline @ git+https://github.com/reichlab/flusion.git#subdirectory=code/data-pipeline',
 ]
 
 [project.optional-dependencies]
@@ -28,18 +40,18 @@ dev = [
 ]
 
 [project.entry-points."console_scripts"]
-reichlab_python_template = "reichlab_python_template.app:main"
+reichlab_python_template = "jacques_flu.app:main"
 
 [build-system]
 # Minimum requirements for the build system to execute.
 requires = ["setuptools", "wheel"]
 
 [tools.setuptools]
-packages = ["reichlab_python_template"]
+packages = ["jacques_flu"]
 
-[tool.reichlab_python_template]
+[tool.jacques_flu]
 # to write json-formatted logs to disk, uncomment the following line specify the file location
-# log_file = "/path/to/log/files/rechlab_python_template.log"
+# log_file = "/path/to/log/files/jacques_flu.log"
 
 [tool.ruff]
 line-length = 120
@@ -52,4 +64,4 @@ inline-quotes = "double"
 quote-style = "double"
 
 [tool.setuptools.dynamic]
-version = {attr = "reichlab_python_template.__version__"}
+version = {attr = "jacques_flu.__version__"}
diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt
@@ -1,65 +1,218 @@
-#
-# This file is autogenerated by pip-compile with Python 3.11
-# by the following command:
-#
-#    pip-compile --extra=dev --output-file=requirements/requirements-dev.txt
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml --extra dev -o requirements/requirements-dev.txt
+absl-py==2.1.0
+    # via
+    #   keras
+    #   tensorboard
+    #   tensorflow
+    #   tensorflow-probability
+astunparse==1.6.3
+    # via tensorflow
+attrs==24.2.0
+    # via pymmwr
+certifi==2024.7.4
+    # via requests
 cfgv==3.4.0
     # via pre-commit
+charset-normalizer==3.3.2
+    # via requests
+cloudpickle==3.0.0
+    # via tensorflow-probability
+contourpy==1.2.1
+    # via matplotlib
 coverage==7.5.1
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
+cycler==0.12.1
+    # via matplotlib
+data-pipeline @ git+https://github.com/reichlab/flusion.git@ab82656e4724f1c33b4cf8b133f49befc4dc8e63#subdirectory=code/data-pipeline
+    # via jacques-flu (pyproject.toml)
+decorator==5.1.1
+    # via tensorflow-probability
 distlib==0.3.8
     # via virtualenv
+dm-tree==0.1.8
+    # via tensorflow-probability
 filelock==3.14.0
     # via virtualenv
+flatbuffers==24.3.25
+    # via tensorflow
+fonttools==4.53.1
+    # via matplotlib
 freezegun==1.5.0
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
+gast==0.6.0
+    # via
+    #   tensorflow
+    #   tensorflow-probability
+google-pasta==0.2.0
+    # via tensorflow
+grpcio==1.66.0
+    # via
+    #   tensorboard
+    #   tensorflow
+h5py==3.11.0
+    # via
+    #   keras
+    #   tensorflow
 identify==2.5.36
     # via pre-commit
+idna==3.8
+    # via requests
 iniconfig==2.0.0
     # via pytest
+jacques @ git+https://github.com/reichlab/jacques@97894a149661a5efa7227fe46518519ffe459ef3#egg=BWRedits
+    # via jacques-flu (pyproject.toml)
+keras==3.5.0
+    # via tensorflow
+kiwisolver==1.4.5
+    # via matplotlib
+libclang==18.1.1
+    # via tensorflow
+markdown==3.7
+    # via tensorboard
 markdown-it-py==3.0.0
     # via rich
+markupsafe==2.1.5
+    # via werkzeug
+matplotlib==3.9.2
+    # via jacques-flu (pyproject.toml)
 mdurl==0.1.2
     # via markdown-it-py
+ml-dtypes==0.4.0
+    # via
+    #   keras
+    #   tensorflow
 mypy==1.10.0
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
 mypy-extensions==1.0.0
     # via mypy
+namex==0.0.8
+    # via keras
 nodeenv==1.8.0
     # via pre-commit
+numpy==1.26.4
+    # via
+    #   jacques-flu (pyproject.toml)
+    #   contourpy
+    #   h5py
+    #   keras
+    #   matplotlib
+    #   ml-dtypes
+    #   opt-einsum
+    #   pandas
+    #   pyarrow
+    #   scipy
+    #   tensorboard
+    #   tensorflow
+    #   tensorflow-probability
+    #   timeseriesutils
+opt-einsum==3.3.0
+    # via tensorflow
+optree==0.12.1
+    # via keras
 packaging==24.0
-    # via pytest
+    # via
+    #   keras
+    #   matplotlib
+    #   pytest
+    #   tensorboard
+    #   tensorflow
+pandas==2.2.2
+    # via
+    #   jacques-flu (pyproject.toml)
+    #   timeseriesutils
+pillow==10.4.0
+    # via matplotlib
 platformdirs==4.2.1
     # via virtualenv
 pluggy==1.5.0
     # via pytest
+polars==1.5.0
+    # via jacques-flu (pyproject.toml)
 pre-commit==3.7.0
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
+protobuf==4.25.4
+    # via
+    #   tensorboard
+    #   tensorflow
+pyarrow==17.0.0
+    # via jacques-flu (pyproject.toml)
 pygments==2.18.0
     # via rich
+pymmwr==0.2.2
+    # via jacques-flu (pyproject.toml)
+pyparsing==3.1.4
+    # via matplotlib
 pytest==8.2.0
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
 python-dateutil==2.9.0.post0
-    # via freezegun
+    # via
+    #   freezegun
+    #   matplotlib
+    #   pandas
+pytz==2024.1
+    # via pandas
 pyyaml==6.0.1
     # via pre-commit
+requests==2.32.3
+    # via tensorflow
 rich==13.7.1
-    # via python-app (pyproject.toml)
+    # via
+    #   jacques-flu (pyproject.toml)
+    #   keras
 ruff==0.4.3
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
+scipy==1.14.1
+    # via timeseriesutils
+setuptools==73.0.1
+    # via
+    #   nodeenv
+    #   tensorboard
+    #   tensorflow
 six==1.16.0
-    # via python-dateutil
+    # via
+    #   astunparse
+    #   google-pasta
+    #   python-dateutil
+    #   tensorboard
+    #   tensorflow
+    #   tensorflow-probability
 structlog==24.1.0
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
+tensorboard==2.17.1
+    # via tensorflow
+tensorboard-data-server==0.7.2
+    # via tensorboard
+tensorflow==2.17.0
+    # via
+    #   jacques-flu (pyproject.toml)
+    #   tf-keras
+tensorflow-probability==0.24.0
+    # via jacques-flu (pyproject.toml)
+termcolor==2.4.0
+    # via tensorflow
+tf-keras==2.17.0
+    # via jacques-flu (pyproject.toml)
+timeseriesutils @ git+https://github.com/reichlab/timeseriesutils@d25f33db30a8d5252329269ec9d205984f980f6c
+    # via jacques-flu (pyproject.toml)
 toml==0.10.2
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
 types-toml==0.10.8.20240310
-    # via python-app (pyproject.toml)
+    # via jacques-flu (pyproject.toml)
 typing-extensions==4.11.0
-    # via mypy
+    # via
+    #   mypy
+    #   optree
+    #   tensorflow
+tzdata==2024.1
+    # via pandas
+urllib3==2.2.2
+    # via requests
 virtualenv==20.26.1
     # via pre-commit
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools
+werkzeug==3.0.4
+    # via tensorboard
+wheel==0.44.0
+    # via astunparse
+wrapt==1.16.0
+    # via tensorflow