Merge pull request #1779 from cmu-delphi/release/indicators_v0.3.30_utils_v0.3.9

Release covidcast-indicators 0.3.30

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.29
+current_version = 0.3.30
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

.github/workflows/build-container-images.yml

@@ -22,6 +22,8 @@ jobs:
           password: ${{ secrets.CMU_DELPHI_DEPLOY_MACHINE_PAT }}
 
       - name: Build, tag, and push image to Github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           baseRef="${GITHUB_REF#*/}"
           baseRef="${baseRef#*/}"

.github/workflows/python-ci.yml

@@ -16,7 +16,7 @@ jobs:
     if: github.event.pull_request.draft == false
     strategy:
       matrix:
-        packages: [_delphi_utils_python, changehc, claims_hosp, doctor_visits, dsew_community_profile, google_symptoms, hhs_hosp, hhs_facilities, jhu, nchs_mortality, nowcast, quidel, quidel_covidtest, safegraph_patterns, sir_complainsalot]
+        packages: [_delphi_utils_python, changehc, claims_hosp, doctor_visits, dsew_community_profile, google_symptoms, hhs_hosp, hhs_facilities, jhu, nchs_mortality, nowcast, quidel_covidtest, safegraph_patterns, sir_complainsalot]
     defaults:
       run:
         working-directory: ${{ matrix.packages }}

Jenkinsfile

@@ -10,7 +10,7 @@
    - TODO: #527 Get this list automatically from python-ci.yml at runtime.
  */
 
-def indicator_list = ["backfill_corrections", "changehc", "claims_hosp", "google_symptoms", "hhs_hosp", "jhu", "nchs_mortality", "quidel", "quidel_covidtest", "safegraph_patterns", "sir_complainsalot", "dsew_community_profile", "doctor_visits"]
+def indicator_list = ["backfill_corrections", "changehc", "claims_hosp", "google_symptoms", "hhs_hosp", "jhu", "nchs_mortality", "quidel_covidtest", "safegraph_patterns", "sir_complainsalot", "dsew_community_profile", "doctor_visits"]
 def build_package_main = [:]
 def build_package_prod = [:]
 def deploy_staging = [:]

_delphi_utils_python/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.8
+current_version = 0.3.9
 commit = True
 message = chore: bump delphi_utils to {new_version}
 tag = False

_delphi_utils_python/delphi_utils/__init__.py

@@ -15,4 +15,4 @@
 from .nancodes import Nans
 from .weekday import Weekday
 
-__version__ = "0.3.8"
+__version__ = "0.3.9"

_delphi_utils_python/delphi_utils/flash_eval/README.md

@@ -0,0 +1,102 @@
+# FlaSH System
+
+THIS README IS IN PROGRESS
+
+FlaSH is a real-time point-outlier detection system. We add the daily evaluation step to this indicators package (retraining is done offline).
+
+FlaSH produces a list of data points that are unusual or surprising so that stakeholders are aware of points that warrant further inspection. 
+
+The guiding principles for the system are: 
+- Flag relevant data points as soon as possible (ideally in an online setting)
+- Be aware of the false positive/false negative rates
+- Reduce cognitive load on data evaluators 
+
+Types of outliers/changes FlaSH intends to catch are: 
+- Out-of-range points 
+- Large spikes 
+- Points that are interesting for a particular weekday
+- Points that are interesting with respect to a particular stream's history
+- Points that are interesting with respect to all other streams 
+- Change in data reporting schedule
+- Changes in health condition [ex: new variant]
+
+## Running FlaSH-eval
+
+First, run the indicator so that there are files for FlaSH to check. 
+
+You can excecute the Python module contained in this
+directory from the main directory of the indicator of interest.
+
+The safest way to do this is to create a virtual environment,
+and install the common DELPHI tools, including flash, and the
+flash module and its dependencies to the virtual environment.
+
+To do this, navigate to the main directory of the indicator of interest and run the following code:
+
+```
+python -m venv env
+source env/bin/activate
+pip install ../_delphi_utils_python/.
+pip install .
+```
+
+To execute the module run the indicator to generate data files and then run
+the flash system , as follows:
+
+```
+env/bin/python -m delphi_INDICATORNAME
+env/bin/python -m delphi_utils.flash_eval
+
+```
+
+Once you are finished with the code, you can deactivate the virtual environment
+and (optionally) remove the environment itself.
+
+```
+deactivate
+rm -r env
+```
+
+### Customization
+
+All of the user-changable parameters are stored in the `flash` field of the indicator's `params.json` file. If `params.json` does not already include a `flash` field, please copy that provided in this module's `params.json.template`.
+
+Please update the follow settings:
+- signals: a list of which signals for that indicator go through FlaSH. 
+
+## Testing the code
+
+To test the code, please create a new virtual environment in the main module directory using the following procedure, similar to above:
+
+```
+make install
+```
+
+To do a static test of the code style, it is recommended to run **pylint** on
+the module. To do this, run the following from the main module directory:
+
+```
+make lint
+```
+
+The most aggressive checks are turned off; only relatively important issues
+should be raised and they should be manually checked (or better, fixed).
+
+Unit tests are also included in the module. To execute these, run the following command from this directory:
+
+```
+make test
+```
+
+or 
+
+```
+(cd tests && ../env/bin/pytest test_file.py --cov=delphi_utils --cov-report=term-missing)
+```
+
+The output will show the number of unit tests that passed and failed, along with the percentage of code covered by the tests. None of the tests should fail and the code lines that are not covered by unit tests should be small and should not include critical sub-routines.
+
+
+## Adding checks
+
+To add a new validation check. Each check should append a descriptive error message to the `raised` attribute if triggered. All checks should allow the user to override exception raising for a specific file using the `suppressed_errors` setting in `params.json`.

quidel/REVIEW.md renamed to _delphi_utils_python/delphi_utils/flash_eval/REVIEW.md

@@ -6,34 +6,34 @@ check the following items.
 
 **Documentation**
 
-- [ ] the README.md file template is filled out and currently accurate; it is
+- [] the README.md file template is filled out and currently accurate; it is
 possible to load and test the code using only the instructions given
-- [ ] minimal docstrings (one line describing what the function does) are
+- [] minimal docstrings (one line describing what the function does) are
 included for all functions; full docstrings describing the inputs and expected
 outputs should be given for non-trivial functions
 
 **Structure**
 
-- [ ] code should use 4 spaces for indentation; other style decisions are
+- [] code should use 4 spaces for indentation; other style decisions are
 flexible, but be consistent within a module
-- [ ] any required metadata files are checked into the repository and placed
+- [] any required metadata files are checked into the repository and placed
 within the directory `static`
-- [ ] any intermediate files that are created and stored by the module should
+- [] any intermediate files that are created and stored by the module should
 be placed in the directory `cache`
-- [ ] final expected output files to be uploaded to the API are placed in the
+- [] final expected output files to be uploaded to the API are placed in the
 `receiving` directory; output files should not be committed to the respository
-- [ ] all options and API keys are passed through the file `params.json`
-- [ ] template parameter file (`params.json.template`) is checked into the
+- [] all options and API keys are passed through the file `params.json`
+- [] template parameter file (`params.json.template`) is checked into the
 code; no personal (i.e., usernames) or private (i.e., API keys) information is
 included in this template file
 
 **Testing**
 
-- [ ] module can be installed in a new virtual environment
-- [ ] pylint with the default `.pylint` settings run over the module produces
+- [] module can be installed in a new virtual environment
+- [] pylint with the default `.pylint` settings run over the module produces
 minimal warnings; warnings that do exist have been confirmed as false positives
-- [ ] reasonably high level of unit test coverage covering all of the main logic
+- [] reasonably high level of unit test coverage covering all of the main logic
 of the code (e.g., missing coverage for raised errors that do not currently seem
 possible to reach are okay; missing coverage for options that will be needed are
 not)
-- [ ] all unit tests run without errors
+- [] all unit tests run without errors

quidel/delphi_quidel/__init__.py renamed to _delphi_utils_python/delphi_utils/flash_eval/__init__.py

@@ -1,15 +1,9 @@
 # -*- coding: utf-8 -*-
-"""Module to pull and clean indicators from the Quidel COVID Test.
+"""Module to flagging interesting or unusual data points.
 
 This file defines the functions that are made public by the module. As the
 module is intended to be executed though the main method, these are primarily
 for testing.
 """
-
 from __future__ import absolute_import
-
-from . import geo_maps
-from . import data_tools
-from . import generate_sensor
-from . import pull
-from . import run
+from .constants import HTML_LINK

quidel/delphi_quidel/__main__.py renamed to _delphi_utils_python/delphi_utils/flash_eval/__main__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Call the function run_module when executed.
 
 This file indicates that calling the module (`python -m MODULE_NAME`) will

_delphi_utils_python/delphi_utils/flash_eval/constants.py

@@ -0,0 +1,12 @@
+"""Constants used in FlaSH."""
+
+#Regions considered under states
+STATES = ['ak', 'al', 'ar', 'as', 'az', 'ca', 'co', 'ct', 'dc', 'de', 'fl', 'ga',
+            'gu', 'hi', 'ia', 'id', 'il', 'in', 'ks', 'ky', 'la',
+            'ma', 'md', 'me', 'mi', 'mn', 'mo', 'mp', 'ms', 'mt', 'nc',
+            'nd', 'ne', 'nh', 'nj', 'nm', 'nv', 'ny', 'oh', 'ok',
+            'or', 'pa', 'pr', 'ri', 'sc', 'sd', 'tn', 'tx', 'ut', 'va', 'vi', 'vt',
+            'wa', 'wi', 'wv', 'wy']
+
+#HTML Link for the visualization tool alerts
+HTML_LINK = "<https://ananya-joshi-visapp-vis-523f3g.streamlitapp.com/?params="