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Merge pull request #1444 from cmu-delphi/new-ci-make
Add make install-ci target to install without editable mode
2 parents 3703b60 + daa52d2 commit ab408fb

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-93
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29 files changed

+144
-93
lines changed

‎.github/workflows/python-ci.yml

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@@ -32,7 +32,7 @@ jobs:
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pip install pylint pytest pydocstyle wheel
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- name: Install
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run: |
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make install
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make install-ci
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- name: Lint
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run: |
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make lint

‎_delphi_utils_python/Makefile

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@@ -8,6 +8,11 @@ install: venv
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pip install wheel ; \
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install .
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lint:
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. env/bin/activate; pylint delphi_utils
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. env/bin/activate; pydocstyle delphi_utils

‎_template_python/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎cdc_covidnet/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎changehc/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎claims_hosp/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎combo_cases_and_deaths/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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3-
dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎covid_act_now/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎doctor_visits/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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3-
dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
4-
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎google_symptoms/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎hhs_facilities/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
76

@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎hhs_hosp/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
76

@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
1211
pip install -e .
1312

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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎jhu/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
76

@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
1211
pip install -e .
1312

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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎nchs_mortality/Makefile

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@@ -1,7 +1,6 @@
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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
76

@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
1211
pip install -e .
1312

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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir)

‎nowcast/.pylintrc

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@@ -16,9 +16,9 @@ disable=logging-format-interpolation,
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[BASIC]
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# Allow arbitrarily short-named variables.
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variable-rgx=[a-z_][a-z0-9_]*
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argument-rgx=[a-z_][a-z0-9_]*
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attr-rgx=[a-z_][a-z0-9_]*
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variable-rgx=[A-Za-z_][a-z0-9_]*
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argument-rgx=[A-Za-z_][a-z0-9_]*
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attr-rgx=[A-Za-z_][a-z0-9_]*
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[DESIGN]
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‎nowcast/Makefile

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.PHONY = venv, lint, test, clean
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*')
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dir = $(shell find ./delphi_* -name __init__.py | grep -o 'delphi_[_[:alnum:]]*' | head -1)
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venv:
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python3.8 -m venv env
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@@ -11,6 +10,12 @@ install: venv
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pip install -e ../_delphi_utils_python ;\
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pip install -e .
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install-ci: venv
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. env/bin/activate; \
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pip install wheel ; \
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pip install ../_delphi_utils_python ;\
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pip install .
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lint:
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. env/bin/activate; pylint $(dir)
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. env/bin/activate; pydocstyle $(dir) --match-dir '(?!nowcast_fusion)'

‎nowcast/delphi_nowcast/deconvolution/__init__.py

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‎nowcast/delphi_nowcast/deconvolution/deconvolution.py

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@@ -74,7 +74,7 @@ def deconvolve_double_smooth_ntf(
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x_k = None
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alpha_0 = np.zeros(n - k - 1)
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u_0 = np.zeros(n - k - 1)
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for t in range(n_iters):
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for _ in range(n_iters):
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x_k = x_update_1 @ (Cty + rho * D.T @ (alpha_0 + u_0))
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Dx = D @ x_k
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alpha_k = _soft_thresh(Dx - u_0, lam / rho)

‎nowcast/delphi_nowcast/deconvolution/ground_truth.py

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This file was deleted.

‎nowcast/delphi_nowcast/nowcast_fusion/__init__.py

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‎nowcast/delphi_nowcast/sensorization/__init__.py

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‎nowcast/delphi_nowcast/sensorization/ar_model.py

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from datetime import datetime, timedelta, date
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"""Fit autoregression models."""
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from datetime import timedelta, date
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from typing import Tuple
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import numpy as np

‎nowcast/delphi_nowcast/sensorization/regression_model.py

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from datetime import datetime, timedelta, date
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"""Fit linear regression mdels."""
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from datetime import timedelta, date
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import numpy as np
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