Add make install-ci target to install without editable mode

.github/workflows/python-ci.yml

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

_delphi_utils_python/Makefile

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

_template_python/Makefile

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

cdc_covidnet/Makefile

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

changehc/Makefile

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

claims_hosp/Makefile

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

combo_cases_and_deaths/Makefile

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

covid_act_now/Makefile

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

doctor_visits/Makefile

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

google_symptoms/Makefile

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

hhs_facilities/Makefile

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

hhs_hosp/Makefile

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

jhu/Makefile

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

nchs_mortality/Makefile

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

nowcast/.pylintrc

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

nowcast/Makefile

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

nowcast/delphi_nowcast/deconvolution/deconvolution.py

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

nowcast/delphi_nowcast/sensorization/ar_model.py

@@ -1,4 +1,6 @@
-from datetime import datetime, timedelta, date
+"""Fit autoregression models."""
+
+from datetime import timedelta, date
 from typing import Tuple
 
 import numpy as np

nowcast/delphi_nowcast/sensorization/regression_model.py

@@ -1,4 +1,6 @@
-from datetime import datetime, timedelta, date
+"""Fit linear regression mdels."""
+
+from datetime import timedelta, date
 
 import numpy as np