Merge pull request #1449 from cmu-delphi/release/indicators_v0.2.19_utils_v0.2.8

Release covidcast-indicators 0.2.19

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.18
+current_version = 0.2.19
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

.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/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.7
+current_version = 0.2.8
 commit = True
 message = chore: bump delphi_utils to {new_version}
 tag = False

_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

_delphi_utils_python/delphi_utils/__init__.py

@@ -15,4 +15,4 @@
 from .nancodes import Nans
 from .weekday import Weekday
 
-__version__ = "0.2.7"
+__version__ = "0.2.8"

_delphi_utils_python/setup.py

@@ -26,7 +26,7 @@
 
 setup(
     name="delphi_utils",
-    version="0.2.7",
+    version="0.2.8",
     description="Shared Utility Functions for Indicators",
     long_description=long_description,
     long_description_content_type="text/markdown",

_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)

changehc/delphi_changehc/constants.py

@@ -9,3 +9,5 @@
 NA = "NA"
 HRR = "hrr"
 FIPS = "fips"
+
+EXPECTED_FILES_PER_DROP = 7

changehc/delphi_changehc/download_ftp_files.py

@@ -8,6 +8,7 @@
 # third party
 import paramiko
 
+from .constants import EXPECTED_FILES_PER_DROP
 
 def print_callback(filename, bytes_so_far, bytes_total):
     """Log file transfer progress."""
@@ -32,8 +33,8 @@ def get_files_from_dir(sftp, filedate, out_path):
                 not path.exists(path.join(out_path, filename)):
             filepaths_to_download[filename] = path.join(out_path, filename)
 
-    # make sure we don't download more than 6 files per day
-    assert len(filepaths_to_download) <= 6, "more files dropped than expected"
+    # make sure we don't download too many files per day
+    assert len(filepaths_to_download) <= EXPECTED_FILES_PER_DROP, "more files dropped than expected"
 
     # download!
     for infile, outfile in filepaths_to_download.items():

changehc/tests/test_download_ftp_files.py

@@ -6,6 +6,7 @@
 
 # first party
 from delphi_changehc.download_ftp_files import *
+from delphi_changehc.constants import EXPECTED_FILES_PER_DROP
 
 class TestDownloadFTPFiles:
 
@@ -51,22 +52,18 @@ def test_get_files(self, mock_path):
         get_files_from_dir(one_new_one_old, "00005566", "")
         assert one_new_one_old.num_gets == 1
 
-        # When seven new files are present, AssertionError
-        new_file1 = self.FileAttr(dt.timestamp(dt.now()), "00001122_foo1")
-        new_file2 = self.FileAttr(dt.timestamp(dt.now()), "00001122_foo2")
-        new_file3 = self.FileAttr(dt.timestamp(dt.now()), "00001122_foo3")
-        new_file4 = self.FileAttr(dt.timestamp(dt.now()), "00001122_foo4")
-        new_file5 = self.FileAttr(dt.timestamp(dt.now()), "00001122_foo5")
-        new_file6 = self.FileAttr(dt.timestamp(dt.now()), "00001122_foo6")
-        new_file7 = self.FileAttr(dt.timestamp(dt.now()), "00001122_foo7")
-        seven_new = self.MockSFTP([new_file1, new_file2, new_file3, new_file4,
-                                    new_file5, new_file6, new_file7])
+        # When too many new files are present, AssertionError
+        file_batch = [
+            self.FileAttr(dt.timestamp(dt.now()), f"00001122_foo{i}")
+            for i in range(EXPECTED_FILES_PER_DROP + 1)
+        ]
+        too_many_new = self.MockSFTP(file_batch)
         with pytest.raises(AssertionError):
-            get_files_from_dir(seven_new, "00001122", "")
+            get_files_from_dir(too_many_new, "00001122", "")
 
         # When the file already exists, no files are downloaded
         mock_path.exists.return_value = True
-        one_exists = self.MockSFTP([new_file1])
+        one_exists = self.MockSFTP([file_batch[0]])
         get_files_from_dir(one_new, "00001122", "")
         assert one_exists.num_gets == 0
 

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]