Merge pull request #1229 from cmu-delphi/release/delphi-epidata-4.1.5

Release Delphi Epidata 4.1.5

Author: melange396

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.4
+current_version = 4.1.5
 commit = False
 tag = False
 

.github/workflows/dependabot-assignments.yml

@@ -0,0 +1,17 @@
+name: Dependabot auto-assign reviewer
+on: pull_request
+
+permissions:
+  pull-requests: write
+
+jobs:
+  dependabot:
+    runs-on: ubuntu-latest
+    env: 
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    if: ${{ github.actor == 'dependabot[bot]' }}
+    steps:
+      - name: Assign team to PR
+        run: gh pr edit "$PR_URL" --add-reviewer "cmu-delphi/code-reviewers"
+        env:
+          PR_URL: ${{github.event.pull_request.html_url}}

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.4
+version = 4.1.5
 
 [options]
 packages =

src/client/delphi_epidata.R

@@ -15,7 +15,7 @@ Epidata <- (function() {
   # API base url
   BASE_URL <- getOption('epidata.url', default = 'https://api.delphi.cmu.edu/epidata/')
 
-  client_version <- '4.1.4'
+  client_version <- '4.1.5'
 
   auth <- getOption("epidata.auth", default = NA)
 

src/client/delphi_epidata.js

@@ -22,7 +22,7 @@
   }
 })(this, function (exports, fetchImpl, jQuery) {
   const BASE_URL = "https://api.delphi.cmu.edu/epidata/";
-  const client_version = "4.1.4";
+  const client_version = "4.1.5";
 
   // Helper function to cast values and/or ranges to strings
   function _listitem(value) {

src/client/packaging/npm/package.json

@@ -2,7 +2,7 @@
   "name": "delphi_epidata",
   "description": "Delphi Epidata API Client",
   "authors": "Delphi Group",
-  "version": "4.1.4",
+  "version": "4.1.5",
   "license": "MIT",
   "homepage": "https://github.com/cmu-delphi/delphi-epidata",
   "bugs": {

src/client/packaging/pypi/delphi_epidata/__init__.py

@@ -1,4 +1,4 @@
 from .delphi_epidata import Epidata
 
 name = 'delphi_epidata'
-__version__ = '4.1.4'
+__version__ = '4.1.5'

src/client/packaging/pypi/setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="delphi_epidata",
-    version="4.1.4",
+    version="4.1.5",
     author="David Farrow",
     author_email="[email protected]",
     description="A programmatic interface to Delphi's Epidata API.",

src/common/covidcast_row.py

@@ -25,6 +25,7 @@
     "value_updated_timestamp": "Int64",
 }
 
+
 @dataclass
 class CovidcastRow:
     """A container for the values of a single covidcast database row.
@@ -35,7 +36,8 @@ class CovidcastRow:
     - converting from and to formats (dict, csv, df, kwargs)
     - creating consistent views, with consistent data types (dict, csv, df)
 
-    The rows are specified in 'v4_schema.sql'. The datatypes are made to match database. When writing to Pandas, the dtypes match the JIT model.py schema.
+    The rows are specified in 'v4_schema.sql'. The datatypes are made to match
+    database. When writing to Pandas, the dtypes match the JIT model.py schema.
     """
 
     # Arguments.
@@ -54,15 +56,20 @@ class CovidcastRow:
     missing_sample_size: int
     issue: int
     lag: int
-    # The following three fields are only the database, but are not ingested at acquisition and not returned by the API.
+    # The following three fields are only in the database, but are not ingested at
+    # acquisition and not returned by the API.
     epimetric_id: Optional[int] = None
     direction: Optional[int] = None
     value_updated_timestamp: Optional[int] = 0
 
     # Classvars.
     _db_row_ignore_fields: ClassVar = []
     _api_row_ignore_fields: ClassVar = ["epimetric_id", "value_updated_timestamp"]
-    _api_row_compatibility_ignore_fields: ClassVar = _api_row_ignore_fields + ["source", "time_type", "geo_type"]
+    _api_row_compatibility_ignore_fields: ClassVar = _api_row_ignore_fields + [
+        "source",
+        "time_type",
+        "geo_type",
+    ]
 
     _pandas_dtypes: ClassVar = PANDAS_DTYPES
 
@@ -72,17 +79,22 @@ def as_dict(self, ignore_fields: Optional[List[str]] = None) -> dict:
             for key in ignore_fields:
                 del d[key]
         return d
-    
+
     def as_api_row_dict(self, ignore_fields: Optional[List[str]] = None) -> dict:
-        """Returns a dict view into the row with the fields returned by the API server."""
+        """Returns a dict view into the row with the fields returned by the API
+        server."""
         return self.as_dict(ignore_fields=self._api_row_ignore_fields + (ignore_fields or []))
 
     def as_api_compatibility_row_dict(self, ignore_fields: Optional[List[str]] = None) -> dict:
-        """Returns a dict view into the row with the fields returned by the old API server (the PHP server)."""
-        return self.as_dict(ignore_fields=self._api_row_compatibility_ignore_fields + (ignore_fields or []))
+        """Returns a dict view into the row with the fields returned by the old
+        API server (the PHP server)."""
+        return self.as_dict(
+            ignore_fields=self._api_row_compatibility_ignore_fields + (ignore_fields or [])
+        )
 
     def as_db_row_dict(self, ignore_fields: Optional[List[str]] = None) -> dict:
-        """Returns a dict view into the row with the fields returned by the database."""
+        """Returns a dict view into the row with the fields returned by the
+        database."""
         return self.as_dict(ignore_fields=self._db_row_ignore_fields + (ignore_fields or []))
 
     def as_dataframe(self, ignore_fields: Optional[List[str]] = None) -> pd.DataFrame:
@@ -92,15 +104,22 @@ def as_dataframe(self, ignore_fields: Optional[List[str]] = None) -> pd.DataFram
         return df
 
     def as_api_row_df(self, ignore_fields: Optional[List[str]] = None) -> pd.DataFrame:
-        """Returns a dataframe view into the row with the fields returned by the API server."""
+        """Returns a dataframe view into the row with the fields returned by the
+        API server."""
         return self.as_dataframe(ignore_fields=self._api_row_ignore_fields + (ignore_fields or []))
 
+    # fmt: off
     def as_api_compatibility_row_df(self, ignore_fields: Optional[List[str]] = None) -> pd.DataFrame:
-        """Returns a dataframe view into the row with the fields returned by the old API server (the PHP server)."""
-        return self.as_dataframe(ignore_fields=self._api_row_compatibility_ignore_fields + (ignore_fields or []))
+        """Returns a dataframe view into the row with the fields returned by the
+        old API server (the PHP server)."""
+        # fmt: on
+        return self.as_dataframe(
+            ignore_fields=self._api_row_compatibility_ignore_fields + (ignore_fields or [])
+        )
 
     def as_db_row_df(self, ignore_fields: Optional[List[str]] = None) -> pd.DataFrame:
-        """Returns a dataframe view into the row with the fields returned by an all-field database query."""
+        """Returns a dataframe view into the row with the fields returned by an
+        all-field database query."""
         return self.as_dataframe(ignore_fields=self._db_row_ignore_fields + (ignore_fields or []))
 
     def signal_pair(self):
@@ -113,7 +132,6 @@ def time_pair(self):
         return f"{self.time_type}:{self.time_value}"
 
 
-
 def check_valid_dtype(dtype):
     try:
         pd.api.types.pandas_dtype(dtype)

src/common/logger.py

@@ -4,11 +4,12 @@
 import threading
 import structlog
 
+
 def handle_exceptions(logger):
     """Handle exceptions using the provided logger."""
+
     def exception_handler(etype, value, traceback):
-        logger.exception("Top-level exception occurred",
-                         exc_info=(etype, value, traceback))
+        logger.exception("Top-level exception occurred", exc_info=(etype, value, traceback))
 
     def multithread_exception_handler(args):
         exception_handler(args.exc_type, args.exc_value, args.exc_traceback)
@@ -17,9 +18,7 @@ def multithread_exception_handler(args):
     threading.excepthook = multithread_exception_handler
 
 
-def get_structured_logger(name=__name__,
-                          filename=None,
-                          log_exceptions=True):
+def get_structured_logger(name=__name__, filename=None, log_exceptions=True):
     """Create a new structlog logger.
 
     Use the logger returned from this in indicator code using the standard
@@ -49,11 +48,7 @@ def get_structured_logger(name=__name__,
     else:
         log_level = logging.INFO
 
-    logging.basicConfig(
-        format="%(message)s",
-        level=log_level,
-        handlers=handlers
-        )
+    logging.basicConfig(format="%(message)s", level=log_level, handlers=handlers)
 
     def add_pid(logger, method_name, event_dict):
         """
@@ -85,7 +80,7 @@ def add_pid(logger, method_name, event_dict):
             # Decode unicode characters
             structlog.processors.UnicodeDecoder(),
             # Render as JSON
-            structlog.processors.JSONRenderer()
+            structlog.processors.JSONRenderer(),
         ],
         # Use a dict class for keeping track of data.
         context_class=dict,

src/server/_config.py

@@ -7,7 +7,7 @@
 
 load_dotenv()
 
-VERSION = "4.1.4"
+VERSION = "4.1.5"
 
 MAX_RESULTS = int(10e6)
 MAX_COMPATIBILITY_RESULTS = int(3650)

src/server/_printer.py

@@ -46,13 +46,14 @@ def __init__(self):
         self.result: int = -1
         self._max_results: int = MAX_COMPATIBILITY_RESULTS if is_compatibility_mode() else MAX_RESULTS
 
-    def make_response(self, gen):
+    def make_response(self, gen, headers=None):
         return Response(
             gen,
             mimetype="application/json",
+            headers=headers,
         )
 
-    def __call__(self, generator: Iterable[Dict[str, Any]]) -> Response:
+    def __call__(self, generator: Iterable[Dict[str, Any]], headers=None) -> Response:
         def gen():
             self.result = -2  # no result, default response
             began = False
@@ -84,7 +85,7 @@ def gen():
             if r is not None:
                 yield r
 
-        return self.make_response(stream_with_context(gen()))
+        return self.make_response(stream_with_context(gen()), headers=headers)
 
     @property
     def remaining_rows(self) -> int:
@@ -223,8 +224,11 @@ def __init__(self, filename: Optional[str] = "epidata"):
         super(CSVPrinter, self).__init__()
         self._filename = filename
 
-    def make_response(self, gen):
-        headers = {"Content-Disposition": f"attachment; filename={self._filename}.csv"} if self._filename else {}
+    def make_response(self, gen, headers=None):
+        if headers is None:
+            headers = {}
+        if self._filename:
+            headers["Content-Disposition"] = f"attachment; filename={self._filename}.csv"
         return Response(gen, mimetype="text/csv; charset=utf8", headers=headers)
 
     def _begin(self):
@@ -296,8 +300,8 @@ class JSONLPrinter(APrinter):
     a printer class writing in JSONLines format
     """
 
-    def make_response(self, gen):
-        return Response(gen, mimetype=" text/plain; charset=utf8")
+    def make_response(self, gen, headers=None):
+        return Response(gen, mimetype=" text/plain; charset=utf8", headers=headers)
 
     def _begin(self):
         if show_hard_api_key_warning():