Remove usage of PHP alias in the Python client

Python-packages/covidcast-py/covidcast/covidcast.py

@@ -7,12 +7,22 @@
 import pandas as pd
 import numpy as np
 from delphi_epidata import Epidata
+from delphi_epidata.delphi_epidata import _HEADERS
+from pkg_resources import get_distribution, DistributionNotFound
 from epiweeks import Week
 
 from .errors import NoDataWarning
 
+
 # Point API requests to the default endpoint
-Epidata.BASE_URL = "https://api.covidcast.cmu.edu/epidata/api.php"
+Epidata.BASE_URL = "https://api.covidcast.cmu.edu/epidata"
+# Prepend to Epidata client's user agent to specify this package and version
+try:
+    _ver = get_distribution("covidcast").version
+except DistributionNotFound:
+    _ver = "0.0.0"
+_HEADERS['user-agent'] = f"covidcast/{_ver} " + _HEADERS['user-agent']
+
 
 VALID_GEO_TYPES = {"county", "hrr", "msa", "dma", "state",  "hhs", "nation"}
 
@@ -463,14 +473,16 @@ def _async_fetch_epidata(data_source: str,
                          issues: Union[date, tuple, list],
                          lag: int,
                          time_type: str = "day") -> Union[pd.DataFrame, None]:
-    """Fetch data from Epidata API asynchronously.
+    """Fetch data from Epidata API asynchronously [DEPRECATED].
 
     signal() wraps this to support fetching data over a range of dates
     and stacks the resulting data frames.
 
     If no data is found, return None, so signal() can easily filter out these
     entries.
     """
+    warnings.warn("`_async_fetch_epidata` is deprecated and will be removed in a future version.",
+                  category=DeprecationWarning)
     dfs = []
     params = []
     date_range = pd.date_range(start_day, end_day, freq="D" if time_type == "day" else "W")

Python-packages/covidcast-py/docs/changelog.rst

@@ -1,6 +1,14 @@
 Changelog
 =========
 
+v0.2.2, October 10, 2023
+--------------------
+
+- New feature: Web requests now identify themselves with a `covidcast`-specific "user agent" string.
+- Update: Now uses newer version of the `delphi-epidata` libarary.
+- Bug fix: Removed usage of PHP alias endpoint for compatibility with new `delphi-epidata` version.
+- Deprecated function: Private method :py:func:`_async_fetch_epidata` has been deprecated.
+
 v0.2.1, June 1, 2023
 --------------------
 

Python-packages/covidcast-py/docs/conf.py

@@ -21,7 +21,7 @@
 author = 'Delphi research group'
 
 # The full version, including alpha/beta/rc tags
-release = '0.2.1'
+release = '0.2.2'
 
 
 # -- General configuration ---------------------------------------------------

Python-packages/covidcast-py/setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="covidcast",
-    version="0.2.1",  # also update in docs/conf.py
+    version="0.2.2",  # also update in docs/conf.py
     author="Alex Reinhart",
     author_email="areinhar@stat.cmu.edu",
     description="Access COVID-19 data through the Delphi COVIDcast API",
@@ -22,7 +22,7 @@
     install_requires=[
         "pandas<2",
         "requests",
-        "delphi-epidata>=4.1.1",
+        "delphi-epidata>=4.1.11,==4.*",
         "geopandas",
         "matplotlib",
         "numpy",

Python-packages/covidcast-py/tests/test_covidcast.py

@@ -265,19 +265,25 @@ def test__async_fetch_epidata(mock_async_epidata):
     with warnings.catch_warnings(record=True) as w:
         covidcast._async_fetch_epidata("source", "signal", date(2020, 4, 2), date(2020, 4, 2),
                                        "*", None, None, None, None)
-        assert len(w) == 1
+        assert len(w) == 2 # including deprecation warning
         assert str(w[0].message) == \
+               "`_async_fetch_epidata` is deprecated and will be removed in a future version."
+        assert w[0].category is DeprecationWarning
+        assert str(w[1].message) == \
                "Problem obtaining source signal data on 20200402 for geography '*': failed"
-        assert w[0].category is RuntimeWarning
+        assert w[1].category is RuntimeWarning
 
     # test warning when a no data response is received
     mock_async_epidata.return_value = [({"message": "no results"}, {"time_values": 20200402})]  # no data API response
     with warnings.catch_warnings(record=True) as w:
         covidcast._async_fetch_epidata("source", "signal", date(2020, 4, 2), date(2020, 4, 2),
                                        "county", None, None, None, None)
-        assert len(w) == 1
-        assert str(w[0].message) == "No source signal data found on 20200402 for geography 'county'"
-        assert w[0].category is NoDataWarning
+        assert len(w) == 2 # including deprecation warning
+        assert str(w[0].message) == \
+               "`_async_fetch_epidata` is deprecated and will be removed in a future version."
+        assert w[0].category is DeprecationWarning
+        assert str(w[1].message) == "No source signal data found on 20200402 for geography 'county'"
+        assert w[1].category is NoDataWarning
 
     # test no epidata yields nothing
     mock_async_epidata.return_value = [({"message": "success"}, None)]  # no epidata

docs/covidcast-py/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: adc91b801928f140c7be8ffe81e03415
+config: cbbd65a1377a79b8be99216462605909
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/covidcast-py/html/_sources/changelog.rst.txt

@@ -1,6 +1,14 @@
 Changelog
 =========
 
+v0.2.2, October 10, 2023
+--------------------
+
+- New feature: Web requests now identify themselves with a `covidcast`-specific "user agent" string.
+- Update: Now uses newer version of the `delphi-epidata` libarary.
+- Bug fix: Removed usage of PHP alias endpoint for compatibility with new `delphi-epidata` version.
+- Deprecated function: Private method :py:func:`_async_fetch_epidata` has been deprecated.
+
 v0.2.1, June 1, 2023
 --------------------
 

docs/covidcast-py/html/_static/basic.css

@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

docs/covidcast-py/html/_static/documentation_options.js

@@ -1,6 +1,5 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.2.1',
+const DOCUMENTATION_OPTIONS = {
+    VERSION: '0.2.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/covidcast-py/html/_static/pygments.css

@@ -22,6 +22,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #8f5902; font-style: italic } /* Comment.Special */
 .highlight .gd { color: #a40000 } /* Generic.Deleted */
 .highlight .ge { color: #000000; font-style: italic } /* Generic.Emph */
+.highlight .ges { color: #000000 } /* Generic.EmphStrong */
 .highlight .gr { color: #ef2929 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */

docs/covidcast-py/html/_static/searchtools.js

@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**

docs/covidcast-py/html/_static/sphinx_highlight.js

@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});