Merge branch 'package-intro' into lee14257/package-eval

Author: krivard

.github/workflows/release_helper.yml

@@ -68,7 +68,7 @@ jobs:
           inv dist
       - uses: actions/upload-artifact@v2
         with:
-          name: delphi_epidata
+          name: epidatpy
       - name: Upload Release Asset
         uses: AButler/[email protected]
         with:

README.md

@@ -1,19 +1,23 @@
-# Delphi Epidata Python Client
+# Delphi Epidata Python Client `epidatpy`
 
 [![License: MIT][mit-image]][mit-url] [![Github Actions][github-actions-image]][github-actions-url] [![PyPi][pypi-image]][pypi-url] [![Read the Docs][docs-image]][docs-url]
 
 ## Install
 
-Install from PyPi:
+**RENAME NOTICE (2022-08-05):** This package will be renamed to `epidatpy`. 
+Please adjust all references to the package name accordingly.
+For a short-term fix, the package can be used with the old name by installing with `ref="delphi_epidata-before-rename"`.
+
+Install latest version:
 
 ```sh
-pip install delphi-epidata
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"
 ```
 
-latest version
+old name version
 
 ```sh
-pip install -e "git+https://github.com/cmu-delphi/delphi-epidata-py.git#egg=delphi_epidata"
+pip install -e "git+https://github.com/cmu-delphi/epidatpy.git@delphi_epidata-before-rename#egg=delphi_epidata"
 ```
 
 ## Usage
@@ -48,20 +52,20 @@ inv release  # upload the current version to pypi
 
 The release consists of multiple steps which can be all done via the GitHub website:
 
-1. Go to [create_release GitHub Action](https://github.com/cmu-delphi/delphi-epidata-py/actions/workflows/create_release.yml) and click the `Run workflow` button. Enter the next version number or one of the magic keywords (patch, minor, major) and hit the green `Run workflow` button.
-1. The action will prepare a new release and will end up with a new [Pull Request](https://github.com/cmu-delphi/delphi-epidata-py/pulls)
+1. Go to [create_release GitHub Action](https://github.com/cmu-delphi/epidatpy/actions/workflows/create_release.yml) and click the `Run workflow` button. Enter the next version number or one of the magic keywords (patch, minor, major) and hit the green `Run workflow` button.
+1. The action will prepare a new release and will end up with a new [Pull Request](https://github.com/cmu-delphi/epidatpy/pulls)
 1. Let the code owner review the PR and its changes and let the CI check whether everything builds successfully
 1. Once approved and merged, another GitHub action job starts which automatically will
    1. create a git tag
-   1. create another [Pull Request](https://github.com/cmu-delphi/delphi-epidata-py/pulls) to merge the changes back to the `dev` branch
-   1. create a [GitHub release](https://github.com/cmu-delphi/delphi-epidata-py/releases) with automatically derived release notes
+   1. create another [Pull Request](https://github.com/cmu-delphi/epidatpy/pulls) to merge the changes back to the `dev` branch
+   1. create a [GitHub release](https://github.com/cmu-delphi/epidatpy/releases) with automatically derived release notes
 1. Done
 
 [mit-image]: https://img.shields.io/badge/License-MIT-yellow.svg
 [mit-url]: https://opensource.org/licenses/MIT
-[github-actions-image]: https://github.com/cmu-delphi/delphi-epidata-py/workflows/ci/badge.svg
-[github-actions-url]: https://github.com/cmu-delphi/delphi-epidata-py/actions
-[pypi-image]: https://img.shields.io/pypi/v/delphi-epidata
-[pypi-url]: https://pypi.python.org/pypi/delphi-epidata/
-[docs-image]: https://readthedocs.org/projects/delphi-epidata/badge/?version=latest
-[docs-url]: https://delphi-epidata.readthedocs.io/en/latest/?badge=latest
+[github-actions-image]: https://github.com/cmu-delphi/epidatpy/workflows/ci/badge.svg
+[github-actions-url]: https://github.com/cmu-delphi/epidatpy/actions
+[pypi-image]: https://img.shields.io/pypi/v/epidatpy
+[pypi-url]: https://pypi.python.org/pypi/epidatpy/
+[docs-image]: https://readthedocs.org/projects/epidatpy/badge/?version=latest
+[docs-url]: https://epidatpy.readthedocs.io/en/latest/?badge=latest

docs/conf.py

@@ -12,17 +12,18 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
-sys.path.insert(0, os.path.abspath('../delphi_epidata'))
+
+sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath("../epidatpy"))
 
 # -- Project information -----------------------------------------------------
 
-project = 'Delphi Epidata API client'
-copyright = '2021, Delphi research group'  # pylint: disable=redefined-builtin
-author = 'Delphi research group'
+project = "Delphi Epidata API client"
+copyright = "2021, Delphi research group"  # pylint: disable=redefined-builtin
+author = "Delphi research group"
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+release = "1.0.0"
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,29 +32,29 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx_autodoc_typehints',
+    "sphinx.ext.autodoc",
+    "sphinx_autodoc_typehints",
     # 'matplotlib.sphinxext.plot_directive'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 add_module_names = False
-autoclass_content = 'class'
-autodoc_typehints = 'description'
+autoclass_content = "class"
+autodoc_typehints = "description"
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -63,7 +64,7 @@
 html_theme_options = {
     "extra_nav_links": {
         "Delphi group": "https://delphi.cmu.edu/",
-        "Delphi Epidata API": "https://cmu-delphi.github.io/delphi-epidata"
+        "Delphi Epidata API": "https://cmu-delphi.github.io/delphi-epidata",
     }
 }
 

docs/getting_started.rst

@@ -168,14 +168,14 @@ An ``EpiRange`` object can be also used to construct a range of epiweeks or date
 
 Basic examples
 --------------
+
 **COVIDcast**
 
 To obtain smoothed estimates of COVID-like illness from our symptom survey,
 distributed through Facebook, for every county in the United States between
 2020-05-01 and 2020-05-07:
 
->>> from datetime import date
->>> from delphi_epidata.request import Epidata, EpiRange
+>>> from epidatpy.request import Epidata, EpiRange
 >>> apicall = Epidata.covidcast("fb-survey", "smoothed_cli", 
 ...                              "day", "county", 
 ...                              EpiRange(20200501, 20200507), "*")
@@ -194,7 +194,7 @@ column. The ``value`` is the requested signal - the smoothed
 estimate of the percentage of people with COVID-like illness based on the
 symptom surveys. The ``issue`` column indicates when this data was reported; in this case, the survey estimates for
 May 1st were updated on September 3rd based on new data, giving a ``lag`` of 125 days.
-See the :py:func:`delphi_epidata.request.Epidata.covidcast` documentation for further details on the returned
+See the :py:func:`epidatpy.request.Epidata.covidcast` documentation for further details on the returned
 columns.
 
 In the above code, the ``.df()`` function on the ``apicall`` variable generated a Pandas DataFrame. We can use 
@@ -259,7 +259,6 @@ command:
  .
  }]
 
-Below are some other examples utilizing other Epidata endpoints and data sources.
 
 |
 

docs/index.rst

@@ -2,12 +2,12 @@ Delphi Epidata
 ===============
 
 This package provides Python access to the `Delphi Epidata API
-<https://cmu-delphi.github.io/delphi-epidata/api>`_ published by
+<https://cmu-delphi.github.io/delphi-epidata/>`_ published by
 the `Delphi group <https://delphi.cmu.edu>`_ at `Carnegie Mellon University
 <https://www.cmu.edu>`_.
 
 The package source code and bug tracker can be found `on GitHub
-<https://github.com/cmu-delphi/delphi-epidata-py>`_.
+<https://github.com/cmu-delphi/epidatpy>`_.
 
 
 .. note :: **You should consider subscribing** to the `API mailing list
@@ -29,12 +29,12 @@ Installation
 ------------
 
 This package is available on PyPI as `covidcast
-<https://pypi.org/project/delphi-epidata/>`_, and can be installed using ``pip`` or
+<https://pypi.org/project/epidatpy/>`_, and can be installed using ``pip`` or
 your favorite Python package manager:
 
 .. code-block:: sh
 
-   pip install delphi-epidata
+   pip install epidatpy
 
 The package requires `pandas <https://pandas.pydata.org/>`_ and `requests
 <https://requests.readthedocs.io/en/master/>`_; these should be installed

docs/signals_covid.rst

@@ -105,7 +105,7 @@ More on COVIDcast (TODO)
 Many data sources and signals are available, so one can also obtain a data frame
 of all signals and their associated metadata:
 
->>> from delphi_epidata.request import CovidcastEpidata
+>>> from epidatpy.request import CovidcastEpidata
 >>> covid_ds = CovidcastEpidata()
 >>> df_source = covid_ds.source_df
 >>> df_signal = covid_ds.signal_df
@@ -115,12 +115,12 @@ which has the property ``source_df`` and ``signal_df``, two data frames containi
 the information of all available sources and signals.
 More details of the two data frames are listed below.
 
-.. autoclass:: delphi_epidata.request.CovidcastDataSources()
+.. autoclass:: epidatpy.request.CovidcastDataSources()
     :members:
 
 More metadata statistics can also be obtained as follows:
 
->>> from delphi_epidata.request import Epidata
+>>> from epidatpy.request import Epidata
 >>> df = Epidata.covidcast_meta().df()
 
-.. autofunction:: delphi_epidata.request.Epidata.covidcast_meta()
+.. autofunction:: epidatpy.request.Epidata.covidcast_meta()

delphi_epidata/__init__.py renamed to epidatpy/__init__.py

@@ -4,6 +4,6 @@
 __version__: Final = "1.0.0"
 
 
-HTTP_HEADERS: Final = {"User-Agent": f"delphi_epidata/{__version__}"}
+HTTP_HEADERS: Final = {"User-Agent": f"epidatpy/{__version__}"}
 
 BASE_URL: Final = "https://delphi.cmu.edu/epidata/"

delphi_epidata/_constants.py renamed to epidatpy/_constants.py

@@ -2,4 +2,4 @@
 [tool.black]
 line-length = 120
 target-version = ['py38']
-include = 'delphi_epidata'
+include = 'epidatpy'

delphi_epidata/_covidcast.py renamed to epidatpy/_covidcast.py

@@ -3,7 +3,7 @@ current_version = 1.0.0
 commit = False
 tag = False
 
-[bumpversion:file:delphi_epidata/_version.py]
+[bumpversion:file:epidatpy/_version.py]
 [bumpversion:file:docs/conf.py]
 
 [bdist_wheel]

delphi_epidata/_endpoints.py renamed to epidatpy/_endpoints.py

@@ -3,14 +3,14 @@
 
 
 setuptools.setup(
-    name="delphi_epidata",
+    name="epidatpy",
     version="1.0.0",
     author="Alex Reinhart",
     author_email="[email protected]",
     description="A programmatic interface to Delphi's Epidata API.",
-    long_description=pathlib.Path('README.md').read_text(),
+    long_description=pathlib.Path("README.md").read_text(),
     long_description_content_type="text/markdown",
-    url="https://github.com/cmu-delphi/delphi-epidata-py",
+    url="https://github.com/cmu-delphi/epidatpy",
     packages=setuptools.find_packages(),
     classifiers=[
         "Programming Language :: Python :: 3",
@@ -20,7 +20,7 @@
         "Natural Language :: English",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
-    python_requires='>=3.6',
-    install_requires=[f.strip() for f in pathlib.Path('requirements.txt').read_text().split('\n') if f],
-    # package_data={'delphi_epidata': []}
+    python_requires=">=3.6",
+    install_requires=[f.strip() for f in pathlib.Path("requirements.txt").read_text().split("\n") if f],
+    # package_data={'epidatpy': []}
 )

delphi_epidata/_model.py renamed to epidatpy/_model.py

@@ -1,4 +1,4 @@
-from delphi_epidata.request import CovidcastEpidata, EpiRange
+from epidatpy.request import CovidcastEpidata, EpiRange
 
 epidata = CovidcastEpidata()
 print(list(epidata.source_names))

delphi_epidata/_parse.py renamed to epidatpy/_parse.py

@@ -1,5 +1,5 @@
 from datetime import date
-from delphi_epidata.request import Epidata, EpiRange
+from epidatpy.request import Epidata, EpiRange
 
 apicall = Epidata.covidcast("fb-survey", "smoothed_cli", "day", "nation", EpiRange(20210405, 20210410), "us")
 

delphi_epidata/async_request.py renamed to epidatpy/async_request.py

@@ -1,5 +1,5 @@
 from asyncio import get_event_loop
-from delphi_epidata.async_request import Epidata
+from epidatpy.async_request import Epidata
 
 
 async def main() -> None:

delphi_epidata/request.py renamed to epidatpy/request.py

@@ -17,7 +17,7 @@
 ROOT_DIR = Path(__file__).parent
 SETUP_FILE = ROOT_DIR.joinpath("setup.py")
 TEST_DIR = ROOT_DIR.joinpath("tests")
-SOURCE_DIR = ROOT_DIR.joinpath("delphi_epidata")
+SOURCE_DIR = ROOT_DIR.joinpath("epidatpy")
 TOX_DIR = ROOT_DIR.joinpath(".tox")
 COVERAGE_FILE = ROOT_DIR.joinpath(".coverage")
 COVERAGE_DIR = ROOT_DIR.joinpath("htmlcov")

pyproject.toml

@@ -1,4 +1,4 @@
-from delphi_epidata import __version__
+from epidatpy import __version__
 
 
 def test_version() -> None:

setup.cfg

@@ -1,4 +1,4 @@
-from delphi_epidata._model import EpiRange, format_item, format_list
+from epidatpy._model import EpiRange, format_item, format_list
 
 
 def test_epirange() -> None: