Merge pull request #53 from UDST/dev

smmaurer · web-flow · commit 0a41626e7faf · 2020-11-09T11:30:28.000-08:00
Finalizing v1.5.4 release
diff --git a/.travis.yml b/.travis.yml
@@ -5,14 +5,13 @@ python:
   - '3.5'
   - '3.6'
   - '3.7'
-  # - '3.8' broken because PyTables binaries aren't available yet
+  - '3.8'
 
 install:
   - pip install .
   - pip install pytest-cov coveralls pycodestyle
   - pip install flask pygments  # for server component tests
   - bin/build_js_bundle.sh complete
-  - pip install numpydoc sphinx sphinx_rtd_theme  # for building docs 
   - pip list
   - pip show orca
 
@@ -22,8 +21,3 @@ script:
 
 after_success:
   - coveralls
-  - bin/build_docs.sh
-
-env:
-  global:
-    secure: DMQgAnged8quDKf3pTLG6RZVMKhrhZfYSRKaPFJrERXEOuRPJjC4QYG24pdyCV2aOQbSOiF16vSctpDmMfjLDARkhNm8FvYYCOKLkE+4ijQ4vE/uQaHsnosGS/1LOOFGjK0h2dvm4CNJqV1JUhCKeOVe/87GGY2JVBy+NJnsl70=
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -1,3 +1,8 @@
+v1.5.4
+======
+
+* Support for PyToolz 0.11+
+
 v1.5.3
 ======
 
diff --git a/README.rst b/README.rst
@@ -1,40 +1,23 @@
-Orca
-====
-
-.. image:: https://img.shields.io/pypi/v/orca.svg
-    :target: https://pypi.python.org/pypi/orca/
-    :alt: PyPI Latest Version
-
-.. image:: https://travis-ci.org/UDST/orca.svg?branch=master
-    :target: https://travis-ci.org/UDST/orca
-    :alt: Build Status
-
 .. image:: https://coveralls.io/repos/UDST/orca/badge.svg?branch=master
   :target: https://coveralls.io/r/UDST/orca?branch=master
   :alt: Coverage
 
-.. image:: https://img.shields.io/pypi/wheel/orca.svg
-    :target: https://pypi.python.org/pypi/orca/
-    :alt: Wheel Status
+Orca
+====
+
+Orca is a Python library for task orchestration. It's designed for workflows like city simulation, where the data representing a model's state is so large that it needs to be managed outside of the task graph.
+
+The building blocks of a workflow are "steps", Python functions that can be assembled on the fly into linear or cyclical pipelines. Steps typically interact with a central data store that persists in memory while the pipeline runs. Derived tables and columns can be updated automatically as base data changes, and pipeline components are evaluated lazily to reduce unnecessary overhead.
 
-Orca is a pipeline orchestration tool that allows you to define dynamic data
-sources and explicitly connect them to processing functions.
-Orca has many features for working with `Pandas <http://pandas.pydata.org/>`__
-data structures, but it can be used with anything.
+Orca is used in `UrbanSim <https://github.com/udst/urbansim>`__ and other projects.
 
-Learn more in the official docs at https://udst.github.io/orca/.
+Documentation
+-------------
 
-Building the Orca UI JS Bundle
-------------------------------
+- `udst.github.io/orca/ <https://udst.github.io/orca/>`__
 
-Orca ships with a bundle of JavaScript for the server UI.
-If you've installed Orca from ``pip`` or ``conda`` you already have the
-bundle, but if you're working on Orca you might need to build it manually:
+Installation
+------------
 
-* Make sure `nodejs <https://nodejs.org/>`__ is installed.
-  (I use `Homebrew <http://brew.sh/>`__ on my Mac.)
-* Install `gulp <http://gulpjs.com/>`__: ``npm install -g gulp``
-* Change directories to ``orca/server/static``
-* Run ``npm install`` to install dependencies
-* Build the bundle: ``gulp js-build``, or
-* Watch JS files to rebuild the bundle on changes: ``gulp js-watch``
+- ``pip install orca``
+- ``conda install orca --channel conda-forge``
diff --git a/docs/README.md b/docs/README.md
@@ -0,0 +1,31 @@
+This folder generates the Orca online documentation, hosted at https://udst.github.io/orca/.
+
+### How it works
+
+HTML files are generated using [Sphinx](http://sphinx-doc.org) and hosted with GitHub Pages from the `gh-pages` branch of the repository. The online documentation is rendered and updated **manually**. 
+
+### Editing the documentation
+
+The files in `docs/source`, along with docstrings in the source code, determine what appears in the rendered documentation. Here's a [good tutorial](https://pythonhosted.org/an_example_pypi_project/sphinx.html) for Sphinx.
+
+### Previewing changes locally
+
+Install the copy of Orca that the documentation is meant to reflect. Install the documentation tools.
+
+```
+pip install . 
+pip install sphinx sphinx_rtd_theme numpydoc
+```
+
+Build the documentation. There should be status messages and warnings, but no errors.
+
+```
+cd docs
+sphinx-build -b html source build
+```
+
+The HTML files will show up in `docs/build/`. 
+
+### Uploading changes
+
+Clone a second copy of the repository and check out the `gh-pages` branch. Copy over the updated HTML files, commit them, and push the changes to GitHub.
diff --git a/docs/build/.gitignore b/docs/build/.gitignore
@@ -0,0 +1 @@
+*/*
diff --git a/docs/source/Makefile b/docs/source/Makefile
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -51,16 +51,16 @@
 
 # General information about the project.
 project = 'Orca'
-copyright = '2019, UrbanSim Inc'
+copyright = '2020, UrbanSim Inc'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.5'
+version = '1.5.4'
 # The full version, including alpha/beta/rc tags.
-release = '1.5.3'
+release = '1.5.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/docs/source/core.rst b/docs/source/core.rst
diff --git a/docs/source/example.rst b/docs/source/example.rst
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -119,19 +119,16 @@ Orca offers some conveniences for streamlining the construction of pipelines:
 Installation
 ------------
 
-Orca depends on Pandas, PyTables, and toolz (or cytoolz).
-Pandas and PyTables are included in `Anaconda <http://docs.continuum.io/anaconda/>`__.
-Toolz may be installed with `pip <https://pip.pypa.io/en/latest/index.html>`__,
-and both toolz and cytoolz are can be installed by
-`conda <http://conda.pydata.org/>`__ (if you are using Anaconda or miniconda).
+Orca requires Pandas, PyTables, and PyToolz, which will be installed automatically if they are not already present in your Python environment.
 
-With the dependencies installed, install Orca with pip::
+
+You can install Orca with pip::
 
     pip install orca
 
-Orca may also be installed with conda::
+Or with conda::
 
-    conda install -c udst orca
+    conda install orca --channel conda-forge
 
 Add the server option to include the optional server dependencies::
 
diff --git a/docs/source/make.bat b/docs/source/make.bat
diff --git a/docs/source/server.rst b/docs/source/server.rst
@@ -22,6 +22,19 @@ Orca by including the ``[server]`` option::
 
     pip install orca[server]
 
+Building the Orca UI JS Bundle
+------------------------------
+
+This is NOT NECESSARY if you've installed Orca from ``pip`` or ``conda``, but these instructions may help if you're working directly with the Orca source code.
+
+* Make sure `nodejs <https://nodejs.org/>`__ is installed.
+  (`Homebrew <http://brew.sh/>`__ is a nice way to do this on Mac.)
+* Install `gulp <http://gulpjs.com/>`__: ``npm install -g gulp``
+* Change directories to ``orca/server/static``
+* Run ``npm install`` to install dependencies
+* Build the bundle: ``gulp js-build``, or
+* Watch JS files to rebuild the bundle on changes: ``gulp js-watch``
+
 Start the Server
 ----------------
 
diff --git a/docs/source/utils.rst b/docs/source/utils.rst
diff --git a/orca/__init__.py b/orca/__init__.py
@@ -4,4 +4,4 @@
 
 from .orca import *
 
-version = __version__ = '1.5.3'
+version = __version__ = '1.5.4'
diff --git a/orca/orca.py b/orca/orca.py
@@ -11,17 +11,21 @@
 import logging
 import time
 import warnings
-from collections import Callable, namedtuple
+from collections import namedtuple
+try:
+    from collections.abc import Callable
+except ImportError:  # Python 2.7
+    from collections import Callable
 from contextlib import contextmanager
 from functools import wraps
 
+
 import pandas as pd
 import tables
 import tlz as tz
 
 from . import utils
 from .utils.logutil import log_start_finish
-from collections import namedtuple
 
 warnings.filterwarnings('ignore', category=tables.NaturalNameWarning)
 logger = logging.getLogger(__name__)
@@ -937,8 +941,8 @@ def _collect_variables(names, expressions=None):
         expressions = []
     offset = len(names) - len(expressions)
     labels_map = dict(tz.concatv(
-        tz.compatibility.zip(names[:offset], names[:offset]),
-        tz.compatibility.zip(names[offset:], expressions)))
+        zip(names[:offset], names[:offset]),
+        zip(names[offset:], expressions)))
 
     all_variables = tz.merge(_INJECTABLES, _TABLES)
     variables = {}
diff --git a/orca/server/server.py b/orca/server/server.py
@@ -336,7 +336,7 @@ def column_csv(table_name, col_name):
     Return a column as CSV using Pandas' default CSV output.
 
     """
-    csv = orca.get_table(table_name).get_column(col_name).to_csv(path=None)
+    csv = orca.get_table(table_name).get_column(col_name).to_csv(path_or_buf=None)
     return csv, 200, {'Content-Type': 'text/csv'}
 
 
diff --git a/orca/server/tests/test_server.py b/orca/server/tests/test_server.py
@@ -1,8 +1,9 @@
 import json
 
 import orca
+import numpy as np
 import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 import pytest
 
 from .. import server
@@ -233,7 +234,7 @@ def test_column_csv(tapp, dfa):
     assert rv.status_code == 200
 
     data = rv.data.decode('utf-8')
-    assert data == dfa.a.to_csv(path=None)
+    assert data == dfa.a.to_csv(path_or_buf=None)
 
 
 def test_no_column_404(tapp):
@@ -420,5 +421,5 @@ def test_table_groupbyagg_level_std(tapp):
     pdt.assert_series_equal(
         test,
         pd.Series(
-            [pd.np.nan, pd.Series([80, 90]).std()],
+            [np.nan, pd.Series([80, 90]).std()],
             index=['a', 'b'], name='b'))
diff --git a/orca/tests/test_orca.py b/orca/tests/test_orca.py
@@ -6,8 +6,8 @@
 import tempfile
 
 import pandas as pd
+import pandas.testing as pdt
 import pytest
-from pandas.util import testing as pdt
 
 from .. import orca
 from ..utils.testing import assert_frames_equal
diff --git a/setup.py b/setup.py
@@ -38,7 +38,7 @@ def run(self):
 
 setup(
     name='orca',
-    version='1.5.3',
+    version='1.5.4',
     description='A pipeline orchestration tool with Pandas support',
     long_description=long_description,
     author='UrbanSim Inc.',
@@ -52,6 +52,7 @@ def run(self):
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
         'License :: OSI Approved :: BSD License'
     ],
     packages=find_packages(exclude=['*.tests']),

-Original file line number
+Diff line change
@@ @@ -1,3 +1,8 @@ @@
 +v1.5.4
 +======
++
 +* Support for PyToolz 0.11+
++
 v1.5.3
 ======