Merge pull request #10 from tsutterley/pip

pip installable version of pointCollection
SmithB · Jun 17, 2020 · 47be54f · 47be54f
2 parents 779cecd + dc27c22
commit 47be54f
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diff --git a/doc/Makefile b/doc/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/doc/make.bat b/doc/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -0,0 +1,3 @@
+sphinx
+recommonmark
+sphinx_markdown_tables
diff --git a/doc/source/Install.md b/doc/source/Install.md
@@ -0,0 +1,18 @@
+Installation
+============
+
+Presently pointCollection is only available for use as a [github repository](https://github.com/SmithB/pointCollection).
+The contents of the repository can be download as a [zipped file](https://github.com/SmithB/pointCollection/archive/master.zip)  or cloned.
+To use this repository, please fork into your own account and then clone onto your system.  
+```bash
+git clone https://github.com/SmithB/pointCollection.git
+```
+Can then install using `setuptools`
+```bash
+python setup.py install
+```
+or `pip`
+```bash
+python3 -m pip install --user .
+```
+Executable versions of this repository can also be tested using [Binder](https://mybinder.org/v2/gh/SmithB/pointCollection/master) and [Pangeo](https://binder.pangeo.io/v2/gh/SmithB/pointCollection/master).
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -0,0 +1,59 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'pointCollection'
+copyright = '2020, Ben Smith'
+author = 'Ben Smith'
+
+# The full version, including alpha/beta/rc tags
+release = '1.0.0.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['recommonmark','sphinx_markdown_tables']
+
+# Add any paths that contain templates here, relative to this directory.
+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 = ['**.ipynb_checkpoints']
+
+# location of master document (by default sphinx looks for contents.rst)
+master_doc = 'index'
+
+# -- Configuration options ---------------------------------------------------
+autosummary_generate = True
+
+# -- 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 = 'bizstyle'
+
+# 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,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -0,0 +1,10 @@
+pointCollection
+===============
+
+Python utilities for organizing and manipulating point data
+
+.. toctree::
+    :maxdepth: 2
+    :caption: Getting Started:
+
+    Install.md
diff --git a/GeoIndex_demo.ipynb → notebooks/GeoIndex_demo.ipynb b/GeoIndex_demo.ipynb → notebooks/GeoIndex_demo.ipynb
@@ -236,7 +236,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "test_dir='test_data/for_geoindex'\n",
+    "test_dir='../test_data/for_geoindex'\n",
     "if not os.path.isdir(test_dir):\n",
     "    os.mkdir(test_dir)\n",
     "for offset in np.arange(-40, 50, 10):\n",
@@ -581,7 +581,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,

diff --git a/Tile_demo.ipynb → notebooks/Tile_demo.ipynb b/Tile_demo.ipynb → notebooks/Tile_demo.ipynb
@@ -106,11 +106,11 @@
     }
    ],
    "source": [
-    "gi_file='test_data/for_geoindex/GeoIndex.h5'\n",
+    "gi_file='../test_data/for_geoindex/GeoIndex.h5'\n",
     "srs_proj4 = '+proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs '\n",
     "\n",
     "\n",
-    "tile_dir='test_Data/for_geoindex/tiles'\n",
+    "tile_dir='../test_Data/for_geoindex/tiles'\n",
     "if not os.path.isdir(tile_dir):\n",
     "    os.mkdir(tile_dir)\n",
     "else:\n",
@@ -175,7 +175,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "test_dir='test_data/for_geoindex/other_diagonal'\n",
+    "test_dir='../test_data/for_geoindex/other_diagonal'\n",
     "\n",
     "x=np.arange(-50, 50, dtype=np.float64)\n",
     "y=-0.8*x\n",
@@ -410,7 +410,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,

diff --git a/map_1415.ipynb → notebooks/map_1415.ipynb b/map_1415.ipynb → notebooks/map_1415.ipynb
diff --git a/map_CS2_fit.ipynb → notebooks/map_CS2_fit.ipynb b/map_CS2_fit.ipynb → notebooks/map_CS2_fit.ipynb
diff --git a/point_demo.ipynb → notebooks/point_demo.ipynb b/point_demo.ipynb → notebooks/point_demo.ipynb
@@ -241,7 +241,7 @@
     }
    ],
    "source": [
-    "ATL06_file=os.path.dirname(pc.__file__)+'/test_data/ATL06_20190205041106_05910210_209_01.h5'\n",
+    "ATL06_file='../test_data/ATL06_20190205041106_05910210_209_01.h5'\n",
     "D_06=pc.ATL06.data().from_h5(ATL06_file)\n",
     "print(D_06)"
    ]
@@ -358,7 +358,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,

diff --git a/tide_demo.ipynb → notebooks/tide_demo.ipynb b/tide_demo.ipynb → notebooks/tide_demo.ipynb
diff --git a/ATL06/__init__.py → pointCollection/ATL06/__init__.py b/ATL06/__init__.py → pointCollection/ATL06/__init__.py
diff --git a/ATL06/data.py → pointCollection/ATL06/data.py b/ATL06/data.py → pointCollection/ATL06/data.py
diff --git a/ATL06/tile.py → pointCollection/ATL06/tile.py b/ATL06/tile.py → pointCollection/ATL06/tile.py
diff --git a/ATL11/__init__.py → pointCollection/ATL11/__init__.py b/ATL11/__init__.py → pointCollection/ATL11/__init__.py
diff --git a/ATL11/crossover_data.py → pointCollection/ATL11/crossover_data.py b/ATL11/crossover_data.py → pointCollection/ATL11/crossover_data.py
diff --git a/ATL11/data.py → pointCollection/ATL11/data.py b/ATL11/data.py → pointCollection/ATL11/data.py
diff --git a/ATL11/demo.py → pointCollection/ATL11/demo.py b/ATL11/demo.py → pointCollection/ATL11/demo.py
diff --git a/ATM_Qfit/__init__.py → pointCollection/ATM_Qfit/__init__.py b/ATM_Qfit/__init__.py → pointCollection/ATM_Qfit/__init__.py
diff --git a/ATM_Qfit/data.py → pointCollection/ATM_Qfit/data.py b/ATM_Qfit/data.py → pointCollection/ATM_Qfit/data.py
diff --git a/ATM_WF/__init__.py → pointCollection/ATM_WF/__init__.py b/ATM_WF/__init__.py → pointCollection/ATM_WF/__init__.py
diff --git a/ATM_WF/data.py → pointCollection/ATM_WF/data.py b/ATM_WF/data.py → pointCollection/ATM_WF/data.py
diff --git a/CS2/__init__.py → pointCollection/CS2/__init__.py b/CS2/__init__.py → pointCollection/CS2/__init__.py
diff --git a/CS2/data.py → pointCollection/CS2/data.py b/CS2/data.py → pointCollection/CS2/data.py
diff --git a/CS2_retracked_POCA/__init__.py → ...Collection/CS2_retracked_POCA/__init__.py b/CS2_retracked_POCA/__init__.py → ...Collection/CS2_retracked_POCA/__init__.py
diff --git a/CS2_retracked_POCA/tile.py → pointCollection/CS2_retracked_POCA/tile.py b/CS2_retracked_POCA/tile.py → pointCollection/CS2_retracked_POCA/tile.py
diff --git a/CS2_retracked_SW/__init__.py → pointCollection/CS2_retracked_SW/__init__.py b/CS2_retracked_SW/__init__.py → pointCollection/CS2_retracked_SW/__init__.py
diff --git a/CS2_retracked_SW/tile.py → pointCollection/CS2_retracked_SW/tile.py b/CS2_retracked_SW/tile.py → pointCollection/CS2_retracked_SW/tile.py
diff --git a/CS2_wfm/__init__.py → pointCollection/CS2_wfm/__init__.py b/CS2_wfm/__init__.py → pointCollection/CS2_wfm/__init__.py
diff --git a/CS2_wfm/data.py → pointCollection/CS2_wfm/data.py b/CS2_wfm/data.py → pointCollection/CS2_wfm/data.py
diff --git a/Qfit.py → pointCollection/Qfit.py b/Qfit.py → pointCollection/Qfit.py
diff --git a/__init__.py → pointCollection/__init__.py b/__init__.py → pointCollection/__init__.py
diff --git a/bin_rows.py → pointCollection/bin_rows.py b/bin_rows.py → pointCollection/bin_rows.py
diff --git a/data.py → pointCollection/data.py b/data.py → pointCollection/data.py
diff --git a/geoIndex.py → pointCollection/geoIndex.py b/geoIndex.py → pointCollection/geoIndex.py
diff --git a/glah12/__init__.py → pointCollection/glah12/__init__.py b/glah12/__init__.py → pointCollection/glah12/__init__.py
diff --git a/glah12/campaign_bias_correction.py → ...ection/glah12/campaign_bias_correction.py b/glah12/campaign_bias_correction.py → ...ection/glah12/campaign_bias_correction.py
diff --git a/glah12/data.py → pointCollection/glah12/data.py b/glah12/data.py → pointCollection/glah12/data.py
diff --git a/grid/WV_date.py → pointCollection/grid/WV_date.py b/grid/WV_date.py → pointCollection/grid/WV_date.py
diff --git a/grid/__init__.py → pointCollection/grid/__init__.py b/grid/__init__.py → pointCollection/grid/__init__.py
diff --git a/grid/data.py → pointCollection/grid/data.py b/grid/data.py → pointCollection/grid/data.py
diff --git a/grid/mosaic.py → pointCollection/grid/mosaic.py b/grid/mosaic.py → pointCollection/grid/mosaic.py
diff --git a/index_glob.py → pointCollection/index_glob.py b/index_glob.py → pointCollection/index_glob.py
diff --git a/indexedH5/__init__.py → pointCollection/indexedH5/__init__.py b/indexedH5/__init__.py → pointCollection/indexedH5/__init__.py
diff --git a/indexedH5/data.py → pointCollection/indexedH5/data.py b/indexedH5/data.py → pointCollection/indexedH5/data.py
diff --git a/is2_calendar.py → pointCollection/is2_calendar.py b/is2_calendar.py → pointCollection/is2_calendar.py
diff --git a/pt_blockmedian.py → pointCollection/pt_blockmedian.py b/pt_blockmedian.py → pointCollection/pt_blockmedian.py
diff --git a/reconstruct_ATL06_tracks.py → pointCollection/reconstruct_ATL06_tracks.py b/reconstruct_ATL06_tracks.py → pointCollection/reconstruct_ATL06_tracks.py
diff --git a/tile.py → pointCollection/tile.py b/tile.py → pointCollection/tile.py
diff --git a/unique_by_rows.py → pointCollection/unique_by_rows.py b/unique_by_rows.py → pointCollection/unique_by_rows.py
diff --git a/readthedocs.yml b/readthedocs.yml
@@ -0,0 +1,19 @@
+# readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: doc/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: []
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+     - requirements: doc/requirements.txt
diff --git a/IndexPicker.py → scripts/IndexPicker.py b/IndexPicker.py → scripts/IndexPicker.py
diff --git a/make_mosaic.py → scripts/make_mosaic.py b/make_mosaic.py → scripts/make_mosaic.py
diff --git a/make_tiles.py → scripts/make_tiles.py b/make_tiles.py → scripts/make_tiles.py
diff --git a/points_to_grid.py → scripts/points_to_grid.py b/points_to_grid.py → scripts/points_to_grid.py
diff --git a/test.py → scripts/test.py b/test.py → scripts/test.py
diff --git a/setup.py b/setup.py
@@ -1,8 +1,14 @@
 from setuptools import setup, find_packages
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
 setup(
-    name='Utilities for organizing and manipulating point data',
+    name='pointCollection',
     version='1.0.0.0',
-    description='Python',
+    description='Utilities for organizing and manipulating point data',
+    long_description=long_description,
+    long_description_content_type="text/markdown",
     url='https://github.com/SmithB/pointCollection',
     author='Ben Smith',
     author_email='besmith@uw.edu',