Merge pull request #75 from brycefrank/develop

Develop

.gitignore

@@ -20,20 +20,12 @@ changelog_0.2.1.md
 pyfortest/temp.*
 /.idea
 /.vs
-/docs/api/setup.rst
-/docs/api/pyfortest.test_pyfor.rst
-/docs/api/pyfortest.test_collection.rst
-/docs/api/pyfortest.rst
-/docs/html/.doctrees/advanced
-/docs/html/.doctrees/api
-/docs/html/.doctrees/topics
-/docs/html/.doctrees
-/docs/html/api/pyfortest.html
-/docs/html/api/pyfortest.test_collection.html
-/docs/html/api/pyfortest.test_pyfor.html
-/docs/html/api/setup.html
-/docs/html/_sources
-/docs/html/_static
-/pyfortest/__pycache__
-/__pycache__
+/environment.yml~
+/CHANGELOG.md~
+/README.md~
+/.environment.yml.un~
+/.CHANGELOG.md.un~
 /temp_tif.tif
+/pyfor.sln
+pyfortest/__pycache__
+pyfor.pyproj

.travis.yml

@@ -1,17 +1,46 @@
-dist: xenial
-language: python
-python:
-  - "3.7"
+language : shell
+
+env:
+  - CONDA_PYTHON=3.7
+
+os:
+  - linux
+  - windows
+
+before_install:
+  # set conda path info
+  - if [[ "$TRAVIS_OS_NAME" != "windows" ]]; then
+      MINICONDA_PATH=$HOME/miniconda;
+      MINICONDA_SUB_PATH=$MINICONDA_PATH/bin;
+    elif [[ "$TRAVIS_OS_NAME" == "windows" ]]; then
+      MINICONDA_PATH=/c/tools/miniconda3/;
+      MINICONDA_PATH_WIN=`cygpath --windows $MINICONDA_PATH`;
+      MINICONDA_SUB_PATH=$MINICONDA_PATH/Scripts;
+    fi;
+  # obtain miniconda installer
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    elif  [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+    fi;
+
 install:
-  - sudo apt-get update
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  - conda info -a
-  - conda config --add channels conda-forge
+  # install miniconda
+  # pip and conda will also need OpenSSL for Windows
+  - if [[ "$TRAVIS_OS_NAME" != "windows" ]]; then
+      bash miniconda.sh -b -p $HOME/miniconda;
+    elif  [[ "$TRAVIS_OS_NAME" == "windows" ]]; then
+      choco install openssl.light;
+      choco install miniconda3 --params="'/AddToPath:1 /D:$MINICONDA_PATH_WIN'";
+    fi;
+  - export PATH="$MINICONDA_PATH:$MINICONDA_SUB_PATH:$PATH";
+  # for conda version 4.4 or later
+  - source $MINICONDA_PATH/etc/profile.d/conda.sh;
+  - hash -r;
+  - conda activate base
+  - conda config --set always_yes yes --set changeps1 no;
+  - conda update -q conda;
+  - echo "Python $CONDA_PYTHON running on $TRAVIS_OS_NAME";
   - conda env create -f environment.yml
   - source activate pyfor_env
   - pip install coveralls

CHANGELOG.md

@@ -1,3 +1,43 @@
+# 0.3.6
+
+Updates between September 9, 2019 and December 1, 2019.
+
+## Changes to Codebase
+
+### Cloud
+1. Added `.from_pdal` class method which converts a `PDAL` `python.filter` `ins` argument to a Cloud object.
+
+### Collection
+1. `._build_polygons` is now multithreaded.
+2. `.create_index` is now multithreaded. Closes #65
+3. `from_dir` now supports glob strings. Closes #66
+4. `par_apply`  accepts optional keyword arguments using the `args` 
+parameter. These are passed to the applying function.
+5. Added date-time parsing to collections.
+
+### GISExport
+1. Removed some deprecated functions that were only used for tree segmentation
+
+### Ground Filter
+1. Fixed a bug where `KrausPfeifer1998.classify` was throwing a key error. Closes #62.
+
+### Metrics
+1. Added `all_returns` metric, that counts the number of returns in a cell.
+
+### Rasterizer
+1. Gridding of points has been simplified. Closes #67.
+
+### Testing Suite
+1. Modified `.travis.yml` for Windows testing environment.
+2. Added additional checks for number of `.lax` files produced and length of tile change on `retile_raster` for
+collection testing. Removed printing statements.
+
+## Installation
+1. `0.3.6` now officially supports conda installation! Dancing in the streets. Check the README for instructions.
+
+## Other
+1. Version numbers must now be set in both `setup.py` and `__init__.py` for compatibility with conda-forge
+
 # 0.3.5
 
 Updates between April 20, 2019 and September 9, 2019

README.md

@@ -16,11 +16,11 @@ memory optimized API for managing large collections of tiles.
 
 ## Release Status
 
-Current Release: 0.3.5
+Current Release: 0.3.6
 
-Release Date: September 9, 2019
+Release Date: December 1st, 2019.
 
-Release Status: 0.3.5 is an adolescent LiDAR data processing package adequate for single tile processing and large acqusitions.
+Release Status: 0.3.6 is an adolescent LiDAR data processing package adequate for single tile processing and large acqusitions.
 
 ## What Does pyfor Do?
 

docs/api/modules.rst

@@ -5,5 +5,3 @@ pyfor
    :maxdepth: 4
 
    pyfor
-   pyfortest
-   setup

docs/conf.py

@@ -19,8 +19,9 @@
 import sphinx_rtd_theme
 import os
 import sys
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../'))
+
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath("../"))
 
 
 # -- General configuration ------------------------------------------------
@@ -32,24 +33,24 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.doctest"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'pyfor'
-copyright = u'2019, Bryce Frank'
-author = u'Bryce Frank'
+project = u"pyfor"
+copyright = u"2019, Bryce Frank"
+author = u"Bryce Frank"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -58,7 +59,7 @@
 try:
     release = pyfor.__version__
 except:
-    with open('../pyfor/__init__.py') as f:
+    with open("../pyfor/__init__.py") as f:
         for line in f:
             if line.find("__version__") >= 0:
                 version = line.split("=")[1].strip()
@@ -75,10 +76,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -89,7 +90,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -100,25 +101,25 @@
 # 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']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
 html_sidebars = {
-    '**': [
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html'
+    "**": [
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
     ]
 }
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pyfordoc'
+htmlhelp_basename = "pyfordoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -127,15 +128,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -145,19 +143,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'pyfor.tex', u'pyfor Documentation',
-     u'Bryce Frank', 'manual'),
+    (master_doc, "pyfor.tex", u"pyfor Documentation", u"Bryce Frank", "manual")
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pyfor', u'pyfor Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pyfor", u"pyfor Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -166,9 +160,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'pyfor', u'pyfor Documentation',
-     author, 'pyfor', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "pyfor",
+        u"pyfor Documentation",
+        author,
+        "pyfor",
+        "One line description of project.",
+        "Miscellaneous",
+    )
 ]
 
 
@@ -178,5 +178,6 @@ def skip(app, what, name, obj, skip, options):
         return False
     return skip
 
+
 def setup(app):
     app.connect("autodoc-skip-member", skip)

docs/html/advanced/groundfilter.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.3.5
+                0.3.6
               </div>
 
 

docs/html/advanced/handlinglargeacquisitions.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.3.5
+                0.3.6
               </div>
 
 

docs/html/advanced/index.html

@@ -36,7 +36,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Handling Large Acquisitions" href="handlinglargeacquisitions.html" />
-    <link rel="prev" title="Normalization" href="../topics/normalization.html" /> 
+    <link rel="prev" title="Area-Based Metrics" href="../topics/metrics.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.3.5
+                0.3.6
               </div>
 
 
@@ -178,7 +178,7 @@ <h1>Advanced<a class="headerlink" href="#advanced" title="Permalink to this head
         <a href="handlinglargeacquisitions.html" class="btn btn-neutral float-right" title="Handling Large Acquisitions" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
-        <a href="../topics/normalization.html" class="btn btn-neutral float-left" title="Normalization" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="../topics/metrics.html" class="btn btn-neutral float-left" title="Area-Based Metrics" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

docs/html/advanced/understandingcomponents.html

@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.3.5
+                0.3.6
               </div>
 
 

docs/html/api/index.html

@@ -60,7 +60,7 @@
 
 
               <div class="version">
-                0.3.5
+                0.3.6
               </div>