Update df to newest branches

.gitignore

@@ -4,9 +4,12 @@ __pycache__/
 build/
 dist/
 stats/
-*.html
 .env
 
+*.html
+**/html/**
+**/_build/**
+
 #tiledb
 **/__fragments/**
 **/__commits/**

README.md

@@ -1,12 +1,34 @@
 ## SilviMetric
 
 
-SilviMetric is an open source library and set of command line utilities for extracting point cloud metrics
-into a TileDB database. See https://silvimetric.com for documentation and tutorials.
+SilviMetric is an open source library and set of command line utilities for extracting point cloud metrics into a TileDB database. See https://silvimetric.com for documentation and tutorials.
 
 [<img src="https://github.com/hobuinc/silvimetric/blob/main/docs/source/logo/Logos/PNG/SilviMeteric_Logo_2c.png?raw=true">](https://silvimetric.com/)
 
 ### Development
 
 GitHub hosts the project at https://github.com/hobuinc/silvimetric
 
+
+### Installation
+These scripts will install `Silvimetric` dependencies as python libraries to the conda environment silvimetric.
+
+`Silvimetric` requires that we install some packages from `conda` (`TileDB`, and `PDAL`) so it's usually easier to use only `conda` to handle your environment. If this is unavailable to you, you will need to install `TileDB` and `PDAL` from source before installing the python packages that are dependent on those (`python-pdal` and `tiledb-py`).
+
+##### Pip and Conda
+
+```
+conda env create -f https://raw.githubusercontent.com/hobuinc/silvimetric/main/environment.yml
+conda activate silvimetric
+pip install silvimetric
+```
+
+##### Source
+
+```
+git clone https://github.com/hobuinc/silvimetric.git && cd silvimetric
+conda env create -f environment.yml && conda activate silvimetric
+pip install .
+# To install for development:
+# pip install -e .
+```

docs/create.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+# This assumes you've already done pip install -r requirements.txt in docs dir
+python -m sphinx -T -b html -d _build/doctrees -D language=en source html

docs/requirements.txt

@@ -3,3 +3,7 @@ sphinxcontrib-bibtex
 sphinx-rtd-theme
 sphinxcontrib-spelling
 sphinx-notfound-page
+numpy
+tiledb
+dask
+.

docs/source/api/commands/delete.rst

@@ -0,0 +1,4 @@
+Delete
+======
+
+.. autofunction:: silvimetric.commands.manage.delete

docs/source/api/commands/extract.rst

@@ -0,0 +1,7 @@
+Extract
+=============================
+
+.. automodule:: silvimetric.commands.extract
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api/commands/index.rst

@@ -0,0 +1,11 @@
+.. toctree::
+    :maxdepth: 1
+
+    initialize
+    scan
+    shatter
+    info
+    extract
+    delete
+    resume
+    restart

docs/source/api/commands/info.rst

@@ -0,0 +1,7 @@
+Info
+===========================
+
+.. automodule:: silvimetric.commands.info
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/commands/initialize.rst

@@ -0,0 +1,7 @@
+Initialize
+========================
+
+.. automodule:: silvimetric.commands.initialize
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/commands/restart.rst

@@ -0,0 +1,4 @@
+Restart
+=======
+
+.. autofunction:: silvimetric.commands.manage.restart

docs/source/api/commands/resume.rst

@@ -0,0 +1,4 @@
+Resume
+======
+
+.. autofunction:: silvimetric.commands.manage.resume

docs/source/api/commands/scan.rst

@@ -0,0 +1,7 @@
+Scan
+===========================
+
+.. automodule:: silvimetric.commands.scan
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/commands/shatter.rst

@@ -0,0 +1,7 @@
+Shatter
+============================
+
+.. automodule:: silvimetric.commands.shatter
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api.rst → docs/source/api/index.rst

@@ -4,7 +4,19 @@
 API
 ================================================================================
 
-.. autosummary::
-   :toctree: generated
 
-   silvimetric
+Resources
+---------
+
+.. toctree::
+    :maxdepth: 1
+
+    resources/index
+
+Commands
+--------
+
+.. toctree::
+    :maxdepth: 1
+
+    commands/index

docs/source/api/resources/bounds.rst

@@ -0,0 +1,6 @@
+Bounds
+==========================
+
+.. automodule:: silvimetric.resources.bounds
+    :members:
+    :undoc-members:

docs/source/api/resources/config.rst

@@ -0,0 +1,5 @@
+Config
+==============================
+
+.. automodule:: silvimetric.resources.config
+   :members:

docs/source/api/resources/data.rst

@@ -0,0 +1,7 @@
+Data
+=====================
+
+.. automodule:: silvimetric.resources.data
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/resources/entry.rst

@@ -0,0 +1,14 @@
+Entry
+----------------------------------
+
+.. autoclass:: silvimetric.resources.entry.Entry
+
+Attribute
+----------------------------------
+
+.. autoclass:: silvimetric.resources.entry.Attribute
+
+Metric
+----------------------------------
+
+.. autoclass:: silvimetric.resources.metric.Metric

docs/source/api/resources/extents.rst

@@ -0,0 +1,5 @@
+Extents
+============================
+
+.. autoclass:: silvimetric.resources.extents.Extents
+    :members:

docs/source/api/resources/index.rst

@@ -0,0 +1,10 @@
+.. toctree::
+    :maxdepth: 1
+
+    config
+    bounds
+    data
+    log
+    storage
+    entry
+    extents

docs/source/api/resources/log.rst

@@ -0,0 +1,7 @@
+Log
+======================
+
+.. automodule:: silvimetric.resources.log
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/resources/storage.rst

@@ -0,0 +1,6 @@
+Storage
+------------------------------------
+
+.. automodule:: silvimetric.resources.storage
+    :members:
+    :undoc-members:

docs/source/cli/extract.rst

@@ -16,16 +16,22 @@ Synopsis
 
 .. code-block::
 
-    Usage: silvimetric DATABASE extract [OPTIONS]
+    Usage: silvimetric [OPTIONS] extract [OPTIONS]
 
     Extract silvimetric metrics from DATABASE
 
     Options:
-    -a, --attributes ATTRS  List of attributes to include in Database
-    -m, --metrics METRICS   List of metrics to include in Database
-    --bounds BOUNDS
-    -o, --outdir TEXT       [required]
+    -a, --attributes ATTRS  List of attributes to include output
+    -m, --metrics METRICS   List of metrics to include in output
+    --bounds BOUNDS         Bounds for data to include in output
+    -o, --outdir PATH       Output directory.  [required]
     --help                  Show this message and exit.
 
+Example
+-------
+
+.. code-block::
+
+    silvimetric -d test.tdb extract -o test_tifs/
 
 .. include:: ../substitutions.txt

docs/source/cli/index.rst

@@ -4,8 +4,44 @@
 Command Line Interface
 ================================================================================
 
+
+.. only:: html
+
+    The command line interface (CLI) will facilitate your interaction with
+    Silvimetric from the terminal.
+
+.. code-block::
+
+    Usage: silvimetric [OPTIONS] COMMAND [ARGS]...
+
+    Options:
+    -d, --database PATH             Database path
+    --debug                         Changes logging level from INFO to DEBUG.
+    --log-dir TEXT                  Directory for log output
+    --progress BOOLEAN              Report progress
+    --workers INTEGER               Number of workers for Dask
+    --threads INTEGER               Number of threads per worker for Dask
+    --watch                         Open dask diagnostic page in default web
+                                    browser.
+    --dasktype [threads|processes]  What Dask uses for parallelization. For
+                                    moreinformation see here https://docs.dask.o
+                                    rg/en/stable/scheduling.html#local-threads
+    --scheduler [distributed|local|single-threaded]
+                                    Type of dask scheduler. Both are local, but
+                                    are run with different dask libraries. See
+                                    more here https://docs.dask.org/en/stable/sc
+                                    heduling.html.
+    --help                          Show this message and exit.
+
+    Commands:
+    extract     Extract silvimetric metrics from DATABASE
+    info        Retrieve information on current state of DATABASE
+    initialize  Create an empty DATABASE
+    scan        Scan point cloud and determine the optimal tile size.
+    shatter     Shatter point clouds into DATABASE cells.
+
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Commands
 
    extract

docs/source/cli/info.rst

@@ -6,7 +6,8 @@ info
 
 .. only:: html
 
-    Info provides detailed information about a SilviMetrics database
+    Info will query the database and output information about the `Shatter`
+    processes that been run as well as the database schema.
 
 .. Index:: info
 
@@ -16,13 +17,26 @@ Synopsis
 
 .. code-block::
 
-    Usage: silvimetric DATABASE info [OPTIONS]
+    Usage: silvimetric [OPTIONS] info [OPTIONS]
 
     Print info about Silvimetric database
 
     Options:
-    --history
-    --help     Show this message and exit.
+        --bounds BOUNDS                 Bounds to filter by
+        --date [%Y-%m-%d|%Y-%m-%dT%H:%M:%SZ]
+                                        Select processes with this date
+        --history                       Show the history section of the output.
+        --metadata                      Show the metadata section of the output.
+        --attributes                    Show the attributes section of the output.
+        --dates <DATETIME DATETIME>...  Select processes within this date range
+        --name TEXT                     Select processes with this name
+        --help                          Show this message and exit.
+
+Example
+-------
 
+.. code-block::
+
+    silvimetric -d test.tdb info
 
 .. include:: ../substitutions.txt

docs/source/cli/initialize.rst

@@ -20,15 +20,26 @@ Synopsis
 
 .. code-block::
 
-    Usage: silvimetric DATABASE initialize [OPTIONS] BOUNDS CRS
+    Usage: silvimetric [OPTIONS] initialize [OPTIONS]
 
     Initialize silvimetrics DATABASE
 
     Options:
+    --bounds BOUNDS         Root bounds that encapsulates all data  [required]
+    --crs CRS               Coordinate system of data  [required]
     -a, --attributes ATTRS  List of attributes to include in Database
     -m, --metrics METRICS   List of metrics to include in Database
     --resolution FLOAT      Summary pixel resolution
     --help                  Show this message and exit.
 
 
+Example
+-------
+
+.. code-block::
+
+    silvimetric --database test.tdb initialize --crs "EPSG:3857" \
+        --bounds '[300, 300, 600, 600]'
+
+
 .. include:: ../substitutions.txt