add patches to solidfiles, #16, implement Run object, #22, incr ver, …

…fix author, url, update docs
hydroframe · Nov 12, 2020 · c4e39d6 · c4e39d6
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diff --git a/README.md b/README.md
@@ -66,6 +66,7 @@ For CONUS1 and CONUS2 domains, local copies of model input files are required.
       PME: PmE.flux.pfb
       SLOPE_X: slopex.pfb
       SLOPE_Y: slopey.pfb
+      CELL_TYPES: Domain_Blank_Mask.tif
     optional_files:
       LAND_COVER: conus1_landcover.sa
       LAT_LON: conus1_Grid_Centers_Short_Deg.format.sa
@@ -74,20 +75,15 @@ For CONUS1 and CONUS2 domains, local copies of model input files are required.
 #### CONUS2 Files
 
     required_files:
-      DOMAIN_MASK: conus_1km_PFmask2.tif
+      DOMAIN_MASK: CONUS2.0.Final1km.SinksAndSelectLakes.Mask.tif
       SUBSURFACE_DATA: 3d-grid.v3.tif
       PME: PME.tif
-      SLOPE_X: Str3Ep0_smth.rvth_1500.mx0.5.mn5.sec0.up_slopex.tif
-      SLOPE_Y: Str3Ep0_smth.rvth_1500.mx0.5.mn5.sec0.up_slopey.tif
-      SINKS: conus_1km_PFmask_manualsinks.tif
-      RESERVOIRS: conus_1km_PFmask_reservoirs.tif
-      LAKE_BORDER: conus_1km_PFmask_selectLakesborder.tif
-      LAKE_MASK: conus_1km_PFmask_selectLakesmask.tif
-      CHANNELS: 1km_upscaledNWM_ChannelOrder5_mod2.tif
-      CELL_TYPES: 1km_PF_BorderCellType.tif
+      SLOPE_X: CONUS2.0.Final1km.slopex.tif
+      SLOPE_Y: CONUS2.0.Final1km.slopey.tif
+      CELL_TYPES: CONUS2.0.Final1km.Border.Type.tif
     optional_files:
       LAND_COVER: 1km_CONUS2_landcover_IGBP.tif
-      LAT_LON: latlonCONUS2.sa
+      LAT_LON: CONUS2.0.Final.LatLong.sa
       DEM: CONUS2.0_RawDEM.tif
 
 **Local Filenames**
@@ -147,13 +143,13 @@ python -m parflow.subset.tools.rasterize_shape -i <path_to_shapefile_parts> -s <
 
 Re-project the shapefile at ~/downloads/shapfiles/WBDHU8.shp to the CONUS1 projection and extent
 ```
-python -m parflow.subset.tools.rasterize_shape -i ~/downloads/shapefiles -s WBDHU8
+python -m parflow.subset.tools.rasterize_shape -i ~/downloads/shapefiles -s WBDHU8 -r ~/conus_inputs/1/Domain_Blank_Mask.tif
 ```
 
 
 #### Use a mask to clip multiple files to PFB or TIF
 
-assumes all files are identically gridded and same as the mask file, if write_tifs=1 then you
+assumes all files are identically gridded and same as the mask file. If setting the `--tif_outs` flag then you
 must supply at least one tif with correct projection and transform information as either the mask file, 
 as a reference dataset with the -r option, or in the list of datafiles to clip
 ```

diff --git a/docs/html/parflow/cli/index.html b/docs/html/parflow/cli/index.html
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+<h1 class="title">Module <code>parflow.cli</code></h1>
+</header>
+<section id="section-intro">
+</section>
+<section>
+<h2 class="section-title" id="header-submodules">Sub-modules</h2>
+<dl>
+<dt><code class="name"><a title="parflow.cli.pfdist_sort" href="pfdist_sort.html">parflow.cli.pfdist_sort</a></code></dt>
+<dd>
+<div class="desc"></div>
+</dd>
+<dt><code class="name"><a title="parflow.cli.tcl2py" href="tcl2py.html">parflow.cli.tcl2py</a></code></dt>
+<dd>
+<div class="desc"></div>
+</dd>
+</dl>
+</section>
+<section>
+</section>
+<section>
+</section>
+<section>
+</section>
+</article>
+<nav id="sidebar">
+<h1>Index</h1>
+<div class="toc">
+<ul></ul>
+</div>
+<ul id="index">
+<li><h3>Super-module</h3>
+<ul>
+<li><code><a title="parflow" href="../index.html">parflow</a></code></li>
+</ul>
+</li>
+<li><h3><a href="#header-submodules">Sub-modules</a></h3>
+<ul>
+<li><code><a title="parflow.cli.pfdist_sort" href="pfdist_sort.html">parflow.cli.pfdist_sort</a></code></li>
+<li><code><a title="parflow.cli.tcl2py" href="tcl2py.html">parflow.cli.tcl2py</a></code></li>
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diff --git a/docs/html/parflow/cli/pfdist_sort.html b/docs/html/parflow/cli/pfdist_sort.html
@@ -0,0 +1,121 @@
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+<article id="content">
+<header>
+<h1 class="title">Module <code>parflow.cli.pfdist_sort</code></h1>
+</header>
+<section id="section-intro">
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">import os
+import sys
+import argparse
+
+from parflow.tools.io import read_pfidb, write_dict_as_pfidb
+from parflow.tools.helper import sort_dict
+
+def writeSortedPFIDB(input_file, output_file=None):
+  if not os.path.exists(input_file):
+    print(f&#39;Input file does not exist: {input_file}&#39;)
+    return
+
+  if output_file is None:
+    output_file = input_file
+
+  write_dict_as_pfidb(sort_dict(read_pfidb(input_file)), output_file)
+
+
+if __name__ == &#34;__main__&#34;:
+  parser = argparse.ArgumentParser(description=&#34;Parflow PFidb sorter&#34;)
+  parser.add_argument(&#34;--input-file&#34;, &#34;-i&#34;,
+                       default=None,
+                       dest=&#34;input&#34;,
+                       help=&#34;Path to ParFlow database file to sort&#34;)
+  parser.add_argument(&#34;--output-file&#34;, &#34;-o&#34;,
+                       default=None,
+                       dest=&#34;output&#34;,
+                       help=&#34;Output file path to write sorted result to&#34;)
+  args = parser.parse_args()
+
+  if args.input is None:
+    parser.print_help()
+    sys.exit(0)
+
+  writeSortedPFIDB(args.input, args.output)</code></pre>
+</details>
+</section>
+<section>
+</section>
+<section>
+</section>
+<section>
+<h2 class="section-title" id="header-functions">Functions</h2>
+<dl>
+<dt id="parflow.cli.pfdist_sort.writeSortedPFIDB"><code class="name flex">
+<span>def <span class="ident">writeSortedPFIDB</span></span>(<span>input_file, output_file=None)</span>
+</code></dt>
+<dd>
+<div class="desc"></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def writeSortedPFIDB(input_file, output_file=None):
+  if not os.path.exists(input_file):
+    print(f&#39;Input file does not exist: {input_file}&#39;)
+    return
+
+  if output_file is None:
+    output_file = input_file
+
+  write_dict_as_pfidb(sort_dict(read_pfidb(input_file)), output_file)</code></pre>
+</details>
+</dd>
+</dl>
+</section>
+<section>
+</section>
+</article>
+<nav id="sidebar">
+<h1>Index</h1>
+<div class="toc">
+<ul></ul>
+</div>
+<ul id="index">
+<li><h3>Super-module</h3>
+<ul>
+<li><code><a title="parflow.cli" href="index.html">parflow.cli</a></code></li>
+</ul>
+</li>
+<li><h3><a href="#header-functions">Functions</a></h3>
+<ul class="">
+<li><code><a title="parflow.cli.pfdist_sort.writeSortedPFIDB" href="#parflow.cli.pfdist_sort.writeSortedPFIDB">writeSortedPFIDB</a></code></li>
+</ul>
+</li>
+</ul>
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