Merge branch 'hawaii-disagg' into 'master'

Repo docs and disagg updates

See merge request ghsc/nshmp/nshmp-haz-v2!524

ACKNOWLEDGEMENTS.md

-# Acknowledgements
-
-This software was developed to meet the U.S. Geological Survey's need for a
-high-performance probabilistic seismic hazard (PSHA) engine capable of supporting
-increasingly complex earthquake hazard models via web-services. It leverages and
-benefits from many design and performance features found in
-[OpenSHA](http://www.opensha.org) and the legacy [USGS fortran codes](/usgs/nshmp-haz-fortran),
-both of which have been supported by the USGS and others over many years. In particular,
-the Southern California Earthquake Center ([SCEC](https://www.scec.org)) has been instrumental
-in the continued development of OpenSHA, which is in use worldwide.
-
-This software is not a replacement for OpenSHA and does not provide a public API for PSHA
-development. In the near future, `nshmp-haz` will likely be added as a dependency in OpenSHA
-so that it's users may gain access to the most current USGS hazard models.

CODE_OF_CONDUCT.md

+# Code of Conduct
+
+All contributions to and interactions surrounding this project will abide by
+the [USGS Code of Scientific Conduct][1].
+
+[1]: https://www2.usgs.gov/fsp/fsp_code_of_scientific_conduct.asp

CONTRIBUTING.md

+# Contributing
+
+Contributions are welcome from the community. Questions can be asked on the
+[issues page][1]. Before creating a new issue, please take a moment to search
+and make sure a similar issue does not already exist. If one does exist, you
+can comment (most simply even with just a `:+1:`) to show your support for that
+issue.
+
+If you have direct contributions you would like considered for incorporation
+into the project you can [fork this repository][2] and
+[submit a merge request][3] for review.
+
+[1]: https://code.usgs.gov/ghsc/nshmp/nshm-fault-sections/issues
+[2]: https://docs.gitlab.com/ee/gitlab-basics/fork-project.html
+[3]: https://docs.gitlab.com/ee/gitlab-basics/add-merge-request.html

DISCLAIMER.md

 # Disclaimer
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
-INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
-PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
-FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
-ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-Information provided by this software may be preliminary or provisional and is subject to
-revision. It is being provided to meet the need for timely best science. The information is
-provided on the condition that neither the U.S. Geological Survey nor the U.S. Government
-shall be held liable for any damages resulting from the authorized or unauthorized use of the information.
+This software has been approved for release by the U.S. Geological Survey
+(USGS). Although the software has been subjected to rigorous review, the USGS
+reserves the right to update the software as needed pursuant to further analysis
+and review. No warranty, expressed or implied, is made by the USGS or the U.S.
+Government as to the functionality of the software and related material nor
+shall the fact of release constitute any such warranty. Furthermore, the
+software is released on condition that neither the USGS nor the U.S. Government
+shall be held liable for any damages resulting from its authorized or
+unauthorized use.

LICENSE.md

 # License
 
-Unless otherwise noted, this software is in the public domain because it contains materials
-that originally came from the U.S. Geological Survey (USGS), an agency of the U.S. Department
-of Interior. For more information, see the official USGS
-[copyright policy](http://www.usgs.gov/visual-id/credit_usgs.html#copyright).
+Unless otherwise noted, this project is in the public domain in the United
+States because it contains materials that originally came from the United
+States Geological Survey, an agency of the United States Department of
+Interior. For more information, see the official USGS copyright policy at
+<https://www2.usgs.gov/visual-id/credit_usgs.html#copyright>
 
-Dependent libraries managed by the [Gradle](https://gradle.org) build tool are distributed
- under open source (or open source-like) licenses. Links to appropriate license agreements
- for each can be found below.
+Additionally, we waive copyright and related rights in the work
+worldwide through the CC0 1.0 Universal public domain dedication.
 
-## Runtime language and libraries
+## CC0 1.0 Universal Summary
 
-- [Java 8](http://www.oracle.com/technetwork/java/javase/terms/license)
-- [Google Guava 26.0](https://github.com/google/guava/blob/master/COPYING)
-- [Google Gson 2.8.5](https://github.com/google/gson/blob/master/LICENSE)
+This is a human-readable summary of the
+[Legal Code (read the full text)](https://creativecommons.org/publicdomain/zero/1.0/legalcode).
 
-## Build tools and libraries
+### No Copyright
 
-- [Gradle](https://github.com/gradle/gradle/blob/master/LICENSE)
-- [JUnit](http://junit.org/junit4/license.html)
-- [JaCoCo](http://www.jacoco.org/jacoco/trunk/doc/license.html)
+The person who associated a work with this deed has dedicated the work to
+the public domain by waiving all of his or her rights to the work worldwide
+under copyright law, including all related and neighboring rights, to the
+extent allowed by law.
+
+You can copy, modify, distribute and perform the work, even for commercial
+purposes, all without asking permission.
+
+### Other Information
+
+In no way are the patent or trademark rights of any person affected by CC0,
+nor are the rights that other persons may have in the work or in how the
+work is used, such as publicity or privacy rights.
+
+Unless expressly stated otherwise, the person who associated a work with
+this deed makes no warranties about the work, and disclaims liability for
+all uses of the work, to the fullest extent permitted by applicable law.
+When using or citing the work, you should not imply endorsement by the
+author or the affirmer.

README.md

 # nshmp-haz
 
-U.S. Geological Survey ([USGS](https://www.usgs.gov)) National Seismic Hazard Mapping Project
-([NSHMP](https://earthquake.usgs.gov/hazards/)) code for performing probabilistic seismic hazard
-(PSHA) and related analyses. These codes are intended for use with seismic hazard models
-developed by the NSHMP for the U.S. and its territories.
+U.S. Geological Survey ([USGS](https://www.usgs.gov)) National Seismic Hazard Model Project
+([NSHMP](https://earthquake.usgs.gov/hazards/)) codes for performing probabilistic seismic
+hazard (PSHA) and related analyses. These codes are intended for use with seismic hazard models
+developed by the NSHMP for the U.S. and its territories. This project includes a variety of
+command line applications and web service classes and relies on the
+[*nshmp-lib*](https://code.usgs.gov/ghsc/nshmp/nshmp-lib) hazard library, among other
+dependencies.
 
-Please see the [wiki](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/wikis/home)
-for more information.
+Please see the [docs](https://code.usgs.gov/ghsc/nshmp/nshmp-haz/docs) for more information.

src/main/java/gov/usgs/earthquake/nshmp/DeaggEpsilon.java

@@ -10,7 +10,6 @@ import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.EnumMap;
-import java.util.EnumSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -91,11 +90,7 @@ public class DeaggEpsilon {
 
       log.info(PROGRAM + ": " + HazardCalc.VERSION);
       Path modelPath = Paths.get(args[0]);
-      Path wusPath = modelPath.resolve("Western US");
-      Path ceusPath = modelPath.resolve("Central & Eastern US");
-
-      HazardModel wusModel = HazardModel.load(wusPath);
-      HazardModel ceusModel = HazardModel.load(ceusPath);
+      HazardModel model = HazardModel.load(modelPath);
 
       log.info("");
       Path siteFile = Paths.get(args[1]);
@@ -105,22 +100,16 @@ public class DeaggEpsilon {
       int colsToSkip = headerCount(siteFile);
       List<Imt> imts = readImtList(siteFile, colsToSkip);
 
-      CalcConfig wusConfig = wusModel.config();
-      CalcConfig ceusConfig = ceusModel.config();
+      CalcConfig config = model.config();
       if (argCount == 3) {
         Path userConfigPath = Paths.get(args[2]);
-        wusConfig = CalcConfig.copyOf(wusModel.config())
-            .extend(CalcConfig.from(userConfigPath))
-            .imts(EnumSet.copyOf(imts))
-            .build();
-        ceusConfig = CalcConfig.copyOf(ceusModel.config())
+        config = CalcConfig.copyOf(model.config())
             .extend(CalcConfig.from(userConfigPath))
-            .imts(EnumSet.copyOf(imts))
             .build();
       }
-      log.info(wusConfig.toString());
+      log.info(config.toString());
 
-      List<Site> sites = ImmutableList.copyOf(Sites.fromCsv(siteFile, wusConfig, true));
+      List<Site> sites = ImmutableList.copyOf(Sites.fromCsv(siteFile, config, true));
       log.info("Sites: " + sites.size());
 
       log.info("Site data columns: " + colsToSkip);
@@ -129,14 +118,14 @@ public class DeaggEpsilon {
 
       checkArgument(sites.size() == imtImlMaps.size(), "Sites and spectra lists different sizes");
 
-      Path out = calc(wusModel, wusConfig, ceusModel, ceusConfig, sites, imtImlMaps, log);
+      Path out = calc(model, config, sites, imtImlMaps, log);
 
       log.info(PROGRAM + ": finished");
 
       /* Transfer log and write config, windows requires fh.close() */
       fh.close();
       Files.move(tmpLog, out.resolve(PROGRAM + ".log"));
-      wusConfig.write(out);
+      config.write(out);
 
       return Optional.empty();
 
@@ -196,16 +185,14 @@ public class DeaggEpsilon {
    * HazardCalc.calc() that will trigger deaggregations if the value is present.
    */
   private static Path calc(
-      HazardModel wusModel,
-      CalcConfig wusConfig,
-      HazardModel ceusModel,
-      CalcConfig ceusConfig,
+      HazardModel model,
+      CalcConfig config,
       List<Site> sites,
       List<Map<Imt, Double>> rtrSpectra,
       Logger log) throws IOException {
 
     ExecutorService exec = null;
-    ThreadCount threadCount = wusConfig.performance.threadCount;
+    ThreadCount threadCount = config.performance.threadCount;
     if (threadCount == ThreadCount.ONE) {
       exec = MoreExecutors.newDirectExecutorService();
       log.info("Threads: Running on calling thread");
@@ -215,7 +202,7 @@ public class DeaggEpsilon {
     }
 
     log.info(PROGRAM + ": calculating ...");
-    Path outDir = createOutputDir(wusConfig.output.directory);
+    Path outDir = createOutputDir(config.output.directory);
     Path siteDir = outDir.resolve("vs30-" + (int) sites.get(0).vs30);
     Files.createDirectory(siteDir);
 
@@ -226,24 +213,11 @@ public class DeaggEpsilon {
       Site site = sites.get(i);
       Map<Imt, Double> spectrum = rtrSpectra.get(i);
 
-      Hazard wusHazard = null;
-      if (site.location.longitude <= -100.0) {
-        wusHazard = HazardCalcs.hazard(wusModel, wusConfig, site, exec);
-      }
-      Hazard ceusHazard = null;
-      if (site.location.longitude > -115.0) {
-        ceusHazard = HazardCalcs.hazard(ceusModel, ceusConfig, site, exec);
-      }
-      Hazard cousHazard = (wusHazard == null)
-          ? ceusHazard
-          : (ceusHazard == null)
-              ? wusHazard
-              : Hazard.merge(wusHazard, ceusHazard);
-
-      Disaggregation disagg = Disaggregation.atImls(cousHazard, spectrum, exec);
+      Hazard hazard = HazardCalcs.hazard(model, config, site, exec);
+      Disaggregation disagg = Disaggregation.atImls(hazard, spectrum, exec);
 
       List<Response> responses = new ArrayList<>(spectrum.size());
-      for (Imt imt : wusConfig.hazard.imts) {
+      for (Imt imt : config.hazard.imts) {
         ResponseData imtMetadata = new ResponseData(
             ImmutableList.of(),
             site,