Merge pull request #127 from baagaard-usgs/update-sfbay-metadata

Update SF-CVM information and update binary build settings

CODE_OF_CONDUCT.md

@@ -1,6 +1,5 @@
 # Code of Conduct
 
-All contributions to- and interactions surrounding- this project will abide by
-the [USGS Code of Scientific Conduct][1].
+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

@@ -1,18 +1,11 @@
 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.
+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 pull request][3] for review.
+If you have direct contributions you would like considered for incorporation into the project you can [fork this repository][2] and [submit a pull request][3] for review.
 
-For additional information, please see the USGS software development
-best practices guide[4] and the USGS Code of Scientific Conduct[5].
+For additional information, please see the USGS software development best practices guide[4] and the USGS Code of Scientific Conduct[5].
 
 
 [1]: https://github.com/baagaard-usgs/geomodelgrids/issues

DISCLAIMER.md

@@ -1,12 +1,5 @@
 ## Disclaimer
 
-This software is preliminary or provisional and is subject to revision. It is
-being provided to meet the need for timely best science. The software has not
-received final approval by the U.S. Geological Survey (USGS). 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. The software is provided on the condition that
-neither the USGS nor the U.S. Government shall be held liable for any damages
-resulting from the authorized or unauthorized use of the software.
+This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). 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. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.
 
 Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

LICENSE.md

@@ -1,10 +1,5 @@
 ## License
 
-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://www.usgs.gov/information-policies-and-instructions/crediting-usgs>.
+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://www.usgs.gov/information-policies-and-instructions/crediting-usgs>.
 
-Additionally, we waive copyright and related rights in the work
-worldwide through the CC0 1.0 Universal public domain dedication.
+Additionally, we waive copyright and related rights in the work worldwide through the CC0 1.0 Universal public domain dedication.

Makefile.am

@@ -25,6 +25,7 @@ EXTRA_DIST = \
 	DISCLAIMER.md \
 	LICENSE.md \
 	setup.py \
+	setup.cfg \
 	code.json \
 	developer/autopep8.cfg \
 	developer/uncrustify.cfg \
@@ -35,14 +36,15 @@ EXTRA_DIST = \
 	docker/debian-stable \
 	docker/debian-testing \
 	docker/ubuntu-20.04 \
-	docker/ubuntu-20.10 \
 	docker/ubuntu-21.04 \
+	docker/ubuntu-21.10 \
 	docker/fedora-33 \
 	docker/fedora-34 \
+	docker/fedora-35 \
 	docker/centos-8 \
 	docker/geomodelgrids-testenv \
 	docker/geomodelgrids-devenv \
-	docker/geomodelgrids-userenv
+	docker/geomodelgrids-userenv \
 	ci-config/run_tests.sh
 
 

README.md

@@ -6,7 +6,7 @@
 
 ## Description
 
-Georeferenced grid-based models composed of blocks with different grid resolutions.
+Georeferenced grid-based Earth models composed of blocks with different grid resolutions.
 
 ## Documentation
 

code.json

@@ -1,45 +1,49 @@
-{
-  "version": "2.0.0",
-  "measurementType": {},
-  "agency": "U.S. Department of Interior",
-  "releases": [
-    {
-        "name": "geomodelgrids",
-        "description": "Generate georeferenced gridded models",
-        "version": "v1.0.0",
-        "status": "??",
-        "organization": "U.S. Geological Survey",
-        "vcs": "git",
-        "repositoryUrl": "https://github.com/baagaard-usgs/geomodelgrids.git",
-        "homepageURL": "https://baagaard-usgs.github.io/geomodelgrids/",
-        "downloadURL": "https://github.com/baagaard-usgs/geomodelgrids/releases/tag/v1.0.0",
-        "disclaimerURL": "https://github.com/baagaard-usgs/geomodelgrids/blob/master/DISCLAIMER.md",
-        "permissions": {
-            "licenses": [
-                {
-                    "name": "Public Domain, CC0-1.0",
-                    "URL": "https://github.com/baagaard-usgs/geomodelgrids/blob/master/LICENSE.md"
-                }
-            ],
-            "usageType": "openSource",
-            "exemptionText": null
-        },
-        "laborHours": null,
-        "languages": [
-            "Python",
-	    "C++"
-        ],
-        "tags": [
-            "seismic velocity model",
-            "HDF5",
-        ],
-        "contact": {
-            "name": "Brad Aagaard",
-            "email": "baagaard@usgs.gov"
-        },
-        "date": {
-            "metadataLastUpdated": "2019-10-24"
+[
+  {
+    "name": "geomodelgrids",
+    "organization": "U.S. Geological Survey",
+    "description": "Georeferenced grid-based Earth models composed of blocks with different grid resolutions.",
+    "version": "1.0.0",
+    "status": "Beta",
+
+    "permissions": {
+      "usageType": "openSource",
+      "licenses": [
+        {
+          "name": "Public Domain, CC0-1.0",
+          "URL": "https://github.com/baagaard-usgs/geomodelgrids/blob/main/LICENSE.md"
         }
+      ]
+    },
+
+    "homepageURL": "https://geomodelgrids.readthedocs.io",
+    "downloadURL": "https://github.com/baagaard-usgs/geomodelgrids/archive/main.zip",
+    "disclaimerURL": "https://github.com/baagaard-usgs/geomodelgrids/blob/main/LICENSE.md",
+    "repositoryURL": "https://github.com/baagaard-usgs/geomodelgrids.git",
+    "vcs": "git",
+
+    "laborHours": 0,
+
+    "tags": [
+      "USGS",
+	"U.S. Geological Survey",
+	"Earth model",
+       "seismic velocity model",
+	"HDF5"
+    ],
+
+    "languages": [
+      "Python",
+      "C++"
+    ],
+
+    "contact": {
+      "name": "Brad Aagaard",
+      "email": "baagaard@usgs.gov"
+    },
+
+    "date": {
+      "metadataLastUpdated": "2021-10-01"
     }
-  ]
-}
+  }
+]

configure.ac

@@ -6,7 +6,7 @@
 # ----------------------------------------------------------------------
 
 AC_PREREQ(2.59)
-AC_INIT([geomodelgrids], [1.0.0rc1], [baagaard@usgs.gov])
+AC_INIT([geomodelgrids], [1.0.0rc2], [baagaard@usgs.gov])
 AC_CONFIG_HEADER([portinfo])
 AC_CONFIG_AUX_DIR([./aux-config])
 AC_CONFIG_MACRO_DIR([m4])

docker/README.md

@@ -1,10 +1,10 @@
 # Docker images
 
-```
+```console
 # Run in top-level source directory
-bash> docker build -t $TAG -f docker/$FILE .
+docker build -t $TAG -f docker/$FILE .
 ```
 
 ```
-bash> docker run --rm -it -v $TOOLS_DIR/earthvision-11:/opt/earthvision -v $HOME/data/cencal-geology:/data/cencal-geology baagaard/earthvision-env /bin/bash
+docker run --rm -it -v $TOOLS_DIR/earthvision-11:/opt/earthvision -v $HOME/data/cencal-geology:/data/cencal-geology baagaard/earthvision-env /bin/bash
 ```

docker/build_binary.py

@@ -12,7 +12,7 @@
 2. Install geomodelgrids
 3. Create setup.sh
 4. Update linking (Darwin only)
-4. Create tarball.
+5. Create tarball.
 """
 
 import argparse
@@ -185,7 +185,7 @@ def configure(self):
 
 # --------------------------------------------------------------------------------------------------
 class OpenSSL(Package):
-    VERSION = "1.1.1k"
+    VERSION = "1.1.1l"
     TARBALL = f"openssl-{VERSION}.tar.gz"
     URL = f"https://www.openssl.org/source/{TARBALL}"
     SRC_DIR = f"openssl-{VERSION}"
@@ -222,7 +222,7 @@ def configure(self):
 
 # --------------------------------------------------------------------------------------------------
 class Proj(Package):
-    VERSION = "7.2.1"
+    VERSION = "8.1.1"
     TARBALL = f"proj-{VERSION}.tar.gz"
     URL = f"https://download.osgeo.org/proj/{TARBALL}"
     BUILD_DIR = "proj-build"
@@ -248,9 +248,9 @@ def install(self):
 
 # --------------------------------------------------------------------------------------------------
 class HDF5(Package):
-    VERSION = "1.12.0"
+    VERSION = "1.12.1"
     TARBALL = f"hdf5-{VERSION}.tar.gz"
-    URL = f"https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_1_12_0/source/{TARBALL}"
+    URL = f"https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-{VERSION}/src/{TARBALL}"
     BUILD_DIR = "hdf5-build"
     SRC_DIR = f"hdf5-{VERSION}"
 

docker/linux-binary

@@ -27,6 +27,7 @@ RUN yum install -y rh-python38
 
 COPY docker/certs/ /usr/share/pki/ca-trust-source/anchors
 RUN update-ca-trust enable
+ENV CERT_PATH=/etc/ssl/certs CERT_FILE=ca-bundle.crt
 
 # ------------------------------------------------------------------------------
 from os-update as build-setup
@@ -39,15 +40,13 @@ ENV INSTALL_DIR=$STORAGE_DIR/dest  HOME=/home/$GMG_USER
 
 RUN mkdir ${STORAGE_DIR} \
   && chown ${GMG_USER} ${STORAGE_DIR} \
-  && chgrp ${GMG_USER} ${STORAGE_DIR}
+  && chgrp ${GMG_USER} ${STORAGE_DIR} \
+  && mkdir ${STORAGE_DIR}/build
 USER ${GMG_USER}
 
-RUN mkdir -p ~/.config/pip \
-  && echo "[global]" > $HOME/.config/pip/pip.conf \
-  && echo "trusted-host = pypi.org files.pythonhosted.org" >> $HOME/.config/pip/pip.conf \
-  && scl enable rh-python38 -- python3 -m pip install requests --user
+RUN scl enable rh-python38 -- python3 -m pip install requests --user
 
-WORKDIR $STORAGE_DIR
+WORKDIR $STORAGE_DIR/build
 
 # To build up to here:
 # docker build -t geomodelgrids-binaryenv -f docker/linux-binary --target build-setup .
@@ -56,11 +55,13 @@ WORKDIR $STORAGE_DIR
 # docker run -ti --rm --name geomodelgrids-binary-workspace -v geomodelgrids-binary:/opt/geomodelgrids geomodelgrids-binaryenv
 # docker cp TARBALL geomodelgrids-binary-workspace:/opt/geomodelgrids/build
 # docker cp docker/build_binary.py geomodelgrids-binary-workspace:/opt/geomodelgrids/build
-# svn enable rh-python38 -- /opt/geomodelgrids/src/docker/build_binary.py --install-dir=$INSTALL_DIR --version=X.X.X --all
+# export SSL_CERT_PATH=/etc/ssl/certs/ca-bundle.crt REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-bundle.crt
+# scl enable rh-python38 -- /opt/geomodelgrids/src/docker/build_binary.py --install-dir=$INSTALL_DIR --version=X.X.X --all
 
 # ------------------------------------------------------------------------------
 from build-setup as build-binary
 
+ENV BUILD_DIR=${STORAGE_DIR}/build
 COPY --chown=gmg-user:gmg-user docker/build_binary.py ${BUILD_DIR}
 
 WORKDIR $BUILD_DIR

geomodelgrids/create/apps/create_model.py

@@ -57,10 +57,11 @@ def main(self, **kwargs):
             self.show_parameters()
             return
 
-        data_path = self.config["geomodelgrids"]["data_source"].split(".")
-        data_obj = getattr(import_module(".".join(data_path[:-1])), data_path[-1])
-        datasrc = data_obj(self.config)
-        datasrc.initialize()
+        if args.import_domain or args.import_surfaces or args.all:
+            data_path = self.config["geomodelgrids"]["data_source"].split(".")
+            data_obj = getattr(import_module(".".join(data_path[:-1])), data_path[-1])
+            datasrc = data_obj(self.config)
+            datasrc.initialize()
         model = core.model.Model(self.config)
 
         if args.import_domain or args.all:

geomodelgrids/create/core/model.py

@@ -385,7 +385,7 @@ def get_attributes(self):
         return attrs
 
 
-@ dataclass
+@dataclass
 class ModelMetadata:
     """Metadata describing model.
     """
@@ -506,8 +506,9 @@ def __init__(self, config):
         self.dim_z = float(config["domain"]["dim_z"])
 
         # Auxiliary data
-        if "auxiliary" in config:
-            self.auxiliary = config["auxiliary"]
+        if "auxiliary" in config["data"]:
+            import json
+            self.auxiliary = json.loads(config["data"]["auxiliary"])
         else:
             self.auxiliary = {}
 

libsrc/geomodelgrids/serial/Query.cc

@@ -196,28 +196,27 @@ geomodelgrids::serial::Query::query(double* const values,
     bool found = false;
     for (size_t i = 0; i < _models.size(); ++i) {
         assert(_models[i]);
-        if (_models[i]->contains(x, y, z)) {
-            double elevationSquash = z;
-            switch (_squash) {
-            case SQUASH_NONE:
-                break;
-            case SQUASH_TOP_SURFACE:
-                if (z > _squashMinElev) {
-                    const double topElev = _models[i]->queryTopElevation(x, y);
-                    elevationSquash = z + topElev;
-                } // if
-                break;
-            case SQUASH_TOPOGRAPHY_BATHYMETRY:
-                if (z > _squashMinElev) {
-                    const double groundElev = _models[i]->queryTopoBathyElevation(x, y);
-                    elevationSquash = z + groundElev;
-                } // if
-                break;
-            default:
-                throw std::logic_error("Unknown squashing type.");
-            } // switch
-
-            const double* modelValues = _models[i]->query(x, y, elevationSquash);
+        double zSquash = z;
+        switch (_squash) {
+        case SQUASH_NONE:
+            break;
+        case SQUASH_TOP_SURFACE:
+            if (z > _squashMinElev) {
+                const double topElev = _models[i]->queryTopElevation(x, y);
+                zSquash = z + topElev;
+            } // if
+            break;
+        case SQUASH_TOPOGRAPHY_BATHYMETRY:
+            if (z > _squashMinElev) {
+                const double groundElev = _models[i]->queryTopoBathyElevation(x, y);
+                zSquash = z + groundElev;
+            } // if
+            break;
+        default:
+            throw std::logic_error("Unknown squashing type.");
+        } // switch
+	if (_models[i]->contains(x, y, zSquash)) {
+            const double* modelValues = _models[i]->query(x, y, zSquash);
             values_map_type& modelMap = _valuesIndex[i];
             for (size_t iValue = 0; iValue < numQueryValues; ++iValue) {
                 values[iValue] = modelValues[modelMap[iValue]];