diff --git a/README.md b/README.md index 44ebc8307d896b325ac289f9704a4f57e6fa3e57..c1aff676bb6574af644a92fc264549f412fdfabf 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,8 @@ Python requires all of the NCM databases: * MineralPhysicsDatabase.nc -These codes are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>) +These codes are part of an effort to produce a three dimensional national crustal mode +for use with seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>) ## Python @@ -36,10 +37,14 @@ See the [README](matlab/README.md) file in the [matlab](matlab) directory for ru ## Help -Any questions regarding the code can be directed to olboyd@usgs.gov. +Any questions regarding the code can be directed to <olboyd@usgs.gov>. ## References *Boyd, O.S., 2020, Calibration of the U.S. Geological Survey National Crustal Model: U.S. Geological Survey Open-File Report 2020–1052, 23 p., <https://doi.org/10.3133/ofr20201052>* + +**Suggested citation:** Boyd, O. S., Clayton, B. S., 2019, GeoPhys—Set of utilities is used +to extract geophysical information from the National Crustal Model: U.S. Geological Survey +software release, <https://doi.org/10.5066/P9NQ5LNU>, IP-116829, BAO Approval 02/24/20. diff --git a/geophys/README.md b/geophys/README.md index 2ec8a2412213ffacd9de6e3b6aba57daeb173fce..186e5ee5619d6c2b29e5d05d71ae12530fd9f66e 100644 --- a/geophys/README.md +++ b/geophys/README.md @@ -1,8 +1,16 @@ # GeoPhys Python routines  -This set of utilities is used to extract geophysical profiles from the NCM (Boyd, 2020). Running the code requires the NCM Calibration dataset (<https://doi.org/10.5066/P9GO3CP8>), NCM Geologic Framework databases (<https://doi.org/10.5066/P9SBQENM>), NCM thermal model, NCM_TemperatureGrids.nc (<https://doi.org/10.5066/P935DT1G>), and the NCM Petrologic and Mineral Physics database (<https://doi.org/10.5066/P9HN170G>). These codes and datasets are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>) - -Profiles can be returned from roughly -126 degrees to -100 degrees longitude and 22 to 53 degrees latitude. If the requested location is outside of the bounds of the NCM, a message to that effect will be returned. +This set of utilities is used to extract geophysical profiles from the NCM (Boyd, 2020). +Running the code requires the NCM Calibration dataset (<https://doi.org/10.5066/P9GO3CP8>), +NCM Geologic Framework databases (<https://doi.org/10.5066/P9SBQENM>), NCM thermal model, +NCM_TemperatureGrids.nc (<https://doi.org/10.5066/P935DT1G>), and the NCM Petrologic and +Mineral Physics database (<https://doi.org/10.5066/P9HN170G>). These codes and datasets +are part of an effort to produce a three dimensional national crustal model for use with +seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>) + +Profiles can be returned from roughly -126 degrees to -100 degrees longitude and 22 to 53 degrees +latitude. If the requested location is outside of the bounds of the NCM, a message to that effect +will be returned. ## Prerequisites @@ -103,7 +111,7 @@ Please see or query the code for help. poetry run help ``` -Any questions regarding the code and data can be directed to olboyd@usgs.gov. +Any questions regarding the code and data can be directed to <olboyd@usgs.gov>. ## Development diff --git a/matlab/README.md b/matlab/README.md index 52fcd5fccd25fac51beee31cd022ef677c09e756..ad0bded50abb8058390f0167324c4e7a0f59dd7f 100644 --- a/matlab/README.md +++ b/matlab/README.md @@ -1,12 +1,24 @@ # GeoPhys MATLAB routines  -This program is used to extract geophysical profiles from the NCM (Boyd, 2020). Running the code requires the NCM Calibration dataset (<https://doi.org/10.5066/P9GO3CP8>), NCM Geologic Framework databases (<https://doi.org/10.5066/P9SBQENM>), NCM thermal model, NCM_TemperatureGrids.nc (<https://doi.org/10.5066/P935DT1G>), and the NCM Petrologic and Mineral Physics database (<https://doi.org/10.5066/P9HN170G>). These codes and datasets are part of an effort to produce a three dimensional national crustal model for use with seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>) - -Profiles can be returned from roughly -126 degrees to -100 degrees longitude and 22 to 53 degrees latitude. If the requested location is outside of the bounds of the NCM, a message to that effect will be returned. +This program is used to extract geophysical profiles from the NCM (Boyd, 2020). +Running the code requires the NCM Calibration dataset (<https://doi.org/10.5066/P9GO3CP8>), +NCM Geologic Framework databases (<https://doi.org/10.5066/P9SBQENM>), NCM thermal model, +NCM_TemperatureGrids.nc (<https://doi.org/10.5066/P935DT1G>), and the NCM Petrologic and +Mineral Physics database (<https://doi.org/10.5066/P9HN170G>). These codes and datasets +are part of an effort to produce a three dimensional national crustal model for use with +seismic hazard studies. (<https://doi.org/10.5066/P9T96Q67>) + +Profiles can be returned from roughly -126 degrees to -100 degrees longitude and 22 to 53 +degrees latitude. If the requested location is outside of the bounds of the NCM, a message +to that effect will be returned. ## Installation -Within matlab, add to your path the location of the GeoPhys matlab scripts. The LoadNCMData.m script assumes that the databases (mentioned above) are installed in NCMBase/database where NCMBase is ../../(Location of LoadNCMData.m). For example, GeoPhys.m might be located in Path/NCM/GeoPhys/matlab. The database directory would then be in Path/NCM/database. LoadNCMData.m can be edited to allow for a different location of the database. +Within matlab, add to your path the location of the GeoPhys matlab scripts. The LoadNCMData.m +script assumes that the databases (mentioned above) are installed in NCMBase/database where +NCMBase is ../../(Location of LoadNCMData.m). For example, GeoPhys.m might be located in +Path/NCM/GeoPhys/matlab. The database directory would then be in Path/NCM/database. +LoadNCMData.m can be edited to allow for a different location of the database. ## Example @@ -16,9 +28,9 @@ See example.m for an example. Please see or query the code for help. -**matlab>> help GeoPhys** +### Matlab Help -Any questions regarding the code and data can be directed to olboyd@usgs.gov. +Any questions regarding the code and data can be directed to <olboyd@usgs.gov>. ## References diff --git a/poetry.lock b/poetry.lock index 8648aa9d214b4c67b1d561fe03884fb9dbd8f1a6..e26836793b89f19a639b0c770bbb1a117d70926e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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@@ -743,6 +893,11 @@ files = [ {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"}, ] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "requests" version = "2.31.0" @@ -764,6 +919,11 @@ urllib3 = ">=1.21.1,<3" socks = ["PySocks (>=1.5.6,!=1.5.7)"] use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "requests-mock" version = "1.11.0" @@ -783,15 +943,20 @@ six = "*" fixture = ["fixtures"] test = ["fixtures", "mock", "purl", "pytest", "requests-futures", "sphinx", "testtools"] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "rich" -version = "13.4.2" +version = "13.5.3" description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" optional = false python-versions = ">=3.7.0" files = [ - {file = "rich-13.4.2-py3-none-any.whl", hash = "sha256:8f87bc7ee54675732fa66a05ebfe489e27264caeeff3728c945d25971b6485ec"}, - {file = "rich-13.4.2.tar.gz", hash = "sha256:d653d6bccede5844304c605d5aac802c7cf9621efd700b46c7ec2b51ea914898"}, + {file = "rich-13.5.3-py3-none-any.whl", hash = "sha256:9257b468badc3d347e146a4faa268ff229039d4c2d176ab0cffb4c4fbc73d5d9"}, + {file = "rich-13.5.3.tar.gz", hash = "sha256:87b43e0543149efa1253f485cd845bb7ee54df16c9617b8a893650ab84b4acb6"}, ] [package.dependencies] @@ -802,6 +967,11 @@ typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9 [package.extras] jupyter = ["ipywidgets (>=7.5.1,<9)"] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "sciencebasepy" version = "2.0.13" @@ -820,6 +990,11 @@ pytest = "*" requests = "*" requests-mock = "*" +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "scipy" version = "1.10.0" @@ -858,6 +1033,11 @@ dev = ["click", "doit (>=0.36.0)", "flake8", "mypy", "pycodestyle", "pydevtool", doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"] test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "six" version = "1.16.0" @@ -869,6 +1049,11 @@ files = [ {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, ] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "thermod" version = "0.3.0" @@ -902,6 +1087,11 @@ files = [ {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"}, ] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "tomlkit" version = "0.12.1" @@ -913,26 +1103,36 @@ files = [ {file = "tomlkit-0.12.1.tar.gz", hash = "sha256:38e1ff8edb991273ec9f6181244a6a391ac30e9f5098e7535640ea6be97a7c86"}, ] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "typing-extensions" -version = "4.7.1" -description = "Backported and Experimental Type Hints for Python 3.7+" +version = "4.8.0" +description = "Backported and Experimental Type Hints for Python 3.8+" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"}, - {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"}, + {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"}, + {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"}, ] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "urllib3" -version = "2.0.4" +version = "2.0.5" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.7" files = [ - {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"}, - {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"}, + {file = "urllib3-2.0.5-py3-none-any.whl", hash = "sha256:ef16afa8ba34a1f989db38e1dbbe0c302e4289a47856990d0682e374563ce35e"}, + {file = "urllib3-2.0.5.tar.gz", hash = "sha256:13abf37382ea2ce6fb744d4dad67838eec857c9f4f57009891805e0b5e123594"}, ] [package.extras] @@ -941,6 +1141,11 @@ secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17. socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [[package]] name = "wrapt" version = "1.15.0" @@ -1025,7 +1230,12 @@ files = [ {file = "wrapt-1.15.0.tar.gz", hash = "sha256:d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a"}, ] +[package.source] +type = "legacy" +url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" +reference = "ncm-database" + [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "83caf92d79068878ffdf2603a566d804cb57d7a396a3b26275a18a22e9dcc0a8" +content-hash = "7f1ffee468da90a0a42acfbc9ae8c77d1e579796c5af0e35bb692670017a2a71" diff --git a/pyproject.toml b/pyproject.toml index b7dde6218774744fb670e7a935d58cc8bc7ca24d..da4447059dfbcf824c526a209fee80d3acfa2c0e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,23 +62,23 @@ build-backend = "poetry.core.masonry.api" [[tool.poetry.source]] name = "ncm-database" url = "https://code.usgs.gov/api/v4/projects/2294/packages/pypi/simple" -priority = "supplemental" +priority = "primary" [[tool.poetry.source]] -name = "MinVel" +name = "GeoFram" url = "https://code.usgs.gov/api/v4/projects/1403/packages/pypi/simple" -priority = "supplemental" +priority = "primary" [[tool.poetry.source]] -name = "GeoFram" +name = "MinVel" url = "https://code.usgs.gov/api/v4/projects/1400/packages/pypi/simple" -priority = "supplemental" +priority = "primary" [[tool.poetry.source]] name = "TherMod" url = "https://code.usgs.gov/api/v4/projects/1404/packages/pypi/simple" -priority = "supplemental" +priority = "primary" [[tool.poetry.source]] name = "PyPI" -priority = "primary" +priority = "supplemental"