Simplify plan-workflow maintenance

container/runner.def

@@ -3,14 +3,15 @@ From: ubuntu:latest
 
 %setup
     [ -d /tmp/EMOD3D ] || git clone --depth 1 [email protected]:ucgmsim/EMOD3D.git /tmp/EMOD3D
-
+    [ -d /tmp/Velocity-Model ] || wget "https://www.dropbox.com/scl/fi/mzf5t4tdnv3qsgtbpx824/Velocity-Model.tar.zst?rlkey=df1uej7hd7xd18jerh357gy53&st=e9n8z0aw&dl=1" -O /tmp/Velocity-Model.tar.zst && cd /tmp && tar xf /tmp/Velocity-Model.tar.zst
 %files
     /tmp/EMOD3D /EMOD3D
-
+    /tmp/Velocity-Model /Velocity-Model
 %post
     apt-get update && apt-get install -y \
                       build-essential \
                       cmake \
+                      curl \
                       gdal-bin \
                       gfortran \
                       ghostscript \
@@ -23,34 +24,35 @@ From: ubuntu:latest
                       libfftw3-dev \
                       libopenmpi-dev \
                       libpapi-dev \
+                      openmpi-bin \
+                      openmpi-common \
                       python-is-python3 \
                       python3-pip \
                       sqlite3 \
-                      wget
 
-    wget "https://www.dropbox.com/scl/fi/b4m9g32x1j70ti69zyybq/genslip_velocity_model.vmod?rlkey=yxurhrdn8uvqh33hsb0inhsq0&st=o77aaccp&dl=0" -O /genslip_velocity_model.vmod
-    wget "https://www.dropbox.com/scl/fi/qakchhg6qu23aclcb02ye/Cant1D_v2-midQ_leer.1d?rlkey=wn1a6nnol2eaf5n6qsy5t1nym&st=8yahw7id&dl=0" -O /Cant1D_v2-midQ_leer.1d
-    wget "https://www.dropbox.com/scl/fi/tw1m15owloi0eo8h3u1kw/geoNet_stats-2023-06-28.vs30?rlkey=plu90zg0ti4lc2nvf51zu9xmg&st=iz8c2ls3&dl=0" -O /stations.vs30
-    wget "https://www.dropbox.com/scl/fi/bb852b1f0rly6cfvs9p9b/geoNet_stats-2023-06-28.ll?rlkey=3y8k5qviy52nbksfdkm1n92yh&st=605h60u6&dl=0" -O /stations.ll
+
+
+    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+    . $HOME/.cargo/env
 
     cd /EMOD3D && \
     mkdir build && \
     cd build && \
-    cmake .. && \
-    make -j $(nproc) genslip_v5.6.2 srf2stoch hb_high_binmod_v6.0.3 hb_high_binmod_v5.4.5
-
+    cmake -DHF_TIME_WINDOW=off -DUSE_FFTW=on -DCMAKE_C_COMPILER=mpicc -DCMAKE_Fotran_COMPILER=mpicc .. && \
+    make -j $(nproc) genslip_v5.6.2 srf2stoch generic_slip2srf hb_high_binmod_v6.0.3 hb_high_binmod_v5.4.5 emod3d-mpi_v3.0.13
+    cd /
     # Remove all folders in EMOD3D except the tools folder
     find /EMOD3D -mindepth 1 -maxdepth 1 ! -name "tools" -exec rm -rf \{\} \;
 
 
-    git clone --depth 1 https://github.com/ucgmsim/Velocity-Model.git /Velocity-Model && \
     cd /Velocity-Model && \
     mkdir build && \
     cd build && \
-    cmake ../ -DCMAKE_C_FLAGS="-fopenmp" -DCMAKE_CXX_FLAGS="-fopenmp" && \
-    make -j $(nproc)
+    cmake ../ -DCMAKE_C_FLAGS="-fopenmp" -DCMAKE_CXX_FLAGS="-fopenmp"  && \
+    make -j $(nproc) && \
+    mv NZVM ..
 
-    pip install "git+https://github.com/ucgmsim/workflow@pegasus" --break-system-packages
+    pip install "git+https://github.com/ucgmsim/workflow@bb_sim_new" --break-system-packages
 
 %environment
-    export PATH="$PATH:/EMOD3D/tools:/Velocity-Model"
+    export PATH="$PATH:/root/.cargo/bin:/EMOD3D/tools:/Velocity-Model"

pyproject.toml

@@ -10,52 +10,46 @@ readme = "README.md"
 requires-python = ">=3.12"
 dynamic = ["version"]
 dependencies = [
-    # UCGMSim Dependencies
-    "im_calculation @ git+https://github.com/ucgmsim/IM_calculation.git",
-    "nshmdb @ git+https://github.com/ucgmsim/NSHM2022DB.git",
-    "oq_wrapper @ git+https://github.com/ucgmsim/Empirical_Engine.git#subdirectory=oq_wrapper",
-    "pygmt_helper @ git+https://github.com/ucgmsim/pygmt_helper.git",
-    "qcore @ git+https://github.com/ucgmsim/qcore.git",
-    "source_modelling @ git+https://github.com/ucgmsim/source_modelling.git",
-    "velocity_modelling @ git+https://github.com/ucgmsim/velocity_modelling.git",
-
-    # Data Formats
-    "geopandas",
-    "h5py",
-    "pandas[parquet, hdf5]",
-    "pyyaml",
-    "xarray[io]",
-
-    # Workflow Planner
-    "jinja2",
-    "networkx",
-    "printree",
-    "pyvis",
-
-    # Numerics
-    "numexpr",
-    "numpy",
-    "scipy",
-    "shapely",
-
-    # CLI
-    "tqdm",
-    "typer",
-
-    # Misc.
-    "requests", # For gcmt-to-realisation
-    "schema", # For loading realisations
-    "structlog", # Logging.
+  # UCGMSim Dependencies
+  "im_calculation @ git+https://github.com/ucgmsim/IM_calculation.git",
+  "nshmdb @ git+https://github.com/ucgmsim/NSHM2022DB.git",
+  "oq_wrapper @ git+https://github.com/ucgmsim/Empirical_Engine.git#subdirectory=oq_wrapper",
+  "pygmt_helper @ git+https://github.com/ucgmsim/pygmt_helper.git",
+  "qcore @ git+https://github.com/ucgmsim/qcore.git",
+  "source_modelling @ git+https://github.com/ucgmsim/source_modelling.git",
+  "velocity_modelling @ git+https://github.com/ucgmsim/velocity_modelling.git",
+
+  # Data Formats
+  "geopandas",
+  "h5py",
+  "pandas[parquet, hdf5]",
+  "pyyaml",
+  "xarray[io]",
+
+  # Workflow Planner
+  "jinja2",
+  "networkx",
+  "printree",
+
+  # Numerics
+  "numexpr",
+  "numpy",
+  "scipy",
+  "shapely",
+
+  # CLI
+  "tqdm",
+  "typer",
+
+  # Misc.
+  "requests",  # For gcmt-to-realisation
+  "schema",    # For loading realisations
+  "structlog", # Logging.
 ]
 
 [project.optional-dependencies]
-test = [
-    "pytest",
-]
-dev = [
-    "ruff",
-    "deptry"
-]
+test = ["pytest"]
+dev = ["ruff", "deptry"]
 
 [tool.deptry]
 pep621_dev_dependency_groups = ["test", "dev"]
@@ -67,7 +61,6 @@ realisation-to-srf = "workflow.scripts.realisation_to_srf:app"
 generate-velocity-model-parameters = "workflow.scripts.generate_velocity_model_parameters:app"
 generate-velocity-model = "workflow.scripts.generate_velocity_model:app"
 generate-station-coordinates = "workflow.scripts.generate_station_coordinates:app"
-generate-model-coordinates = "workflow.scripts.generate_model_coordinates:app"
 generate-rupture-propagation = "workflow.scripts.generate_rupture_propagation:app"
 copy-domain-parameters = "workflow.scripts.copy_velocity_model_parameters:app"
 create-e3d-par = "workflow.scripts.create_e3d_par:app"
@@ -86,40 +79,38 @@ import-realisation = "workflow.scripts.import_realisation:app"
 workflow = "workflow"
 
 
-
-
 [tool.setuptools_scm]
 
 
 [tool.ruff.lint]
 extend-select = [
-    # isort imports
-    "I",
-    # Use r'\s+' rather than '\s+'
-    "W605",
-    # All the naming errors, like using camel case for function names.
-    "N",
-    # Missing docstrings in classes, methods, and functions
-    "D101",
-    "D102",
-    "D103",
-    "D105",
-    "D107",
-    # Use f-string instead of a format call
-    "UP032",
-    # Standard library import is deprecated
-    "UP035",
-    # Missing function argument type-annotation
-    "ANN001",
-    "ANN002",
-    "ANN003",
-    "ANN201",
-    "ANN202",
-    "ANN204",
-    "ANN205",
-    "ANN206",
-    # Using except without specifying an exception type to catch
-    "BLE001",
+  # isort imports
+  "I",
+  # Use r'\s+' rather than '\s+'
+  "W605",
+  # All the naming errors, like using camel case for function names.
+  "N",
+  # Missing docstrings in classes, methods, and functions
+  "D101",
+  "D102",
+  "D103",
+  "D105",
+  "D107",
+  # Use f-string instead of a format call
+  "UP032",
+  # Standard library import is deprecated
+  "UP035",
+  # Missing function argument type-annotation
+  "ANN001",
+  "ANN002",
+  "ANN003",
+  "ANN201",
+  "ANN202",
+  "ANN204",
+  "ANN205",
+  "ANN206",
+  # Using except without specifying an exception type to catch
+  "BLE001",
 ]
 ignore = ["D104"]
 
@@ -128,15 +119,15 @@ convention = "numpy"
 
 [tool.ruff.lint.isort]
 known-first-party = [
-    "source_modelling",
-    "workflow",
-    "pygmt_helper",
-    "qcore",
-    "empirical",
-    "nshmdb",
-    "IM",
-    "mera",
-    "velocity_modelling",
+  "source_modelling",
+  "workflow",
+  "pygmt_helper",
+  "qcore",
+  "empirical",
+  "nshmdb",
+  "IM",
+  "mera",
+  "velocity_modelling",
 ]
 
 [tool.ruff.lint.per-file-ignores]
@@ -150,24 +141,24 @@ omit = ["workflow/scripts/*.py"]
 
 [tool.numpydoc_validation]
 checks = [
-    "GL05",
-    "GL08",
-    "GL10",
-    "PR01",
-    "PR02",
-    "PR03",
-    "PR04",
-    "PR05",
-    "PR06",
-    "PR07",
-    "RT01",
-    "RT02",
-    "RT03",
-    "RT04",
-    "YD01",
+  "GL05",
+  "GL08",
+  "GL10",
+  "PR01",
+  "PR02",
+  "PR03",
+  "PR04",
+  "PR05",
+  "PR06",
+  "PR07",
+  "RT01",
+  "RT02",
+  "RT03",
+  "RT04",
+  "YD01",
 ]
 # remember to use single quotes for regex in TOML
 exclude = [ # don't report on objects that match any of these regex
-    '\.undocumented_method$',
-    '\.__repr__$',
+  '\.undocumented_method$',
+  '\.__repr__$',
 ]