From e18d42bf8b43df2402f3bc64554d576ac04abcef Mon Sep 17 00:00:00 2001 From: jdhughes-usgs Date: Fri, 20 Dec 2024 16:12:09 -0600 Subject: [PATCH] update for mf6.6.0 (#203) * fix fortran submodule evaluation * update sutra and mfusg_gsi versions. * update pixi version --- .github/workflows/ci.yml | 4 +- .github/workflows/pymake-linting-install.yml | 2 +- .github/workflows/pymake-requests.yml | 2 +- pixi.lock | 12239 +++++++++-------- pymake/utils/_dag.py | 10 +- pymake/utils/_usgs_src_update.py | 10 +- pymake/utils/usgsprograms.txt | 16 +- 7 files changed, 6354 insertions(+), 5929 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 70c4869..bc8a00a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -57,7 +57,7 @@ jobs: - name: Setup pixi uses: prefix-dev/setup-pixi@v0.8.1 with: - pixi-version: v0.19.1 + pixi-version: v0.34.0 manifest-path: "pixi.toml" - name: pixi post-install @@ -148,7 +148,7 @@ jobs: - name: Setup pixi uses: prefix-dev/setup-pixi@v0.8.1 with: - pixi-version: v0.19.1 + pixi-version: v0.34.0 manifest-path: "pixi.toml" - name: pixi post-install diff --git a/.github/workflows/pymake-linting-install.yml b/.github/workflows/pymake-linting-install.yml index 589551c..f30698f 100644 --- a/.github/workflows/pymake-linting-install.yml +++ b/.github/workflows/pymake-linting-install.yml @@ -26,7 +26,7 @@ jobs: - name: Setup pixi uses: prefix-dev/setup-pixi@v0.8.1 with: - pixi-version: v0.19.1 + pixi-version: v0.34.0 manifest-path: "pixi.toml" - name: Lint diff --git a/.github/workflows/pymake-requests.yml b/.github/workflows/pymake-requests.yml index 472efb9..f96dc6d 100644 --- a/.github/workflows/pymake-requests.yml +++ b/.github/workflows/pymake-requests.yml @@ -33,7 +33,7 @@ jobs: - name: Setup pixi uses: prefix-dev/setup-pixi@v0.8.1 with: - pixi-version: v0.19.1 + pixi-version: v0.34.0 manifest-path: "pixi.toml" - name: pixi post-install diff --git a/pixi.lock b/pixi.lock index 692465a..1744dd1 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,4 +1,4 @@ -version: 4 +version: 5 environments: default: channels: @@ -7,776 +7,795 @@ environments: linux-64: - 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timestamp: 1716874280334 + - cffi >=1.11 + - python >=3.9,<3.10.0a0 + - python >=3.9,<3.10.0a0 *_cpython + - python_abi 3.9.* *_cp39 + - zstd >=1.5.6,<1.5.7.0a0 + - zstd >=1.5.6,<1.6.0a0 + license: BSD-3-Clause + license_family: BSD + size: 320027 + timestamp: 1725305723442 - kind: conda name: zstd version: 1.5.6 diff --git a/pymake/utils/_dag.py b/pymake/utils/_dag.py index 7e55fa2..11f195d 100644 --- a/pymake/utils/_dag.py +++ b/pymake/utils/_dag.py @@ -12,6 +12,7 @@ __status__ = "Production" import os +import re class Node: @@ -125,6 +126,7 @@ def _get_f_nodelist(srcfiles): # create a dictionary that has a list of modules used within each source # create a list of Nodes for later ordering # create a dictionary of nodes + submodule_pattern = r"\(([^)]+)\)" module_dict = {} sourcefile_module_dict = {} nodelist = [] @@ -148,13 +150,17 @@ def _get_f_nodelist(srcfiles): linelist = line.strip().split() if len(linelist) == 0: continue - if linelist[0].upper() in ["MODULE", "SUBMODULE"]: + if linelist[0].upper() == "MODULE": modulename = linelist[1].upper() module_dict[modulename] = srcfile if linelist[0].upper() == "USE": modulename = linelist[1].split(",")[0].upper() if modulename not in modulelist: modulelist.append(modulename) + if line.strip().upper().startswith("SUBMODULE"): + modulename = re.findall(submodule_pattern, line)[0].upper() + if modulename not in modulelist: + modulelist.append(modulename) # update the dictionary if any entries have been found sourcefile_module_dict[srcfile] = modulelist @@ -171,7 +177,7 @@ def _get_f_nodelist(srcfiles): if m in module_dict: mlocation = module_dict[m] if mlocation != srcfile: - # print 'adding dependency: ', srcfile, mlocation + # print(f"adding dependency: {srcfile} {mlocation}") node.add_dependency(nodedict[mlocation]) except: print(f"get_f_nodelist: {srcfile} key does not exist") diff --git a/pymake/utils/_usgs_src_update.py b/pymake/utils/_usgs_src_update.py index a167e7d..c8fe616 100644 --- a/pymake/utils/_usgs_src_update.py +++ b/pymake/utils/_usgs_src_update.py @@ -737,7 +737,7 @@ def _update_mf6_external_dependencies( target: str = "mf6", ) -> None: """ - Remove MODFLOW 6 files with external library dependencies (PETSc, MPI). + Remove MODFLOW 6 files with external library dependencies (PETSc, MPI, NetCDF). Parameters @@ -769,6 +769,14 @@ def _update_mf6_external_dependencies( "Solution/ParallelSolution.f90", "Distributed/MpiUnitCache.f90", "Distributed/MpiMessageCache.f90", + "Utilities/Export/DisNCMesh.f90", + "Utilities/Export/DisNCStructured.f90", + "Utilities/Export/DisvNCMesh.f90", + "Utilities/Export/MeshNCModel.f90", + "Utilities/Export/NCExportCreate.f90", + "Utilities/Idm/netcdf/NCArrayReader.f90", + "Utilities/Idm/netcdf/NCContextBuild.f90", + "Utilities/Idm/netcdf/NetCDFCommon.f90", ) for file in parallel_files: path = srcdir / file diff --git a/pymake/utils/usgsprograms.txt b/pymake/utils/usgsprograms.txt index cef494a..7e0cb3a 100644 --- a/pymake/utils/usgsprograms.txt +++ b/pymake/utils/usgsprograms.txt @@ -1,7 +1,7 @@ target , version, current, url , dirname , srcdir , standard_switch, double_switch, shared_object -mf6 , 6.5.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.5.0/mf6.5.0_linux.zip , mf6.5.0_linux , src , True , False , False -zbud6 , 6.5.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.5.0/mf6.5.0_linux.zip , mf6.5.0_linux , utils/zonebudget/src, True , False , False -libmf6 , 6.5.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.5.0/mf6.5.0_linux.zip , mf6.5.0_linux , srcbmi , True , False , True +mf6 , 6.6.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.6.0/mf6.6.0_linux.zip , mf6.6.0_linux , src , True , False , False +zbud6 , 6.6.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.6.0/mf6.6.0_linux.zip , mf6.6.0_linux , utils/zonebudget/src, True , False , False +libmf6 , 6.6.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.6.0/mf6.6.0_linux.zip , mf6.6.0_linux , srcbmi , True , False , True mp7 , 7.2.001, True , https://water.usgs.gov/water-resources/software/MODPATH/modpath_7_2_001.zip , modpath_7_2_001 , source , True , False , False mt3dms , 5.3.0 , True , https://github.com/MODFLOW-USGS/mt3dms/releases/download/2.0/mt3dms-2.0.zip , mt3dms-2.0 , true-binary , True , False , False mt3dusgs , 1.1.0 , True , https://water.usgs.gov/water-resources/software/MT3D-USGS/mt3dusgs1.1.0.zip , mt3dusgs1.1.0 , src , True , False , False @@ -9,7 +9,7 @@ vs2dt , 3.3 , True , https://water.usgs.gov/water-resources/software triangle , 1.6 , True , https://github.com/MODFLOW-USGS/triangle/releases/download/1.0/triangle-1.0.zip , triangle-1.0 , src , True , False , False gridgen , 1.0.02 , True , https://water.usgs.gov/water-resources/software/GRIDGEN/gridgen.1.0.02.zip , gridgen.1.0.02 , src , True , False , False crt , 1.3.1 , True , https://water.usgs.gov/ogw/CRT/CRT_1.3.1.zip , CRT_1.3.1 , SOURCE , True , False , False -sutra , 3.0 , True , https://water.usgs.gov/water-resources/software/sutra/SUTRA_3_0_0.zip , SutraSuite , SUTRA_3_0/source , True , False , False +sutra , 4.0 , True , https://water.usgs.gov/water-resources/software/sutra/4.0/SUTRA_4_0_0.zip , SutraSuite , SUTRA_4_0/source , True , False , False mf2000 , 1.19.01, True , https://water.usgs.gov/nrp/gwsoftware/modflow2000/mf2k1_19_01.tar.gz , mf2k.1_19 , src , True , False , False mf2005 , 1.12.00, True , https://github.com/MODFLOW-USGS/mf2005/releases/download/v.1.12.00/MF2005.1_12u.zip , MF2005.1_12u , src , True , False , False mfusg , 1.5 , True , https://water.usgs.gov/water-resources/software/MODFLOW-USG/mfusg1_5.zip , mfusg1_5 , src , True , False , False @@ -20,7 +20,7 @@ mflgr , 2.0.0 , True , https://water.usgs.gov/ogw/modflow-lgr/modflow- zonbud3 , 3.01 , True , https://water.usgs.gov/water-resources/software/ZONEBUDGET/zonbud3_01.exe , Zonbud.3_01 , Src , True , False , False mfnwt1.1.4 , 1.1.4 , False , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.1.4.zip , MODFLOW-NWT_1.1.4 , src , True , False , False mfnwt , 1.3.0 , True , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.3.0.zip , MODFLOW-NWT , src , True , False , False -mfusg_gsi , 2.3.0 , True , https://www.gsienv.com/wp-content/uploads/2024/03/USG-Transport_Version-2.3.0.zip , USGT-v2-3-0-Source , . , True , False , False -mf6dev , 6.6.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , src , True , False , False -zbud6dev , 6.6.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , utils/zonebudget/src, True , False , False -libmf6dev , 6.6.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , srcbmi , True , False , True \ No newline at end of file +mfusg_gsi , 2.4.0 , True , https://www.gsienv.com/wp-content/uploads/2024/07/USG-Transport_Version-2.4.0.zip , USGT-v2-4-0-Source , . , True , False , False +mf6dev , 6.7.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , src , True , False , False +zbud6dev , 6.7.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , utils/zonebudget/src, True , False , False +libmf6dev , 6.7.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , srcbmi , True , False , True \ No newline at end of file