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release(1.2.8): update mf6 version (#132)
* Add latest version of mfusg_gsi (v2.1.1). * Update test_request.py::test_latest_assets with latest asset list * Update pymake calls in GH Actions workflows to use working-directory
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‎.github/workflows/main.yml

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on:
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schedule:
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- cron: '0 3 * * 3' # run at 3 AM UTC every Wednesday
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- cron: '0 7 * * *' # run at 7 AM UTC every day
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push:
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branches: [ master ]
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pull_request:
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- name: test on Linux
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if: runner.os == 'Linux'
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working-directory: ./autotest
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run: |
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pytest -v -n=auto --dist=loadfile -m="base or regression" --durations=0 --cov=pymake --cov-report=xml autotest/
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pytest -v -n=auto --dist=loadfile -m="base or regression" --durations=0 --cov=pymake --cov-report=xml
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- name: test on MacOS
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if: runner.os == 'macOS'
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working-directory: ./autotest
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run: |
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pytest -v -n=auto --dist=loadfile -m="base" --durations=0 --cov=pymake --cov-report=xml autotest/
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pytest -v -n=auto --dist=loadfile -m="base" --durations=0 --cov=pymake --cov-report=xml
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- name: test on Windows
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if: runner.os == 'Windows'
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working-directory: ./autotest
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shell: cmd
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run: |
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pytest -v -m="base" --durations=0 --cov=pymake --cov-report=xml autotest/
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pytest -v -m="base" --durations=0 --cov=pymake --cov-report=xml
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- name: Print coverage report before upload
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working-directory: ./autotest
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run: |
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coverage report
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- name: Upload coverage to Codecov
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uses: codecov/[email protected]
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file: ./coverage.xml
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file: ./autotest/coverage.xml

‎.github/workflows/pymake-gcc.yml

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on:
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schedule:
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- cron: '0 3 * * 3' # run at 3 AM UTC every Wednesday
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- cron: '0 7 * * *' # run at 7 AM UTC every day
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push:
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branches: [ master ]
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pull_request:
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.github/common/download-examples.sh
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- name: Run pytest
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working-directory: ./autotest
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run: |
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pytest -v --dist=loadfile -n=auto -m="base or regression" --durations=0 --cov=pymake --cov-report=xml autotest/
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pytest -v --dist=loadfile -n=auto -m="base or regression" --durations=0 --cov=pymake --cov-report=xml
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- name: Print coverage report before upload
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working-directory: ./autotest
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run: |
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coverage report
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- name: Upload coverage to Codecov
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uses: codecov/[email protected]
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with:
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file: ./coverage.xml
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file: ./autotest/coverage.xml
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pymakeCI-gcc-prev:
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name: pymake CI GCC 9 and 8
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.github/common/download-examples.sh
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- name: Run pytest
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working-directory: ./autotest
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run: |
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pytest -v --dist=loadfile -n=auto -m="base" --durations=0 --cov=pymake --cov-report=xml autotest/
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pytest -v --dist=loadfile -n=auto -m="base" --durations=0 --cov=pymake --cov-report=xml
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- name: Print coverage report before upload
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working-directory: ./autotest
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run: |
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coverage report
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- name: Upload coverage to Codecov
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uses: codecov/[email protected]
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with:
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file: ./coverage.xml
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file: ./autotest/coverage.xml
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pymakeCI-python-prev:
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name: pymake CI with previous python versions

‎.github/workflows/pymake-requests.yml

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on:
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schedule:
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- cron: '0 3 * * 3' # run at 3 AM UTC every Wednesday
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- cron: '0 7 * * *' # run at 7 AM UTC every day
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branches: [ master ]
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pull_request:
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.github/common/install-python.sh
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- name: Run pytest
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working-directory: ./autotest
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run: |
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pytest -v -n=auto -m requests --durations=0 --cov=pymake --cov-report=xml autotest/
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pytest -v -n=auto -m requests --durations=0 --cov=pymake --cov-report=xml
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- name: Run scheduled tests
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if: ${{ github.event_name == 'schedule' }}
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working-directory: ./autotest
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run: |
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pytest -v -m="schedule" --durations=0 --cov=pymake --cov-report=xml autotest/
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pytest -v -m="schedule" --durations=0 --cov=pymake --cov-report=xml
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- name: Print coverage report before upload
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working-directory: ./autotest
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coverage report
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- name: Upload coverage to Codecov
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uses: codecov/[email protected]
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file: ./coverage.xml
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file: ./autotest/coverage.xml

‎README.md

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Python package for building MODFLOW-based programs from source files.
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### Version 1.2.7
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### Version 1.2.8
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![pymake continuous integration](https://github.com/modflowpy/pymake/workflows/pymake%20continuous%20integration/badge.svg)
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[![codecov](https://codecov.io/gh/modflowpy/pymake/branch/master/graph/badge.svg)](https://codecov.io/gh/modflowpy/pymake)

‎autotest/test_cli_cmds.py

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import pathlib as pl
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import shutil
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import subprocess
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import sys
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import pytest
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‎autotest/test_mf6_existing_meson.py

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import contextlib
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import os
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import shutil
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import sys
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import time
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import flopy
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import pytest

‎autotest/test_requests.py

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@@ -107,9 +107,9 @@ def test_latest_assets():
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keys = assets.keys()
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test_keys = [
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"code.json",
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"code.md",
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"mac.zip",
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"linux.zip",
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"win32.zip",
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"win64.zip",
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]
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for key in keys:

‎pymake/config.py

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__author__ = "Joseph D. Hughes"
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__date__ = "December 8, 2022"
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__version__ = "1.2.7"
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__date__ = "July 5, 2023"
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__version__ = "1.2.8"
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__maintainer__ = "Joseph D. Hughes"
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__email__ = "[email protected]"
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__status__ = "Production"

‎pymake/utils/_usgs_src_update.py

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@@ -7,6 +7,7 @@
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import shutil
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import sys
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import types
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from typing import Union
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from .usgsprograms import usgs_program_data
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# remove exe extension from targets
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for idx, target in enumerate(targets):
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if ".exe" in target.lower():
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targets[idx] = target[:-4]
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targets[idx] = pl.Path(target).with_suffix("").name
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# get a dictionary of update functions
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funcs = _get_function_names(sys.modules[__name__], select_name="_update_")
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"FMTARG = 'BINARY'": "FMTARG = 'UNFORMATTED'\n ACCARG = 'STREAM'",
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",SHARED,ACCESS='SEQUENTIAL'": ",ACCESS='SEQUENTIAL'",
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"FORM=FMTARG,SHARED,": "FORM=FMTARG,",
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",BUFFERED='YES',": ",",
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", BUFFERED='NO')": ")",
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",SHARE = 'DENYNONE'": ",",
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", SHARE = 'DENYNONE',": ",",
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"FORM='FORMATTED',ACCESS='SEQUENTIAL',": "FORM='FORMATTED',ACCESS='SEQUENTIAL'",
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}
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fpth = pl.Path(srcdir) / "glo2basu1.f"
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f.close()
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454+
tags = {",share='DENYNONE',": ","}
455+
456+
fpth = pl.Path(srcdir) / "UpdtSt.for"
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if fpth.exists():
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with open(fpth) as f:
459+
lines = f.readlines()
460+
f = open(fpth, "w")
461+
for idx, line in enumerate(lines):
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for key, value in tags.items():
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if key in line:
464+
line = line.replace(key, value)
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f.write(line)
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f.close()
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tag = "DEALLOCATE(ITHFLG)"
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tag2 = "DEALLOCATE(LAYTYP)"
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fpth = pl.Path(srcdir) / "gwf2bcf-lpf-u1.f"
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def _update_mf6_files(
852+
srcdir: Union[str, os.PathLike],
853+
fc: str,
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cc: str,
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arch: str,
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double: bool,
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) -> None:
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"""
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Update MODFLOW 6 source files to remove files with external dependencies.
860+
This was required for releases >= 6.4.2
861+
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Parameters
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----------
864+
srcdir : str
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path to directory with source files
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fc : str
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fortran compiler
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cc : str
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c/c++ compiler
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arch : str
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architecture
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double : bool
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boolean indicating if compiler switches are used to build a
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double precision target
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Returns
877+
-------
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"""
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_update_mf6_external_dependencies(srcdir)
881+
return
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def _update_libmf6_files(
885+
srcdir: Union[str, os.PathLike],
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fc: str,
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cc: str,
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arch: str,
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double: bool,
890+
) -> None:
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"""
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Update MODFLOW 6 shared object source files to remove files with external
893+
dependencies. This was required for releases >= 6.4.2
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Parameters
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----------
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srcdir : str
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path to directory with source files
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fc : str
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fortran compiler
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cc : str
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c/c++ compiler
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arch : str
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architecture
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double : bool
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boolean indicating if compiler switches are used to build a
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double precision target
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Returns
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-------
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"""
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_update_mf6_external_dependencies(srcdir, target="libmf6")
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return
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# common source file replacement functions
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def _update_mf6_external_dependencies(
919+
srcdir: Union[str, os.PathLike],
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target: str = "mf6",
921+
) -> None:
922+
"""
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Remove MODFLOW 6 files with external library dependencies (PETSc, MPI).
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Parameters
927+
----------
928+
srcdir : os.PathLike
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path to directory with source files
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target: str
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target to create (Default is mf6)
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Returns
934+
-------
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None
936+
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"""
938+
if not isinstance(srcdir, pl.Path):
939+
srcdir = pl.Path(srcdir)
940+
if target == "libmf6":
941+
srcdir = srcdir.parent / "src"
942+
parallel_files = (
943+
"Utilities/Vector/PetscVector.F90",
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"Utilities/Matrix/PetscMatrix.F90",
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"Solution/PETSc/PetscSolver.F90",
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"Solution/PETSc/PetscConvergence.F90",
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"Distributed/MpiMessageBuilder.f90",
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"Distributed/MpiRouter.f90",
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"Distributed/MpiRunControl.F90",
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"Distributed/MpiWorld.f90",
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"Solution/ParallelSolution.f90",
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)
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for file in parallel_files:
954+
path = srcdir / file
955+
if path.is_file():
956+
print(f'Removing..."{path}"')
957+
os.remove(path)
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return
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def _update_utl7(srcdir):
834962
"""Update utl7.f source file
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‎pymake/utils/usgsprograms.txt

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target , version, current, url , dirname , srcdir , standard_switch, double_switch, shared_object
2-
mf6 , 6.4.1 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.1/mf6.4.1_linux.zip , mf6.4.1_linux , src , True , False , False
3-
zbud6 , 6.4.1 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.1/mf6.4.1_linux.zip , mf6.4.1_linux , utils/zonebudget/src, True , False , False
4-
libmf6 , 6.4.1 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.1/mf6.4.1_linux.zip , mf6.4.1_linux , srcbmi , True , False , True
2+
mf6 , 6.4.2 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip , mf6.4.2_linux , src , True , False , False
3+
zbud6 , 6.4.2 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip , mf6.4.2_linux , utils/zonebudget/src, True , False , False
4+
libmf6 , 6.4.2 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip , mf6.4.2_linux , srcbmi , True , False , True
55
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
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mt3dms , 5.3.0 , True , https://hydro.geo.ua.edu/mt3d/mt3dms_530.exe , mt3dms5.3.0 , src/true-binary , True , False , False
77
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
@@ -18,6 +18,6 @@ swtv4 , 4.00.05, True , https://water.usgs.gov/water-resources/software
1818
mp6 , 6.0.1 , True , https://water.usgs.gov/water-resources/software/MODPATH/modpath.6_0_01.zip , modpath.6_0 , src , True , False , False
1919
mflgr , 2.0.0 , True , https://water.usgs.gov/ogw/modflow-lgr/modflow-lgr-v2.0.0/mflgrv2_0_00.zip , mflgr.2_0 , src , True , True , False
2020
zonbud3 , 3.01 , True , https://water.usgs.gov/water-resources/software/ZONEBUDGET/zonbud3_01.exe , Zonbud.3_01 , Src , True , False , False
21-
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
22-
mfnwt , 1.3.0 , True , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.3.0.zip , MODFLOW-NWT , src , True , True , False
23-
mfusg_gsi , 2.01.0 , True , https://www.gsienv.com/wp-content/uploads/2023/01/USG-Transport-V_2.1.0-1.zip , . , Source , True , True , False
21+
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
22+
mfnwt , 1.3.0 , True , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.3.0.zip , MODFLOW-NWT , src , True , True , False
23+
mfusg_gsi , 2.1.1 , True , https://www.gsienv.com/wp-content/uploads/2023/04/USG-Transport-V_2.1.1.zip , USGT-v2-1-1-source , . , True , False , False

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