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refactor(usgsprograms): update triangle and mt3d to use GitHub repos #133

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merged 3 commits into from
Jul 6, 2023
Merged

refactor(usgsprograms): update triangle and mt3d to use GitHub repos #133

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445adac
refactor(usgsprograms): update triangle and mt3d to use github repos
jdhughes-usgs Jul 5, 2023
254996e
* add flaky to test_cli_cmds::test_make_program
jdhughes-usgs Jul 5, 2023
79f1a22
* use triangle and mt3dms GitHub releases
jdhughes-usgs Jul 5, 2023
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4 changes: 4 additions & 0 deletions autotest/test_cli_cmds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,9 @@
import subprocess

import pytest
from flaky import flaky

RERUNS = 3

targets = (
"triangle",
Expand Down Expand Up @@ -47,6 +50,7 @@ def clean_up() -> None:

@pytest.mark.dependency(name="make_program")
@pytest.mark.base
@flaky(max_runs=RERUNS)
@pytest.mark.parametrize("target", targets)
def test_make_program(target: str) -> None:
cmd = [
Expand Down
92 changes: 1 addition & 91 deletions pymake/utils/_usgs_src_update.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,6 @@
import types
from typing import Union

from .usgsprograms import usgs_program_data


def _get_function_names(module, select_name=None):
"""Get a dictionary of functions available in a user-specified source file.
Expand Down Expand Up @@ -111,15 +109,9 @@ def _update_triangle_files(srcdir, fc, cc, arch, double):
-------

"""
# move the downloaded files
rootdir = os.path.join(*(srcdir.split(os.path.sep)[:1]))
prog_dict = usgs_program_data().get_target("triangle")
dirname = prog_dict.dirname
dstpth = os.path.join(rootdir, dirname)

# modify long to long long on windows
if "win32" in sys.platform.lower() and cc in ("icl", "cl"):
src = os.path.join(rootdir, "triangle.c")
src = os.path.join(srcdir, "triangle.c")
with open(src, "r") as f:
lines = f.readlines()
for idx, line in enumerate(lines):
Expand All @@ -129,28 +121,6 @@ def _update_triangle_files(srcdir, fc, cc, arch, double):
with open(src, "w") as f:
for line in lines:
f.write(line)

# make destination directory
if not os.path.exists(dstpth):
os.makedirs(dstpth, exist_ok=True)

# make src directory
if not os.path.exists(srcdir):
os.makedirs(srcdir)

# move the source files
src = os.path.join(rootdir, "triangle.c")
dst = os.path.join(srcdir, "triangle.c")
shutil.move(src, dst)
src = os.path.join(rootdir, "triangle.h")
dst = os.path.join(srcdir, "triangle.h")
shutil.move(src, dst)

# remove remaining downloaded files
for file in os.listdir(rootdir):
src = os.path.join(rootdir, file)
if os.path.isfile(src):
os.remove(src)
return


Expand All @@ -175,66 +145,6 @@ def _update_mt3dms_files(srcdir, fc, cc, arch, double):
-------

"""
# move the downloaded files
rootdir = os.path.join(*(srcdir.split(os.path.sep)[:1]))
prog_dict = usgs_program_data().get_target("mt3dms")
dirname = prog_dict.dirname
dstpth = os.path.join(rootdir, dirname)

# Clean up unneeded files
for f in ["ReadMe_MT3DMS.pdf", "upgrade.pdf"]:
fpth = os.path.join(rootdir, f)
if os.path.isfile(fpth):
print(f'Removing..."{f}"')
os.remove(fpth)

# remove some unneeded folders
dir_list = ["bin", "doc", "examples", "utility"]
for d in dir_list:
dname = os.path.join(rootdir, d)
if os.path.isdir(dname):
print(f'Removing..."{dname}"')
shutil.rmtree(dname)

# make destination directory
if not os.path.exists(dstpth):
os.makedirs(dstpth, exist_ok=True)

# move the files
for src_dir, _, files in os.walk(rootdir):
# skip target directory (dirname)
if dirname in src_dir:
continue
if src_dir is rootdir:
continue
else:
dst_dir = src_dir.replace(rootdir + os.path.sep, "")
dst_dir = os.path.join(dstpth, dst_dir)
if not os.path.exists(dst_dir):
os.mkdir(dst_dir)
for file_ in files:
src_file = os.path.join(src_dir, file_)
dst_file = os.path.join(dst_dir, file_)
if os.path.exists(dst_file):
os.remove(dst_file)
print(f"{src_file} -> {dst_dir}")
# shutil.copy(src_file, dst_dir)
shutil.move(src_file, dst_file)

# remove the original source directory
dname = os.path.join(rootdir, "src")
if os.path.isdir(dname):
print(f'Removing..."{dname}"')
shutil.rmtree(dname)

# remove some unneeded files
file_list = ["automake.fig", "mt3dms5b.exe"]
for f in file_list:
dname = os.path.join(srcdir, f)
if os.path.isfile(dname):
print(f'Removing..."{dname}"')
os.remove(dname)

# Replace the getcl command with getarg
f1 = open(os.path.join(srcdir, "mt3dms5.for"), "r")
f2 = open(os.path.join(srcdir, "mt3dms5.for.tmp"), "w")
Expand Down
4 changes: 2 additions & 2 deletions pymake/utils/usgsprograms.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,10 @@ mf6 , 6.4.2 , True , https://github.com/MODFLOW-USGS/modflow6/releas
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
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
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://hydro.geo.ua.edu/mt3d/mt3dms_530.exe , mt3dms5.3.0 , src/true-binary , 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
vs2dt , 3.3 , True , https://water.usgs.gov/water-resources/software/VS2DI/vs2dt3_3.zip , vs2dt3_3 , include , True , False , False
triangle , 1.6 , True , https://www.netlib.org/voronoi/triangle.zip , triangle1.6 , src , True , False , False
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
Expand Down