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Feat sim pathlib support #1712

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Merged
wpbonelli merged 3 commits into from
Feb 13, 2023
Merged

Feat sim pathlib support #1712

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00aa044
feat: add pathlib support for MFSimulation.__init__() and MFSimulatio…
aleaf Feb 8, 2023
9198778
etc: add pip to environment.yml to avoid admonishment when creating e…
aleaf Feb 8, 2023
976079a
refactor(mf6/mfbase.py): isort imports and remove old code
aleaf Feb 8, 2023
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16 changes: 8 additions & 8 deletions autotest/test_mf6.py
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Original file line number Diff line number Diff line change
Expand Up @@ -264,7 +264,7 @@ def test_string_to_file_path():


def test_subdir(function_tmpdir):
sim = MFSimulation(sim_ws=str(function_tmpdir))
sim = MFSimulation(sim_ws=function_tmpdir)
tdis = ModflowTdis(sim)
gwf = ModflowGwf(sim, model_rel_path="level2")
ims = ModflowIms(sim)
Expand Down Expand Up @@ -942,7 +942,7 @@ def test_get_set_data_record(function_tmpdir):
@requires_exe("mf6")
def test_output(function_tmpdir, example_data_path):
ex_name = "test001e_UZF_3lay"
sim_ws = str(example_data_path / "mf6" / ex_name)
sim_ws = example_data_path / "mf6" / ex_name
sim = MFSimulation.load(sim_ws=sim_ws, exe_name="mf6")
sim.set_sim_path(str(function_tmpdir))
sim.write_simulation()
Expand Down Expand Up @@ -1034,8 +1034,8 @@ def test_output_add_observation(function_tmpdir, example_data_path):
def test_sfr_connections(function_tmpdir, example_data_path):
'''MODFLOW just warns if any reaches are unconnected
flopy fails to load model if reach 1 is unconnected, fine with other unconnected'''
data_path = str(example_data_path / "mf6" / "test666_sfrconnections")
sim_ws = str(function_tmpdir)
data_path = example_data_path / "mf6" / "test666_sfrconnections"
sim_ws = function_tmpdir
for test in ['sfr0', 'sfr1']:
sim_name = "test_sfr"
model_name = "test_sfr"
Expand Down Expand Up @@ -1081,11 +1081,11 @@ def test_sfr_connections(function_tmpdir, example_data_path):
cnfile = f'mf6_{test}_connection.txt'
pkfile = f'mf6_{test}_package.txt'

with open(os.path.join(data_path, pkfile), 'r') as f:
with open(data_path / pkfile, 'r') as f:
nreaches = len(f.readlines())
sfr = ModflowGwfsfr(model,
packagedata={'filename': os.path.join(data_path, pkfile)},
connectiondata={'filename': os.path.join(data_path, cnfile)},
packagedata={'filename': str(data_path / pkfile)},
connectiondata={'filename': str(data_path / cnfile)},
nreaches=nreaches,
pname='sfr',
unit_conversion=86400
Expand Down Expand Up @@ -1114,7 +1114,7 @@ def test_array(function_tmpdir):

sim_name = "test_array"
model_name = "test_array"
out_dir = str(function_tmpdir)
out_dir = function_tmpdir
tdis_name = "{}.tdis".format(sim_name)
sim = MFSimulation(
sim_name=sim_name, version="mf6", exe_name="mf6", sim_ws=out_dir
Expand Down
1 change: 1 addition & 0 deletions etc/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ dependencies:
- filelock
- jupyter
- jupytext
- pip
- pip:
- modflow-devtools
- pytest
Expand Down
12 changes: 4 additions & 8 deletions flopy/mf6/mfbase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import warnings
from collections.abc import Iterable
from enum import Enum
from pathlib import Path
from shutil import copyfile


Expand Down Expand Up @@ -416,14 +417,9 @@ def set_sim_path(self, path, internal_use=False):
if self.simulation is not None:
self.simulation.set_sim_path(path)
return
# recalculate paths for everything
# resolve path type
path = self.string_to_file_path(path)
if os.path.isabs(path):
self._sim_path = path
else:
# assume path is relative to working directory
self._sim_path = os.path.join(os.getcwd(), path)
# ensure that _sim_path is absolute
path = Path(path)
self._sim_path = path.absolute()
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@wpbonelli wpbonelli Feb 13, 2023

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Maybe worth calling path.expanduser().absolute() to get tilde expansion too? Just an extra convenience. Could do this in a followup PR, supporting PathLike more broadly throughout flopy seems worthwhile


def resolve_path(
self, path, model_name, last_loaded_path=False, move_abs_paths=False
Expand Down