From a07aab955542c9d2a6a4bc9a8db3d234e2732480 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Mon, 15 Jul 2024 12:18:23 -0400
Subject: [PATCH 01/15] adds filepath and data tests for get runscripts

---
 tests/test_parflow_run.py | 75 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index 3ca588ce..abc6d639 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -14,6 +14,81 @@ def test_get_ref_yaml_path(tmp_path):
     assert run.GeomInput.domaininput.InputType == "Box"
 
 
+@pytest.mark.parametrize(
+    "grid, mode, input_file_type",
+    [
+        pytest.param("conus1", "spinup", "box"),
+        pytest.param("conus2", "spinup", "box"),
+        pytest.param("conus1", "transient", "box"),
+        pytest.param("conus2", "transient", "box"),
+        pytest.param("conus1", "spinup", "solid"),
+        pytest.param("conus2", "spinup", "solid"),
+        pytest.param("conus1", "transient", "solid"),
+        pytest.param("conus2", "transient", "solid"),
+
+    ]
+)
+def test_get_template_runscript_filepaths(grid, mode, input_file_type, tmp_path):
+    test_dir = tmp_path / "test_runscript"
+    test_dir.mkdir()
+    runscript_path = st.get_template_runscript(
+        grid=grid,
+        mode=mode,
+        input_file_type=input_file_type,
+        write_dir=test_dir,
+)
+    output=f"{test_dir}/{grid}_{mode}_{input_file_type}.yaml"
+    print(os.path.exists(runscript_path))
+    assert runscript_path == output
+    assert os.path.exists(runscript_path)
+
+
+@pytest.mark.parametrize(
+    "grid, mode, input_file_type",
+    [
+        pytest.param("conus1", "spinup", "box"),
+        pytest.param("conus2", "spinup", "box"),
+        pytest.param("conus1", "transient", "box"),
+        pytest.param("conus2", "transient", "box"),
+        pytest.param("conus1", "spinup", "solid"),
+        pytest.param("conus2", "spinup", "solid"),
+        pytest.param("conus1", "transient", "solid"),
+        pytest.param("conus2", "transient", "solid"),
+
+    ]
+)
+def test_get_template_runscript_data(grid, mode, input_file_type, tmp_path):
+    test_dir = tmp_path / "test_runscript_data"
+    test_dir.mkdir()
+    runscript_path = st.get_template_runscript(
+    grid=grid,
+    mode=mode,
+    input_file_type=input_file_type,
+    write_dir=test_dir
+)
+    run = Run.from_definition(runscript_path)
+
+    #check mode
+    if mode == "transient":
+        assert run.Solver.LSM == "CLM"
+    else:
+        assert run.Solver.LSM == "none"
+    #check grid
+    if grid == "conus1":
+        assert run.ComputationalGrid.NX == 3342
+        assert run.ComputationalGrid.NY == 1888
+    else:
+        assert run.ComputationalGrid.NX == 4442
+        assert run.ComputationalGrid.NY == 3256
+    #check input_file_type
+    if input_file_type == "box":
+        assert run.Geom.domain.Upper.X == run.ComputationalGrid.NX*1000.0
+        assert run.Geom.domain.Upper.Y == run.ComputationalGrid.NY*1000.0
+    else:
+        assert run.Geom.domain.Upper.X == None
+        assert run.Geom.domain.Upper.Y == None
+
+
 def test_edit_runscript_for_subset_1(tmp_path):
     """Check the edited fiedls of the runscript file."""
     test_dir = tmp_path / "test"

From 97b49f854a10074ef5c5816445669dc9b41b8204 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Tue, 16 Jul 2024 10:15:25 -0400
Subject: [PATCH 02/15] adds filename and data tests for edit parflow run

---
 tests/test_parflow_run.py | 92 +++++++++++++++++++++++++++++++--------
 1 file changed, 74 insertions(+), 18 deletions(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index abc6d639..e10f160e 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -4,16 +4,6 @@
 import subsettools as st
 
 
-def test_get_ref_yaml_path(tmp_path):
-    test_dir = tmp_path / "test"
-    test_dir.mkdir()
-    runscript = st.get_template_runscript("conus1", "transient", "box", test_dir)
-    assert runscript == os.path.join(test_dir, "conus1_transient_box.yaml")
-    run = Run.from_definition(runscript)
-    assert run.ComputationalGrid.NX == 3342
-    assert run.GeomInput.domaininput.InputType == "Box"
-
-
 @pytest.mark.parametrize(
     "grid, mode, input_file_type",
     [
@@ -37,9 +27,7 @@ def test_get_template_runscript_filepaths(grid, mode, input_file_type, tmp_path)
         input_file_type=input_file_type,
         write_dir=test_dir,
 )
-    output=f"{test_dir}/{grid}_{mode}_{input_file_type}.yaml"
-    print(os.path.exists(runscript_path))
-    assert runscript_path == output
+    assert runscript_path == os.path.join(test_dir, os.listdir(test_dir)[0])
     assert os.path.exists(runscript_path)
 
 
@@ -61,11 +49,11 @@ def test_get_template_runscript_data(grid, mode, input_file_type, tmp_path):
     test_dir = tmp_path / "test_runscript_data"
     test_dir.mkdir()
     runscript_path = st.get_template_runscript(
-    grid=grid,
-    mode=mode,
-    input_file_type=input_file_type,
-    write_dir=test_dir
-)
+        grid=grid,
+        mode=mode,
+        input_file_type=input_file_type,
+        write_dir=test_dir
+    )
     run = Run.from_definition(runscript_path)
 
     #check mode
@@ -89,6 +77,74 @@ def test_get_template_runscript_data(grid, mode, input_file_type, tmp_path):
         assert run.Geom.domain.Upper.Y == None
 
 
+def test_edit_runscript_filepaths(tmp_path):
+    test_dir = tmp_path / "test"
+    test_dir.mkdir()
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    forcing_dir = tmp_path / "forcing"
+    forcing_dir.mkdir()
+    runscript_path = st.get_template_runscript("conus1", "transient", "box",test_dir)
+    ij_bounds = (10, 10, 25, 25)
+    runname = "test-edit-runscript"
+
+    new_runscript_path = st.edit_runscript_for_subset(
+        ij_bounds=ij_bounds, 
+        runscript_path=runscript_path, 
+        write_dir=write_dir,
+        runname=runname, 
+        forcing_dir=forcing_dir,
+    )
+    assert os.path.exists(new_runscript_path)
+    assert os.path.join(write_dir, os.listdir(write_dir)[0]) == new_runscript_path
+
+@pytest.mark.parametrize(
+    "runname, ij_bounds",
+    [
+        pytest.param("new_runscript", (10,10,25,25)),
+        pytest.param(None, (10,10,25,23))
+    ]
+)
+def test_edit_runscript_data(runname, ij_bounds, tmp_path):
+    test_dir = tmp_path / "test"
+    test_dir.mkdir()
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    forcing_dir = tmp_path / "forcing"
+    forcing_dir.mkdir()
+    old_runscript_path = st.get_template_runscript("conus1", "transient", "box", test_dir)
+    new_runscript_path = st.edit_runscript_for_subset(
+        ij_bounds=ij_bounds,
+        runscript_path=old_runscript_path,
+        write_dir=write_dir,
+        runname=runname,
+        forcing_dir=str(forcing_dir),
+    )
+    i_min, j_min, i_max, j_max = ij_bounds
+    nx, ny = (i_max-i_min, j_max-j_min)
+    new_run = Run.from_definition(new_runscript_path)
+    old_run = Run.from_definition(old_runscript_path)
+
+    if runname:
+        assert new_run.get_name() == runname
+    else:
+        assert new_run.get_name() == old_run.get_name()
+    assert new_run.ComputationalGrid.NX == nx
+    assert new_run.ComputationalGrid.NY == ny
+    assert new_run.Geom.domain.Upper.X == nx*1000
+    assert new_run.Geom.domain.Upper.Y == ny*1000
+
+
+def test_get_ref_yaml_path(tmp_path):
+    test_dir = tmp_path / "test"
+    test_dir.mkdir()
+    runscript = st.get_template_runscript("conus1", "transient", "box", test_dir)
+    assert runscript == os.path.join(test_dir, "conus1_transient_box.yaml")
+    run = Run.from_definition(runscript)
+    assert run.ComputationalGrid.NX == 3342
+    assert run.GeomInput.domaininput.InputType == "Box"
+
+
 def test_edit_runscript_for_subset_1(tmp_path):
     """Check the edited fiedls of the runscript file."""
     test_dir = tmp_path / "test"

From f0a7f476fa344a96a4f8aa2e117f9492f67b3cf7 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Thu, 18 Jul 2024 13:35:06 -0400
Subject: [PATCH 03/15] adds tests for copy_files

---
 tests/test_parflow_run.py | 37 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index e10f160e..77f1c0d7 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -2,6 +2,7 @@
 import pytest
 from parflow import Run
 import subsettools as st
+import filecmp
 
 
 @pytest.mark.parametrize(
@@ -27,8 +28,8 @@ def test_get_template_runscript_filepaths(grid, mode, input_file_type, tmp_path)
         input_file_type=input_file_type,
         write_dir=test_dir,
 )
-    assert runscript_path == os.path.join(test_dir, os.listdir(test_dir)[0])
     assert os.path.exists(runscript_path)
+    assert runscript_path == os.path.join(test_dir, os.listdir(test_dir)[0])
 
 
 @pytest.mark.parametrize(
@@ -135,6 +136,40 @@ def test_edit_runscript_data(runname, ij_bounds, tmp_path):
     assert new_run.Geom.domain.Upper.Y == ny*1000
 
 
+def test_copy_single_file(tmp_path):
+    read_dir = tmp_path / "read"
+    read_dir.mkdir()
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    runscript_path = st.get_template_runscript(
+        grid="conus1",
+        mode="transient",
+        input_file_type="box",
+        write_dir=read_dir,
+    )
+    st.copy_files(read_dir, write_dir)
+    f1 = runscript_path
+    f2 = f"{write_dir}/{os.path.basename(runscript_path)}"
+    assert os.path.exists(f2)
+    assert filecmp.cmp(f1, f2, shallow=False)
+
+
+def test_copy_multiple_files(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    correct_output_dir = os.path.join(
+        os.getcwd(), "tests", "correct_output", "conus1_upper_verde"
+    )
+    st.copy_files(read_dir=correct_output_dir, write_dir=write_dir)
+    match, mismatch, errors = filecmp.cmpfiles(
+        write_dir, correct_output_dir, ["mask.pfb", "solidfile.pfsol", "drv_clmin.dat"], shallow=True
+    )
+    assert len(match) == 3
+    assert len(mismatch) == 0
+    assert len(errors) == 0
+    
+
+
 def test_get_ref_yaml_path(tmp_path):
     test_dir = tmp_path / "test"
     test_dir.mkdir()

From 2b6789e60106349c93a0aff7e2f5f78b20b6c698 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Thu, 18 Jul 2024 13:51:22 -0400
Subject: [PATCH 04/15] adds check for forcing_dir in edit_runscript_data

---
 tests/test_parflow_run.py | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index 77f1c0d7..08d52723 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -100,36 +100,46 @@ def test_edit_runscript_filepaths(tmp_path):
     assert os.path.join(write_dir, os.listdir(write_dir)[0]) == new_runscript_path
 
 @pytest.mark.parametrize(
-    "runname, ij_bounds",
+    "runname, ij_bounds, forcing",
     [
-        pytest.param("new_runscript", (10,10,25,25)),
-        pytest.param(None, (10,10,25,23))
+        pytest.param("new_runscript", (10,10,25,25), False),
+        pytest.param(None, (10,10,25,23), True)
     ]
 )
-def test_edit_runscript_data(runname, ij_bounds, tmp_path):
+def test_edit_runscript_data(runname, ij_bounds, forcing, tmp_path):
     test_dir = tmp_path / "test"
     test_dir.mkdir()
     write_dir = tmp_path / "write"
     write_dir.mkdir()
-    forcing_dir = tmp_path / "forcing"
-    forcing_dir.mkdir()
+    if forcing:
+        forcing_dir = tmp_path / "forcing"
+        forcing_dir.mkdir()
+        forcing_dir = str(forcing_dir)
+    else:
+        forcing_dir = None
     old_runscript_path = st.get_template_runscript("conus1", "transient", "box", test_dir)
     new_runscript_path = st.edit_runscript_for_subset(
         ij_bounds=ij_bounds,
         runscript_path=old_runscript_path,
         write_dir=write_dir,
         runname=runname,
-        forcing_dir=str(forcing_dir),
+        forcing_dir=forcing_dir,
     )
     i_min, j_min, i_max, j_max = ij_bounds
     nx, ny = (i_max-i_min, j_max-j_min)
     new_run = Run.from_definition(new_runscript_path)
     old_run = Run.from_definition(old_runscript_path)
-
+    #  check runname
     if runname:
         assert new_run.get_name() == runname
     else:
         assert new_run.get_name() == old_run.get_name()
+    #  check forcing_dir
+    if forcing:
+        assert new_run.Solver.CLM.MetFilePath == str(forcing_dir)
+    else:
+        assert new_run.Solver.CLM.MetFilePath == old_run.Solver.CLM.MetFilePath
+    #  check ij_bounds
     assert new_run.ComputationalGrid.NX == nx
     assert new_run.ComputationalGrid.NY == ny
     assert new_run.Geom.domain.Upper.X == nx*1000

From 9f69dab59ebc48effaa871a1ab40009317a34477 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Thu, 18 Jul 2024 14:41:12 -0400
Subject: [PATCH 05/15] checks all files are copied in test_copy_multiple_files

---
 tests/test_parflow_run.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index 08d52723..a080abac 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -16,7 +16,6 @@
         pytest.param("conus2", "spinup", "solid"),
         pytest.param("conus1", "transient", "solid"),
         pytest.param("conus2", "transient", "solid"),
-
     ]
 )
 def test_get_template_runscript_filepaths(grid, mode, input_file_type, tmp_path):
@@ -56,7 +55,6 @@ def test_get_template_runscript_data(grid, mode, input_file_type, tmp_path):
         write_dir=test_dir
     )
     run = Run.from_definition(runscript_path)
-
     #check mode
     if mode == "transient":
         assert run.Solver.LSM == "CLM"
@@ -83,22 +81,19 @@ def test_edit_runscript_filepaths(tmp_path):
     test_dir.mkdir()
     write_dir = tmp_path / "write"
     write_dir.mkdir()
-    forcing_dir = tmp_path / "forcing"
-    forcing_dir.mkdir()
     runscript_path = st.get_template_runscript("conus1", "transient", "box",test_dir)
     ij_bounds = (10, 10, 25, 25)
     runname = "test-edit-runscript"
-
     new_runscript_path = st.edit_runscript_for_subset(
         ij_bounds=ij_bounds, 
         runscript_path=runscript_path, 
         write_dir=write_dir,
         runname=runname, 
-        forcing_dir=forcing_dir,
     )
     assert os.path.exists(new_runscript_path)
     assert os.path.join(write_dir, os.listdir(write_dir)[0]) == new_runscript_path
 
+
 @pytest.mark.parametrize(
     "runname, ij_bounds, forcing",
     [
@@ -172,12 +167,11 @@ def test_copy_multiple_files(tmp_path):
     )
     st.copy_files(read_dir=correct_output_dir, write_dir=write_dir)
     match, mismatch, errors = filecmp.cmpfiles(
-        write_dir, correct_output_dir, ["mask.pfb", "solidfile.pfsol", "drv_clmin.dat"], shallow=True
+        write_dir, correct_output_dir, os.listdir(correct_output_dir), shallow=True
     )
-    assert len(match) == 3
+    assert len(match) == len(os.listdir(correct_output_dir))
     assert len(mismatch) == 0
     assert len(errors) == 0
-    
 
 
 def test_get_ref_yaml_path(tmp_path):

From 71cde12be163c6e8d54d8fc2888d7bd3764acaab Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Thu, 18 Jul 2024 14:50:50 -0400
Subject: [PATCH 06/15] empty commit to trigger build


From 9a50c0a8a41f0e1c1853cd522d2a1f0dda27a91b Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Thu, 18 Jul 2024 15:59:59 -0400
Subject: [PATCH 07/15] adds dummy files for copy_files test

---
 tests/test_parflow_run.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index a080abac..ee08c765 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -71,9 +71,12 @@ def test_get_template_runscript_data(grid, mode, input_file_type, tmp_path):
     if input_file_type == "box":
         assert run.Geom.domain.Upper.X == run.ComputationalGrid.NX*1000.0
         assert run.Geom.domain.Upper.Y == run.ComputationalGrid.NY*1000.0
+        assert run.GeomInput.domaininput.InputType == "Box"
     else:
         assert run.Geom.domain.Upper.X == None
         assert run.Geom.domain.Upper.Y == None
+        assert run.GeomInput.domaininput.InputType == "SolidFile"
+
 
 
 def test_edit_runscript_filepaths(tmp_path):
@@ -146,15 +149,11 @@ def test_copy_single_file(tmp_path):
     read_dir.mkdir()
     write_dir = tmp_path / "write"
     write_dir.mkdir()
-    runscript_path = st.get_template_runscript(
-        grid="conus1",
-        mode="transient",
-        input_file_type="box",
-        write_dir=read_dir,
-    )
+    test_file = read_dir / "myfile"
+    test_file.write_text("file contents")
     st.copy_files(read_dir, write_dir)
-    f1 = runscript_path
-    f2 = f"{write_dir}/{os.path.basename(runscript_path)}"
+    f1 = test_file
+    f2 = f"{write_dir}/{os.path.basename(test_file)}"
     assert os.path.exists(f2)
     assert filecmp.cmp(f1, f2, shallow=False)
 

From d7ed8f16f5c4d62252d30d6e2e9d1e08c788a5f4 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Fri, 19 Jul 2024 10:25:36 -0400
Subject: [PATCH 08/15] adds dummy files for test_copy_multiple_files

---
 tests/test_parflow_run.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index ee08c765..2b1340a1 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -161,14 +161,18 @@ def test_copy_single_file(tmp_path):
 def test_copy_multiple_files(tmp_path):
     write_dir = tmp_path / "write"
     write_dir.mkdir()
-    correct_output_dir = os.path.join(
-        os.getcwd(), "tests", "correct_output", "conus1_upper_verde"
-    )
-    st.copy_files(read_dir=correct_output_dir, write_dir=write_dir)
+    read_dir = tmp_path / "read"
+    read_dir.mkdir()
+    test_file1 = read_dir / "myfile1"
+    test_file1.write_text("this is the first file in this folder")    
+    test_file2 = read_dir / "myfile2"
+    test_file2.write_text("this is the second file in this folder")   
+
+    st.copy_files(read_dir, write_dir)
     match, mismatch, errors = filecmp.cmpfiles(
-        write_dir, correct_output_dir, os.listdir(correct_output_dir), shallow=True
+        write_dir, read_dir, os.listdir(read_dir), shallow=False
     )
-    assert len(match) == len(os.listdir(correct_output_dir))
+    assert len(match) == 2
     assert len(mismatch) == 0
     assert len(errors) == 0
 

From 6dc8a6e8b107a7acc4f3f639726238cb0cb6d595 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Mon, 22 Jul 2024 15:25:59 -0400
Subject: [PATCH 09/15] adds filename tests for change_filename_values

---
 tests/test_parflow_run.py | 36 +++++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index 2b1340a1..88da58f9 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -177,6 +177,40 @@ def test_copy_multiple_files(tmp_path):
     assert len(errors) == 0
 
 
+def test_change_filename_values_filepaths1(tmp_path):
+#   saves new runscript in new dir with new runname
+    working_dir = tmp_path / "working"
+    working_dir.mkdir()
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    original_runscript_path = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=working_dir)
+    new_runscript_path = st.change_filename_values(runscript_path=original_runscript_path, write_dir=write_dir, runname="new_runscript")
+    assert original_runscript_path != new_runscript_path
+    assert os.path.dirname(new_runscript_path) != os.path.dirname(original_runscript_path)
+    assert os.path.basename(new_runscript_path) == "new_runscript.yaml"
+
+
+def test_change_filename_values_filepaths2(tmp_path):
+#   saves new runscript in same dir with new runname
+    working_dir = tmp_path / "working"
+    working_dir.mkdir()
+    original_runscript_path = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=working_dir)
+    new_runscript_path = st.change_filename_values(runscript_path=original_runscript_path, runname="new_runscript")
+    assert original_runscript_path != new_runscript_path
+    assert os.path.dirname(new_runscript_path) == os.path.dirname(original_runscript_path)
+    assert os.path.basename(new_runscript_path) == "new_runscript.yaml"
+
+
+def test_change_filename_values_filepaths3(tmp_path):
+#   overwrites existing runscript with new runscript
+    working_dir = tmp_path / "working"
+    working_dir.mkdir()
+    original_runscript_path = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=working_dir)
+    new_runscript_path = st.change_filename_values(runscript_path=original_runscript_path)
+    assert original_runscript_path == new_runscript_path
+
+   
+# ------ Previously written tests ------ #
 def test_get_ref_yaml_path(tmp_path):
     test_dir = tmp_path / "test"
     test_dir.mkdir()
@@ -242,7 +276,7 @@ def test_edit_runscript_for_subset_3(tmp_path):
 
 
 def test_change_filename_values_1(tmp_path):
-    """Check the edited fiedls of the runscript file."""
+    """Check the edited fields of the runscript file."""
     test_dir = tmp_path / "test"
     test_dir.mkdir()
     old_runscript = st.get_template_runscript("conus1", "transient", "box", test_dir)

From 4c8e9f1f5b2444b48cce10c930885f4f198efabe Mon Sep 17 00:00:00 2001
From: gartavanis <32808713+gartavanis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 14:46:42 -0400
Subject: [PATCH 10/15] Fix HUC picker reference (#95)

Co-authored-by: gartavanis <gartavanis@users.noreply.github.com>
---
 docs/examples/definte_subset.ipynb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/examples/definte_subset.ipynb b/docs/examples/definte_subset.ipynb
index 9a01a8d8..c155f947 100644
--- a/docs/examples/definte_subset.ipynb
+++ b/docs/examples/definte_subset.ipynb
@@ -125,7 +125,7 @@
    "metadata": {},
    "source": [
     "## 4. Defining bounds for a HUC watershed\n",
-    "The subsettools [`define_huc_domain`](https://hydroframesubsettools.readthedocs.io/en/latest/autoapi/subsettools/subsettools/index.html#subsettools.subsettools.define_huc_domain) function returns a tuple `(imin, jmin, imax, jmax)` of grid indices that define a bounding box containing any HUC, and a mask for that domain. You can provide 2, 4, 6, 8 or 10-digit HUCs.  For help finding your HUC you can refer to the [USGS HUC picker](https://water.usgs.gov/wsc/map_index.html)."
+    "The subsettools [`define_huc_domain`](https://hydroframesubsettools.readthedocs.io/en/latest/autoapi/subsettools/subsettools/index.html#subsettools.subsettools.define_huc_domain) function returns a tuple `(imin, jmin, imax, jmax)` of grid indices that define a bounding box containing any HUC, and a mask for that domain. You can provide 2, 4, 6, 8 or 10-digit HUCs.  For help finding your HUC you can refer to the [USGS HUC picker](https://water.usgs.gov/wsc/a_api/wbd/index_wbd.html). **Make sure to use the new (up to 12-digit) USGS HUC maps rather than the legacy 8-digit ones.**"
    ]
   },
   {
@@ -269,7 +269,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

From e932459db465fae8aeb2f199db94e3dcd8bbe06e Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Thu, 18 Jul 2024 14:50:50 -0400
Subject: [PATCH 11/15] empty commit to trigger build


From 932a9db2bc293930b37de021d92c0418daad9d9d Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Tue, 23 Jul 2024 13:07:36 -0400
Subject: [PATCH 12/15] adds individual unit tests for change_filename_values
 data

---
 tests/test_parflow_run.py | 82 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 81 insertions(+), 1 deletion(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index 88da58f9..5500f53b 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -209,7 +209,87 @@ def test_change_filename_values_filepaths3(tmp_path):
     new_runscript_path = st.change_filename_values(runscript_path=original_runscript_path)
     assert original_runscript_path == new_runscript_path
 
-   
+
+def test_change_filename_values_slopex(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    test_file = "dummy_test_file.pfb"
+    original_runscript = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=write_dir)
+    new_runscript = st.change_filename_values(original_runscript, write_dir, runname="new_runscript", slopex=test_file)
+    run = Run.from_definition(new_runscript)
+    assert run.TopoSlopesX.FileName == test_file
+
+
+def test_change_filename_values_slopey(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    test_file = "dummy_test_file.pfb"
+    original_runscript = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=write_dir)
+    new_runscript = st.change_filename_values(original_runscript, write_dir, runname="new_runscript", slopey=test_file)
+    run = Run.from_definition(new_runscript)
+    assert run.TopoSlopesY.FileName == test_file
+
+
+def test_change_filename_values_solidfile(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    test_file = "dummy_test_file.pfb"
+    original_runscript = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=write_dir)
+    new_runscript = st.change_filename_values(original_runscript, write_dir, runname="new_runscript", solidfile=test_file)
+    run = Run.from_definition(new_runscript)
+    assert run.GeomInput.domaininput.FileName == test_file
+
+
+def test_change_filename_values_init_press(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    test_file = "dummy_test_file.pfb"
+    original_runscript = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=write_dir)
+    new_runscript = st.change_filename_values(original_runscript, write_dir, runname="new_runscript", init_press=test_file)
+    run = Run.from_definition(new_runscript)
+    assert  run.Geom.domain.ICPressure.FileName == test_file
+
+
+def test_change_filename_values_indicator(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    test_file = "dummy_test_file.pfb"
+    original_runscript = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=write_dir)
+    new_runscript = st.change_filename_values(original_runscript, write_dir, runname="new_runscript", indicator=test_file)
+    run = Run.from_definition(new_runscript)
+    assert run.Geom.indi_input.FileName == test_file
+
+
+def test_change_filename_values_depth_to_bedrock(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    test_file = "dummy_test_file.pfb"
+    original_runscript = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=write_dir)
+    new_runscript = st.change_filename_values(original_runscript, write_dir, runname="new_runscript", depth_to_bedrock=test_file)
+    run = Run.from_definition(new_runscript)
+    assert run.Geom.domain.FBz.FileName == test_file
+
+
+def test_change_filename_values_mannings(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    test_file = "dummy_test_file.pfb"
+    original_runscript = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=write_dir)
+    new_runscript = st.change_filename_values(original_runscript, write_dir, runname="new_runscript", mannings=test_file)
+    run = Run.from_definition(new_runscript)
+    assert run.Mannings.FileName == test_file
+
+
+def test_change_filename_values_evap_trans(tmp_path):
+    write_dir = tmp_path / "write"
+    write_dir.mkdir()
+    test_file = "dummy_test_file.pfb"
+    original_runscript = st.get_template_runscript(grid="conus1", mode="transient", input_file_type="box", write_dir=write_dir)
+    new_runscript = st.change_filename_values(original_runscript, write_dir, runname="new_runscript", evap_trans=test_file)
+    run = Run.from_definition(new_runscript)
+    assert run.Solver.EvapTrans.FileName == test_file
+    
+
 # ------ Previously written tests ------ #
 def test_get_ref_yaml_path(tmp_path):
     test_dir = tmp_path / "test"

From 38bf80f39b771bc17c89d826c66b511fd94ecb34 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Tue, 23 Jul 2024 16:18:45 -0400
Subject: [PATCH 13/15] adds dist_run tests for filepaths and data

---
 tests/test_parflow_run.py | 99 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index 5500f53b..abeb10ac 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -1,6 +1,9 @@
 import os
 import pytest
+import numpy as np
 from parflow import Run
+from parflow.tools.io import write_pfb, read_pfb
+from parflow import ParflowBinaryReader
 import subsettools as st
 import filecmp
 
@@ -290,6 +293,102 @@ def test_change_filename_values_evap_trans(tmp_path):
     assert run.Solver.EvapTrans.FileName == test_file
     
 
+def test_dist_run_filepaths_1(tmp_path):
+#  no working directory provided
+    runscript_dir = tmp_path / "runscript"
+    runscript_dir.mkdir()
+    original_runscript_path = st.get_template_runscript(
+        grid="conus1", 
+        mode="transient", 
+        input_file_type="box", 
+        write_dir=runscript_dir
+    )
+    new_runscript_path = st.dist_run(topo_p=4,topo_q=4,runscript_path=original_runscript_path,dist_clim_forcing=False)
+    assert new_runscript_path == original_runscript_path
+    
+
+def test_dist_run_filepaths_2(tmp_path):
+#  no working directory provided
+    runscript_dir = tmp_path / "runscript"
+    runscript_dir.mkdir()
+    working_dir = tmp_path / "working"
+    working_dir.mkdir()
+    original_runscript_path = st.get_template_runscript(
+        grid="conus1", 
+        mode="transient", 
+        input_file_type="box", 
+        write_dir=runscript_dir
+    )
+    new_runscript_path = st.dist_run(topo_p=4,topo_q=4,runscript_path=original_runscript_path,dist_clim_forcing=False, working_dir=working_dir)
+    assert original_runscript_path != new_runscript_path
+    assert os.path.basename(new_runscript_path) == os.path.basename(original_runscript_path)
+    assert os.path.dirname(new_runscript_path) != os.path.dirname(original_runscript_path)
+
+
+def test_dist_run_runscript(tmp_path):
+    working_dir = tmp_path / "working"
+    working_dir.mkdir()
+    runscript_path = st.get_template_runscript(
+        grid="conus1", 
+        mode="transient", 
+        input_file_type="box", 
+        write_dir=working_dir
+    )
+    new_path = st.dist_run(
+        topo_p=3,
+        topo_q=2,
+        runscript_path=runscript_path,
+        dist_clim_forcing=False
+    )
+    run = Run.from_definition(new_path)
+    assert run.Process.Topology.P == 3
+    assert run.Process.Topology.Q == 2
+
+
+def test_dist_run_forcing_data(tmp_path):
+#   checks header of distributed forcing data
+    runscript_dir = tmp_path / "runscript"
+    runscript_dir.mkdir()
+    working_dir = tmp_path / "working"
+    working_dir.mkdir()
+    test_file = working_dir / "test_file.pfb"
+    data = np.ones((10,10))
+    write_pfb(str(test_file), data)
+    topo_p = 2
+    topo_q = 3
+    runscript_path = st.get_template_runscript("conus1", "transient", "box", runscript_dir)
+    temp_run = Run.from_definition(runscript_path)
+    temp_run.Solver.CLM.MetFilePath = str(working_dir)
+    temp_run.write(
+        working_directory=runscript_dir, file_format="yaml"
+    )
+    new_path = st.dist_run(topo_p, topo_q,runscript_path, dist_clim_forcing=True, working_dir=str(working_dir))
+    run = Run.from_definition(new_path)
+    with ParflowBinaryReader(test_file) as pfb:
+        data = pfb.read_header()
+    assert data['n_subgrids'] == topo_p*topo_q
+
+
+def test_dist_run_runfile_data(tmp_path):
+#   checks header of distributed forcing data
+    runscript_dir = tmp_path / "runscript"
+    runscript_dir.mkdir()
+    working_dir = tmp_path / "working"
+    working_dir.mkdir()
+    test_file = working_dir / "test_run_file.pfb"
+    data = np.ones((10,10))
+    write_pfb(str(test_file), data)
+    topo_p = 2
+    topo_q = 3
+    runscript_path = st.get_template_runscript("conus1", "transient", "box", runscript_dir)
+    new_path = st.dist_run(topo_p, topo_q,runscript_path, dist_clim_forcing=False, working_dir=str(working_dir))
+    run = Run.from_definition(new_path)
+    with ParflowBinaryReader(test_file) as pfb:
+        data = pfb.read_header()
+    assert data['n_subgrids'] == topo_p*topo_q
+
+
+
 # ------ Previously written tests ------ #
 def test_get_ref_yaml_path(tmp_path):
     test_dir = tmp_path / "test"

From 44751422ff1fdd491a2d2298304c8279010ef1a8 Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Wed, 24 Jul 2024 09:46:52 -0400
Subject: [PATCH 14/15] small fixes

---
 tests/test_parflow_run.py | 33 +++++++--------------------------
 1 file changed, 7 insertions(+), 26 deletions(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index abeb10ac..17dd4f80 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -297,28 +297,18 @@ def test_dist_run_filepaths_1(tmp_path):
 #  no working directory provided
     runscript_dir = tmp_path / "runscript"
     runscript_dir.mkdir()
-    original_runscript_path = st.get_template_runscript(
-        grid="conus1", 
-        mode="transient", 
-        input_file_type="box", 
-        write_dir=runscript_dir
-    )
+    original_runscript_path = st.get_template_runscript("conus1", "transient", "box", runscript_dir)
     new_runscript_path = st.dist_run(topo_p=4,topo_q=4,runscript_path=original_runscript_path,dist_clim_forcing=False)
     assert new_runscript_path == original_runscript_path
     
 
 def test_dist_run_filepaths_2(tmp_path):
-#  no working directory provided
+#  working directory provided
     runscript_dir = tmp_path / "runscript"
     runscript_dir.mkdir()
     working_dir = tmp_path / "working"
     working_dir.mkdir()
-    original_runscript_path = st.get_template_runscript(
-        grid="conus1", 
-        mode="transient", 
-        input_file_type="box", 
-        write_dir=runscript_dir
-    )
+    original_runscript_path = st.get_template_runscript("conus1", "transient", "box", runscript_dir)
     new_runscript_path = st.dist_run(topo_p=4,topo_q=4,runscript_path=original_runscript_path,dist_clim_forcing=False, working_dir=working_dir)
     assert original_runscript_path != new_runscript_path
     assert os.path.basename(new_runscript_path) == os.path.basename(original_runscript_path)
@@ -326,20 +316,11 @@ def test_dist_run_filepaths_2(tmp_path):
 
 
 def test_dist_run_runscript(tmp_path):
+#   checks runscript object to ensure topo_p and q changes were made
     working_dir = tmp_path / "working"
     working_dir.mkdir()
-    runscript_path = st.get_template_runscript(
-        grid="conus1", 
-        mode="transient", 
-        input_file_type="box", 
-        write_dir=working_dir
-    )
-    new_path = st.dist_run(
-        topo_p=3,
-        topo_q=2,
-        runscript_path=runscript_path,
-        dist_clim_forcing=False
-    )
+    runscript_path = st.get_template_runscript("conus1", "transient", "box", working_dir)
+    new_path = st.dist_run(topo_p=3, topo_q=2, runscript_path=runscript_path, dist_clim_forcing=False)
     run = Run.from_definition(new_path)
     assert run.Process.Topology.P == 3
     assert run.Process.Topology.Q == 2
@@ -370,7 +351,7 @@ def test_dist_run_forcing_data(tmp_path):
 
 
 def test_dist_run_runfile_data(tmp_path):
-#   checks header of distributed forcing data
+#   checks header of distributed run data
     runscript_dir = tmp_path / "runscript"
     runscript_dir.mkdir()
     working_dir = tmp_path / "working"

From 3d93fe8c201baf4b3f19dd343754dc501788ee8c Mon Sep 17 00:00:00 2001
From: egwilborn <egwilborn@gmail.com>
Date: Thu, 25 Jul 2024 14:32:22 -0400
Subject: [PATCH 15/15] changes directory for forcing data

---
 tests/test_parflow_run.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/test_parflow_run.py b/tests/test_parflow_run.py
index 17dd4f80..ec215190 100644
--- a/tests/test_parflow_run.py
+++ b/tests/test_parflow_run.py
@@ -330,20 +330,20 @@ def test_dist_run_forcing_data(tmp_path):
 #   checks header of distributed forcing data
     runscript_dir = tmp_path / "runscript"
     runscript_dir.mkdir()
-    working_dir = tmp_path / "working"
-    working_dir.mkdir()
-    test_file = working_dir / "test_file.pfb"
+    forcing_dir = tmp_path / "forcing"
+    forcing_dir.mkdir()
+    test_file = forcing_dir / "test_file.pfb"
     data = np.ones((10,10))
     write_pfb(str(test_file), data)
     topo_p = 2
     topo_q = 3
     runscript_path = st.get_template_runscript("conus1", "transient", "box", runscript_dir)
     temp_run = Run.from_definition(runscript_path)
-    temp_run.Solver.CLM.MetFilePath = str(working_dir)
+    temp_run.Solver.CLM.MetFilePath = str(forcing_dir)
     temp_run.write(
         working_directory=runscript_dir, file_format="yaml"
     )
-    new_path = st.dist_run(topo_p, topo_q,runscript_path, dist_clim_forcing=True, working_dir=str(working_dir))
+    new_path = st.dist_run(topo_p, topo_q,runscript_path, dist_clim_forcing=True)
     run = Run.from_definition(new_path)
     with ParflowBinaryReader(test_file) as pfb:
         data = pfb.read_header()