FIx output reader

doc/requirements.txt

@@ -1,6 +1,6 @@
 pygmsh
 seaborn
-sphinx == 5.3
+sphinx
 sphinx-argparse
 sphinx-gallery
 pydata-sphinx-theme

doc/source/conf.py

@@ -17,7 +17,7 @@
 import toughio
 
 project = "toughio"
-copyright = "2022, Keurfon Luu"
+copyright = "2023, Keurfon Luu"
 author = "Keurfon Luu"
 
 version = toughio.__version__

tests/test_run.py

@@ -0,0 +1,87 @@
+import os
+import platform
+import sys
+
+import pytest
+
+import toughio
+
+
+@pytest.mark.parametrize(
+    "exec, workers, docker, wsl, cmd",
+    [
+        ("tough-exec", None, None, False, "tough-exec INFILE INFILE.out"),
+        ("tough-exec", 8, None, False, "mpiexec -n 8 tough-exec INFILE INFILE.out"),
+    ],
+)
+def test_run(exec, workers, docker, wsl, cmd):
+    status = toughio.run(
+        exec,
+        {},
+        workers=workers,
+        docker=docker,
+        wsl=wsl,
+        use_temp=sys.version_info
+        >= (3, 8),  # dirs_exist_ok only works with Python > 3.8
+        silent=True,
+    )
+
+    assert status.args == cmd
+
+
+@pytest.mark.skipif(
+    not platform.system().startswith("Win"), reason="requires Windows platform"
+)
+@pytest.mark.parametrize(
+    "exec, workers, docker, wsl, cmd",
+    [
+        (
+            "tough-exec",
+            None,
+            "docker-image",
+            False,
+            "docker run --rm  -v PLACEHOLDER:/shared -w /shared docker-image tough-exec INFILE INFILE.out",
+        ),
+        ("tough-exec", None, None, True, "bash -c 'tough-exec INFILE INFILE.out'"),
+        (
+            "tough-exec",
+            8,
+            "docker-image",
+            True,
+            """bash -c 'docker run --rm  -v PLACEHOLDER:/shared -w /shared docker-image mpiexec -n 8 tough-exec INFILE INFILE.out'""",
+        ),
+    ],
+)
+def test_run_windows(exec, workers, docker, wsl, cmd):
+    if os.getenv("ComSpec").endswith("cmd.exe"):
+        cmd = cmd.replace("PLACEHOLDER", '"%cd%"')
+
+    else:
+        cmd = cmd.replace("PLACEHOLDER", "${PWD}")
+
+    test_run(exec, workers, docker, wsl, cmd)
+
+
+@pytest.mark.skipif(
+    platform.system().startswith("Win"), reason="requires Unix platform"
+)
+@pytest.mark.parametrize(
+    "exec, workers, docker, cmd",
+    [
+        (
+            "tough-exec",
+            None,
+            "docker-image",
+            "docker run --rm PLACEHOLDER -v ${PWD}:/shared -w /shared docker-image tough-exec INFILE INFILE.out",
+        ),
+        (
+            "tough-exec",
+            8,
+            "docker-image",
+            "docker run --rm PLACEHOLDER -v ${PWD}:/shared -w /shared docker-image mpiexec -n 8 tough-exec INFILE INFILE.out",
+        ),
+    ],
+)
+def test_run_unix(exec, workers, docker, cmd):
+    cmd = cmd.replace("PLACEHOLDER", f"-e LOCAL_USER_ID={os.getuid()}")
+    test_run(exec, workers, docker, False, cmd)

toughio/VERSION

@@ -1 +1 @@
-1.13.0
+1.13.1

toughio/_io/output/tough/_tough.py

@@ -126,15 +126,7 @@ def _read_table(f, file_type):
                 if line[:nwsp].strip() and not line.strip().startswith("ELEM"):
                     if first:
                         # Find first floating point
-                        for xf in line.split()[::-1]:
-                            try:
-                                _ = int(xf)
-
-                            except ValueError:
-                                x = xf
-                                continue
-
-                            break
+                        x = line.split()[-headers[::-1].index("INDEX")]
 
                         # Find end of label(s)
                         tmp = line[: line.index(x)].rstrip()

toughio/_run.py

@@ -152,20 +152,26 @@ def run(
         cmd = f"mpiexec -n {workers} {cmd}"
 
     # Use Docker
+    is_windows = platform.system().startswith("Win")
+
     if docker:
-        if platform.system().startswith("Win") and os.getenv("ComSpec").endswith(
-            "cmd.exe"
-        ):
-            cwd = "%cd%"
+        if is_windows and os.getenv("ComSpec").endswith("cmd.exe"):
+            cwd = '"%cd%"'
 
         else:
             cwd = "${PWD}"
 
-        cmd = f"docker run --rm -v {cwd}:/work -w /work {docker} {cmd}"
+        try:
+            uid = f"-e LOCAL_USER_ID={os.getuid()}"
+
+        except AttributeError:
+            uid = ""
+
+        cmd = f"docker run --rm {uid} -v {cwd}:/shared -w /shared {docker} {cmd}"
 
     # Use WSL
-    if wsl and platform.system().startswith("Win"):
-        cmd = f'bash -c "{cmd}"'
+    if wsl and is_windows:
+        cmd = f"bash -c '{cmd}'"
 
     kwargs = {}
     if silent:
@@ -184,7 +190,7 @@ def run(
             simulation_dir,
             working_dir,
             ignore=shutil.ignore_patterns(*ignore_patterns),
-            dirs_exist_ok=True,
+            dirs_exist_ok=True,  # Doesn't work with Python 3.7
         )
         shutil.rmtree(simulation_dir, ignore_errors=True)
         os.remove(working_dir / "tempdir.txt")