feat: remove use_shell option

This PR fixes issue #30

README.md

@@ -65,8 +65,9 @@ Create a template and place it in the `.datalad/make/methods` directory:
 > cat > .datalad/make/methods/one-to-many <<EOF
 parameters = ['first', 'second', 'output']
 
-use_shell = 'true'
 command = [
+    "bash",
+    "-c",
     "echo content: {first} > '{output}-1.txt'; echo content: {second} > '{output}-2.txt'",
 ]
 EOF

datalad_remake/annexremotes/tests/test_hierarchies.py

@@ -10,26 +10,28 @@
     create_simple_computation_dataset,
 )
 
-test_method = """
-parameters = ['first', 'second', 'third']
-use_shell = 'true'
-command = [
-    "echo content: {first} > 'a.txt';",
-    "mkdir -p 'd2_subds0/d2_subds1/d2_subds2';",
-    "echo content: {second} > 'b.txt';",
-    "echo content: {third} > 'new.txt';",
-    "echo content: {first} > 'd2_subds0/a0.txt';",
-    "echo content: {second} > 'd2_subds0/b0.txt';",
-    "echo content: {third} > 'd2_subds0/new.txt';",
-    "echo content: {first} > 'd2_subds0/d2_subds1/a1.txt';",
-    "echo content: {second} > 'd2_subds0/d2_subds1/b1.txt';",
-    "echo content: {third} > 'd2_subds0/d2_subds1/new.txt';",
-    "echo content: {first} > 'd2_subds0/d2_subds1/d2_subds2/a2.txt';",
-    "echo content: {second} > 'd2_subds0/d2_subds1/d2_subds2/b2.txt';",
-    "echo content: {third} > 'd2_subds0/d2_subds1/d2_subds2/new.txt';",
-]
-"""
+script = (
+    "echo content: {first} > 'a.txt';"
+    "mkdir -p 'd2_subds0/d2_subds1/d2_subds2';"
+    "echo content: {second} > 'b.txt';"
+    "echo content: {third} > 'new.txt';"
+    "echo content: {first} > 'd2_subds0/a0.txt';"
+    "echo content: {second} > 'd2_subds0/b0.txt';"
+    "echo content: {third} > 'd2_subds0/new.txt';"
+    "echo content: {first} > 'd2_subds0/d2_subds1/a1.txt';"
+    "echo content: {second} > 'd2_subds0/d2_subds1/b1.txt';"
+    "echo content: {third} > 'd2_subds0/d2_subds1/new.txt';"
+    "echo content: {first} > 'd2_subds0/d2_subds1/d2_subds2/a2.txt';"
+    "echo content: {second} > 'd2_subds0/d2_subds1/d2_subds2/b2.txt';"
+    "echo content: {third} > 'd2_subds0/d2_subds1/d2_subds2/new.txt'"
+)
 
+test_method = '\n'.join(
+    [
+        "parameters = ['first', 'second', 'third']",
+        'command = ["bash", "-c", "' + script + '"]',
+    ]
+)
 
 output_pattern_static = [
     'a.txt',

datalad_remake/annexremotes/tests/test_priority.py

@@ -23,8 +23,7 @@
 # priority code.
 template = """
 parameters = ['content']
-use_shell = 'true'
-command = ["echo from {label}: {{content}} > 'a.txt'"]
+command = ["bash", "-c", "echo from {label}: {{content}} > 'a.txt'"]
 """
 
 

datalad_remake/annexremotes/tests/test_remake_remote.py

@@ -18,10 +18,7 @@
 
 template = """
 parameters = ['content']
-
-use_shell = 'true'
-
-command = ["echo content: {content} > 'a.txt'"]
+command = ["bash", "-c", "echo content: {content} > 'a.txt'"]
 """
 
 

datalad_remake/commands/tests/test_make.py

@@ -12,8 +12,7 @@
 
 test_method = """
 parameters = ['name', 'file']
-use_shell = 'true'
-command = ["echo Hello {name} > {file}"]
+command = ["bash", "-c", "echo Hello {name} > {file}"]
 """
 
 output_pattern = ['a.txt']

datalad_remake/tests/test_complex_cases.py

@@ -7,22 +7,17 @@
 
 template = """
 parameters = ['line']
-
-use_shell = 'true'
-
-command = ["echo {line} >> 'a.txt'"]
+command = ["bash", "-c", "echo {line} >> 'a.txt'"]
 """
 
 template_c1 = """
 parameters = ['line']
-use_shell = 'true'
-command = ["cat a.txt > c1.txt;  echo {line} >> c1.txt"]
+command = ["bash", "-c", "cat a.txt > c1.txt;  echo {line} >> c1.txt"]
 """
 
 template_c2 = """
 parameters = ['line']
-use_shell = 'true'
-command = ["cat c1.txt > c2.txt; echo {line} >> c2.txt"]
+command = ["bash", "-c", "cat c1.txt > c2.txt; echo {line} >> c2.txt"]
 """
 
 

datalad_remake/utils/compute.py

@@ -74,10 +74,5 @@ def compute(
     substituted_command = substitute_arguments(template, substitutions, 'command')
 
     with chdir(root_directory):
-        if template.get('use_shell', 'false') == 'true':
-            cmd = ' '.join(substituted_command)
-            lgr.debug(f'compute: RUNNING: with shell=True: {cmd}')
-            subprocess.run(cmd, shell=True, check=True)  # noqa: S602
-        else:
-            lgr.debug(f'compute: RUNNING: {substituted_command}')
-            subprocess.run(substituted_command, check=True)
+        lgr.debug(f'compute: RUNNING: {substituted_command}')
+        subprocess.run(substituted_command, check=True)

examples/fmriprep-docker/fmriprep-docker

@@ -18,8 +18,6 @@
 
 parameters = ['input_dir', 'output_dir', 'participant_label', 'license_file']
 
-use_shell = 'false'
-
 # Note: `{root_directory}` resolves to the directory of the dataset in which the
 # computation was started with `datalad make`.
 

examples/fmriprep-singularity/fmriprep-singularity

@@ -19,8 +19,6 @@
 
 parameters = ['container', 'input_dir', 'output_dir', 'participant_label', 'license_file']
 
-use_shell = 'false'
-
 # Note: `{root_directory}` resolves to the directory of the dataset in which the
 # computation was started with `datalad make`.
 

examples/one-to-many

@@ -8,12 +8,12 @@
 
 parameters = ['first', 'second', 'output']
 
-use_shell = 'true'
-
 # The command line that should be executed. The curly braces are placeholders
 # for the parameters that were defined above. They will be replaced with
 # the values provided in the parameter arguments of `datalad make`.
 #
 command = [
+    "bash",
+    "-c",
     "echo content: {first} > '{output}-1.txt'; echo content: {second} > '{output}-2.txt'",
 ]