toil 6.1.0a1__py3-none-any.whl → 8.0.0__py3-none-any.whl

toil/test/cwl/measure_default_memory.cwl

@@ -0,0 +1,12 @@
+cwlVersion: v1.2
+class: CommandLineTool
+inputs: []
+baseCommand: ["bash", "-c", "ulimit -m"]
+stdout: memory.txt
+outputs:
+  memory:
+    type: string
+    outputBinding:
+      glob: memory.txt
+      loadContents: True
+      outputEval: $(self[0].contents)

toil/test/cwl/not_run_required_input.cwl

@@ -0,0 +1,29 @@
+# This workflow fills in a required int from an optional int, but only when the
+# int is really present. But it also uses the value to compute the conditional
+# task's resource requirements, so Toil can't just schedule the task and then
+# check the condition.
+# See <https://github.com/DataBiosphere/toil/issues/4930#issue-2297563321>
+cwlVersion: v1.2
+class: Workflow
+requirements:
+  InlineJavascriptRequirement: {}
+inputs:
+  optional_input: int?
+steps:
+  the_step:
+    in:
+      required_input:
+        source: optional_input
+    when: $(inputs.required_input != null)
+    run:
+      cwlVersion: v1.2
+      class: CommandLineTool
+      inputs:
+        required_input: int
+      requirements:
+        ResourceRequirement:
+          coresMax: $(inputs.required_input)
+      baseCommand: "nproc"
+      outputs: []
+    out: []
+outputs: []

toil/test/cwl/scatter_duplicate_outputs.cwl

@@ -0,0 +1,40 @@
+cwlVersion: v1.2
+class: Workflow
+id: scatter-duplicate-outputs
+
+inputs:
+  - id: toScatterOver
+    type: string[]
+    default: ['this','is','an','array','of','more','than','two','things']
+
+steps:
+  echo:
+    run:
+      id: scatter
+      class: CommandLineTool
+      inputs:
+        s: string
+      baseCommand: [echo]
+      arguments: [ $(inputs.s)]
+      stdout: scatter.out
+      stderr: scatter.err
+      outputs:
+        out: stdout
+        err: stderr
+    in:
+      - id: s
+        source: toScatterOver
+    scatter:
+     - s
+    out:
+      - id: out
+      - id: err
+
+outputs:
+  - id: echo_out
+    type: File[]
+    outputSource: ["echo/out"]
+
+
+requirements:
+  - class: ScatterFeatureRequirement

toil/test/cwl/seqtk_seq.cwl

@@ -21,4 +21,4 @@ hints:
     packages:
     - package: seqtk
       version:
-      - r93
+      - '1.4'

toil/test/docs/scriptsTest.py

@@ -5,15 +5,18 @@ import subprocess
 import sys
 import unittest
 
-pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))  # noqa
+import pytest
+
+pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))  # noqa
 sys.path.insert(0, pkg_root)  # noqa
 
-from toil.test import ToilTest, needs_cwl, needs_docker
+from toil.test import ToilTest, needs_docker
 from toil.version import python
 
 
 class ToilDocumentationTest(ToilTest):
     """Tests for scripts in the toil tutorials."""
+
     @classmethod
     def setUpClass(cls):
         super(ToilTest, cls).setUpClass()
@@ -21,14 +24,8 @@ class ToilDocumentationTest(ToilTest):
 
     def tearDown(self) -> None:
         super(ToilTest, self).tearDown()
-        # src/toil/test/docs/scripts/cwlExampleFiles/sample_1_output.txt
-        output_files = ["sample_1_output.txt", "sample_2_output.txt", "sample_3_output.txt"]
-        for output in output_files:
-            output_file = os.path.join(self.directory, 'scripts/cwlExampleFiles', output)
-            if os.path.exists(output_file):
-                os.remove(output_file)
-
-        jobstores = ['/mnt/ephemeral/workspace/toil-pull-requests/toilWorkflowRun']
+
+        jobstores = ["/mnt/ephemeral/workspace/toil-pull-requests/toilWorkflowRun"]
         for jobstore in jobstores:
             if os.path.exists(jobstore):
                 shutil.rmtree(jobstore)
@@ -36,19 +33,24 @@ class ToilDocumentationTest(ToilTest):
         unittest.TestCase.tearDown(self)
 
     """Just check the exit code"""
-    def checkExitCode(self, script):
+
+    def checkExitCode(self, script, extra_args: list[str] = []):
         program = os.path.join(self.directory, "scripts", script)
-        process = subprocess.Popen([python, program, "file:my-jobstore", "--clean=always"],
-                                   stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        process = subprocess.Popen(
+            [python, program, "file:my-jobstore", "--clean=always"] + extra_args,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
         stdout, stderr = process.communicate()
         if isinstance(stdout, bytes):
-            stdout = stdout.decode('utf-8')
-            stderr = stderr.decode('utf-8')
+            stdout = stdout.decode("utf-8")
+            stderr = stderr.decode("utf-8")
         if not process.returncode == 0:
             raise RuntimeError(stderr)
-        return stdout + ' ' + stderr
+        return stdout + " " + stderr
 
     """Check the exit code and the output"""
+
     def checkExpectedOut(self, script, expectedOutput):
         outerr = self.checkExitCode(script)
 
@@ -57,6 +59,7 @@ class ToilDocumentationTest(ToilTest):
         self.assertGreater(index, -1, f"Expected:\n{expectedOutput}\nOutput:\n{outerr}")
 
     """Check the exit code and look for a pattern"""
+
     def checkExpectedPattern(self, script, expectedPattern):
         outerr = self.checkExitCode(script)
 
@@ -65,13 +68,11 @@ class ToilDocumentationTest(ToilTest):
         n = re.search(pattern, outerr)
         self.assertNotEqual(n, None, f"Pattern:\n{expectedPattern}\nOutput:\n{outerr}")
 
-    @needs_cwl
-    def testCwlexample(self):
-        self.checkExitCode("tutorial_cwlexample.py")
-
-    def testDiscoverfiles(self):
-        self.checkExitCode("tutorial_discoverfiles.py")
+    def testStats(self):
+        # This script asks for 4 cores but we might need to run the tests in only 3.
+        self.checkExitCode("tutorial_stats.py", ["--scale=0.5"])
 
+    @pytest.mark.timeout(1200)
     def testDynamic(self):
         self.checkExitCode("tutorial_dynamic.py")
 
@@ -82,16 +83,24 @@ class ToilDocumentationTest(ToilTest):
         self.checkExitCode("tutorial_encapsulation2.py")
 
     def testHelloworld(self):
-        self.checkExpectedOut("tutorial_helloworld.py", "Hello, world!, here's a message: You did it!\n")
+        self.checkExpectedOut(
+            "tutorial_helloworld.py", "Hello, world!, here's a message: You did it!\n"
+        )
 
     def testInvokeworkflow(self):
-        self.checkExpectedOut("tutorial_invokeworkflow.py", "Hello, world!, here's a message: Woot\n")
+        self.checkExpectedOut(
+            "tutorial_invokeworkflow.py", "Hello, world!, here's a message: Woot\n"
+        )
 
     def testInvokeworkflow2(self):
-        self.checkExpectedOut("tutorial_invokeworkflow2.py", "Hello, world!, I have a message: Woot!\n")
+        self.checkExpectedOut(
+            "tutorial_invokeworkflow2.py", "Hello, world!, I have a message: Woot!\n"
+        )
 
     def testJobFunctions(self):
-        self.checkExpectedOut("tutorial_jobfunctions.py", "Hello world, I have a message: Woot!\n")
+        self.checkExpectedOut(
+            "tutorial_jobfunctions.py", "Hello world, I have a message: Woot!\n"
+        )
 
     def testManaging(self):
         self.checkExitCode("tutorial_managing.py")
@@ -100,38 +109,51 @@ class ToilDocumentationTest(ToilTest):
         self.checkExitCode("tutorial_managing2.py")
 
     def testMultiplejobs(self):
-        self.checkExpectedPattern("tutorial_multiplejobs.py",
-                                  "Hello world, I have a message: first.*Hello world, I have a message: "
-                                  "second or third.*Hello world, I have a message: second or third.*Hello world,"
-                                  " I have a message: last")
+        self.checkExpectedPattern(
+            "tutorial_multiplejobs.py",
+            "Hello world, I have a message: first.*Hello world, I have a message: "
+            "second or third.*Hello world, I have a message: second or third.*Hello world,"
+            " I have a message: last",
+        )
 
     def testMultiplejobs2(self):
-        self.checkExpectedPattern("tutorial_multiplejobs2.py",
-                                  "Hello world, I have a message: first.*Hello world, I have a message: "
-                                  "second or third.*Hello world, I have a message: second or third.*Hello world,"
-                                  " I have a message: last")
+        self.checkExpectedPattern(
+            "tutorial_multiplejobs2.py",
+            "Hello world, I have a message: first.*Hello world, I have a message: "
+            "second or third.*Hello world, I have a message: second or third.*Hello world,"
+            " I have a message: last",
+        )
 
     def testMultiplejobs3(self):
-        self.checkExpectedPattern("tutorial_multiplejobs3.py",
-                                  "Hello world, I have a message: first.*Hello world, I have a message: "
-                                  "second or third.*Hello world, I have a message: second or third.*Hello world,"
-                                  " I have a message: last")
-
+        self.checkExpectedPattern(
+            "tutorial_multiplejobs3.py",
+            "Hello world, I have a message: first.*Hello world, I have a message: "
+            "second or third.*Hello world, I have a message: second or third.*Hello world,"
+            " I have a message: last",
+        )
+
+    @pytest.mark.timeout(1200)
     def testPromises2(self):
-        self.checkExpectedOut("tutorial_promises2.py",
-                              "['00000', '00001', '00010', '00011', '00100', '00101', '00110', '00111',"
-                              " '01000', '01001', '01010', '01011', '01100', '01101', '01110', '01111',"
-                              " '10000', '10001', '10010', '10011', '10100', '10101', '10110', '10111',"
-                              " '11000', '11001', '11010', '11011', '11100', '11101', '11110', '11111']")
+        self.checkExpectedOut(
+            "tutorial_promises2.py",
+            "['00000', '00001', '00010', '00011', '00100', '00101', '00110', '00111',"
+            " '01000', '01001', '01010', '01011', '01100', '01101', '01110', '01111',"
+            " '10000', '10001', '10010', '10011', '10100', '10101', '10110', '10111',"
+            " '11000', '11001', '11010', '11011', '11100', '11101', '11110', '11111']",
+        )
 
     def testQuickstart(self):
-        self.checkExpectedOut("tutorial_quickstart.py", "Hello, world!, here's a message: Woot\n")
+        self.checkExpectedOut(
+            "tutorial_quickstart.py", "Hello, world!, here's a message: Woot\n"
+        )
 
     def testRequirements(self):
         self.checkExitCode("tutorial_requirements.py")
 
     def testArguments(self):
-        self.checkExpectedOut("tutorial_arguments.py", "Hello, world!, here's a message: Woot")
+        self.checkExpectedOut(
+            "tutorial_arguments.py", "Hello, world!, here's a message: Woot"
+        )
 
     @needs_docker
     def testDocker(self):
@@ -146,5 +168,6 @@ class ToilDocumentationTest(ToilTest):
     def testStaging(self):
         self.checkExitCode("tutorial_staging.py")
 
+
 if __name__ == "__main__":
     unittest.main()