Remove the WDL compiler.

.gitlab-ci.yml

@@ -61,7 +61,6 @@ stages:
   - main_tests
   - integration
 
-
 lint:
   rules:
     - if: $CI_PIPELINE_SOURCE != "schedule"
@@ -75,7 +74,6 @@ lint:
     - make docs
     # - make diff_pydocstyle_report
 
-
 cwl_dependency_is_stand_alone:
   rules:
     - if: $CI_PIPELINE_SOURCE != "schedule"
@@ -85,15 +83,14 @@ cwl_dependency_is_stand_alone:
     - ${MAIN_PYTHON_PKG} -m virtualenv venv && . venv/bin/activate && make prepare && make develop extras=[cwl]
     - make test threads="${TEST_THREADS}" marker="${MARKER}" tests=src/toil/test/docs/scriptsTest.py::ToilDocumentationTest::testCwlexample
 
-
 wdl_dependency_is_stand_alone:
   rules:
     - if: $CI_PIPELINE_SOURCE != "schedule"
   stage: linting_and_dependencies
   script:
     - pwd
     - ${MAIN_PYTHON_PKG} -m virtualenv venv && . venv/bin/activate && make prepare && make develop extras=[wdl]
-    - make test threads="${TEST_THREADS}" marker="${MARKER}" tests=src/toil/test/wdl/toilwdlTest.py::ToilWdlTest::testMD5sum
+    - make test threads="${TEST_THREADS}" marker="${MARKER}" tests=src/toil/test/wdl/wdltoil_test.py::WDLTests::test_MD5sum
 
 quick_test_offline:
   rules:

contrib/admin/mypy-with-ignore.py

@@ -33,14 +33,6 @@ def main():
         'src/toil/__init__.py',
         'src/toil/deferred.py',
         'src/toil/version.py',
-        'src/toil/wdl/utils.py',
-        'src/toil/wdl/wdl_synthesis.py',
-        'src/toil/wdl/wdl_analysis.py',
-        'src/toil/wdl/wdl_functions.py',
-        'src/toil/wdl/toilwdl.py',
-        'src/toil/wdl/versions/draft2.py',
-        'src/toil/wdl/versions/v1.py',
-        'src/toil/wdl/versions/dev.py',
         'src/toil/provisioners/abstractProvisioner.py',
         'src/toil/provisioners/gceProvisioner.py',
         'src/toil/provisioners/__init__.py',
@@ -104,7 +96,6 @@ def ignore(file_path):
             if file_path.startswith(prefix):
                 return True
         return False
-
 
     filtered_files_to_check = []
     for file_path in all_files_to_check:

setup.py

@@ -116,7 +116,6 @@ def run_setup():
                 'cwltoil = toil.cwl.cwltoil:cwltoil_was_removed [cwl]',
                 'toil-cwl-runner = toil.cwl.cwltoil:main [cwl]',
                 'toil-wdl-runner = toil.wdl.wdltoil:main [wdl]',
-                'toil-wdl-runner-old = toil.wdl.toilwdl:main [wdl]',
                 'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server]',
                 '_toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos]',
                 '_toil_contained_executor = toil.batchSystems.contained_executor:executor']})

src/toil/server/cli/wes_cwl_runner.py

@@ -147,7 +147,7 @@ def parse_params(self, workflow_params_file: str) -> Dict[str, Any]:
 
         :param workflow_params_file: The URL or path to the CWL input file.
         """
-        loader = schema_salad.ref_resolver.Loader(
+        loader = schema_salad.ref_resolver.Loader(  # type:ignore
             {"location": {"@type": "@id"}, "path": {"@type": "@id"}}
         )
 

src/toil/test/utils/toilDebugTest.py

@@ -1,4 +1,3 @@
-"""A set of test cases for toilwdl.py"""
 # Copyright (C) 2015-2021 Regents of the University of California
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -15,47 +14,44 @@
 import logging
 import os
 import subprocess
-from pathlib import Path
+import tempfile
 
 from toil.lib.resources import glob
 from toil.test import slow
 from toil.version import python
 
-import pytest
 
 logger = logging.getLogger(__name__)
 
 
-@pytest.fixture
-def workflow_debug_jobstore(tmp_path: Path) -> str:
-    jobStorePath = str(tmp_path / "toilWorkflowRun")
+def workflow_debug_jobstore() -> str:
+    job_store_path = os.path.join(tempfile.mkdtemp(), "toilWorkflowRun")
     subprocess.check_call(
         [
             python,
             os.path.abspath("src/toil/test/utils/ABCWorkflowDebug/debugWorkflow.py"),
-            jobStorePath,
+            job_store_path,
         ]
     )
-    return jobStorePath
+    return job_store_path
 
 
 @slow
-def testJobStoreContents(workflow_debug_jobstore: str):
+def testJobStoreContents():
     """
     Test toilDebugFile.printContentsOfJobStore().
 
     Runs a workflow that imports 'B.txt' and 'mkFile.py' into the
     jobStore.  'A.txt', 'C.txt', 'ABC.txt' are then created.  This checks to
     make sure these contents are found in the jobStore and printed.
     """
-    jobStoreDir = workflow_debug_jobstore
     contents = ["A.txt", "B.txt", "C.txt", "ABC.txt", "mkFile.py"]
 
     subprocess.check_call(
         [
             python,
             os.path.abspath("src/toil/utils/toilDebugFile.py"),
-            jobStoreDir,
+            workflow_debug_jobstore(),
             "--logDebug",
             "--listFilesInJobStore=True",
         ]
@@ -78,7 +74,7 @@ def testJobStoreContents(workflow_debug_jobstore: str):
     os.remove(jobstoreFileContents)
 
 
-def fetchFiles(symLink, jobStoreDir: str, outputDir):
+def fetchFiles(symLink: bool, jobStoreDir: str, outputDir: str):
     """
     Fn for testFetchJobStoreFiles() and testFetchJobStoreFilesWSymlinks().
 
@@ -99,8 +95,8 @@ def fetchFiles(symLink, jobStoreDir: str, outputDir):
         "*C.txt",
         "*ABC.txt",
         "*mkFile.py",
-        "--localFilePath=" + outputDir,
-        "--useSymlinks=" + str(symLink),
+        f"--localFilePath={outputDir}",
+        f"--useSymlinks={symLink}",
     ]
     print(cmd)
     subprocess.check_call(cmd)
@@ -114,22 +110,10 @@ def fetchFiles(symLink, jobStoreDir: str, outputDir):
 
 
 # expected run time = 4s
-def testFetchJobStoreFiles(tmp_path: Path, workflow_debug_jobstore: str) -> None:
-    """Test toilDebugFile.fetchJobStoreFiles() without using symlinks."""
-    outputDir = tmp_path / "testoutput"
-    outputDir.mkdir()
-    fetchFiles(
-        symLink=False, jobStoreDir=workflow_debug_jobstore, outputDir=str(outputDir)
-    )
-
-
-# expected run time = 4s
-def testFetchJobStoreFilesWSymlinks(
-    tmp_path: Path, workflow_debug_jobstore: str
-) -> None:
-    """Test toilDebugFile.fetchJobStoreFiles() using symlinks."""
-    outputDir = tmp_path / "testoutput"
-    outputDir.mkdir()
-    fetchFiles(
-        symLink=True, jobStoreDir=workflow_debug_jobstore, outputDir=str(outputDir)
-    )
+def testFetchJobStoreFiles() -> None:
+    """Test toilDebugFile.fetchJobStoreFiles() symlinks."""
+    job_store_dir = workflow_debug_jobstore()
+    output_dir = os.path.join(os.path.dirname(job_store_dir), "testoutput")
+    os.makedirs(output_dir, exist_ok=True)
+    for symlink in (True, False):
+        fetchFiles(symLink=symlink, jobStoreDir=job_store_dir, outputDir=output_dir)