toil 9.0.0__py3-none-any.whl → 9.1.1__py3-none-any.whl

toil/worker.py

@@ -544,6 +544,7 @@ def workerScript(
         startClock = ResourceMonitor.get_total_cpu_time()
 
         startTime = time.time()
+        fileStore = None
         while True:
             ##########################################
             # Run the job body, if there is one
@@ -689,8 +690,10 @@ def workerScript(
         totalCPUTime, totalMemoryUsage = (
             ResourceMonitor.get_total_cpu_time_and_memory_usage()
         )
-        statsDict.workers.time = str(time.time() - startTime)
-        statsDict.workers.clock = str(totalCPUTime - startClock)
+        chain_wall_time = time.time() - startTime
+        chain_cpu_time = totalCPUTime - startClock
+        statsDict.workers.time = str(chain_wall_time)
+        statsDict.workers.clock = str(chain_cpu_time)
         statsDict.workers.memory = str(totalMemoryUsage)
         # Say the worker used the max disk we saw from any job
         max_bytes = 0

{toil-9.0.0.dist-info → toil-9.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: toil
-Version: 9.0.0
+Version: 9.1.1
 Summary: Pipeline management software for clusters.
 Home-page: https://github.com/DataBiosphere/toil
 Author: Benedict Paten and the Toil community
@@ -33,7 +33,7 @@ Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: dill<0.4,>=0.3.2
-Requires-Dist: requests<=2.31.0
+Requires-Dist: requests<=2.32.5
 Requires-Dist: docker<8,>=6.1.0
 Requires-Dist: urllib3<3,>=1.26.0
 Requires-Dist: python-dateutil
@@ -55,10 +55,10 @@ Requires-Dist: mypy-boto3-s3<2,>=1.28.3.post2; extra == "aws"
 Requires-Dist: moto<6,>=5.0.3; extra == "aws"
 Requires-Dist: ec2_metadata<3,>=2.14.0; extra == "aws"
 Provides-Extra: cwl
-Requires-Dist: cwltool==3.1.20250110105449; extra == "cwl"
+Requires-Dist: cwltool==3.1.20250715140722; extra == "cwl"
 Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "cwl"
 Requires-Dist: galaxy-tool-util<26; extra == "cwl"
-Requires-Dist: galaxy-util<25; extra == "cwl"
+Requires-Dist: galaxy-util<26; extra == "cwl"
 Requires-Dist: ruamel.yaml<=0.19,>=0.15; extra == "cwl"
 Requires-Dist: ruamel.yaml.clib>=0.2.6; extra == "cwl"
 Requires-Dist: networkx!=2.8.1,<4; extra == "cwl"
@@ -67,11 +67,11 @@ Requires-Dist: cwl-utils>=0.36; extra == "cwl"
 Provides-Extra: encryption
 Requires-Dist: pynacl<2,>=1.4.0; extra == "encryption"
 Provides-Extra: google
-Requires-Dist: apache-libcloud<3,>=2.2.1; extra == "google"
+Requires-Dist: apache-libcloud<4,>=3.6.1; extra == "google"
 Requires-Dist: google-cloud-storage<=2.8.0,>=2; extra == "google"
 Requires-Dist: google-auth<3,>=2.18.1; extra == "google"
 Provides-Extra: kubernetes
-Requires-Dist: kubernetes<33,>=12.0.1; extra == "kubernetes"
+Requires-Dist: kubernetes<34,>=12.0.1; extra == "kubernetes"
 Requires-Dist: kubernetes-stubs==v22.6.0post1; extra == "kubernetes"
 Requires-Dist: types-urllib3; extra == "kubernetes"
 Requires-Dist: types-PyYAML; extra == "kubernetes"
@@ -84,7 +84,7 @@ Provides-Extra: server
 Requires-Dist: connexion[swagger-ui]<4,>=3; extra == "server"
 Requires-Dist: flask<4,>=3; extra == "server"
 Requires-Dist: werkzeug<4,>=3; extra == "server"
-Requires-Dist: flask-cors<6,>=5.0.1; extra == "server"
+Requires-Dist: flask-cors<7,>=5.0.1; extra == "server"
 Requires-Dist: gunicorn<24,>=23.0.0; extra == "server"
 Requires-Dist: celery<6,>=5.4.0; extra == "server"
 Requires-Dist: wes-service<6,>=5.0.0; extra == "server"
@@ -99,20 +99,20 @@ Requires-Dist: mypy-boto3-iam<2,>=1.28.3.post2; extra == "all"
 Requires-Dist: mypy-boto3-s3<2,>=1.28.3.post2; extra == "all"
 Requires-Dist: moto<6,>=5.0.3; extra == "all"
 Requires-Dist: ec2_metadata<3,>=2.14.0; extra == "all"
-Requires-Dist: cwltool==3.1.20250110105449; extra == "all"
+Requires-Dist: cwltool==3.1.20250715140722; extra == "all"
 Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "all"
 Requires-Dist: galaxy-tool-util<26; extra == "all"
-Requires-Dist: galaxy-util<25; extra == "all"
+Requires-Dist: galaxy-util<26; extra == "all"
 Requires-Dist: ruamel.yaml<=0.19,>=0.15; extra == "all"
 Requires-Dist: ruamel.yaml.clib>=0.2.6; extra == "all"
 Requires-Dist: networkx!=2.8.1,<4; extra == "all"
 Requires-Dist: CacheControl[filecache]; extra == "all"
 Requires-Dist: cwl-utils>=0.36; extra == "all"
 Requires-Dist: pynacl<2,>=1.4.0; extra == "all"
-Requires-Dist: apache-libcloud<3,>=2.2.1; extra == "all"
+Requires-Dist: apache-libcloud<4,>=3.6.1; extra == "all"
 Requires-Dist: google-cloud-storage<=2.8.0,>=2; extra == "all"
 Requires-Dist: google-auth<3,>=2.18.1; extra == "all"
-Requires-Dist: kubernetes<33,>=12.0.1; extra == "all"
+Requires-Dist: kubernetes<34,>=12.0.1; extra == "all"
 Requires-Dist: kubernetes-stubs==v22.6.0post1; extra == "all"
 Requires-Dist: types-urllib3; extra == "all"
 Requires-Dist: types-PyYAML; extra == "all"
@@ -123,7 +123,7 @@ Requires-Dist: graphlib-backport==1.0; python_version < "3.9" and extra == "all"
 Requires-Dist: connexion[swagger-ui]<4,>=3; extra == "all"
 Requires-Dist: flask<4,>=3; extra == "all"
 Requires-Dist: werkzeug<4,>=3; extra == "all"
-Requires-Dist: flask-cors<6,>=5.0.1; extra == "all"
+Requires-Dist: flask-cors<7,>=5.0.1; extra == "all"
 Requires-Dist: gunicorn<24,>=23.0.0; extra == "all"
 Requires-Dist: celery<6,>=5.4.0; extra == "all"
 Requires-Dist: wes-service<6,>=5.0.0; extra == "all"

{toil-9.0.0.dist-info → toil-9.1.1.dist-info}/RECORD

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 toil/common.py,sha256=SCcqojtspk3oqwStKUx-daP7fMCgWQ8TWBgh7WNcSRY,83253
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 toil/exceptions.py,sha256=oL2d9uutwtcPkMcEUGrixKUd4y1JLSA0-N7hNJqCLSk,1883
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-toil/leader.py,sha256=qae1vsJYuuJW9fYYAl4nd-hVMvjfaWJ3Yf6eVsJwMLc,85512
+toil/job.py,sha256=KGcmuzoCFtWakl_y4LwBlo8Uuh1-FnGqHOXc_BwAF0A,175901
+toil/leader.py,sha256=abI47MI8zUlWZCjFce2QMwoFF9-QQ1aF8kWn7qKtrpM,85829
 toil/realtimeLogger.py,sha256=2O4AUaKtvItzzCAQKORIEHZ2cDoLf_6njoKWv_uzdFc,9878
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 toil/serviceManager.py,sha256=GE5IUjQmNrekYv9tclim0RlCFf4ueOQ2H4qHjMBrOcg,19978
 toil/statsAndLogging.py,sha256=JXir7TCV8OdDaAdt3VsDR2rbdNWk4ILyOwlKHVdoXT0,18696
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+toil/lib/web.py,sha256=zboNkhbCv4AzvyqxIkSnnirZJHZLeXhl5KG3Xwu6U4Q,1550
 toil/lib/aws/__init__.py,sha256=VI77J2o4IehFBpEUjS4eHmXlxEplFnKYHq6w8ZyotEk,7905
 toil/lib/aws/ami.py,sha256=SD728qocULXqWZmxPslcymukG-MxfNniMsBE9d1VVcM,9341
+toil/lib/aws/config.py,sha256=sXSMBHGGBUVXXcDLPJFi9nr7pQVDzuKE75tFYg5MC1U,859
 toil/lib/aws/iam.py,sha256=6qNJ6C61XVzbuPX1p-tcnEcabCjIultrVe9MrgcME04,18550
-toil/lib/aws/s3.py,sha256=accn7bSneZttfb91pZR_80gDhCgVX7Z4ZOKOwM-6u9w,1156
+toil/lib/aws/s3.py,sha256=8C9ed6hk6TZyffsvvgUJaLExwq7k3WlL8-Nv3rFu_jo,22750
 toil/lib/aws/session.py,sha256=96l_AGsyA3CpTJiOqPemuLWtGsV28K4DU6vjtDR-pxA,15033
-toil/lib/aws/utils.py,sha256=gk75XIj1Nlw8fN_KoaRb8n-rONmAtAuF2wYUqiev_2E,22205
+toil/lib/aws/utils.py,sha256=JNGcvAPgYHXpUGUVlJ374cLVUfEl8344m13qwz6HUYs,21812
 toil/lib/aws/utils.py.orig,sha256=1zR2bg0-mP-SM46MRZb-7s4O_9K5IOZ5_v92WItpmUs,22244
 toil/lib/encryption/__init__.py,sha256=HP19EUYJeIMdjZq11fLn_dXIGU98sIkpTxvMxvPaUSs,705
 toil/lib/encryption/_dummy.py,sha256=6e2fthd6YdgFUgY0kjGb2052KLWUeXD_ejeoCTAThLU,1082
@@ -96,13 +99,13 @@ toil/options/common.py,sha256=vUMadLlEze1Wks7F1ZcVk9tsAIQMbxVQePJx-KxCNVk,46257
 toil/options/cwl.py,sha256=aPcbaCA8h739e1GW2oUbymYBpPaDEnCDrPZowI6zMII,14578
 toil/options/runner.py,sha256=gr5D8PJ_eNu-VGhAYdhDlhDCkfd_id5_FrTQyZoiD5c,2614
 toil/options/wdl.py,sha256=kqM3AElkX00-34DSDnHRViahL6C0vsE9-wyosKvU2Fk,3790
-toil/provisioners/__init__.py,sha256=Z3OV95yx77LBVRUtjX_J8r_0OSC2glAIo5y7irbB-S0,9794
+toil/provisioners/__init__.py,sha256=TPsr-qc9P_fYbeCeo7FCGrU8UQxH4D3Rdhpzh6-nM7A,9885
 toil/provisioners/abstractProvisioner.py,sha256=R3OuUV2p8GWWuRs2PbaHkjHufOLyoknUaHq4vKPVGMc,58000
 toil/provisioners/clusterScaler.py,sha256=9FgnSPbn2U_FYUSJUeN67A0kdh-Yl0roi5nZLeJVr_I,64980
 toil/provisioners/gceProvisioner.py,sha256=8OsbSZeMgAB9l03zQ9WdKZ2-zFrHyzgXoLNdGKjdYcU,24212
-toil/provisioners/node.py,sha256=RFLXufNQhjiHUO5fBfbEBd4cbtSUWsNmiGcDDodioMI,15198
-toil/provisioners/aws/__init__.py,sha256=XmVkSuHGMvaMbDJ36yZHGkH5fsUJYJyi3V4R9MYw0Gs,8621
-toil/provisioners/aws/awsProvisioner.py,sha256=UOw4wmRy_7biTIsc0i5fhW7rvyXv0Mv-tTGIRlM2Fo0,90358
+toil/provisioners/node.py,sha256=zIr-JLEC-yn1umzCxreY1BMLWohxwHL1MFYW61Wwr28,17066
+toil/provisioners/aws/__init__.py,sha256=SO_2wlt8h1NtwYR9eqfqbYnDoUoyIAarlA2lFrbm_pA,9019
+toil/provisioners/aws/awsProvisioner.py,sha256=jDpM3s5M8BZGBG9cv6izyRIne00T3lPAh83dtrIco9U,90902
 toil/server/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/server/app.py,sha256=Rldi7Wwft7Zxl3jrqh6HVHc4gMNiMjZ3CJhc7nVLW-w,7431
 toil/server/celery_app.py,sha256=PbdwRb7tY5MU4PkPgFZkq7CMiCe6LHBxw5YgcbdsKIE,663
@@ -119,14 +122,14 @@ toil/server/wes/abstract_backend.py,sha256=BXmM_jrescRYuN4phgEjag6Xl-tXRPYz_PtwV
 toil/server/wes/amazon_wes_utils.py,sha256=xRrV7hiWoWVwxJykgL2HQdMf1FZg73eqEBltKXya1Fc,10287
 toil/server/wes/tasks.py,sha256=DBjUUbxY6mq0H4aB8qiGhatmz6qWJWHkHPgfAqSr37w,24746
 toil/server/wes/toil_backend.py,sha256=u7aA-Tb3QRH5mX5hJW1DWWjBNaSjgoo-C2jvvNic7v4,27518
-toil/test/__init__.py,sha256=ZuMmiG2Il-MiziEEiGetNyY8gJQOyH_ftxCkwIe-2Ig,49238
+toil/test/__init__.py,sha256=YmDLhPdigktTP_hE90epOJOeCKuSx1TVnaRiVFgqGG4,49144
 toil/test/conftest.py,sha256=JADYg_YbV_b28B970KcOqh4UYAhjpqwHxdQj4vt0xeE,237
 toil/test/batchSystems/__init__.py,sha256=9h1rcqYjjnn97DpDEJf8tlNOIDx0XiXyQwh0F_81y0k,612
 toil/test/batchSystems/batchSystemTest.py,sha256=5NkxMJ-mHOgN9oZoSK9zjPGZJf5CR2cQOuQ3V1P3g4I,56410
 toil/test/batchSystems/batch_system_plugin_test.py,sha256=eZlOOzdL7ja_EymnD_veY3fnAhz_6hE4CJwDKVyss-w,2991
 toil/test/batchSystems/test_gridengine.py,sha256=kZCF7WIAmCF1LTPPWd4zC6piQr0UaKJ3kYKz5tsBal0,6353
 toil/test/batchSystems/test_lsf_helper.py,sha256=JICnAPvU7HfqJ0RhIpC-IFfHLKftOAAQF2Iqc7nFs30,4697
-toil/test/batchSystems/test_slurm.py,sha256=998C-m8sKBlYGSIz8XJ5Br_TnuCZT2JOaHtUUz4WHkQ,28565
+toil/test/batchSystems/test_slurm.py,sha256=1leONjEsU_bcAjTfgoXzwJwgtmANOpUeDcAcOXRqm-Q,32041
 toil/test/cactus/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/test/cactus/pestis.tar.gz,sha256=pIzVl3PiXRAIZBtOQTlPD-tzzrC95JxJax5ykWeozD0,5762005
 toil/test/cactus/test_cactus_integration.py,sha256=4sRlsm7b29a08HNHFUbFu_gDW36TQeTfGBvRYUXNF_U,2219
@@ -183,12 +186,16 @@ toil/test/cwl/scatter_duplicate_outputs.cwl,sha256=1ubeij5YQhjHe0igq5xL-Caje6ghe
 toil/test/cwl/seqtk_seq.cwl,sha256=uR7wlwxlNLkA_hIFglgiWGoOftQqFk4sH7Wo5zF60-c,406
 toil/test/cwl/seqtk_seq_job.json,sha256=R7ZKDllKq33U0vLRK7yvRAjKr26wU5cbdgdixG_4bnY,69
 toil/test/cwl/sorttool.cwl,sha256=c1fhFZ_ekTMuEAM0nikUPd2j-etPQL8MqyuSJLNadtc,1060
+toil/test/cwl/staging_cat.cwl,sha256=7rswT6E6ldaA2I9t0DxMyuqiSepGMsIerhGZLyItpvA,625
+toil/test/cwl/staging_make_file.cwl,sha256=l6HEfkg3Wd8JUBCFoMd86a6hvIJXMGF4THHd8FiO2hE,359
+toil/test/cwl/staging_workflow.cwl,sha256=bCNyjI_CvValQOU3nDq_dl4ZO2uMwkUTLdL0TBmt5TI,789
 toil/test/cwl/stream.cwl,sha256=jtyYdmSyCeI6uoOeX5Nb_LMIXhR5Sqmu8dGSr_Y2Z8g,732
 toil/test/cwl/stream.json,sha256=9-UG9jmoMeNKHcB0yfKiEURPsuBe8Btr80iob3tEKzo,132
 toil/test/cwl/test_filename_conflict_detection.cwl,sha256=wVrc9EXmO74tgaEe4oE-EMpmQiHIuUFbLh0-qVisVZo,699
 toil/test/cwl/test_filename_conflict_detection_at_root.cwl,sha256=G3clUTFeeGZt5xPi2SNs05W7I-RT0OEN2C8xKHzQ300,695
 toil/test/cwl/test_filename_conflict_resolution.cwl,sha256=sIoXi61RzCkzD1MTCoglRYAXo8xaE1JiC6irvSANK0I,717
 toil/test/cwl/whale.txt,sha256=MS7gbKfWkYSmPTP52eIzQFHSzZiRMwvCNleCZ1YTmhE,1111
+toil/test/cwl/zero_default.cwl,sha256=9fO0kdTpx1gfEc9mldtwBnMPPjHadSjLtQEGxnYFS5Q,1112
 toil/test/cwl/directory/directory/file.txt,sha256=vRp5WUxW_LwWXs2loofRuWHwB8gIR2XE7lzCGRBBRbU,146
 toil/test/cwl/mock_mpi/fake_mpi.yml,sha256=YtxcavXA2BbTx098_6pFRs4T9E34j-PrlJnuGCr7x9w,113
 toil/test/cwl/mock_mpi/fake_mpi_run.py,sha256=CvV6oDK_vGYZEIaINRxev1TaKs7NtzJSG8eMk3MrgeE,1165
@@ -232,12 +239,11 @@ toil/test/docs/scripts/tutorial_promises2.py,sha256=wSmEGzhkcbDdu5kk4lLj1e93ZpiN
 toil/test/docs/scripts/tutorial_quickstart.py,sha256=n6rdO1cUvB70K_UgLyE3MpRbs5AyhNCSgMOvvSmt9j4,544
 toil/test/docs/scripts/tutorial_requirements.py,sha256=4A93_9OQEUeVpmA7bPknaSdKEi5adMfGHKBaRO4R7bg,1012
 toil/test/docs/scripts/tutorial_services.py,sha256=IkH-JpG4ymR1yd8AUIbhOgPwNlltWFEmiMpV2w-lYxw,1124
-toil/test/docs/scripts/tutorial_staging.py,sha256=LXM9obfyrGHeU36yFfbcvbmJ79czedvok58RkBwxlf8,1365
+toil/test/docs/scripts/tutorial_staging.py,sha256=MMwaxWJaZFUJk3WZFknBF0AHddcvSA_zAqGwbk2JvQw,1740
 toil/test/docs/scripts/tutorial_stats.py,sha256=eM0m4sjdgm9bkLpgf41nnX7MND9-JUWm_MuPfSFVk68,1762
-toil/test/docs/scripts/stagingExampleFiles/in.txt,sha256=gjjOyS8yW5TTMD-HmYuFwcfD5tQhbl23pv-x42qGK6s,7
 toil/test/docs/scripts/stagingExampleFiles/out.txt,sha256=1itR1QTwJkLatQA5Wa8MFVcJTH1J3MVEq6N6Cl2NHQ0,13
 toil/test/jobStores/__init__.py,sha256=9h1rcqYjjnn97DpDEJf8tlNOIDx0XiXyQwh0F_81y0k,612
-toil/test/jobStores/jobStoreTest.py,sha256=QEma-WTO-9kzp298LJXVUifXc1yP3OutKa3D0G7opkY,69620
+toil/test/jobStores/jobStoreTest.py,sha256=WPuC1PYSwZ56aZKOjznmClFHbUgUAaHQZjdGm5k3kg4,64763
 toil/test/lib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/test/lib/dockerTest.py,sha256=uvxPeXwJg7FTK9t9JXDHTQHecg1I9jC86-CFcR05mvY,17221
 toil/test/lib/test_conversions.py,sha256=JSwdTRYklpofPV3VANHC7vHZ7WcpEWOZD6G9Tkjd45w,7232
@@ -248,9 +254,9 @@ toil/test/lib/test_trs.py,sha256=mcGn3boLFkjS_aPMOS-gwlFd7QcMVM-vpLadBnZb8SE,691
 toil/test/lib/test_url.py,sha256=fWsi6yJEBahwfwWBKqcpalF2cUDfYG4aCk6BicJg-p0,2388
 toil/test/lib/url_plugin_test.py,sha256=7aXCIEIZ4cThcSqWwsfu5U_3QwhNxaI8WN-DTnB7CrA,3636
 toil/test/lib/aws/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-toil/test/lib/aws/test_iam.py,sha256=uSZZdGwwjJvxRDYfGoKGbWPx1kx6A61gVmb73LepLMU,7076
-toil/test/lib/aws/test_s3.py,sha256=NpYO0GnACbGpaKPwM0yeObxqBoFYJv92RUP7VdtompE,3061
-toil/test/lib/aws/test_utils.py,sha256=_JI_FfpyONfLE4HduibcAPF7_Y39MUx4H6wk7KqdWw8,2253
+toil/test/lib/aws/test_iam.py,sha256=Yx8vawHeo7tvGe1WTjajYD_Pw81ymb3Lluxi1ZVtNUc,7098
+toil/test/lib/aws/test_s3.py,sha256=WQp96eq4pSx7mjBWKeEyoZ2Cpne7cnSwgQ1lC10cLCk,3142
+toil/test/lib/aws/test_utils.py,sha256=OBgOhMeXHR4IefbzfBGACGOKoNm2K6xMC4MXSRi7UuA,2285
 toil/test/mesos/MesosDataStructuresTest.py,sha256=IcV-bNWJcMnij0WruhTk4RTmGROTTcU3pav5e4gHPfA,3225
 toil/test/mesos/__init__.py,sha256=9h1rcqYjjnn97DpDEJf8tlNOIDx0XiXyQwh0F_81y0k,612
 toil/test/mesos/helloWorld.py,sha256=xX65tKSBIKAxguBoAe-6Twp2XcBK1QEnKp5LRVImgK4,2204
@@ -264,7 +270,7 @@ toil/test/provisioners/gceProvisionerTest.py,sha256=eL3G66PzMqjB2ahXMTUd6rBGByJg
 toil/test/provisioners/provisionerTest.py,sha256=_JAvTs9bjynVpRkJI0VLPHZw-Y7kHI9B1vaWR4RomKA,2179
 toil/test/provisioners/restartScript.py,sha256=GodLqsIiYNxXFWQtyYHrxACI1fSUeGzcltO6qOdznj4,416
 toil/test/provisioners/aws/__init__.py,sha256=9h1rcqYjjnn97DpDEJf8tlNOIDx0XiXyQwh0F_81y0k,612
-toil/test/provisioners/aws/awsProvisionerTest.py,sha256=M1XN80n_NSO31b8zhqEvxDMfoyJIwKoNUaQ9f7ypegY,23753
+toil/test/provisioners/aws/awsProvisionerTest.py,sha256=JHkXHVez95-KQBSAwJwbfxy-j5_WYYD_9uesyw9WSgY,25266
 toil/test/server/__init__.py,sha256=9h1rcqYjjnn97DpDEJf8tlNOIDx0XiXyQwh0F_81y0k,612
 toil/test/server/serverTest.py,sha256=2T9FD32-9uoGjtRC2mtJh67j9_3OWZgFONQmkA4f2tU,29399
 toil/test/sort/__init__.py,sha256=9h1rcqYjjnn97DpDEJf8tlNOIDx0XiXyQwh0F_81y0k,612
@@ -272,13 +278,13 @@ toil/test/sort/restart_sort.py,sha256=A-1pWMhSIHSbtib-u1rvOFbhRqW_mQlf6dEbelFs7Q
 toil/test/sort/sort.py,sha256=H_f4DzLGSnkHpFRayYtJKkxlCAVcikuVR48MnuybrDI,11258
 toil/test/sort/sortTest.py,sha256=0dUZ0RCzE66bRcmOHJUD5MFg4UkSRbwhnHVkzX54wI4,12239
 toil/test/src/__init__.py,sha256=9h1rcqYjjnn97DpDEJf8tlNOIDx0XiXyQwh0F_81y0k,612
-toil/test/src/autoDeploymentTest.py,sha256=Oqy3j-jBeMCgu66wrxkDVUKFdqvkQ7aMj7GN6gKG7cE,23947
+toil/test/src/autoDeploymentTest.py,sha256=GSflx0XQ_gQQ8tHVouR0GJ_1oDyVYdS8gaK9tpIV9Rg,23898
 toil/test/src/busTest.py,sha256=N49fTwZFT7kTt5a-9xxoxJTjoMnjvIPwyJdmX9N7nac,5353
 toil/test/src/checkpointTest.py,sha256=LahYir7B3FNttP4OhbiYFKjxIftjTiuIXHC83xsxzNI,4464
 toil/test/src/deferredFunctionTest.py,sha256=y8AAnmmn7VYbJozukKQFE3mx-vw9O6o6oeCiGv4PkeA,13355
 toil/test/src/dockerCheckTest.py,sha256=CuXBewb1ba4rOO3YOrmChxPvdOfJGXNcT8P47HcaY1g,4407
 toil/test/src/environmentTest.py,sha256=k-WsZ3-9Xn0Vctd8tBQTPR_fVqY-f1VHC5U3_d7qdd4,4239
-toil/test/src/fileStoreTest.py,sha256=7Rh9qRGEB5nBdcerRz-7QLfq47pyfS1XQSKCOaQQS3w,73186
+toil/test/src/fileStoreTest.py,sha256=AZ9OazR5zRhUnH4eYYGiGsr8ZFcpX50ng3WGT00w0OQ,72970
 toil/test/src/helloWorldTest.py,sha256=vPxXEYDZZuMynm_yQ5ZZPcm3AzXdYLT9bs0kP72OM2w,1727
 toil/test/src/importExportFileTest.py,sha256=jqQQzQta0BH6QtxidFs8s-snpLIAS6P5y89oAU_gXAA,7974
 toil/test/src/jobDescriptionTest.py,sha256=ops9NpnUa1aKGPrTOXU3jTwiDszCRJzHHAZzQx8bF10,4335
@@ -302,10 +308,11 @@ toil/test/src/userDefinedJobArgTypeTest.py,sha256=5PaS_418DbCAk7csGmgx3VC90mB-9Y
 toil/test/src/workerTest.py,sha256=88Mz9ES62IijTkLdnzCxB3ZVEtLS2fxbIVlfhjI4SwI,6334
 toil/test/utils/__init__.py,sha256=9h1rcqYjjnn97DpDEJf8tlNOIDx0XiXyQwh0F_81y0k,612
 toil/test/utils/toilDebugTest.py,sha256=Qp3_MaTyhjQOs4WkI2J7BwRSdx-MyjjcghTnPZ-EWKA,9757
-toil/test/utils/toilKillTest.py,sha256=fuigiHip4tR4HkYiqSojkiagMGUajRFprGS2LPAOMHk,3747
+toil/test/utils/toilKillTest.py,sha256=iFApgCjKKgmeuq1FSCn04-9VJijOjmBCn-RdjlqSuKw,4136
 toil/test/utils/utilsTest.py,sha256=RuiYS5ogRz_rid2YqsRGhylpW3oGofe8ssGvUbXSBiE,22008
+toil/test/utils/ABCWorkflowDebug/ABC.txt,sha256=tdQEXD9Gb6kf4sxqvnkjKhpXzfEE96JucW4KHieJ33g,3
 toil/test/utils/ABCWorkflowDebug/B_file.txt,sha256=wM3nf6j--X1HbBCq09LVT8wvM2FA0HNlHC3Mzx43n9Y,2
-toil/test/utils/ABCWorkflowDebug/debugWorkflow.py,sha256=BdzJE1TFGnBmO7aO8sGG4Noe2CpM0rad8te9_wvAKlI,6812
+toil/test/utils/ABCWorkflowDebug/debugWorkflow.py,sha256=QF8tfoEVYdZbR7vyL43El4G_Q613zdGo_xF_m_zi7sk,6785
 toil/test/utils/ABCWorkflowDebug/mkFile.py,sha256=x0DSfKGpd-39F1X1lXHzY_CpGvFvsMFDneOJRRimDXE,454
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 toil/test/utils/ABCWorkflowDebug/sleep.yaml,sha256=9kNrGjaLOSTdsnC7zw36Em2YLueoHFdraKBLiQY3WEQ,13
@@ -313,13 +320,13 @@ toil/test/wdl/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-toil/test/wdl/wdltoil_test.py,sha256=vGaoxuY_H_s_wHzPHXrPSVMLz0Wx1KVsx1rJGwKmo8M,47907
-toil/test/wdl/wdltoil_test_kubernetes.py,sha256=MJs8w6LXISSCM3fXfBw6kCUtvNb_jM0yTsbenSWXf0s,2839
+toil/test/wdl/wdltoil_test.py,sha256=GajkwQqFCcbUYqALEpW2KIUYhVvgnCcQH_qXwfHAzh4,51302
+toil/test/wdl/wdltoil_test_kubernetes.py,sha256=vJdmSuQJslvrfF6nadjORkdanED99xElG54EC7L2rR4,2996
 toil/test/wdl/md5sum/empty_file.json,sha256=Y4Yb2dygeV8J7wowyUuTi8qOwmRR-znb70r3jsPw688,27
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 toil/test/wdl/md5sum/md5sum.1.0.wdl,sha256=BJMdlruHIRcuBLQY738T_eyHZms-8obz4-P6VxrwW30,445
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+toil/test/wdl/md5sum/md5sum.json,sha256=Qact-pZ-Bqy2016DharLO3vFhok_RiWEKtTWSn0V6oQ,39
 toil/test/wdl/md5sum/md5sum.wdl,sha256=rOMK3chqHY8TvJljL715ZDGokmN3z-eUtIzDXTFYw5w,447
 toil/test/wdl/miniwdl_self_test/inputs-namespaced.json,sha256=uUaurpDKWYaPET2tEkiIZ1ciEti_4s2_j0ZsUwiDdPo,107
 toil/test/wdl/miniwdl_self_test/inputs.json,sha256=Q_e331sBPLgqfALukm1eWxR1n5zQp2l5YRtiGpWjBW4,94
@@ -396,6 +403,7 @@ toil/test/wdl/testfiles/croo.wdl,sha256=LglQ9WjDYmMI6fsDE_CacTRMHtTRu84LX-H05IIS
 toil/test/wdl/testfiles/drop_files.wdl,sha256=6pR3s6IOIg6tvZesvF4Fh78QvzlKGz3HP3X4PUQgIWs,1929
 toil/test/wdl/testfiles/drop_files_subworkflow.wdl,sha256=Qrq7LPfQGmD8ALWUVyp3AlZ8_KcD1nqKCb5bVf9wDb4,158
 toil/test/wdl/testfiles/empty.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+toil/test/wdl/testfiles/gather.wdl,sha256=kzycmVYei6LkZkcAtCM1JD6g498bMALiO-JVjBwa3hc,637
 toil/test/wdl/testfiles/not_enough_outputs.wdl,sha256=AO3v20B5nR28MZmmKYCTiqh3hRJgg6LCENAZ2nC4IYg,438
 toil/test/wdl/testfiles/random.wdl,sha256=74vORE5a-fcQs_z73uyjUzkRqpGLv22bWmlNuvE83nw,1017
 toil/test/wdl/testfiles/read_file.wdl,sha256=9UkeiNK7QQJfzARfWfApL_zQ_7O3cTAF3_IyJfBhQJs,296
@@ -421,7 +429,7 @@ toil/test/wdl/wdl_specification/v1_spec_declaration.wdl,sha256=-9YcGU3YotQP3vn4-
 toil/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/utils/toilClean.py,sha256=X6Fws6LVqa-ScUITMTomV5iohXa3yz_rAIFnUfXlqZU,1850
 toil/utils/toilConfig.py,sha256=Ki6gGV-9d21z06u-A0meE2H0MjJUCT4mQEsMmERHn8o,1502
-toil/utils/toilDebugFile.py,sha256=HdBOe6IX6xyzGjDf_ZDxCTWaeA9lFO94UexGV1oeptE,6302
+toil/utils/toilDebugFile.py,sha256=tRlsJgfCnPCV-1w4eS9WPIBDlywIxLgxzAXeQjjqhhk,6334
 toil/utils/toilDebugJob.py,sha256=K3j5wqDBzLHRGwThE_PDVN0-yKFl7xETDWXrNe6EnQc,10796
 toil/utils/toilDestroyCluster.py,sha256=OvwlKgomHiLptN8GjLouBzfFCo-SyLfrRWF4sv0kPww,1416
 toil/utils/toilKill.py,sha256=21zOstvFb32cwQlhMsG5Q4lPT2CSnZ7OXEK1mmyLmtk,2751
@@ -430,15 +438,15 @@ toil/utils/toilMain.py,sha256=Lz7dtkpE8urTRgimRjewKvbh4Xgh6l0OJRtxX203LyI,2790
 toil/utils/toilRsyncCluster.py,sha256=cR-4o9KpoyBdObCwQgpAqpO30VK3gGzwHKOGyQHGQeQ,2150
 toil/utils/toilServer.py,sha256=4XbyOHQHgMWWrCWj9Uz1M-jLQheV2Ju-DQ_fNdnBg1o,1178
 toil/utils/toilSshCluster.py,sha256=yjNOjbtC1CdvTRK1vOygamXvlUYHnbmWtsOyH5lBNkg,3580
-toil/utils/toilStats.py,sha256=I8ERYFA0NxYDC8meBoMkxABmVfTlvYWnOBRP8BfVGEc,25615
+toil/utils/toilStats.py,sha256=k6llhv5HOolSO4yQCoMuYVwbOpauGrPiGb5jSAWYAtM,26301
 toil/utils/toilStatus.py,sha256=qacxW5lcguvmhUi1b4cjm1acJik0zpsP7CsUuZyX-fo,20424
 toil/utils/toilUpdateEC2Instances.py,sha256=47972f1_oRvKOZv77EcBr3QjP2YNl8SZWhTsw6mWG-4,1318
 toil/wdl/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/wdl/utils.py,sha256=U0TqbVTsap0VdeZjrUf4l71A7Zns-Hkso1B1Zdp2LRk,1316
-toil/wdl/wdltoil.py,sha256=Jo9b-QH9bdBAERQteLv4cwh4gE-6BXVZakNHBuwH6rg,243539
-toil-9.0.0.dist-info/licenses/LICENSE,sha256=YVxVi652J1ZDmtC3EMP5r0EbK85-hm_pzogiULmlqUA,12862
-toil-9.0.0.dist-info/METADATA,sha256=HCWcmygjuGJXxNgNKCjsY9e8FACTRcWzhEEcJNG5kfM,8695
-toil-9.0.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-toil-9.0.0.dist-info/entry_points.txt,sha256=EF2yFhV2UYuJGr-OjMkUOd3RyOCgRWQbS6XJtBJ25eM,436
-toil-9.0.0.dist-info/top_level.txt,sha256=1ydj7IXvHS9tMT5OVTSSpub6ZOaQeIn3KGCgJqaikF0,5
-toil-9.0.0.dist-info/RECORD,,
+toil/wdl/wdltoil.py,sha256=DKGkqbGjjEaXt9QrnSKDzEE3JuAMNzE_jc9cxyibk7c,265992
+toil-9.1.1.dist-info/licenses/LICENSE,sha256=YVxVi652J1ZDmtC3EMP5r0EbK85-hm_pzogiULmlqUA,12862
+toil-9.1.1.dist-info/METADATA,sha256=__E7Qc3gMoOZf0U8AWTtBXtarqwFA8e-zpegiV35-Do,8695
+toil-9.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+toil-9.1.1.dist-info/entry_points.txt,sha256=EF2yFhV2UYuJGr-OjMkUOd3RyOCgRWQbS6XJtBJ25eM,436
+toil-9.1.1.dist-info/top_level.txt,sha256=1ydj7IXvHS9tMT5OVTSSpub6ZOaQeIn3KGCgJqaikF0,5
+toil-9.1.1.dist-info/RECORD,,

toil/lib/iterables.py

@@ -1,112 +0,0 @@
-# Copyright (C) 2015-2021 Regents of the University of California
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-from collections.abc import Iterable, Iterator
-
-# 5.14.2018: copied into Toil from https://github.com/BD2KGenomics/bd2k-python-lib
-from typing import Any, TypeVar
-
-IT = TypeVar("IT")
-
-
-def flatten(iterables: Iterable[IT]) -> Iterator[IT]:
-    """Flatten an iterable, except for string elements."""
-    for it in iterables:
-        if isinstance(it, str):
-            yield it
-        else:
-            yield from it
-
-
-# noinspection PyPep8Naming
-class concat:
-    """
-    A literal iterable to combine sequence literals (lists, set) with generators or list comprehensions.
-
-    Instead of
-
-    >>> [ -1 ] + [ x * 2 for x in range( 3 ) ] + [ -1 ]
-    [-1, 0, 2, 4, -1]
-
-    you can write
-
-    >>> list( concat( -1, ( x * 2 for x in range( 3 ) ), -1 ) )
-    [-1, 0, 2, 4, -1]
-
-    This is slightly shorter (not counting the list constructor) and does not involve array
-    construction or concatenation.
-
-    Note that concat() flattens (or chains) all iterable arguments into a single
-    result iterable:
-
-    >>> list( concat( 1, range( 2, 4 ), 4 ) )
-    [1, 2, 3, 4]
-
-    It only does so one level deep. If you need to recursively flatten a data structure,
-    check out crush().
-
-    If you want to prevent that flattening for an iterable argument, wrap it in concat():
-
-    >>> list( concat( 1, concat( range( 2, 4 ) ), 4 ) )
-    [1, range(2, 4), 4]
-
-    Some more example.
-
-    >>> list( concat() ) # empty concat
-    []
-    >>> list( concat( 1 ) ) # non-iterable
-    [1]
-    >>> list( concat( concat() ) ) # empty iterable
-    []
-    >>> list( concat( concat( 1 ) ) ) # singleton iterable
-    [1]
-    >>> list( concat( 1, concat( 2 ), 3 ) ) # flattened iterable
-    [1, 2, 3]
-    >>> list( concat( 1, [2], 3 ) ) # flattened iterable
-    [1, 2, 3]
-    >>> list( concat( 1, concat( [2] ), 3 ) ) # protecting an iterable from being flattened
-    [1, [2], 3]
-    >>> list( concat( 1, concat( [2], 3 ), 4 ) ) # protection only works with a single argument
-    [1, 2, 3, 4]
-    >>> list( concat( 1, 2, concat( 3, 4 ), 5, 6 ) )
-    [1, 2, 3, 4, 5, 6]
-    >>> list( concat( 1, 2, concat( [ 3, 4 ] ), 5, 6 ) )
-    [1, 2, [3, 4], 5, 6]
-
-    Note that while strings are technically iterable, concat() does not flatten them.
-
-    >>> list( concat( 'ab' ) )
-    ['ab']
-    >>> list( concat( concat( 'ab' ) ) )
-    ['ab']
-    """
-
-    def __init__(self, *args: Any) -> None:
-        super().__init__()
-        self.args = args
-
-    def __iter__(self) -> Iterator[Any]:
-        def expand(x):
-            if isinstance(x, concat) and len(x.args) == 1:
-                i = x.args
-            elif not isinstance(x, str):
-                try:
-                    i = x.__iter__()
-                except AttributeError:
-                    i = (x,)
-            else:
-                i = x
-            return i
-
-        return flatten(map(expand, self.args))

toil/test/docs/scripts/stagingExampleFiles/in.txt

@@ -1 +0,0 @@
-Hello,