From 53c685d676f173063dc9dd0053e08dea06e8ebbc Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 7 Oct 2020 10:56:29 +0200 Subject: [PATCH 01/58] Fix db-skip-locked invocation grabbing for pool members --- lib/galaxy/web_stack/__init__.py | 5 ++++- .../test_workflow_handler_configuration.py | 22 +++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/web_stack/__init__.py b/lib/galaxy/web_stack/__init__.py index 211b190b121..ee0d90c7647 100644 --- a/lib/galaxy/web_stack/__init__.py +++ b/lib/galaxy/web_stack/__init__.py @@ -528,6 +528,9 @@ class WeblessApplicationStack(ApplicationStack): # # Disable DB_SELF if a valid pool is configured. Use DB "SKIP LOCKED" if the DB engine supports it, transaction # isolation if it doesn't, or DB_PREASSIGN if the job_config doesn't allow either. + # + # Set handler_assignment_methods_configured to True, so that pool members initialize grabbing + job_config.handler_assignment_methods_configured = True conf_class_name = job_config.__class__.__name__ remove_methods = [HANDLER_ASSIGNMENT_METHODS.DB_SELF] with self.app.model.session.connection(): @@ -547,7 +550,7 @@ class WeblessApplicationStack(ApplicationStack): for m in remove_methods: try: job_config.handler_assignment_methods.remove(m) - log.debug("%s: Removed '%s' from handler assignment methods due to use of mules", conf_class_name, m) + log.debug("%s: Removed '%s' from handler assignment methods due to use of --attach-to-pool", conf_class_name, m) except ValueError: pass if add_method not in job_config.handler_assignment_methods: diff --git a/test/integration/test_workflow_handler_configuration.py b/test/integration/test_workflow_handler_configuration.py index f6c33aeadb6..c9672cb65a4 100644 --- a/test/integration/test_workflow_handler_configuration.py +++ b/test/integration/test_workflow_handler_configuration.py @@ -42,6 +42,19 @@ WORKFLOW_HANDLER_JOB_CONFIG_TEMPLATE = string.Template(""" """) +POOL_JOB_CONFIG_TEMPLATE = string.Template(""" + + + + + + + + + + +""") + WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE = string.Template(""" @@ -220,6 +233,15 @@ class JobHandlerAsWorkflowHandlerWithDbSkipLocked(BaseWorkflowHandlerConfigurati assert self.is_app_workflow_scheduler +class JobHandlerAsWorkflowHandlerWithDbSkipLockedAttachToPool(JobHandlerAsWorkflowHandlerWithDbSkipLocked): + + @classmethod + def handle_galaxy_config_kwds(cls, config): + config["job_config_file"] = config_file(POOL_JOB_CONFIG_TEMPLATE, assign_with=cls.assign_with) + config["server_name"] = "handler0" + config["attach_to_pools"] = ["job-handlers"] + + class DefaultWorkflowHandlerIfJobHandlerOffTestCase(BaseWorkflowHandlerConfigurationTestCase): @classmethod From 4989a921e0eb8f3ba943e697de4b0359210d1667 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 7 Oct 2020 11:21:31 +0200 Subject: [PATCH 02/58] Setup invocation_grabber if handler_assignment method permits it Probably the better fix. --- lib/galaxy/jobs/handler.py | 9 ++++---- lib/galaxy/web_stack/__init__.py | 3 --- lib/galaxy/workflow/scheduling_manager.py | 25 +++++++++++------------ 3 files changed, 17 insertions(+), 20 deletions(-) diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py index 047727e993d..f27af3cfa8f 100644 --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -96,10 +96,11 @@ class ItemGrabber: HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION, HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED, } - try: - return [m for m in handler_assignment_methods if m in grabbable_methods][0] - except IndexError: - return + if handler_assignment_methods: + try: + return [m for m in handler_assignment_methods if m in grabbable_methods][0] + except IndexError: + return def grab_unhandled_items(self): """ diff --git a/lib/galaxy/web_stack/__init__.py b/lib/galaxy/web_stack/__init__.py index ee0d90c7647..77116c1fdf9 100644 --- a/lib/galaxy/web_stack/__init__.py +++ b/lib/galaxy/web_stack/__init__.py @@ -528,9 +528,6 @@ class WeblessApplicationStack(ApplicationStack): # # Disable DB_SELF if a valid pool is configured. Use DB "SKIP LOCKED" if the DB engine supports it, transaction # isolation if it doesn't, or DB_PREASSIGN if the job_config doesn't allow either. - # - # Set handler_assignment_methods_configured to True, so that pool members initialize grabbing - job_config.handler_assignment_methods_configured = True conf_class_name = job_config.__class__.__name__ remove_methods = [HANDLER_ASSIGNMENT_METHODS.DB_SELF] with self.app.model.session.connection(): diff --git a/lib/galaxy/workflow/scheduling_manager.py b/lib/galaxy/workflow/scheduling_manager.py index 031950cfba4..46764ec3815 100644 --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -267,19 +267,18 @@ class WorkflowRequestMonitor(Monitors): self.workflow_scheduling_manager = workflow_scheduling_manager self._init_monitor_thread(name="WorkflowRequestMonitor.monitor_thread", target=self.__monitor, config=app.config) self.invocation_grabber = None - if self.workflow_scheduling_manager.handler_assignment_methods_configured: - self_handler_tags = set(self.app.job_config.self_handler_tags) - self_handler_tags.add(self.workflow_scheduling_manager.default_handler_id) - handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(self.workflow_scheduling_manager.handler_assignment_methods) - if handler_assignment_method: - self.invocation_grabber = ItemGrabber( - app=app, - grab_type='WorkflowInvocation', - handler_assignment_method=handler_assignment_method, - max_grab=self.workflow_scheduling_manager.handler_max_grab, - self_handler_tags=self_handler_tags, - handler_tags=self_handler_tags, - ) + self_handler_tags = set(self.app.job_config.self_handler_tags) + self_handler_tags.add(self.workflow_scheduling_manager.default_handler_id) + handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(self.workflow_scheduling_manager.handler_assignment_methods) + if handler_assignment_method: + self.invocation_grabber = ItemGrabber( + app=app, + grab_type='WorkflowInvocation', + handler_assignment_method=handler_assignment_method, + max_grab=self.workflow_scheduling_manager.handler_max_grab, + self_handler_tags=self_handler_tags, + handler_tags=self_handler_tags, + ) def __monitor(self): to_monitor = self.workflow_scheduling_manager.active_workflow_schedulers From ea38dc655b5345dd8bb27e394ceeade3df25bace Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Mon, 28 Sep 2020 12:52:12 -0700 Subject: [PATCH 03/58] Change k8s runner to use k8s assigned uid to track jobs rather than name --- lib/galaxy/jobs/runners/kubernetes.py | 62 ++++++++------------- lib/galaxy/jobs/runners/util/pykube_util.py | 34 ++++------- 2 files changed, 34 insertions(+), 62 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index 003a32ed2f7..77aabfb2707 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -6,7 +6,6 @@ import logging import math import os import re -from time import sleep import yaml @@ -19,9 +18,11 @@ from galaxy.jobs.runners import ( from galaxy.jobs.runners.util.pykube_util import ( DEFAULT_JOB_API_VERSION, ensure_pykube, - find_job_object_by_name, + find_job_object_by_id, + find_pod_object_by_id, galaxy_instance_id, Job, + JOB_ID_LABEL, job_object_dict, Pod, produce_unique_k8s_job_name, @@ -126,36 +127,21 @@ class KubernetesJobRunner(AsynchronousJobRunner): self.__get_k8s_job_spec(ajs) ) - # Checks if job exists and is trusted, or if it needs re-creation. job = Job(self._pykube_api, k8s_job_obj) - job_exists = job.exists() - if job_exists and not self._galaxy_instance_id: - # if galaxy instance id is not set, then we don't trust matching jobs and we simply delete and - # re-create the job - log.debug("Matching job exists, but Job is not trusted, so it will be deleted and a new one created.") - job.delete() - elapsed_seconds = 0 - while job.exists(): - sleep(3) - elapsed_seconds += 3 - if elapsed_seconds > self.runner_params['k8s_timeout_seconds_job_deletion']: - log.debug( - "Timed out before k8s could delete existing untrusted job %s, not queuing associated Galaxy job." - % k8s_job_name) - return - log.debug("Waiting for job to be deleted " + k8s_job_name) - - Job(self._pykube_api, k8s_job_obj).create() - elif job_exists and self._galaxy_instance_id: - # The job exists and we trust the identifier. - log.debug("Matching job exists, but Job is trusted, so we simply use the existing one for " + k8s_job_name) - # We simply leave the k8s job to be handled later on by check_watched_item(). - else: - # Creates the Kubernetes Job if it doesn't exist. - job.create() + job.create() + job_id = job.labels.get(JOB_ID_LABEL, False) + if not job_id: + ## Recover uid label because it wasn't set + #job.labels[JOB_ID_LABEL] = job.metadata.uid + #job.update() + #job_id = job.labels.get(JOB_ID_LABEL, False) + #if not job_id: + job_wrapper.fail("Unexpected value from job runner", exception=True) + log.exception("%s not assigned by k8s to job on invocation: %s" % (JOB_ID_LABEL, job.obj)) + return # define job attributes in the AsyncronousJobState for follow-up - ajs.job_id = k8s_job_name + ajs.job_id = job_id # store runner information for tracking if Galaxy restarts job_wrapper.set_external_id(k8s_job_name) self.monitor_queue.put(ajs) @@ -399,8 +385,8 @@ class KubernetesJobRunner(AsynchronousJobRunner): def check_watched_item(self, job_state): """Checks the state of a job already submitted on k8s. Job state is an AsynchronousJobState""" - jobs = Job.objects(self._pykube_api).filter(selector="app=" + job_state.job_id, - namespace=self.runner_params['k8s_namespace']) + jobs = find_job_object_by_id(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) + if len(jobs.response['items']) == 1: job = Job(self._pykube_api, jobs.response['items'][0]) job_destination = job_state.job_wrapper.job_destination @@ -504,8 +490,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): marks the job for resubmission (resubmit logic is part of destinations). """ - pods = Pod.objects(self._pykube_api).filter(selector="app=%s" % job_state.job_id, - namespace=self.runner_params['k8s_namespace']) + pods = find_pod_object_by_id(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) if not pods.response['items']: return False @@ -520,17 +505,15 @@ class KubernetesJobRunner(AsynchronousJobRunner): """Attempts to delete a dispatched job to the k8s cluster""" job = job_wrapper.get_job() try: - name = job.job_runner_external_id - namespace = self.runner_params['k8s_namespace'] - job_to_delete = find_job_object_by_name(self._pykube_api, name, namespace) + job_to_delete = find_job_object_by_id(self._pykube_api, job.get_job_runner_external_id(), self.runner_params['k8s_namespace']) if job_to_delete: self.__cleanup_k8s_job(job_to_delete) # TODO assert whether job parallelism == 0 # assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists" - log.debug("({}/{}) Terminated at user's request".format(job.id, job.job_runner_external_id)) + log.debug("({}/{}) Terminated at user's request".format(job.id, job.get_job_runner_external_id())) except Exception as e: log.exception("({}/{}) User killed running job, but error encountered during termination: {}".format( - job.id, job.job_runner_external_id, e)) + job.id, job.get_job_runner_external_id(), e)) def recover(self, job, job_wrapper): """Recovers jobs stuck in the queued/running state when Galaxy started""" @@ -559,8 +542,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): def finish_job(self, job_state): super().finish_job(job_state) - jobs = Job.objects(self._pykube_api).filter(selector="app=" + job_state.job_id, - namespace=self.runner_params['k8s_namespace']) + jobs = find_job_object_by_id(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) if len(jobs.response['items']) != 1: log.warning("More than one job matches selector. Possible configuration error" " in job id '%s'", job_state.job_id) diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py index 8c00c75b445..8668c3d9d2d 100644 --- a/lib/galaxy/jobs/runners/util/pykube_util.py +++ b/lib/galaxy/jobs/runners/util/pykube_util.py @@ -26,6 +26,7 @@ DEFAULT_NAMESPACE = "default" INSTANCE_ID_INVALID_MESSAGE = ("Galaxy instance [%s] is either too long " "(>20 characters) or it includes non DNS " "acceptable characters, ignoring it.") +JOB_ID_LABEL = "controller-uid" def ensure_pykube(): @@ -68,24 +69,14 @@ def pull_policy(params): return None -def find_job_object_by_name(pykube_api, job_name, namespace=None): - return _find_object_by_name(Job, pykube_api, job_name, namespace=namespace) +def find_job_object_by_id(pykube_api, job_id, namespace=None): + if not job_id: + raise ValueError("job_id must not be empty") + return Job.objects(pykube_api).filter(selector=JOB_ID_LABEL + "=" + job_id, namespace=namespace) -def find_pod_object_by_name(pykube_api, pod_name, namespace=None): - return _find_object_by_name(Pod, pykube_api, pod_name, namespace=namespace) - - -def _find_object_by_name(clazz, pykube_api, object_name, namespace=None): - filter_kwd = dict(selector="app=%s" % object_name) - if namespace is not None: - filter_kwd["namespace"] = namespace - - objs = clazz.objects(pykube_api).filter(**filter_kwd) - obj = None - if len(objs.response['items']) > 0: - obj = clazz(pykube_api, objs.response['items'][0]) - return obj +def find_pod_object_by_id(pykube_api, job_id, namespace=None): + return Pod.objects(pykube_api).filter(selector=JOB_ID_LABEL + "=" + job_id, namespace=namespace) def stop_job(job, cleanup="always"): @@ -111,11 +102,9 @@ def job_object_dict(params, job_name, spec): "apiVersion": params.get('k8s_job_api_version', DEFAULT_JOB_API_VERSION), "kind": "Job", "metadata": { - # metadata.name is the name of the pod resource created, and must be unique - # http://kubernetes.io/docs/user-guide/configuring-containers/ - "name": job_name, + # labels must not be set so that the automatically generated ones are used that include controller-uid + "generateName": job_name + "-", "namespace": params.get('k8s_namespace', DEFAULT_NAMESPACE), - "labels": {"app": job_name} }, "spec": spec, } @@ -145,9 +134,10 @@ def galaxy_instance_id(params): __all__ = ( "DEFAULT_JOB_API_VERSION", + "JOB_ID_LABEL", "ensure_pykube", - "find_job_object_by_name", - "find_pod_object_by_name", + "find_job_object_by_id", + "find_pod_object_by_id", "galaxy_instance_id", "Job", "job_object_dict", From 377248f696cd8fa21c206ae1c4e01a20f540e9c3 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Tue, 6 Oct 2020 00:11:32 -0700 Subject: [PATCH 04/58] Add code to recover uid label in unlikely event k8s labelling behavior changes --- lib/galaxy/jobs/runners/kubernetes.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index 77aabfb2707..fd1a3115b19 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -131,14 +131,14 @@ class KubernetesJobRunner(AsynchronousJobRunner): job.create() job_id = job.labels.get(JOB_ID_LABEL, False) if not job_id: - ## Recover uid label because it wasn't set - #job.labels[JOB_ID_LABEL] = job.metadata.uid - #job.update() - #job_id = job.labels.get(JOB_ID_LABEL, False) - #if not job_id: - job_wrapper.fail("Unexpected value from job runner", exception=True) - log.exception("%s not assigned by k8s to job on invocation: %s" % (JOB_ID_LABEL, job.obj)) - return + # Recover uid label because it wasn't set + job.labels[JOB_ID_LABEL] = job.metadata.uid + job.update() + job_id = job.labels.get(JOB_ID_LABEL, False) + if not job_id: + job_wrapper.fail("Unexpected value from job runner", exception=True) + log.exception("%s not assigned by k8s to job on invocation: %s" % (JOB_ID_LABEL, job.obj)) + return # define job attributes in the AsyncronousJobState for follow-up ajs.job_id = job_id From 96e5aed4df7fdd911ddc0a9d1cecbdafb40ede56 Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Tue, 6 Oct 2020 19:55:42 +0530 Subject: [PATCH 05/58] Use generated job name to filter objects in k8s --- lib/galaxy/jobs/runners/kubernetes.py | 35 +++++++----------- lib/galaxy/jobs/runners/util/pykube_util.py | 40 ++++++++------------- 2 files changed, 26 insertions(+), 49 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index fd1a3115b19..a6fea745c7e 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -18,14 +18,13 @@ from galaxy.jobs.runners import ( from galaxy.jobs.runners.util.pykube_util import ( DEFAULT_JOB_API_VERSION, ensure_pykube, - find_job_object_by_id, - find_pod_object_by_id, + find_job_object_by_name, + find_pod_object_by_name, galaxy_instance_id, Job, - JOB_ID_LABEL, job_object_dict, Pod, - produce_unique_k8s_job_name, + produce_k8s_job_prefix, pull_policy, pykube_client_from_dict, stop_job, @@ -120,25 +119,16 @@ class KubernetesJobRunner(AsynchronousJobRunner): return # Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/ - k8s_job_name = self.__produce_unique_k8s_job_name(job_wrapper.get_id_tag()) + k8s_job_prefix = self.__produce_k8s_job_prefix(job_wrapper) k8s_job_obj = job_object_dict( self.runner_params, - k8s_job_name, + k8s_job_prefix, self.__get_k8s_job_spec(ajs) ) job = Job(self._pykube_api, k8s_job_obj) job.create() - job_id = job.labels.get(JOB_ID_LABEL, False) - if not job_id: - # Recover uid label because it wasn't set - job.labels[JOB_ID_LABEL] = job.metadata.uid - job.update() - job_id = job.labels.get(JOB_ID_LABEL, False) - if not job_id: - job_wrapper.fail("Unexpected value from job runner", exception=True) - log.exception("%s not assigned by k8s to job on invocation: %s" % (JOB_ID_LABEL, job.obj)) - return + job_id = job.metadata['name'] # define job attributes in the AsyncronousJobState for follow-up ajs.job_id = job_id @@ -191,8 +181,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): """Parse the ID of the Galaxy instance from runner params.""" return galaxy_instance_id(self.runner_params) - def __produce_unique_k8s_job_name(self, galaxy_internal_job_id): - # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers. + def __produce_k8s_job_prefix(self, job_wrapper): instance_id = self._galaxy_instance_id or '' return produce_unique_k8s_job_name(app_prefix='gxy', instance_id=instance_id, job_id=galaxy_internal_job_id) @@ -212,7 +201,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): (see pod selector) and an appropriate restart policy.""" k8s_spec_template = { "metadata": { - "labels": {"app": self.__produce_unique_k8s_job_name(ajs.job_wrapper.get_id_tag())[:-5]} + "labels": {"app": self.__produce_k8s_job_prefix(ajs.job_wrapper)} }, "spec": { "volumes": self.runner_params['k8s_mountable_volumes'], @@ -385,7 +374,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): def check_watched_item(self, job_state): """Checks the state of a job already submitted on k8s. Job state is an AsynchronousJobState""" - jobs = find_job_object_by_id(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) + jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) if len(jobs.response['items']) == 1: job = Job(self._pykube_api, jobs.response['items'][0]) @@ -490,7 +479,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): marks the job for resubmission (resubmit logic is part of destinations). """ - pods = find_pod_object_by_id(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) + pods = find_pod_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) if not pods.response['items']: return False @@ -505,7 +494,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): """Attempts to delete a dispatched job to the k8s cluster""" job = job_wrapper.get_job() try: - job_to_delete = find_job_object_by_id(self._pykube_api, job.get_job_runner_external_id(), self.runner_params['k8s_namespace']) + job_to_delete = find_job_object_by_name(self._pykube_api, job.get_job_runner_external_id(), self.runner_params['k8s_namespace']) if job_to_delete: self.__cleanup_k8s_job(job_to_delete) # TODO assert whether job parallelism == 0 @@ -542,7 +531,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): def finish_job(self, job_state): super().finish_job(job_state) - jobs = find_job_object_by_id(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) + jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) if len(jobs.response['items']) != 1: log.warning("More than one job matches selector. Possible configuration error" " in job id '%s'", job_state.job_id) diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py index 8668c3d9d2d..b844c50ecb6 100644 --- a/lib/galaxy/jobs/runners/util/pykube_util.py +++ b/lib/galaxy/jobs/runners/util/pykube_util.py @@ -26,7 +26,6 @@ DEFAULT_NAMESPACE = "default" INSTANCE_ID_INVALID_MESSAGE = ("Galaxy instance [%s] is either too long " "(>20 characters) or it includes non DNS " "acceptable characters, ignoring it.") -JOB_ID_LABEL = "controller-uid" def ensure_pykube(): @@ -47,18 +46,9 @@ def pykube_client_from_dict(params): return pykube_client -def produce_unique_k8s_job_name(app_prefix=None, instance_id=None, job_id=None): - if job_id is None: - job_id = str(uuid.uuid4()) - - job_name = "" - if app_prefix: - job_name += "%s-" % app_prefix - - if instance_id and len(instance_id) > 0: - job_name += "%s-" % instance_id - - return "{}{}-{}".format(job_name, job_id, uuid.uuid4())[-63:] +def produce_k8s_job_prefix(app_prefix=None, instance_id=None, job_id=None): + job_name_elems = [app_prefix or "", instance_id or "", job_id or str(uuid.uuid4())] + return '-'.join(elem for elem in job_name_elems if elem) def pull_policy(params): @@ -69,14 +59,14 @@ def pull_policy(params): return None -def find_job_object_by_id(pykube_api, job_id, namespace=None): - if not job_id: - raise ValueError("job_id must not be empty") - return Job.objects(pykube_api).filter(selector=JOB_ID_LABEL + "=" + job_id, namespace=namespace) +def find_job_object_by_name(pykube_api, job_name, namespace=None): + if not job_name: + raise ValueError("job name must not be empty") + return Job.objects(pykube_api).filter(field_selector={"metadata.name": job_name}, namespace=namespace) -def find_pod_object_by_id(pykube_api, job_id, namespace=None): - return Pod.objects(pykube_api).filter(selector=JOB_ID_LABEL + "=" + job_id, namespace=namespace) +def find_pod_object_by_name(pykube_api, job_name, namespace=None): + return Pod.objects(pykube_api).filter(selector="job-name=" + job_name, namespace=namespace) def stop_job(job, cleanup="always"): @@ -97,13 +87,12 @@ def stop_job(job, cleanup="always"): job.api.raise_for_status(r) -def job_object_dict(params, job_name, spec): +def job_object_dict(params, job_prefix, spec): k8s_job_obj = { "apiVersion": params.get('k8s_job_api_version', DEFAULT_JOB_API_VERSION), "kind": "Job", "metadata": { - # labels must not be set so that the automatically generated ones are used that include controller-uid - "generateName": job_name + "-", + "generateName": job_prefix + "-", "namespace": params.get('k8s_namespace', DEFAULT_NAMESPACE), }, "spec": spec, @@ -134,15 +123,14 @@ def galaxy_instance_id(params): __all__ = ( "DEFAULT_JOB_API_VERSION", - "JOB_ID_LABEL", "ensure_pykube", - "find_job_object_by_id", - "find_pod_object_by_id", + "find_job_object_by_name", + "find_pod_object_by_name", "galaxy_instance_id", "Job", "job_object_dict", "Pod", - "produce_unique_k8s_job_name", + "produce_k8s_job_prefix", "pull_policy", "pykube_client_from_dict", "stop_job", From 56a71c7437559473f18a99d5858fae12219884be Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Wed, 7 Oct 2020 14:26:25 +0530 Subject: [PATCH 06/58] Improve handling of empty pvcs and fix job deletion --- lib/galaxy/jobs/runners/kubernetes.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index a6fea745c7e..bc0868b5443 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -87,7 +87,10 @@ class KubernetesJobRunner(AsynchronousJobRunner): self.setup_volumes() def setup_volumes(self): - volume_claims = dict(volume.split(":") for volume in self.runner_params['k8s_persistent_volume_claims'].split(',')) + if self.runner_params.get('k8s_persistent_volume_claims'): + volume_claims = dict(volume.split(":") for volume in self.runner_params['k8s_persistent_volume_claims'].split(',')) + else: + volume_claims = {} mountable_volumes = [{'name': claim_name, 'persistentVolumeClaim': {'claimName': claim_name}} for claim_name in volume_claims] self.runner_params['k8s_mountable_volumes'] = mountable_volumes volume_mounts = [{'name': claim_name, 'mountPath': mount_path} for claim_name, mount_path in volume_claims.items()] @@ -495,8 +498,9 @@ class KubernetesJobRunner(AsynchronousJobRunner): job = job_wrapper.get_job() try: job_to_delete = find_job_object_by_name(self._pykube_api, job.get_job_runner_external_id(), self.runner_params['k8s_namespace']) - if job_to_delete: - self.__cleanup_k8s_job(job_to_delete) + if job_to_delete and len(job_to_delete.response['items']) > 0: + k8s_job = Job(self._pykube_api, job_to_delete.response['items'][0]) + self.__cleanup_k8s_job(k8s_job) # TODO assert whether job parallelism == 0 # assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists" log.debug("({}/{}) Terminated at user's request".format(job.id, job.get_job_runner_external_id())) From 06d2830a4be22e81911cf95321d97eeef2a69c21 Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Wed, 14 Oct 2020 00:44:20 +0530 Subject: [PATCH 07/58] Fix incorrect variable references in k8s runner --- lib/galaxy/jobs/runners/kubernetes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index bc0868b5443..e2fdfd9b477 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -136,7 +136,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): # define job attributes in the AsyncronousJobState for follow-up ajs.job_id = job_id # store runner information for tracking if Galaxy restarts - job_wrapper.set_external_id(k8s_job_name) + job_wrapper.set_external_id(job_id) self.monitor_queue.put(ajs) def __get_pull_policy(self): From 016e231f2daf62f8c0d6a43cae73ef23f1283cc9 Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Wed, 14 Oct 2020 09:24:39 +0530 Subject: [PATCH 08/58] Remove job_id from k8s job prefix --- lib/galaxy/jobs/runners/kubernetes.py | 2 +- lib/galaxy/jobs/runners/util/pykube_util.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index e2fdfd9b477..c8121ae7dcc 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -186,7 +186,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): def __produce_k8s_job_prefix(self, job_wrapper): instance_id = self._galaxy_instance_id or '' - return produce_unique_k8s_job_name(app_prefix='gxy', instance_id=instance_id, job_id=galaxy_internal_job_id) + return produce_k8s_job_prefix(app_prefix='gxy', instance_id=instance_id) def __get_k8s_job_spec(self, ajs): """Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template. diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py index b844c50ecb6..1c2c482f74a 100644 --- a/lib/galaxy/jobs/runners/util/pykube_util.py +++ b/lib/galaxy/jobs/runners/util/pykube_util.py @@ -46,8 +46,8 @@ def pykube_client_from_dict(params): return pykube_client -def produce_k8s_job_prefix(app_prefix=None, instance_id=None, job_id=None): - job_name_elems = [app_prefix or "", instance_id or "", job_id or str(uuid.uuid4())] +def produce_k8s_job_prefix(app_prefix=None, instance_id=None): + job_name_elems = [app_prefix or "", instance_id or ""] return '-'.join(elem for elem in job_name_elems if elem) From 0fe859911969ee163e60bd7f911e9f592cbe05ff Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 14 Oct 2020 10:02:49 +0200 Subject: [PATCH 09/58] Drop unused import --- lib/galaxy/jobs/runners/util/pykube_util.py | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/galaxy/jobs/runners/util/pykube_util.py b/lib/galaxy/jobs/runners/util/pykube_util.py index 1c2c482f74a..bee2ae3920a 100644 --- a/lib/galaxy/jobs/runners/util/pykube_util.py +++ b/lib/galaxy/jobs/runners/util/pykube_util.py @@ -2,7 +2,6 @@ import logging import os import re -import uuid try: from pykube.config import KubeConfig From 7b837f5fea1590c4a38b078300aaca7c8a9112fe Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Wed, 7 Oct 2020 08:55:11 -0700 Subject: [PATCH 10/58] Add k8s recommended labels --- lib/galaxy/jobs/runners/kubernetes.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index c8121ae7dcc..755b9ee28d2 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -204,7 +204,14 @@ class KubernetesJobRunner(AsynchronousJobRunner): (see pod selector) and an appropriate restart policy.""" k8s_spec_template = { "metadata": { - "labels": {"app": self.__produce_k8s_job_prefix(ajs.job_wrapper)} + "labels": { + "app.kubernetes.io/name": ajs.tool_wrapper.tool.id, + "app.kubernetes.io/instance": self.__produce_k8s_job_prefix(ajs.job_wrapper), + "app.kubernetes.io/version": ajs.tool_wrapper.tool.version, + "app.kubernetes.io/component": "tool", + "app.kubernetes.io/part-of": self._galaxy_instance_id or "galaxy", + "app.kubernetes.io/managed-by": "galaxy", + } }, "spec": { "volumes": self.runner_params['k8s_mountable_volumes'], From aa1b306cc41b2e54f286ce6537ff2075837a2588 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Wed, 7 Oct 2020 09:13:22 -0700 Subject: [PATCH 11/58] Add more labels and refine --- lib/galaxy/jobs/runners/kubernetes.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index 755b9ee28d2..a67afd02cdf 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -209,8 +209,11 @@ class KubernetesJobRunner(AsynchronousJobRunner): "app.kubernetes.io/instance": self.__produce_k8s_job_prefix(ajs.job_wrapper), "app.kubernetes.io/version": ajs.tool_wrapper.tool.version, "app.kubernetes.io/component": "tool", - "app.kubernetes.io/part-of": self._galaxy_instance_id or "galaxy", + "app.kubernetes.io/part-of": "galaxy", "app.kubernetes.io/managed-by": "galaxy", + "app.galaxy.org/job_id": ajs.job_wrapper.get_id_tag(), + "app.galaxy.org/instance": self._galaxy_instance_id or "", + "app.galaxy.org/handler": self.app.config.server_name, } }, "spec": { From 3379ea699bf3240b6009d9500493e7c6cd9317f5 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Wed, 7 Oct 2020 09:18:18 -0700 Subject: [PATCH 12/58] Fix galaxy domain name --- lib/galaxy/jobs/runners/kubernetes.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index a67afd02cdf..d9e3ab5f95b 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -211,9 +211,9 @@ class KubernetesJobRunner(AsynchronousJobRunner): "app.kubernetes.io/component": "tool", "app.kubernetes.io/part-of": "galaxy", "app.kubernetes.io/managed-by": "galaxy", - "app.galaxy.org/job_id": ajs.job_wrapper.get_id_tag(), - "app.galaxy.org/instance": self._galaxy_instance_id or "", - "app.galaxy.org/handler": self.app.config.server_name, + "app.galaxyproject.org/job_id": ajs.job_wrapper.get_id_tag(), + "app.galaxyproject.org/instance": self._galaxy_instance_id or "", + "app.galaxyproject.org/handler": self.app.config.server_name, } }, "spec": { From f2848748da8379b916c9d5ff89f0c3c8e2d251ee Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Wed, 7 Oct 2020 11:26:25 -0700 Subject: [PATCH 13/58] Add destination_id to labels --- lib/galaxy/jobs/runners/kubernetes.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index d9e3ab5f95b..b7bae723400 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -214,6 +214,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): "app.galaxyproject.org/job_id": ajs.job_wrapper.get_id_tag(), "app.galaxyproject.org/instance": self._galaxy_instance_id or "", "app.galaxyproject.org/handler": self.app.config.server_name, + "app.galaxyproject.org/destination": ajs.job_wrapper.job_destination.id, } }, "spec": { From 75c25950b24815c51a62f5635350bc99167ceb08 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Tue, 13 Oct 2020 14:11:32 -0700 Subject: [PATCH 14/58] Move full tool id label to annotation as it is not valid label. Fix var ref. --- lib/galaxy/jobs/runners/kubernetes.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index b7bae723400..db365e9437c 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -205,9 +205,9 @@ class KubernetesJobRunner(AsynchronousJobRunner): k8s_spec_template = { "metadata": { "labels": { - "app.kubernetes.io/name": ajs.tool_wrapper.tool.id, - "app.kubernetes.io/instance": self.__produce_k8s_job_prefix(ajs.job_wrapper), - "app.kubernetes.io/version": ajs.tool_wrapper.tool.version, + "app.kubernetes.io/name": ajs.job_wrapper.tool.tool_id, + "app.kubernetes.io/instance": self.__produce_unique_k8s_job_name(ajs.job_wrapper.get_id_tag()), + "app.kubernetes.io/version": ajs.job_wrapper.tool.version, "app.kubernetes.io/component": "tool", "app.kubernetes.io/part-of": "galaxy", "app.kubernetes.io/managed-by": "galaxy", @@ -215,6 +215,9 @@ class KubernetesJobRunner(AsynchronousJobRunner): "app.galaxyproject.org/instance": self._galaxy_instance_id or "", "app.galaxyproject.org/handler": self.app.config.server_name, "app.galaxyproject.org/destination": ajs.job_wrapper.job_destination.id, + }, + "annotations": { + "app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id, } }, "spec": { From 4d3db19c9cc70e0b68c3547d426651704b73d33d Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Wed, 14 Oct 2020 13:55:15 +0530 Subject: [PATCH 15/58] Remove unused variable and fix references --- lib/galaxy/jobs/runners/kubernetes.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index db365e9437c..b5436d93da5 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -122,7 +122,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): return # Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/ - k8s_job_prefix = self.__produce_k8s_job_prefix(job_wrapper) + k8s_job_prefix = self.__produce_k8s_job_prefix() k8s_job_obj = job_object_dict( self.runner_params, k8s_job_prefix, @@ -184,7 +184,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): """Parse the ID of the Galaxy instance from runner params.""" return galaxy_instance_id(self.runner_params) - def __produce_k8s_job_prefix(self, job_wrapper): + def __produce_k8s_job_prefix(self): instance_id = self._galaxy_instance_id or '' return produce_k8s_job_prefix(app_prefix='gxy', instance_id=instance_id) @@ -206,7 +206,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): "metadata": { "labels": { "app.kubernetes.io/name": ajs.job_wrapper.tool.tool_id, - "app.kubernetes.io/instance": self.__produce_unique_k8s_job_name(ajs.job_wrapper.get_id_tag()), + "app.kubernetes.io/instance": self.__produce_k8s_job_prefix(), "app.kubernetes.io/version": ajs.job_wrapper.tool.version, "app.kubernetes.io/component": "tool", "app.kubernetes.io/part-of": "galaxy", From 204fe1d21db55571e54e953e10446e6bb66572cb Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Wed, 14 Oct 2020 11:03:00 +0200 Subject: [PATCH 16/58] Use ajs.job_wrapper.tool.id tool_id is not a valid attributes of a Tool instance --- lib/galaxy/jobs/runners/kubernetes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index b5436d93da5..08cf307947f 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -205,7 +205,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): k8s_spec_template = { "metadata": { "labels": { - "app.kubernetes.io/name": ajs.job_wrapper.tool.tool_id, + "app.kubernetes.io/name": ajs.job_wrapper.tool.id, "app.kubernetes.io/instance": self.__produce_k8s_job_prefix(), "app.kubernetes.io/version": ajs.job_wrapper.tool.version, "app.kubernetes.io/component": "tool", From 1869d948b9a2322b765805e6b0fb277e0f474d84 Mon Sep 17 00:00:00 2001 From: Nolan Woods Date: Wed, 14 Oct 2020 10:59:55 -0700 Subject: [PATCH 17/58] Use old_id instead of id --- lib/galaxy/jobs/runners/kubernetes.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index 08cf307947f..f2b5e556152 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -205,7 +205,7 @@ class KubernetesJobRunner(AsynchronousJobRunner): k8s_spec_template = { "metadata": { "labels": { - "app.kubernetes.io/name": ajs.job_wrapper.tool.id, + "app.kubernetes.io/name": ajs.job_wrapper.tool.old_id, "app.kubernetes.io/instance": self.__produce_k8s_job_prefix(), "app.kubernetes.io/version": ajs.job_wrapper.tool.version, "app.kubernetes.io/component": "tool", From 55a8aba55819e9694d2c5f748e89817f32defb61 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 11:49:24 -0400 Subject: [PATCH 18/58] Version 20.9.0 of util (tag galaxy-util-20.9.0). --- packages/util/HISTORY.rst | 2 +- packages/util/galaxy/project_galaxy_util.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index 2816300aea2..ca446f4a6bb 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.5.1 (2020-10-15) --------------------- diff --git a/packages/util/galaxy/project_galaxy_util.py b/packages/util/galaxy/project_galaxy_util.py index dd0d57feb07..a95e19b5a59 100644 --- a/packages/util/galaxy/project_galaxy_util.py +++ b/packages/util/galaxy/project_galaxy_util.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-util" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From ca4831d0d183ab741e4bcb4dfdbd1bcf25365884 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 11:50:17 -0400 Subject: [PATCH 19/58] Starting work on util 20.9.1 --- packages/util/HISTORY.rst | 6 ++++++ packages/util/galaxy/project_galaxy_util.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index ca446f4a6bb..8af37d22a72 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.5.1 (2020-10-15) --------------------- diff --git a/packages/util/galaxy/project_galaxy_util.py b/packages/util/galaxy/project_galaxy_util.py index a95e19b5a59..f70e4153805 100644 --- a/packages/util/galaxy/project_galaxy_util.py +++ b/packages/util/galaxy/project_galaxy_util.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-util" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 82a807ee1747c9bf3f694c648d3548d1d201382c Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 11:53:11 -0400 Subject: [PATCH 20/58] Prepare first release of galaxy-selenium package. --- packages/selenium/HISTORY.rst | 4 ++-- packages/selenium/galaxy/project_galaxy_selenium.py | 2 +- packages/util/HISTORY.rst | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 72090ac4c88..03e6b93bb36 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/selenium/galaxy/project_galaxy_selenium.py b/packages/selenium/galaxy/project_galaxy_selenium.py index 8682a60d8ee..228f659f9f8 100644 --- a/packages/selenium/galaxy/project_galaxy_selenium.py +++ b/packages/selenium/galaxy/project_galaxy_selenium.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-selenium" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index 8af37d22a72..f1ec00b6172 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -12,10 +12,10 @@ History --------------------- -20.5.1 (2020-10-15) +20.9.0 (2020-10-15) --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-03) From 593d61dbb2da57c1f3d7392bedce66fc52818b03 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 11:53:57 -0400 Subject: [PATCH 21/58] Version 20.9.0 of selenium (tag galaxy-selenium-20.9.0). --- packages/selenium/HISTORY.rst | 2 +- packages/selenium/galaxy/project_galaxy_selenium.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 03e6b93bb36..f69ace2191a 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/selenium/galaxy/project_galaxy_selenium.py b/packages/selenium/galaxy/project_galaxy_selenium.py index 228f659f9f8..eec4cc1971a 100644 --- a/packages/selenium/galaxy/project_galaxy_selenium.py +++ b/packages/selenium/galaxy/project_galaxy_selenium.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-selenium" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 87a566e8c74c64b048242779cebee66ec89c8b95 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 11:54:13 -0400 Subject: [PATCH 22/58] Starting work on selenium 20.9.1 --- packages/selenium/HISTORY.rst | 6 ++++++ packages/selenium/galaxy/project_galaxy_selenium.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index f69ace2191a..47e0dd9ab2c 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/selenium/galaxy/project_galaxy_selenium.py b/packages/selenium/galaxy/project_galaxy_selenium.py index eec4cc1971a..da0a5600b20 100644 --- a/packages/selenium/galaxy/project_galaxy_selenium.py +++ b/packages/selenium/galaxy/project_galaxy_selenium.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-selenium" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 7c9b123a6f01d52d95b01ec4a4785eba65e24854 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 11:55:31 -0400 Subject: [PATCH 23/58] Prep release of galaxy-objectstore 20.9.0. --- packages/objectstore/HISTORY.rst | 4 ++-- packages/objectstore/galaxy/project_galaxy_objectstore.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 7879816905a..040cfe067ee 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py index cc83b9e9564..07ff9659b18 100644 --- a/packages/objectstore/galaxy/project_galaxy_objectstore.py +++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-objectstore" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From f5b0d2b10961c7ed4248002394267e6b0ecb942e Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 11:55:51 -0400 Subject: [PATCH 24/58] Version 20.9.0 of objectstore (tag galaxy-objectstore-20.9.0). --- packages/objectstore/HISTORY.rst | 2 +- packages/objectstore/galaxy/project_galaxy_objectstore.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 040cfe067ee..08f5f139c36 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py index 07ff9659b18..7501a05e22c 100644 --- a/packages/objectstore/galaxy/project_galaxy_objectstore.py +++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-objectstore" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From c31a2745f68cf3eade9b33b21df1bcb3f44d5269 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 11:56:04 -0400 Subject: [PATCH 25/58] Starting work on objectstore 20.9.1 --- packages/objectstore/HISTORY.rst | 6 ++++++ packages/objectstore/galaxy/project_galaxy_objectstore.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 08f5f139c36..08c9654f4a5 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py index 7501a05e22c..0ff5f53bfcf 100644 --- a/packages/objectstore/galaxy/project_galaxy_objectstore.py +++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-objectstore" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 8f10728629dfff66271208553471f1d90564c9d8 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:04:17 -0400 Subject: [PATCH 26/58] Version 20.9.0 of tool-util (tag galaxy-tool-util-20.9.0). --- packages/tool_util/HISTORY.rst | 1 + packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 6969c9bae0b..e89cfb0c2f1 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -9,6 +9,7 @@ History 20.9.0.dev2 --------------------- +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py index bcb85b77313..babbca309bb 100644 --- a/packages/tool_util/galaxy/project_galaxy_tool_util.py +++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev3' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-tool-util" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 8edc8f6c11ce2ab64435ac1ea5a4e2185aa05732 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:04:37 -0400 Subject: [PATCH 27/58] Starting work on tool-util 20.9.1 --- packages/tool_util/HISTORY.rst | 6 ++++++ packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index e89cfb0c2f1..c4d31a3e8bb 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0.dev2 --------------------- diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py index babbca309bb..39e55909cc8 100644 --- a/packages/tool_util/galaxy/project_galaxy_tool_util.py +++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-tool-util" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From b8f96b1aea5391a8dc8a67e5d94a92ee10e8dda7 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:07:58 -0400 Subject: [PATCH 28/58] Prep 20.9.0 release of galaxy-data. --- packages/data/HISTORY.rst | 4 ++-- packages/data/galaxy/project_galaxy_data.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 4f7ba0c7b9d..deb0190eca3 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py index 25e11b314df..679e00b715d 100644 --- a/packages/data/galaxy/project_galaxy_data.py +++ b/packages/data/galaxy/project_galaxy_data.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-data" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From aa6028421bfb310133eae6c118dc8d4822a42560 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:08:30 -0400 Subject: [PATCH 29/58] Version 20.9.0 of data (tag galaxy-data-20.9.0). --- packages/data/HISTORY.rst | 2 +- packages/data/galaxy/project_galaxy_data.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index deb0190eca3..7ee2b5ffd88 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py index 679e00b715d..26317963dba 100644 --- a/packages/data/galaxy/project_galaxy_data.py +++ b/packages/data/galaxy/project_galaxy_data.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-data" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From be2aa9274a176aeb2d5d9e36ad7687854fea7e4d Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:09:04 -0400 Subject: [PATCH 30/58] Starting work on data 20.9.1 --- packages/data/HISTORY.rst | 6 ++++++ packages/data/galaxy/project_galaxy_data.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 7ee2b5ffd88..243f3eeb0c4 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py index 26317963dba..35bc7ed8335 100644 --- a/packages/data/galaxy/project_galaxy_data.py +++ b/packages/data/galaxy/project_galaxy_data.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-data" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 7c6923d3ed7b4f8f1045d105e95a0fe89f465d3d Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:13:10 -0400 Subject: [PATCH 31/58] Prep release of job metrics for 20.09. --- packages/job_metrics/HISTORY.rst | 4 ++-- packages/job_metrics/galaxy/project_galaxy_job_metrics.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 7879816905a..040cfe067ee 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py index 1b7831b5354..3276059edc2 100644 --- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py +++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-job-metrics" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 8f68a210cae549d89c4d2f2041779594f0e4c1b1 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:13:25 -0400 Subject: [PATCH 32/58] Version 20.9.0 of job-metrics (tag galaxy-job-metrics-20.9.0). --- packages/job_metrics/HISTORY.rst | 2 +- packages/job_metrics/galaxy/project_galaxy_job_metrics.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 040cfe067ee..08f5f139c36 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py index 3276059edc2..109e4488def 100644 --- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py +++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-job-metrics" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 82de4aed5b7f5a097061fab6d7f408358ed0ab62 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:13:40 -0400 Subject: [PATCH 33/58] Starting work on job-metrics 20.9.1 --- packages/job_metrics/HISTORY.rst | 6 ++++++ packages/job_metrics/galaxy/project_galaxy_job_metrics.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 08f5f139c36..08c9654f4a5 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py index 109e4488def..73b7d0bf1b6 100644 --- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py +++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-job-metrics" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 472395821e23b0f138e985425ad0984a03e3f5bf Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:15:00 -0400 Subject: [PATCH 34/58] Prep the next release of galaxy-web-framework. --- packages/web_framework/HISTORY.rst | 4 ++-- packages/web_framework/galaxy/project_galaxy_web_framework.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index 72090ac4c88..03e6b93bb36 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py index 79a5de41962..c48ce2f1d2d 100644 --- a/packages/web_framework/galaxy/project_galaxy_web_framework.py +++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-web-framework" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 74eca3c953c6c99c3a5ccdc780c0ea273a5c305e Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:15:17 -0400 Subject: [PATCH 35/58] Version 20.9.0 of web-framework (tag galaxy-web-framework-20.9.0). --- packages/web_framework/HISTORY.rst | 2 +- packages/web_framework/galaxy/project_galaxy_web_framework.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index 03e6b93bb36..f69ace2191a 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py index c48ce2f1d2d..cc6b4100896 100644 --- a/packages/web_framework/galaxy/project_galaxy_web_framework.py +++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-web-framework" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 80e1af9bc339c88d560086528a09d5761954e6e2 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:15:30 -0400 Subject: [PATCH 36/58] Starting work on web-framework 20.9.1 --- packages/web_framework/HISTORY.rst | 6 ++++++ .../web_framework/galaxy/project_galaxy_web_framework.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index f69ace2191a..47e0dd9ab2c 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py index cc6b4100896..b04c269331f 100644 --- a/packages/web_framework/galaxy/project_galaxy_web_framework.py +++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-web-framework" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From fe87facf9e104bd8a7dec8175627e99be75fedd4 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:16:48 -0400 Subject: [PATCH 37/58] Prep release of galaxy-job-execution. --- packages/job_execution/HISTORY.rst | 4 ++-- packages/job_execution/galaxy/project_galaxy_job_execution.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 72090ac4c88..03e6b93bb36 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py index c88e1f230ac..779f7ef4a78 100644 --- a/packages/job_execution/galaxy/project_galaxy_job_execution.py +++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-job-execution" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From a29ebebbba45fdcdcd66b17ea0fdf052ee31904d Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:17:01 -0400 Subject: [PATCH 38/58] Version 20.9.0 of job-execution (tag galaxy-job-execution-20.9.0). --- packages/job_execution/HISTORY.rst | 2 +- packages/job_execution/galaxy/project_galaxy_job_execution.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 03e6b93bb36..f69ace2191a 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py index 779f7ef4a78..a78799c83ac 100644 --- a/packages/job_execution/galaxy/project_galaxy_job_execution.py +++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-job-execution" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 7326a92a647664da6ac61ee0c113ef513d218e08 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:17:13 -0400 Subject: [PATCH 39/58] Starting work on job-execution 20.9.1 --- packages/job_execution/HISTORY.rst | 6 ++++++ .../job_execution/galaxy/project_galaxy_job_execution.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index f69ace2191a..47e0dd9ab2c 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py index a78799c83ac..a1e0b67e8e2 100644 --- a/packages/job_execution/galaxy/project_galaxy_job_execution.py +++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-job-execution" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 99398aff4f5eab8c83963526c9ce33df6f864116 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:18:48 -0400 Subject: [PATCH 40/58] Prep next release of galaxy-auth. --- packages/auth/HISTORY.rst | 4 ++-- packages/auth/galaxy/project_galaxy_auth.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index 72090ac4c88..03e6b93bb36 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py index a15658b18cb..9c7e602fbbc 100644 --- a/packages/auth/galaxy/project_galaxy_auth.py +++ b/packages/auth/galaxy/project_galaxy_auth.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-auth" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From b974a018c1e19698697af6c905b3637149e3e714 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:19:00 -0400 Subject: [PATCH 41/58] Version 20.9.0 of auth (tag galaxy-auth-20.9.0). --- packages/auth/HISTORY.rst | 2 +- packages/auth/galaxy/project_galaxy_auth.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index 03e6b93bb36..f69ace2191a 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py index 9c7e602fbbc..d9099c872fc 100644 --- a/packages/auth/galaxy/project_galaxy_auth.py +++ b/packages/auth/galaxy/project_galaxy_auth.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-auth" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From b6a3c2fe87f634e9fdbd1ba961ec6342e8eff83e Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:19:13 -0400 Subject: [PATCH 42/58] Starting work on auth 20.9.1 --- packages/auth/HISTORY.rst | 6 ++++++ packages/auth/galaxy/project_galaxy_auth.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index f69ace2191a..47e0dd9ab2c 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py index d9099c872fc..e92f5030833 100644 --- a/packages/auth/galaxy/project_galaxy_auth.py +++ b/packages/auth/galaxy/project_galaxy_auth.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-auth" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 6544ce579949b5fd892a1aa74cb94be9656d71aa Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:20:27 -0400 Subject: [PATCH 43/58] Prepare next release of galaxy-app. --- packages/app/HISTORY.rst | 4 ++-- packages/app/galaxy/project_galaxy_app.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index 72090ac4c88..03e6b93bb36 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py index 61a6ae88785..a1d9ce5ef84 100644 --- a/packages/app/galaxy/project_galaxy_app.py +++ b/packages/app/galaxy/project_galaxy_app.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-app" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From ee01836e84d82f2da43dd001922d433e860769e5 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:21:04 -0400 Subject: [PATCH 44/58] Version 20.9.0 of app (tag galaxy-app-20.9.0). --- packages/app/HISTORY.rst | 2 +- packages/app/galaxy/project_galaxy_app.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index 03e6b93bb36..f69ace2191a 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py index a1d9ce5ef84..05f82135772 100644 --- a/packages/app/galaxy/project_galaxy_app.py +++ b/packages/app/galaxy/project_galaxy_app.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-app" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From cf34b35f5570f0d1998206519dc7edc4fc1a1fc6 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:21:20 -0400 Subject: [PATCH 45/58] Starting work on app 20.9.1 --- packages/app/HISTORY.rst | 6 ++++++ packages/app/galaxy/project_galaxy_app.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index f69ace2191a..47e0dd9ab2c 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py index 05f82135772..c596495f381 100644 --- a/packages/app/galaxy/project_galaxy_app.py +++ b/packages/app/galaxy/project_galaxy_app.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-app" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From c2d76372afea7f619a4bf9a062758433e18c9120 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:23:19 -0400 Subject: [PATCH 46/58] Prep next release of galaxy-test-base. --- packages/test_base/HISTORY.rst | 4 ++-- packages/test_base/galaxy/project_galaxy_test_base.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index b8a2e6045e6..fbefceda0e7 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* Initial release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/test_base/galaxy/project_galaxy_test_base.py b/packages/test_base/galaxy/project_galaxy_test_base.py index d2ae57543f9..7d0dc677435 100644 --- a/packages/test_base/galaxy/project_galaxy_test_base.py +++ b/packages/test_base/galaxy/project_galaxy_test_base.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-test-base" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From f546e5097a383d8e029150c833562bf26d744303 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:23:35 -0400 Subject: [PATCH 47/58] Version 20.9.0 of test-base (tag galaxy-test-base-20.9.0). --- packages/test_base/HISTORY.rst | 2 +- packages/test_base/galaxy/project_galaxy_test_base.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index fbefceda0e7..9a1b46a519c 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * Initial release from the 20.09 branch of Galaxy. diff --git a/packages/test_base/galaxy/project_galaxy_test_base.py b/packages/test_base/galaxy/project_galaxy_test_base.py index 7d0dc677435..58d86925dcf 100644 --- a/packages/test_base/galaxy/project_galaxy_test_base.py +++ b/packages/test_base/galaxy/project_galaxy_test_base.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-test-base" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From d79324f5bffc8575988c72f6b92f8ef5b8fbd214 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:23:48 -0400 Subject: [PATCH 48/58] Starting work on test-base 20.9.1 --- packages/test_base/HISTORY.rst | 6 ++++++ packages/test_base/galaxy/project_galaxy_test_base.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 9a1b46a519c..bd4cac54775 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/test_base/galaxy/project_galaxy_test_base.py b/packages/test_base/galaxy/project_galaxy_test_base.py index 58d86925dcf..0517aeb43e8 100644 --- a/packages/test_base/galaxy/project_galaxy_test_base.py +++ b/packages/test_base/galaxy/project_galaxy_test_base.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-test-base" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 5471d5fac005e64639b98cbd0211481d5ec6e71a Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:28:56 -0400 Subject: [PATCH 49/58] Prep release of galaxy-test-api. --- packages/test_api/HISTORY.rst | 5 +++-- packages/test_api/galaxy/project_galaxy_test_api.py | 2 +- packages/test_api/requirements.txt | 3 +-- packages/test_selenium/requirements.txt | 5 ++--- 4 files changed, 7 insertions(+), 8 deletions(-) diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 7cb67f838f8..fc6d5bb6cbf 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -6,7 +6,8 @@ History .. to_doc --------------------- -20.1.0.dev0 +20.9.0.dev0 --------------------- -* Initial import from dev branch of Galaxy during 20.01 development cycle. +* Initial import from dev branch of Galaxy during 20.09 branch of Galaxy. + diff --git a/packages/test_api/galaxy/project_galaxy_test_api.py b/packages/test_api/galaxy/project_galaxy_test_api.py index eb9c6e2d8eb..d16e186532b 100644 --- a/packages/test_api/galaxy/project_galaxy_test_api.py +++ b/packages/test_api/galaxy/project_galaxy_test_api.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.1.0.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-test-api" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" diff --git a/packages/test_api/requirements.txt b/packages/test_api/requirements.txt index e548169079b..735bffa9c07 100644 --- a/packages/test_api/requirements.txt +++ b/packages/test_api/requirements.txt @@ -1,2 +1 @@ -galaxy-test-driver - +galaxy-test-base diff --git a/packages/test_selenium/requirements.txt b/packages/test_selenium/requirements.txt index e8566b22706..95f090dd641 100644 --- a/packages/test_selenium/requirements.txt +++ b/packages/test_selenium/requirements.txt @@ -1,4 +1,3 @@ -galaxy-data -nose -pytest +galaxy-test-base + From f49308317336cfa24c49d5c52b2544248b039628 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:29:22 -0400 Subject: [PATCH 50/58] Version 20.9.0 of test-api (tag galaxy-test-api-20.9.0). --- packages/test_api/HISTORY.rst | 2 +- packages/test_api/galaxy/project_galaxy_test_api.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index fc6d5bb6cbf..7b70fb0084b 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * Initial import from dev branch of Galaxy during 20.09 branch of Galaxy. diff --git a/packages/test_api/galaxy/project_galaxy_test_api.py b/packages/test_api/galaxy/project_galaxy_test_api.py index d16e186532b..380526982a0 100644 --- a/packages/test_api/galaxy/project_galaxy_test_api.py +++ b/packages/test_api/galaxy/project_galaxy_test_api.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-test-api" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From dc34d270292ab80bd1fcff4eb82205c0b37da0b7 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:29:38 -0400 Subject: [PATCH 51/58] Starting work on test-api 20.9.1 --- packages/test_api/HISTORY.rst | 6 ++++++ packages/test_api/galaxy/project_galaxy_test_api.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 7b70fb0084b..3647c319467 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/test_api/galaxy/project_galaxy_test_api.py b/packages/test_api/galaxy/project_galaxy_test_api.py index 380526982a0..2a6a0c9accd 100644 --- a/packages/test_api/galaxy/project_galaxy_test_api.py +++ b/packages/test_api/galaxy/project_galaxy_test_api.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-test-api" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 803e9e19ad0eca3961fba70132459fbb2266d9f4 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:31:39 -0400 Subject: [PATCH 52/58] Prep release of galaxy-test-selenium. --- packages/test_selenium/HISTORY.rst | 4 ++-- packages/test_selenium/galaxy/project_galaxy_test_selenium.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/test_selenium/HISTORY.rst b/packages/test_selenium/HISTORY.rst index 7cb67f838f8..ac7f5cd8a5b 100644 --- a/packages/test_selenium/HISTORY.rst +++ b/packages/test_selenium/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.1.0.dev0 +20.9.0.dev0 --------------------- -* Initial import from dev branch of Galaxy during 20.01 development cycle. +* First release from the 20.09 branch of Galaxy. diff --git a/packages/test_selenium/galaxy/project_galaxy_test_selenium.py b/packages/test_selenium/galaxy/project_galaxy_test_selenium.py index f9042bac1c0..ab7e8f30e3d 100644 --- a/packages/test_selenium/galaxy/project_galaxy_test_selenium.py +++ b/packages/test_selenium/galaxy/project_galaxy_test_selenium.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.1.0.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-test-selenium" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 05b173c8dd974d26c4e47b61a4dba457f7122b95 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:31:55 -0400 Subject: [PATCH 53/58] Version 20.9.0 of test-selenium (tag galaxy-test-selenium-20.9.0). --- packages/test_selenium/HISTORY.rst | 2 +- packages/test_selenium/galaxy/project_galaxy_test_selenium.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/test_selenium/HISTORY.rst b/packages/test_selenium/HISTORY.rst index ac7f5cd8a5b..2da85e87e2a 100644 --- a/packages/test_selenium/HISTORY.rst +++ b/packages/test_selenium/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/test_selenium/galaxy/project_galaxy_test_selenium.py b/packages/test_selenium/galaxy/project_galaxy_test_selenium.py index ab7e8f30e3d..9f4c4f925b1 100644 --- a/packages/test_selenium/galaxy/project_galaxy_test_selenium.py +++ b/packages/test_selenium/galaxy/project_galaxy_test_selenium.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-test-selenium" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From b31bcb986d55277ad32ae5668d662d39fa14d45e Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:32:12 -0400 Subject: [PATCH 54/58] Starting work on test-selenium 20.9.1 --- packages/test_selenium/HISTORY.rst | 6 ++++++ .../test_selenium/galaxy/project_galaxy_test_selenium.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/test_selenium/HISTORY.rst b/packages/test_selenium/HISTORY.rst index 2da85e87e2a..135ed311ff6 100644 --- a/packages/test_selenium/HISTORY.rst +++ b/packages/test_selenium/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/test_selenium/galaxy/project_galaxy_test_selenium.py b/packages/test_selenium/galaxy/project_galaxy_test_selenium.py index 9f4c4f925b1..710669ebdea 100644 --- a/packages/test_selenium/galaxy/project_galaxy_test_selenium.py +++ b/packages/test_selenium/galaxy/project_galaxy_test_selenium.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-test-selenium" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 2bccaf35fbbc63a80d389cb17985387431c610d2 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:33:25 -0400 Subject: [PATCH 55/58] Prep release of galaxy-test-driver package. --- packages/test_driver/HISTORY.rst | 4 ++-- packages/test_driver/galaxy/project_galaxy_test_driver.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 72090ac4c88..03e6b93bb36 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -6,10 +6,10 @@ History .. to_doc --------------------- -20.5.1.dev0 +20.9.0.dev0 --------------------- - +* First release from the 20.09 branch of Galaxy. --------------------- 20.5.0 (2020-07-04) diff --git a/packages/test_driver/galaxy/project_galaxy_test_driver.py b/packages/test_driver/galaxy/project_galaxy_test_driver.py index ccf9c1596b8..fd6156ec7fa 100644 --- a/packages/test_driver/galaxy/project_galaxy_test_driver.py +++ b/packages/test_driver/galaxy/project_galaxy_test_driver.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.5.1.dev0' +__version__ = '20.9.0.dev0' PROJECT_NAME = "galaxy-test-driver" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 568a30c5973d7e1934ff10dd37d5ecabc46915b8 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:33:41 -0400 Subject: [PATCH 56/58] Version 20.9.0 of test-driver (tag galaxy-test-driver-20.9.0). --- packages/test_driver/HISTORY.rst | 2 +- packages/test_driver/galaxy/project_galaxy_test_driver.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 03e6b93bb36..f69ace2191a 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.0.dev0 +20.9.0 (2020-10-15) --------------------- * First release from the 20.09 branch of Galaxy. diff --git a/packages/test_driver/galaxy/project_galaxy_test_driver.py b/packages/test_driver/galaxy/project_galaxy_test_driver.py index fd6156ec7fa..455f55d69ed 100644 --- a/packages/test_driver/galaxy/project_galaxy_test_driver.py +++ b/packages/test_driver/galaxy/project_galaxy_test_driver.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0.dev0' +__version__ = '20.9.0' PROJECT_NAME = "galaxy-test-driver" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From acf949d341b65403aadf3bb6d456c24e40714a55 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 15 Oct 2020 12:33:54 -0400 Subject: [PATCH 57/58] Starting work on test-driver 20.9.1 --- packages/test_driver/HISTORY.rst | 6 ++++++ packages/test_driver/galaxy/project_galaxy_test_driver.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index f69ace2191a..47e0dd9ab2c 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -5,6 +5,12 @@ History .. to_doc +--------------------- +20.9.1.dev0 +--------------------- + + + --------------------- 20.9.0 (2020-10-15) --------------------- diff --git a/packages/test_driver/galaxy/project_galaxy_test_driver.py b/packages/test_driver/galaxy/project_galaxy_test_driver.py index 455f55d69ed..837a78922f9 100644 --- a/packages/test_driver/galaxy/project_galaxy_test_driver.py +++ b/packages/test_driver/galaxy/project_galaxy_test_driver.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.0' +__version__ = '20.9.1.dev0' PROJECT_NAME = "galaxy-test-driver" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From cf97ffcf6ad7f32201e5f035eb9e192bbd0e743b Mon Sep 17 00:00:00 2001 From: Alexandru Mahmoud Date: Fri, 16 Oct 2020 18:41:53 -0400 Subject: [PATCH 58/58] [19.09] Fixing bug in k8s runner's k8s_pod_retrials --- lib/galaxy/jobs/runners/kubernetes.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/lib/galaxy/jobs/runners/kubernetes.py index 14eb11bab09..3c79f5bd440 100644 --- a/lib/galaxy/jobs/runners/kubernetes.py +++ b/lib/galaxy/jobs/runners/kubernetes.py @@ -58,8 +58,8 @@ class KubernetesJobRunner(AsynchronousJobRunner): k8s_default_limits_cpu=dict(map=str, default=None), k8s_default_limits_memory=dict(map=str, default=None), k8s_cleanup_job=dict(map=str, valid=lambda s: s in {"onsuccess", "always", "never"}, default="always"), - k8s_pod_retries=dict(map=int, valid=lambda x: int >= 0, default=3), - k8s_pod_retrials=dict(map=int, valid=lambda x: int >= 0, default=3), + k8s_pod_retries=dict(map=int, valid=lambda x: int(x) >= 0, default=3), + k8s_pod_retrials=dict(map=int, valid=lambda x: int(x) >= 0, default=3), k8s_walltime_limit=dict(map=int, valid=lambda x: int(x) >= 0, default=172800)) if 'runner_param_specs' not in kwargs: