Bug fix, add histogram of pod tasks

README.md

@@ -1,19 +1,21 @@
 KubeCustom
 ==============================
 [//]: # (Badges)
-[![GitHub Actions Build Status](https://github.com/jaclark5/kubecustom/workflows/CI/badge.svg)](https://github.com/jaclark5/kubecustom/actions?query=workflow%3ACI)
+[![GitHub Actions Build Status](https://github.com/openforcefield/kubecustom/workflows/CI/badge.svg)](https://github.com/openforcefield/kubecustom/actions?query=workflow%3ACI)
 [![Documentation Status](https://readthedocs.org/projects/kubecustom/badge/?version=latest)](https://kubecustom.readthedocs.io/en/latest/?badge=latest)
 <!--
-[![codecov](https://codecov.io/gh/jaclark5/kubecustom/branch/main/graph/badge.svg)](https://codecov.io/gh/jaclark5/kubecustom/branch/main)
+[![codecov](https://codecov.io/gh/openforcefield/kubecustom/branch/main/graph/badge.svg)](https://codecov.io/gh/openforcefield/kubecustom/branch/main)
 -->
 
 Kubernetes assessment  and combined control functions to handle multiple deployments.
 
+**This is a set of informal tools for internal use. We make no guarantees of versioning, functionality, or support.**
+
 ## Installation
 
 * Step 1: Download the main branch from our GitHub page as a zip file, or clone it to your working directory with:
 
-    ``git clone https://github.com/jaclark5/kubecustom``
+    ``git clone https://github.com/openforcefield/kubecustom``
 
 * Step 2 (Optional): If you are using conda and you want to create a new environment for this package you may install with:
 

kubecustom/__main__.py

@@ -7,7 +7,7 @@
 parser = get_parser()
 args = parser.parse_args()
 kwargs = {key: value for key, value in args.__dict__.items()}
-timelag = kwargs.pop("timelag")
+timelag = int(kwargs.pop("timelag"))
 
 
 def repeat_task(scheduler):

kubecustom/deployment.py

@@ -307,7 +307,6 @@ def scale_deployment(deployment_name, replicas, namespace=None, verbose=True):
     namespace = MyDataInstance.get_namespace() if namespace is None else namespace
 
     config.load_kube_config()
-    apps_v1_api = client.AppsV1Api()
 
     dep_info = get_deployment_info(deployment_name, namespace=namespace)
     if dep_info["replicas"] == replicas:
@@ -325,11 +324,13 @@ def scale_deployment(deployment_name, replicas, namespace=None, verbose=True):
             delete_pod(pod_list[i], namespace=namespace)
 
     try:
-        deployment = apps_v1_api.read_namespaced_deployment(deployment_name, namespace)
+        deployment = client.AppsV1Api().read_namespaced_deployment(
+            deployment_name, namespace
+        )
         deployment.spec.replicas = replicas
 
         # Apply the patch to update the deployment
-        apps_v1_api.patch_namespaced_deployment(
+        client.AppsV1Api().patch_namespaced_deployment(
             name=deployment_name, namespace=namespace, body=deployment
         )
 

kubecustom/pod.py

@@ -1,7 +1,7 @@
 """Create, delete, and extract information for pods"""
 
 import warnings
-from collections import defaultdict
+from collections import defaultdict, Counter
 
 from kubernetes import client, config
 from kubernetes.client.exceptions import ApiException
@@ -192,13 +192,17 @@ def get_pods_status_info(previous=False, deployment_name=None, namespace=None):
     pod_info = {}
     for pod in pods:
         state, status, status_info = pod_state(pod, previous=previous)
+        try:
+            restart_count = pod.status.container_statuses[0].restart_count
+        except Exception:
+            restart_count = None
         pod_info[pod.metadata.name] = {
             "pod_name": pod.metadata.name,
             "node_name": pod.spec.node_name,
             "host_ip": pod.status.host_ip,
             "pod_ip": pod.status.pod_ip,
             "phase": pod.status.phase,
-            "restart_count": pod.status.container_statuses[0].restart_count,
+            "restart_count": restart_count,
             "state": state,
             "status": status,
             "status_info": status_info,
@@ -267,7 +271,7 @@ def get_pods_resource_info(
             if verbose:
                 print(
                     f"Pod: {pod_name}, Container: {container_name}, CPU: {container['usage']['cpu']} {cpu_usage},\t"
-                    "Memory: {container['usage']['memory']} {memory_usage}GB,\tLabels: {pod['metadata']['labels']}"
+                    f"Memory: {container['usage']['memory']} {memory_usage}GB,\tLabels: {pod['metadata']['labels']}"
                 )
 
             output[pod_name] = {
@@ -289,12 +293,15 @@ def get_active_tasks(pod_list, verbose=True, namespace=None):
         :func:`kubecustom.secret.MyData.get_namespace`.
 
     Returns:
-        dict: Dictionary of pod names and the number of active tasks each pod has
+        pod_tasks (dict): Dictionary of pod names and the number of active tasks each pod has
+        stats (dict): Dictionary of the number of tasks a pod could have, and the number of pods
+        in that state.
     """
 
     namespace = MyDataInstance.get_namespace() if namespace is None else namespace
 
-    output = {}
+    output = defaultdict(int)
+    stats = Counter()
     for pod in pod_list:
         pod_name = pod.metadata.name
         try:
@@ -312,22 +319,27 @@ def get_active_tasks(pod_list, verbose=True, namespace=None):
                     line_array = line.split()
                     tasks = int(line_array[-7])
                     output[pod_name] = tasks
+                    stats[tasks] += 1
                     if verbose:
                         print(f"    Pod: {pod_name}, Number of Tasks {tasks}")
                     break
-                elif "new tasks" in line:
-                    line_array = line.split()
-                    tasks = int(line_array[-3])
-                    output[pod_name] = tasks
-                    if verbose:
-                        print(f"    Pod: {pod_name}, Number of Tasks {tasks} new")
-                    break
+
+            if pod_name not in output:
+                output[pod_name] = None
+                stats["None Yet"] += 1
+                if verbose:
+                    print(f"    Pod: {pod_name}, Number of Tasks None Yet")
+
         except Exception:
+            stats[None] += 1
             output[pod_name] = None
             if verbose:
                 print(f"    Pod: {pod_name}, Number of Tasks NA")
 
-    return output
+    if verbose:
+        print(stats)
+
+    return output, stats
 
 
 def print_pods_summary(deployment_name=None, namespace=None):

kubecustom/secret.py

@@ -132,7 +132,8 @@ def _update_file(self):
         with open(_init_filename, "w") as f:
             for i, line in enumerate(_file_contents):
                 line_array = line.split()
-                line_array = [line_array[0], str(getattr(self, self._attributes[i]))]
+                attr = getattr(self, self._attributes[i])
+                line_array = [line_array[0], str(attr if attr is not None else "None")]
                 f.write(" ".join(line_array) + "\n")
 
     def get_username(self):

kubecustom/utils.py

@@ -80,7 +80,7 @@ def convert_memory_use(mem_usage):
         "M": 0.001,
         "k": 1e-6,
         "b": 1e-9,
-        "": 1 - 9,
+        "": 1e-9,
         "m": 9.3132257461548e-13,
     }
     mem_usage.replace(" ", "")

pyproject.toml

@@ -29,7 +29,7 @@ dependencies = [
 
 # Update the urls once the hosting is set up.
 [project.urls]
-"Source" = "https://github.com/jaclark5/kubecustom/"
+"Source" = "https://github.com/openforcefield/kubecustom/"
 "Documentation" = "https://kubecustom.readthedocs.io/"
 
 [project.optional-dependencies]