feat(poetry): refactor to use poetry instead of pipenv and GH actions… (

#94)

* feat(poetry): refactor to use poetry instead of pipenv and GH actions instead of Travis

* fix(ci): only run on push to master or PRs

* feat(ci): do pypi test push on PRs

* fix(ci): pass secrets in

* fix(ci): pass secrets explicitly

* chore(deps): less restrictive

* chore(deps): flexible deps

* feat(ci): update to latest PyPI support

* Update pypi.yaml

.github/workflows/ci.yaml

@@ -0,0 +1,22 @@
+name: CI
+
+on:
+  # run on pushed commits to master and on new commits on pull requests
+  push:
+    branches:
+      - master
+  pull_request:
+    types: [opened, synchronize]
+
+jobs:
+  Security:
+    name: Security Pipeline
+    uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
+    with:
+       python-poetry: 'false'
+    secrets: inherit  # pragma: allowlist secret
+  UnitTest:
+    name: Python Unit Test
+    uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
+    with:
+        python-version: '3.9'

.github/workflows/pypi.yaml

@@ -0,0 +1,18 @@
+name: PyPI
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - '*'
+jobs:
+  PyPIPoetryPublish:
+    name: PyPI Poetry Publish
+    uses: uc-cdis/.github/.github/workflows/python_package_index_publish.yaml@master
+    with:
+        PYTHON_VERSION: '3.9'
+        DO_TEST_PUBLISH_FIRST: true
+    secrets:
+      PYPI_TEST_API_TOKEN: ${{ secrets.PYPI_TEST_API_TOKEN }}
+      PYPI_PROD_API_TOKEN: ${{ secrets.PYPI_PROD_API_TOKEN }}

docs/create_docs.py

@@ -15,7 +15,7 @@
 import getpass
 from io import open
 
-PROJECT_NAME = "cirrus"
+PROJECT_NAME = "gen3cirrus"
 DOCUMENTATION_DIR = os.path.dirname(os.path.realpath(__file__))
 SOURCE_CODE_DIR = os.path.abspath(DOCUMENTATION_DIR + "/../")
 

docs/source/conf.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# cirrus documentation build configuration file, created by
+# gen3cirrus documentation build configuration file, created by
 # sphinx-quickstart on Thu Jan  4 12:06:39 2018.
 #
 # This file is execfile()d with the current directory set to its
@@ -55,7 +55,7 @@
 master_doc = "index"
 
 # General information about the project.
-project = "cirrus"
+project = "gen3cirrus"
 copyright = "2018, avantol"
 author = "avantol"
 
@@ -145,15 +145,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "cirrus.tex", "cirrus Documentation", "avantol", "manual")
+    (master_doc, "gen3cirrus.tex", "gen3cirrus Documentation", "avantol", "manual")
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "cirrus", "cirrus Documentation", [author], 1)]
+man_pages = [(master_doc, "gen3cirrus", "gen3cirrus Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -164,10 +164,10 @@
 texinfo_documents = [
     (
         master_doc,
-        "cirrus",
-        "cirrus Documentation",
+        "gen3cirrus",
+        "gen3cirrus Documentation",
         author,
-        "cirrus",
+        "gen3cirrus",
         "One line description of project.",
         "Miscellaneous",
     )

cirrus/backoff.py → gen3cirrus/backoff.py

@@ -6,7 +6,7 @@
 import json
 import sys
 
-from cirrus.errors import CirrusError
+from gen3cirrus.errors import CirrusError
 
 logger = get_logger(__name__)
 

cirrus/config.py → gen3cirrus/config.py

@@ -1,5 +1,5 @@
 """
-cirrus Configuration
+gen3cirrus Configuration
 
 - Contains the necessary information to manage a google project, including
   some info about it and credentials. Usually the credentials supplied

cirrus/core.py → gen3cirrus/core.py

@@ -1,5 +1,5 @@
 """
-cirrus - Cloud API Wrapper Layer exposing easier Cloud Management
+gen3cirrus - Cloud API Wrapper Layer exposing easier Cloud Management
 
 Current Capabilities:
 - Manage Google resources, policies, and access (specific Google APIs

cirrus/errors.py → gen3cirrus/errors.py

@@ -1,5 +1,5 @@
 class CirrusError(Exception):
-    def __init__(self, message="There was an error within the cirrus library.", *args):
+    def __init__(self, message="There was an error within the gen3cirrus library.", *args):
         super(CirrusError, self).__init__(message)
 
 

cirrus/google_cloud/errors.py → gen3cirrus/google_cloud/errors.py

@@ -1,4 +1,4 @@
-from cirrus.errors import CirrusError
+from gen3cirrus.errors import CirrusError
 
 
 class GoogleNamingError(CirrusError):
@@ -20,7 +20,7 @@ def __init__(
             "This action requires an authed session. Please use "
             "Python's `with <Class> as <name>` syntax for a context manager "
             "that automatically enters and exits authorized sessions using "
-            "default credentials. See cirrus's README for setup instructions."
+            "default credentials. See gen3cirrus's README for setup instructions."
         )
 
 

cirrus/google_cloud/manager.py → gen3cirrus/google_cloud/manager.py

@@ -24,24 +24,24 @@
 from requests.exceptions import HTTPError as requestsHttpError
 from urllib.parse import quote as urlquote
 
-from cirrus.backoff import BACKOFF_SETTINGS
-from cirrus.config import config
-from cirrus.core import CloudManager
-from cirrus.errors import CirrusError, CirrusUserError, CirrusNotFound
-from cirrus.google_cloud.errors import (
+from gen3cirrus.backoff import BACKOFF_SETTINGS
+from gen3cirrus.config import config
+from gen3cirrus.core import CloudManager
+from gen3cirrus.errors import CirrusError, CirrusUserError, CirrusNotFound
+from gen3cirrus.google_cloud.errors import (
     GoogleAuthError,
     GoogleAPIError,
     GoogleNamingError,
 )
-from cirrus.google_cloud.iam import (
+from gen3cirrus.google_cloud.iam import (
     GooglePolicy,
     GooglePolicyBinding,
     GooglePolicyMember,
     GooglePolicyRole,
     get_iam_service_account_email,
 )
-from cirrus.google_cloud.services import GoogleAdminService, GoogleService
-from cirrus.google_cloud.utils import (
+from gen3cirrus.google_cloud.services import GoogleAdminService, GoogleService
+from gen3cirrus.google_cloud.utils import (
     get_valid_service_account_id_for_user,
     get_service_account_cred_from_key_response,
     get_proxy_group_name_for_user,
@@ -515,7 +515,7 @@ def give_group_access_to_bucket(self, group_email, bucket_name, access=None):
             bucket_name (str): Bucket to provide access to
 
         Raises:
-            cirrus.google_cloud.errors.CirrusNotFound: No bucket found with given name
+            gen3cirrus.google_cloud.errors.CirrusNotFound: No bucket found with given name
         """
         access = access or ["read"]
         try:
@@ -542,7 +542,7 @@ def give_group_access_to_bucket(self, group_email, bucket_name, access=None):
             else:
                 raise CirrusUserError(
                     "Unable to grant {access_level} access to {group_email} "
-                    "on bucket {bucket_name}. cirrus "
+                    "on bucket {bucket_name}. gen3cirrus "
                     "does not support the access level {access_level}.".format(
                         access_level=access_level,
                         group_email=group_email,

cirrus/google_cloud/services.py → gen3cirrus/google_cloud/services.py

@@ -6,8 +6,8 @@
 from googleapiclient.discovery import build
 import backoff
 
-from cirrus.config import config
-from cirrus.google_cloud.manager import BACKOFF_SETTINGS
+from gen3cirrus.config import config
+from gen3cirrus.google_cloud.manager import BACKOFF_SETTINGS
 
 
 class GoogleService(object):

cirrus/google_cloud/utils.py → gen3cirrus/google_cloud/utils.py

@@ -11,8 +11,8 @@
 from google.oauth2 import service_account
 from cdislogging import get_logger
 
-from cirrus.config import config
-from cirrus.google_cloud.errors import GoogleNamingError
+from gen3cirrus.config import config
+from gen3cirrus.google_cloud.errors import GoogleNamingError
 
 GOOGLE_SERVICE_ACCOUNT_REGEX = "[a-z][a-z\d\-]*[a-z\d]"
 logger = get_logger(__name__, log_level="info")