Merge pull request #1506 from alan-turing-institute/hatch

Pulumi: Migrate pyproject to PyPA standard and hatch

.github/workflows/lint_code.yaml

@@ -4,9 +4,9 @@ name: Lint code
 # Run workflow on pushes to matching branches
 on:  # yamllint disable-line rule:truthy
   push:
-    branches: [develop]
+    branches: [develop, python-migration]
   pull_request:
-    branches: [develop]
+    branches: [develop, python-migration]
 
 jobs:
   lint_json:
@@ -53,12 +53,14 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - name: Install requirements
-        shell: bash
-        run: pip install flake8
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: Install hatch
+        run: pip install hatch
       - name: Lint Python
-        shell: bash
-        run: flake8 . --statistics --count
+        run: hatch run lint:style
 
   lint_shell:
     runs-on: ubuntu-latest

.gitignore

@@ -42,5 +42,5 @@ expanded.yaml
 # mypy cache
 .mypy_cache
 
-# Pulumi secrets files
-pulumi/Pulumi.*.yaml
+# ruff cache
+.ruff_cache

data_safe_haven/README.md

@@ -5,10 +5,7 @@ Install the following requirements before starting
 - [Poetry](https://python-poetry.org/docs/#installation)
 - [Pulumi](https://www.pulumi.com/docs/get-started/install/)
 
-# Deploying a Data Safe Haven
-
-Create a directory where you want to store local configuration files for this deployment.
-This is the `project directory`
+## Deploying a Data Safe Haven
 
 - Run the following to initialise the deployment [approx 5 minutes]:
 
@@ -25,42 +22,41 @@ If you prefer to enter these at the command line, run `dsh init -h` to see the n
 > dsh deploy shm
 ```
 
-You will be prompted for various project settings.
-If you prefer to enter these at the command line, run `dsh deploy shm -h` to see the necessary command line flags.
+You will be prompted for various settings.
+Run `dsh deploy shm -h` to see the necessary command line flags and provide them as arguments.
 
 - Add one or more users from a CSV file with columns named (`GivenName`, `Surname`, `Phone`, `Email`). Note that the phone number must be in full international format.
 
 ```bash
-> dsh users add <my CSV users file>
+> dsh admin add-users <my CSV users file>
 ```
 
 - Next deploy the infrastructure for one or more Secure Research Environments (SREs) [approx 30 minutes]:
 
 ```bash
-> dsh deploy sre <SRE name> -r <VM1 SKU> -r <VM2 SKU>
+> dsh deploy sre <SRE name>
 ```
 
-where you must specify a VM SKU for each user-accessible secure research desktop that you want to deploy
-On first run, you will be prompted for various project settings.
-If you prefer to enter these at the command line, run `dsh deploy sre -h` to see the necessary command line flags.
+You will be prompted for various settings.
+Run `dsh deploy sre -h` to see the necessary command line flags and provide them as arguments.
 
 - Next add one or more existing users to your SRE
 
 ```bash
-> dsh users register -s <SRE name> <username1> <username2>
+> dsh admin register-users -s <SRE name> <username1> <username2>
 ```
 
 where you must specify the usernames for each user you want to add to this SRE
 
-# Administering a Data Safe Haven
+## Administering a Data Safe Haven
 
 - Run the following to list the currently available users
 
 ```bash
-> dsh users list
+> dsh admin list-users
 ```
 
-# Removing a deployed Data Safe Haven
+## Removing a deployed Data Safe Haven
 
 - Run the following if you want to teardown a deployed SRE:
 

data_safe_haven/__init__.py

@@ -1,4 +1,5 @@
 """Data Safe Haven"""
-import pkg_resources
 
-__version__ = pkg_resources.get_distribution("data-safe-haven").version
+from .version import __version__, __version_info__
+
+__all__ = ["__version__", "__version_info__"]

data_safe_haven/administration/users/active_directory_users.py

@@ -1,14 +1,14 @@
 """Interact with users in an Azure Active Directory"""
-# Standard library imports
 import pathlib
-from typing import Any, Optional, Sequence
+from collections.abc import Sequence
+from typing import Any
 
-# Local imports
 from data_safe_haven.config import Config
 from data_safe_haven.external import AzureApi
 from data_safe_haven.functions import b64encode
 from data_safe_haven.pulumi import PulumiSHMStack
 from data_safe_haven.utility import FileReader, Logger
+
 from .research_user import ResearchUser
 
 
@@ -70,7 +70,7 @@ def add(self, new_users: Sequence[ResearchUser]) -> None:
         for line in output.split("\n"):
             self.logger.parse(line)
 
-    def list(self, sre_name: Optional[str] = None) -> Sequence[ResearchUser]:
+    def list(self, sre_name: str | None = None) -> Sequence[ResearchUser]:  # noqa: A003
         """List users in a local Active Directory"""
         list_users_script = FileReader(
             self.resources_path / "active_directory" / "list_users.ps1"
@@ -85,7 +85,7 @@ def list(self, sre_name: Optional[str] = None) -> Sequence[ResearchUser]:
         users = []
         for line in output.split("\n"):
             tokens = line.split(";")
-            if len(tokens) >= 6:
+            if len(tokens) >= 6:  # noqa: PLR2004
                 users.append(
                     ResearchUser(
                         email_address=tokens[4],
@@ -127,7 +127,7 @@ def remove(self, users: Sequence[ResearchUser]) -> None:
         for line in output.split("\n"):
             self.logger.parse(line)
 
-    def set(self, users: Sequence[ResearchUser]) -> None:
+    def set(self, users: Sequence[ResearchUser]) -> None:  # noqa: A003
         """Set local Active Directory users to specified list"""
         users_to_remove = [user for user in self.list() if user not in users]
         self.remove(users_to_remove)

data_safe_haven/administration/users/azure_ad_users.py

@@ -1,11 +1,11 @@
 """Interact with users in an Azure Active Directory"""
-# Standard library imports
-from typing import Any, Sequence
+from collections.abc import Sequence
+from typing import Any
 
-# Local imports
 from data_safe_haven.external import GraphApi
 from data_safe_haven.functions import password
 from data_safe_haven.utility import Logger
+
 from .research_user import ResearchUser
 
 
@@ -25,11 +25,11 @@ def __init__(
     def add(self, new_users: Sequence[ResearchUser]) -> None:
         """Add list of users to AzureAD"""
         # Get the default domain
-        default_domain = [
+        default_domain = next(
             domain["id"]
             for domain in self.graph_api.read_domains()
             if domain["isDefault"]
-        ][0]
+        )
         for user in new_users:
             request_json = {
                 "accountEnabled": user.account_enabled,
@@ -56,7 +56,7 @@ def add(self, new_users: Sequence[ResearchUser]) -> None:
         #     # Also add the user to the research users group
         #     self.graph_api.add_user_to_group(user.username, self.researchers_group_name)
 
-    def list(self) -> Sequence[ResearchUser]:
+    def list(self) -> Sequence[ResearchUser]:  # noqa: A003
         user_list = self.graph_api.read_users()
         return [
             ResearchUser(
@@ -98,14 +98,14 @@ def remove(self, users: Sequence[ResearchUser]) -> None:
         #                 f"Removed '{user.preferred_username}' from group '{self.researchers_group_name}'"
         #             )
         #         else:
-        #             raise DataSafeHavenMicrosoftGraphException
-        #     except DataSafeHavenMicrosoftGraphException:
+        #             raise DataSafeHavenMicrosoftGraphError
+        #     except DataSafeHavenMicrosoftGraphError:
         #         self.logger.error(
         #             f"Unable to remove '{user.preferred_username}' from group '{self.researchers_group_name}'"
         #         )
         pass
 
-    def set(self, users: Sequence[ResearchUser]) -> None:
+    def set(self, users: Sequence[ResearchUser]) -> None:  # noqa: A003
         """Set Guacamole users to specified list"""
         users_to_remove = [user for user in self.list() if user not in users]
         self.remove(users_to_remove)

data_safe_haven/administration/users/guacamole_users.py

@@ -1,11 +1,11 @@
-# Standard library imports
 import pathlib
-from typing import Any, Optional, Sequence
+from collections.abc import Sequence
+from typing import Any
 
-# Local imports
 from data_safe_haven.config import Config
 from data_safe_haven.external import AzurePostgreSQLDatabase
 from data_safe_haven.pulumi import PulumiSREStack
+
 from .research_user import ResearchUser
 
 
@@ -20,7 +20,7 @@ def __init__(self, config: Config, sre_name: str, *args: Any, **kwargs: Any):
             sre_stack.output("remote_desktop")["resource_group_name"],
             config.subscription_name,
         )
-        self.users_: Optional[Sequence[ResearchUser]] = None
+        self.users_: Sequence[ResearchUser] | None = None
         self.postgres_script_path: pathlib.Path = (
             pathlib.Path(__file__).parent.parent.parent
             / "resources"
@@ -30,14 +30,17 @@ def __init__(self, config: Config, sre_name: str, *args: Any, **kwargs: Any):
         self.sre_name = sre_name
         self.group_name = f"Data Safe Haven Users SRE {sre_name}"
 
-    def list(self) -> Sequence[ResearchUser]:
+    def list(self) -> Sequence[ResearchUser]:  # noqa: A003
         """List all Guacamole users"""
         if self.users_ is None:  # Allow for the possibility of an empty list of users
             postgres_output = self.postgres_provisioner.execute_scripts(
                 [self.postgres_script_path / "list_users.mustache.sql"],
                 mustache_values={"group_name": self.group_name},
             )
-            # The output is of the form [["sam_account_name1", "email_address1"], ["sam_account_name2", "email_address2"]]
+            # The output is of the form [
+            #   ["sam_account_name1", "email_address1"],
+            #   ["sam_account_name2", "email_address2"]
+            # ]
             self.users_ = [
                 ResearchUser(
                     sam_account_name=user_details[0].split("@")[0],

data_safe_haven/administration/users/research_user.py

@@ -1,18 +1,17 @@
-# Standard library imports
-from typing import Any, Optional
+from typing import Any
 
 
 class ResearchUser:
     def __init__(
         self,
-        account_enabled: Optional[bool] = None,
-        country: Optional[str] = None,
-        email_address: Optional[str] = None,
-        given_name: Optional[str] = None,
-        phone_number: Optional[str] = None,
-        sam_account_name: Optional[str] = None,
-        surname: Optional[str] = None,
-        user_principal_name: Optional[str] = None,
+        account_enabled: bool | None = None,
+        country: str | None = None,
+        email_address: str | None = None,
+        given_name: str | None = None,
+        phone_number: str | None = None,
+        sam_account_name: str | None = None,
+        surname: str | None = None,
+        user_principal_name: str | None = None,
     ) -> None:
         self.account_enabled = account_enabled
         self.country = country