Merge pull request #185 from openradx/replace-invoke-with-typer

Replace invoke with typer

.devcontainer/Dockerfile

@@ -3,7 +3,6 @@ FROM mcr.microsoft.com/devcontainers/python:3.13
 USER root
 
 # Install system dependencies
-# - bash-completion for shell completions of invoke
 # - gettext for Django translations
 # - postgresql-common for the apt.postgresql.org.sh script
 # - postgresql-client-17 for a current version of psql
@@ -19,10 +18,5 @@ RUN sudo apt-get update \
 
 USER vscode
 
-# pipx is already installed in the base devcontainers Python image
-RUN pipx install invoke \
-  && invoke --print-completion-script=bash >> ~/.bash_completion \
-  pipx uninstall invoke
-
 RUN pipx install poetry \
   && poetry completions bash >> ~/.bash_completion

.devcontainer/devcontainer.json

@@ -8,7 +8,7 @@
   },
   // https://github.com/orgs/community/discussions/50403
   // "initializeCommand": "docker system prune --all --force",
-  "postCreateCommand": "poetry install && poetry run invoke init-workspace",
+  "postCreateCommand": "poetry install && poetry run ./cli.py init-workspace",
   "customizations": {
     "vscode": {
       "extensions": [

.github/workflows/ci.yml

@@ -28,7 +28,7 @@ jobs:
       - name: Install dependencies
         run: poetry install
       - name: Configure environment
-        run: poetry run invoke init-workspace
+        run: poetry run ./cli.py init-workspace
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
       - name: Build and cache Docker images
@@ -41,14 +41,14 @@ jobs:
           cache-from: type=gha
           cache-to: type=gha,mode=max
       - name: Start Docker containers
-        run: poetry run invoke compose-up --no-build
+        run: poetry run ./cli.py compose-up --no-build
       - name: Run linting
         # https://github.com/actions/runner/issues/241#issuecomment-745902718
         shell: 'script -q -e -c "bash {0}"'
-        run: poetry run invoke lint
+        run: poetry run ./cli.py lint
       - name: Run tests
         shell: 'script -q -e -c "bash {0}"'
-        run: poetry run invoke test --cov
+        run: poetry run ./cli.py test --cov
       - name: Stop Docker containers
         if: ${{ always() }}
-        run: poetry run invoke compose-down
+        run: poetry run ./cli.py compose-down

.gitpod.Dockerfile

@@ -3,7 +3,6 @@ FROM gitpod/workspace-python-3.12
 USER root
 
 # Install system dependencies
-# - bash-completion for shell completions of invoke
 # - gettext for Django translations
 # - postgresql-common for the apt.postgresql.org.sh script
 # - postgresql-client-17 for a current version of psql
@@ -33,10 +32,7 @@ RUN mkdir $NVM_DIR \
   && nvm use default
 
 RUN python3 -m pip install --user pipx \
-  && python3 -m pipx ensurepath \
-  && python3 -m pipx install invoke \
-  && invoke --print-completion-script=bash >> $HOME/.bash_completion \
-  && pipx uninstall invoke
+  && python3 -m pipx ensurepath
 
 # Poetry is already installed in the base Gitpod Python image,
 # but we need to upgrade it

.gitpod.yml

@@ -5,7 +5,7 @@ tasks:
   - name: setup
     init: |
       poetry install
-      poetry run invoke init-workspace
+      poetry run ./cli.py init-workspace
 
 ports:
   - port: 8000

CONTRIBUTING.md

@@ -14,10 +14,10 @@ git clone https://github.com/openradx/adit.git
 cd adit
 poetry install
 poetry shell
-invoke compose-up
+poetry run ./cli.py compose-up
 ```
 
 The development server of the example project will be started on <http://localhost:8000>
 
 If a library dependency is changed, the containers need to be rebuilt (e.g. by running
-`invoke compose-down && invoke compose-up`).
+`poetry run ./cli.py compose-down && poetry run ./cli.py compose-up`).

TODO.md

@@ -141,12 +141,6 @@
   - Can be work around by wrapping another zip file in an encrypted zip file <https://unix.stackexchange.com/a/290088/469228>
 - Rewrite dicom_connector to use asyncio (wrap all pynetdicom calls in asyncio.to_thread)
   - I don't think that this will gain any performance improvements, so maybe not worth it
-- Evaluate other task runners
-  - <https://www.pyinvoke.org/> # used currently
-  - <https://github.com/taskipy/taskipy>
-  - <https://github.com/nat-n/poethepoet>
-  - <https://just.systems/>
-  - <https://taskfile.dev/>
 - Make a job urgent retrospectively (maybe only staff members can do this)
   - A current workaround is to cancel the job, change urgency with Django Admin and then resume the job
 - Try to bring channels_liver_server in official pytest_django release

adit/core/management/commands/populate_orthancs.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 from django.conf import settings
 from django.core.management.base import BaseCommand
 
@@ -11,8 +13,12 @@ def add_arguments(self, parser):
         parser.add_argument("--reset", action="store_true")
 
     def handle(self, *args, **options):
-        orthanc1 = OrthancRestHandler(host=settings.ORTHANC1_HOST, port=settings.ORTHANC1_HTTP_PORT)
-        orthanc2 = OrthancRestHandler(host=settings.ORTHANC2_HOST, port=settings.ORTHANC2_HTTP_PORT)
+        orthanc1_host: str = settings.ORTHANC1_HOST
+        orthanc1_http_port: int = settings.ORTHANC1_HTTP_PORT
+        orthanc2_host: str = settings.ORTHANC2_HOST
+        orthanc2_http_port: int = settings.ORTHANC2_HTTP_PORT
+        orthanc1 = OrthancRestHandler(host=orthanc1_host, port=orthanc1_http_port)
+        orthanc2 = OrthancRestHandler(host=orthanc2_host, port=orthanc2_http_port)
 
         if options["reset"]:
             self.stdout.write("Resetting Orthancs...", ending="")
@@ -27,6 +33,7 @@ def handle(self, *args, **options):
 
         self.stdout.write("Populating Orthanc1 with example DICOMs...", ending="")
         self.stdout.flush()
-        dicoms_folder = settings.BASE_DIR / "samples" / "dicoms"
+        base_path: Path = settings.BASE_PATH
+        dicoms_folder = base_path / "samples" / "dicoms"
         orthanc1.upload(dicoms_folder)
         self.stdout.write("Done")

adit/core/management/commands/receiver.py

@@ -21,7 +21,7 @@ class Command(AsyncServerCommand):
         "files to subscribing workers."
     )
     server_name = "DICOM receiver"
-    paths_to_watch = settings.SOURCE_FOLDERS
+    paths_to_watch = settings.SOURCE_PATHS
 
     async def run_server_async(self, **options):
         with tempfile.TemporaryDirectory(prefix="adit_receiver_") as tmpdir:

adit/core/tests/utils/test_dicom_operator.py

@@ -129,7 +129,7 @@ def test_download_series_with_c_get(mocker: MockerFixture):
     association_mock = create_association_mock()
     associate_mock.return_value = association_mock
     association_mock.send_c_get.return_value = DicomTestHelper.create_successful_c_get_response()
-    path = Path(settings.BASE_DIR) / "samples" / "dicoms"
+    path = Path(settings.BASE_PATH) / "samples" / "dicoms"
     ds = read_dataset(next(path.rglob("*.dcm")))
     received_ds = []
     dicom_operator = create_dicom_operator()
@@ -158,7 +158,7 @@ def test_download_series_with_c_move(settings: SettingsWrapper, mocker: MockerFi
     dicom_operator = create_dicom_operator()
     dicom_operator.server.study_root_get_support = False
     dicom_operator.server.patient_root_get_support = False
-    path = Path(settings.BASE_DIR) / "samples" / "dicoms"
+    path = Path(settings.BASE_PATH) / "samples" / "dicoms"
     file_path = next(path.rglob("*.dcm"))
     ds = read_dataset(file_path)
     responses = [{"SOPInstanceUID": ds.SOPInstanceUID}]

adit/core/tests/utils/test_file_transmit.py

@@ -15,7 +15,7 @@
 
 @pytest.mark.asyncio
 async def test_start_transmit_file():
-    samples_path = Path(f"{settings.BASE_DIR}/samples/dicoms")
+    samples_path = Path(f"{settings.BASE_PATH}/samples/dicoms")
     sample_files = list(samples_path.rglob("*.dcm"))
 
     server = FileTransmitServer(HOST, PORT)

adit/core/utils/testing_helpers.py

@@ -161,7 +161,7 @@ def create_dicom_web_client(server_url: str, ae_title: str, token_string: str) -
 
 
 def load_sample_dicoms(patient_id: str | None = None) -> Iterable[Dataset]:
-    test_dicoms_path = settings.BASE_DIR / "samples" / "dicoms"
+    test_dicoms_path = settings.BASE_PATH / "samples" / "dicoms"
     if patient_id:
         test_dicoms_path = test_dicoms_path / patient_id
 

adit/settings/base.py

@@ -22,10 +22,10 @@
     env.read_env()
 
 # The base directory of the project (the root of the repository)
-BASE_DIR = Path(__file__).resolve(strict=True).parent.parent.parent
+BASE_PATH = Path(__file__).resolve(strict=True).parent.parent.parent
 
-# Used to monitor files for autoreload
-SOURCE_FOLDERS = [BASE_DIR / "adit"]
+# The source paths of the project
+SOURCE_PATHS = [BASE_PATH / "adit"]
 
 # Fetch version from the environment which is passed through from the latest git version tag
 PROJECT_VERSION = env.str("PROJECT_VERSION", default="vX.Y.Z")
@@ -274,7 +274,7 @@
 STATIC_URL = "/static/"
 
 # Additional (project wide) static files
-STATICFILES_DIRS = (BASE_DIR / "adit" / "static",)
+STATICFILES_DIRS = (BASE_PATH / "adit" / "static",)
 
 # For crispy forms
 CRISPY_ALLOWED_TEMPLATE_PACKS = "bootstrap5"
@@ -295,14 +295,14 @@
 DBBACKUP_CLEANUP_KEEP = 30
 
 # Orthanc servers are integrated in ADIT by using a reverse proxy (django-revproxy).
-ORTHANC1_HOST = env.str("ORTHANC1_HOST")
-ORTHANC1_HTTP_PORT = env.int("ORTHANC1_HTTP_PORT")
-ORTHANC1_DICOM_PORT = env.int("ORTHANC1_DICOM_PORT")
-ORTHANC1_DICOMWEB_ROOT = env.str("ORTHANC1_DICOMWEB_ROOT")
-ORTHANC2_HOST = env.str("ORTHANC2_HOST")
-ORTHANC2_HTTP_PORT = env.int("ORTHANC2_HTTP_PORT")
-ORTHANC2_DICOM_PORT = env.int("ORTHANC2_DICOM_PORT")
-ORTHANC2_DICOMWEB_ROOT = env.str("ORTHANC2_DICOMWEB_ROOT")
+ORTHANC1_HOST = env.str("ORTHANC1_HOST", default="localhost")
+ORTHANC1_HTTP_PORT = env.int("ORTHANC1_HTTP_PORT", default=6501)
+ORTHANC1_DICOM_PORT = env.int("ORTHANC1_DICOM_PORT", default=7501)
+ORTHANC1_DICOMWEB_ROOT = env.str("ORTHANC1_DICOMWEB_ROOT", "dicom-web")
+ORTHANC2_HOST = env.str("ORTHANC2_HOST", default="localhost")
+ORTHANC2_HTTP_PORT = env.int("ORTHANC2_HTTP_PORT", default=6502)
+ORTHANC2_DICOM_PORT = env.int("ORTHANC2_DICOM_PORT", default=7502)
+ORTHANC2_DICOMWEB_ROOT = env.str("ORTHANC2_DICOMWEB_ROOT", "dicom-web")
 
 # Used by django-filter
 FILTERS_EMPTY_CHOICE_LABEL = "Show All"
@@ -318,16 +318,16 @@
 
 # The address and port of the STORE SCP server (part of the receiver).
 # By default the STORE SCP server listens to all interfaces (empty string)
-STORE_SCP_HOST = env.str("STORE_SCP_HOST")
-STORE_SCP_PORT = env.int("STORE_SCP_PORT")
+STORE_SCP_HOST = env.str("STORE_SCP_HOST", "localhost")
+STORE_SCP_PORT = env.int("STORE_SCP_PORT", 11112)
 
 # The address and port of the file transmit socket server (part of the receiver)
 # that is used to transfer DICOM files from the receiver to the workers (when
 # the PACS server does not support C-GET).
 # By default the file transmit socket server listens to all interfaces (should
 # not be a problem as it is inside the docker network).
-FILE_TRANSMIT_HOST = env.str("FILE_TRANSMIT_HOST")
-FILE_TRANSMIT_PORT = env.int("FILE_TRANSMIT_PORT")
+FILE_TRANSMIT_HOST = env.str("FILE_TRANSMIT_HOST", "localhost")
+FILE_TRANSMIT_PORT = env.int("FILE_TRANSMIT_PORT", 14638)
 
 # Usually a transfer job must be verified by an admin. By setting
 # this option to True ADIT will schedule unverified transfers

cli.py

@@ -0,0 +1,53 @@
+#! /usr/bin/env python3
+
+from pathlib import Path
+from typing import Annotated
+
+import typer
+from adit_radis_shared import cli_commands as commands
+from adit_radis_shared import cli_helpers as helpers
+
+helpers.PROJECT_ID = "adit"
+helpers.ROOT_PATH = Path(__file__).resolve().parent
+
+app = typer.Typer()
+
+extra_args = {"allow_extra_args": True, "ignore_unknown_options": True}
+
+app.command()(commands.init_workspace)
+app.command()(commands.compose_up)
+app.command()(commands.compose_down)
+app.command()(commands.stack_deploy)
+app.command()(commands.stack_rm)
+app.command()(commands.lint)
+app.command()(commands.format_code)
+app.command(context_settings=extra_args)(commands.test)
+app.command()(commands.show_outdated)
+app.command()(commands.backup_db)
+app.command()(commands.restore_db)
+app.command()(commands.shell)
+app.command()(commands.generate_certificate_files)
+app.command()(commands.generate_certificate_chain)
+app.command()(commands.generate_django_secret_key)
+app.command()(commands.generate_secure_password)
+app.command()(commands.generate_auth_token)
+app.command()(commands.randomize_env_secrets)
+app.command()(commands.try_github_actions)
+
+
+@app.command()
+def populate_orthancs(
+    reset: Annotated[bool, typer.Option(help="Do not build images")] = False,
+    simulate: Annotated[bool, typer.Option(help="Simulate the command")] = False,
+):
+    """Populate Orthancs with example DICOMs"""
+
+    cmd = f"{helpers.build_compose_cmd()} exec web python manage.py populate_orthancs"
+    if reset:
+        cmd += " --reset"
+
+    helpers.execute_cmd(cmd, simulate=simulate)
+
+
+if __name__ == "__main__":
+    app()

docs/Backups.md

@@ -1,3 +1,3 @@
 # Backups
 
-For database backups django-dbbackup app is used. The backups are done every night at 3 am by a periodic task using the dbbackup management command and stored in the `backups` directory which is mounted as a volume. The dbbackup command can also be called manually with `invoke backup_db`.
+For database backups django-dbbackup app is used. The backups are done every night at 3 am by a periodic task using the dbbackup management command and stored in the `backups` directory which is mounted as a volume. The dbbackup command can also be called manually with `poetry run ./cli.py backup-db`.

docs/Maintenance.md

@@ -5,11 +5,11 @@
 There are different things that can be upgraded:
 
 - The python package dependencies (normal dependencies and dev dependencies)
-  - Check outdated Python packages: `inv show-outdated` (check Python section in output)
+  - Check outdated Python packages: `poetry run ./cli.py show-outdated` (check Python section in output)
   - `poetry update` will update packages according to their version range in `pyproject.toml`
   - Other upgrades (e.g. major versions) must be upgraded by modifying the version range in `pyproject.toml` before calling `poetry update`
 - Javascript dependencies
-  - Check outdated Javascript packages: `inv show-outdated` (check Javascript section in output)
+  - Check outdated Javascript packages: `poetry run ./cli.py show-outdated` (check Javascript section in output)
   - `npm update` will update packages according to their version range in `package.json`
   - Other upgrades (e.g. major versions) must be upgraded by modifying the version range in `packages.json` before calling `npm update`
   - After an upgrade make sure the files in `static/vendor` still link to the correct files in `node_modules`1

example.env

@@ -68,7 +68,7 @@ SITE_DOMAIN=localhost
 # These variables are used to create a certificate key, self-signed certificate,
 # and the corresponding certificate chain. If you have an existing certificate
 # key and signed certificate from your CA, you can generate the corresponding
-# certificate chain using 'invoke generate-certificate-chain'.
+# certificate chain using 'poetry run ./cli.py generate-certificate-chain'.
 SSL_HOSTNAME=localhost
 SSL_IP_ADDRESSES=127.0.0.1
 SSL_SERVER_CERT_FILE="./cert.pem"