Allow PIXL CLI to be installed in non-editable mode

.github/workflows/main.yml

@@ -101,10 +101,8 @@ jobs:
                   enable-cache: true
 
             - name: Install Python dependencies
-              # Editable install required here due to the way the
-              # code determines the export directory. See issue #318.
               run: |
-                  uv sync
+                  uv sync --no-editable
 
             - name: Create .secrets.env
               run: touch test/.secrets.env

cli/README.md

@@ -41,8 +41,13 @@ pixl dc up
 will run `docker compose --project pixl_{pixl_env} up --wait --build --remove-orphans`, where `pixl_env`
 is determined by the `ENV` environment variable.
 
+Note, if your `.env` file is in a different directory from the `docker-compose.yml` file, you can pass in the
+path to you `.env` file using the `--env-file` argument.
+
 ### Configuration
 
+#### Rabbit MQ and PostgreSQL
+
 The `rabbitmq` and PIXL DB `postgres` services are configured by setting the following environment variables
 (default values shown):
 
@@ -69,6 +74,30 @@ PIXL_IMAGING_API_RATE=1
 
 where the `*_RATE` variables set the default querying rate for the message queues.
 
+#### Host directories
+
+The PIXL root and export directories on the host machine can be configured using
+the following environment variables:
+
+```sh
+PIXL_ROOT=../
+HOST_EXPORT_ROOT_DIR=../projects/exports
+HOST_EXPORT_ROOT_DIR_MOUNT=./projects/exports
+```
+
+The `PIXL_ROOT` directory must contain the `docker-compose.yml` file and `projects/configs` folders
+from the top-level directory of this repository. `PIXL_ROOT` must also contain the `.sample.env` file
+if you would like to use the `pixl check_env` command. This path can be absolute or relative to your
+`.env` file (which must be in your current working directory). This variable is used by the PIXL CLI
+when running PIXL.
+
+The `HOST_EXPORT_ROOT_DIR` is the directory on your host machine that data will be exported to. This path
+can be absolute or relative to your `.env` file. This variable is used by the PIXL CLI when running PIXL.
+
+The `HOST_EXPORT_ROOT_DIR_MOUNT` is the directory on your host machine that will be mounted for exporting data to.
+The path can be absolute or relative to the `PIXL_ROOT`. This variable is used by docker-compose to mount the
+export directory when starting PIXL.
+
 ### Running the pipeline
 
 Populate queue for Imaging using parquet files:

cli/src/pixl_cli/_config.py

@@ -21,6 +21,21 @@
 env_file = Path.cwd() / ".env"
 config = Config(RepositoryEnv(env_file)) if env_file.exists() else Config(RepositoryEmpty())
 
+# The PIXL root and export root directories from the point of view of the docker host (which
+# is where the CLI runs). For the export directory within the export-api container, see
+# pixl_export/main.py: EXPORT_API_EXPORT_ROOT_DIR
+PIXL_ROOT = config(
+    "PIXL_ROOT",
+    default=Path(__file__).parents[3],
+    cast=Path,
+).resolve()
+
+HOST_EXPORT_ROOT_DIR = config(
+    "HOST_EXPORT_ROOT_DIR",
+    default=Path(__file__).parents[3] / "projects" / "exports",
+    cast=Path,
+).resolve()
+
 SERVICE_SETTINGS = {
     "rabbitmq": {
         "host": config("RABBITMQ_HOST"),

cli/src/pixl_cli/_docker_commands.py

@@ -18,10 +18,9 @@
 from typing import Optional
 
 import click
-from decouple import config
 from loguru import logger
 
-PIXL_ROOT = Path(__file__).parents[3].resolve()
+from pixl_cli._config import PIXL_ROOT, config
 
 
 # Required to allow passing unkown options to docker-compose

cli/src/pixl_cli/_io.py

@@ -18,20 +18,19 @@
 import json
 from datetime import datetime
 from enum import StrEnum, auto
-from pathlib import Path
 from typing import TYPE_CHECKING
 
 import numpy as np
 import pandas as pd
 from core.exports import ParquetExport
 from loguru import logger
 
+from pixl_cli._config import HOST_EXPORT_ROOT_DIR
+
 if TYPE_CHECKING:
-    from core.db.models import Image
+    from pathlib import Path
 
-# The export root dir from the point of view of the docker host (which is where the CLI runs)
-# For the view from inside, see pixl_export/main.py: EXPORT_API_EXPORT_ROOT_DIR
-HOST_EXPORT_ROOT_DIR = Path(__file__).parents[3] / "projects" / "exports"
+    from core.db.models import Image
 
 
 def project_info(resources_path: Path) -> tuple[str, datetime]:

cli/src/pixl_cli/main.py

@@ -25,14 +25,19 @@
 import requests
 from core.exports import ParquetExport
 from core.patient_queue.producer import PixlProducer
-from decouple import RepositoryEnv, UndefinedValueError, config
+from decouple import RepositoryEnv, UndefinedValueError
 from loguru import logger
 
-from pixl_cli._config import SERVICE_SETTINGS, api_config_for_queue
+from pixl_cli._config import (
+    HOST_EXPORT_ROOT_DIR,
+    PIXL_ROOT,
+    SERVICE_SETTINGS,
+    api_config_for_queue,
+    config,
+)
 from pixl_cli._database import exported_images_for_project
 from pixl_cli._docker_commands import dc
 from pixl_cli._io import (
-    HOST_EXPORT_ROOT_DIR,
     make_radiology_linker_table,
     project_info,
     read_patient_info,
@@ -45,8 +50,6 @@
 # localhost needs to be added to the NO_PROXY environment variables on GAEs
 os.environ["NO_PROXY"] = os.environ["no_proxy"] = "localhost"
 
-PIXL_ROOT = Path(__file__).parents[3].resolve()
-
 
 @click.group()
 @click.option("--debug/--no-debug", default=False)

docker-compose.yml

@@ -305,7 +305,7 @@ services:
         extra_hosts:
             - "host.docker.internal:host-gateway"
         volumes:
-            - ${PWD}/projects/exports:/run/projects/exports
+            - ${HOST_EXPORT_ROOT_DIR_MOUNT:-${PWD}/projects/exports}:/run/projects/exports
             - ${PWD}/projects/configs:/${PROJECT_CONFIGS_DIR:-/projects/configs}:ro
 
     imaging-api:

docs/setup/developer.md

@@ -30,6 +30,18 @@ uv sync
 
 See each service's README for instructions for individual developing and testing instructions.
 
+### Non-editable installation
+
+By default, `uv` will install `pixl` and its workspace members in editable mode. To install in non-editable mode:
+
+```shell
+uv sync --no-editable
+```
+
+You will need to set the `PIXL_ROOT`, `HOST_EXPORT_ROOT_DIR`, and `HOST_EXPORT_ROOT_DIR_MOUNT` environment
+variables if you install PIXL in non-editable mode. See the [`cli` docs](../../cli/README.md#host-directories)
+for more info.
+
 ## Testing
 
 ### Module-level testing

pyproject.toml

@@ -67,3 +67,7 @@ dev = [
     "nibabel==5.3.2",
 ]
 
+[tool.coverage.report]
+exclude_also = [
+  "if TYPE_CHECKING:"
+]

pytest-pixl/src/pytest_pixl/ftpserver.py

@@ -13,6 +13,7 @@
 #  limitations under the License.
 """A ligthweight FTPS server supporting implicit SSL for use in PIXL tests."""
 
+import importlib.resources
 from pathlib import Path
 
 from decouple import config
@@ -89,12 +90,12 @@ def __init__(self, home_root: Path, host_address: str) -> None:
         self.home_dir: Path = home_root / self.user_name
         self.home_dir.mkdir()
 
-        self.certfile = Path(__file__).parents[1] / "resources" / "ssl" / "localhost.crt"
-        self.keyfile = Path(__file__).parents[1] / "resources" / "ssl" / "localhost.key"
+        ssl_dir = importlib.resources.files("pytest-pixl") / "src" / "resources" / "ssl"
+        self.certfile = Path(str(ssl_dir.joinpath("localhost.crt")))
+        self.keyfile = Path(str(ssl_dir.joinpath("localhost.key")))
 
         self.authorizer = DummyAuthorizer()
         self.handler = SSLImplicitFTPHandler
-
         self._add_user()
         self._setup_TLS_handler()
         self._create_server()
@@ -116,8 +117,8 @@ def _setup_TLS_handler(self) -> None:
 
     def _check_ssl_files(self) -> None:
         # Make sure we have access to the SSL certificates
-        certfile_path = Path(self.certfile)
-        keyfile_path = Path(self.keyfile)
+        certfile_path = self.certfile
+        keyfile_path = self.keyfile
         assert certfile_path.exists(), f"Could not find certfile at {certfile_path.absolute()}"
         assert keyfile_path.exists(), f"Could not find keyfile at {keyfile_path.absolute()}"
 

test/.env

@@ -89,3 +89,8 @@ FTP_USER_PASSWORD=longpassword
 
 # Project configs directory
 PROJECT_CONFIGS_DIR=projects/configs
+
+# Host env variables
+PIXL_ROOT=../
+HOST_EXPORT_ROOT_DIR=../projects/exports
+HOST_EXPORT_ROOT_DIR_MOUNT=./projects/exports