Adding READMEs to all directories

.dockerignore

@@ -0,0 +1,7 @@
+**/build
+.git
+**/.mypy_cache
+.venv*
+**/.pytest_cache
+**/.ruff_cache
+**/__pycache__

.env.sample

@@ -54,7 +54,6 @@ ORTHANC_ANON_URL=http://orthanc-anon:8042
 ORTHANC_ANON_USERNAME=
 ORTHANC_ANON_PASSWORD=
 ORTHANC_ANON_AE_TITLE=
-ORTHANC_ANON_HTTP_TIMEOUT=60
 ORTHANC_AUTOROUTE_ANON_TO_ENDPOINT=false
 ENABLE_DICOM_WEB=true
 STUDY_TIME_OFFSET=

.github/workflows/main.yml

@@ -28,11 +28,11 @@ concurrency:
 
 jobs:
     lint:
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-24.04
         timeout-minutes: 5
         steps:
             - name: Checkout
-              uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+              uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
             - name: Run pre-commit
               uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
@@ -46,64 +46,65 @@ jobs:
                   docker compose config --quiet
 
     test:
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-24.04
         timeout-minutes: 30
         strategy:
             fail-fast: false # run all tests if even if one fails
             matrix:
                 package_dir: [pixl_core, hasher, pixl_dcmd, cli, pixl_export, pixl_imaging, pytest-pixl]
 
         steps:
-            - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+            - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-            - name: Init Python
-              uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
+            - name: Install uv
+              uses: astral-sh/setup-uv@v4
               with:
+                  version: "0.5.10"
                   python-version: "3.11"
-                  cache: "pip"
+                  enable-cache: true
+
 
             - name: Install Python dependencies
               run: |
-                  python -m pip install --upgrade pip
-                  pip install -e pytest-pixl/
-                  pip install -e pixl_core/[test]
-                  pip install -e ${{ matrix.package_dir }}/[test]
+                  uv sync
 
             - name: Run tests and generate coverage report
               working-directory: ${{ matrix.package_dir }}
-              run: COV_CORE_SOURCE=src COV_CORE_CONFIG=.coveragerc COV_CORE_DATAFILE=.coverage.eager pytest --cov=src --cov-append --cov-report=xml --cov-report=term-missing
+              run: |
+                  source ../.venv/bin/activate
+                  COV_CORE_SOURCE=src COV_CORE_CONFIG=.coveragerc COV_CORE_DATAFILE=.coverage.eager pytest --cov=src --cov-append --cov-report=xml --cov-report=term-missing
               env:
                   ENV: test
                   AZURE_KEY_VAULT_NAME: test
                   AZURE_KEY_VAULT_SECRET_NAME: test
 
             - name: Upload coverage reports to Codecov
-              uses: codecov/codecov-action@e28ff129e5465c2c0dcc6f003fc735cb6ae0c673 # v4.5.0
+              uses: codecov/codecov-action@7f8b4b4bde536c465e797be725718b88c5d95e0e # v5.1.1
               with:
                   directory: ${{ matrix.package_dir }}
               env:
                   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     system-test:
         if: ${{ ! github.event.pull_request.draft || contains(github.event.pull_request.title, '[force-system-test]') }}
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-24.04
         timeout-minutes: 30
         steps:
-            - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-            - uses: docker/setup-buildx-action@988b5a0280414f521da01fcc63a27aeeb4b104db # v3
-            - name: Init Python
-              uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
+            - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+            - uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349 # v3
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v4
               with:
+                  version: "0.5.10"
                   python-version: "3.11"
-                  cache: "pip"
+                  enable-cache: true
 
             - name: Install Python dependencies
-              # The -e option is required here due to the way the
+              # Editable install required here due to the way the
               # code determines the export directory. See issue #318.
               run: |
-                  pip install -e pytest-pixl/
-                  pip install -e pixl_core/[test]
-                  pip install -e cli/[test]
+                  uv sync
 
             - name: Create .secrets.env
               run: touch test/.secrets.env
@@ -129,7 +130,7 @@ jobs:
                   HASHER_API_AZ_TENANT_ID: ${{ secrets.EXPORT_AZ_TENANT_ID }}
                   HASHER_API_AZ_KEY_VAULT_NAME: ${{ secrets.EXPORT_AZ_KEY_VAULT_NAME }}
               run: |
-                  ./run-system-test.sh coverage
+                  uv run ./run-system-test.sh coverage
                   echo FINISHED SYSTEM TEST SCRIPT
 
             - name: Dump queue docker logs for debugging
@@ -179,8 +180,8 @@ jobs:
 
 
             - name: Upload coverage reports to Codecov
-              uses: codecov/codecov-action@e28ff129e5465c2c0dcc6f003fc735cb6ae0c673 # v4.5.0
+              uses: codecov/codecov-action@7f8b4b4bde536c465e797be725718b88c5d95e0e # v5.1.1
               with:
                 directory: test
               env:
-                CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+                CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -53,3 +53,9 @@ repos:
             language: script
             types_or: [python, shell, yaml, dockerfile]
             entry: bin/linters/check_headers_exist.sh
+
+    # avoid forgetting to update the lock file after pyproject.toml changes
+    - repo: https://github.com/astral-sh/uv-pre-commit
+      rev: 0.5.15
+      hooks:
+        - id: uv-lock

.renovaterc.json5

@@ -2,6 +2,36 @@
   $schema: "https://docs.renovatebot.com/renovate-schema.json",
   extends: [
     "github>UCL-ARC/.github//renovate/default-config.json",
-    "schedule:monthly",
+    ":assignAndReview(team:arc-dev)",
+    "group:allNonMajor"
   ],
-}
+  customDatasources: {
+    dicomSpec: {
+      defaultRegistryUrlTemplate: "https://dicom.nema.org/medical/dicom",
+      format: "html",
+    },
+  },
+  customManagers: [
+    {
+      customType: "regex",
+      description: "Update DICOM Spec edition used for validation",
+      fileMatch: [
+        "orthanc/orthanc-anon/plugin/download_dicom_spec.py",
+        "pixl_dcmd/src/pixl_dcmd/main.py",
+      ],
+      matchStrings: [
+        'edition\\s?=\\s?"(?<currentValue>.*?)"\n',
+        '.*\\(edition\\s?=\\s?"(?<currentValue>.*?)"\\)\n',
+      ],
+      depNameTemplate: "dicomSpec",
+      datasourceTemplate: "custom.dicomSpec",
+    },
+  ],
+  packageRules: [
+    {
+      matchDatasources: ["custom.dicomSpec"],
+      extractVersion: "/medical/dicom/(?<version>\\d{4}[a-z])/",
+      versioning: "loose",
+    }
+  ]
+}

README.md

@@ -20,18 +20,17 @@ Please request access to Slab and add further details in a [new blank issue](htt
 </details>
 
 
-## Installation
+## Installation in production
 
 Install the PIXL Python modules by running the following commands from the top-level `PIXL/` directory:
 
 ```shell
-python -m pip install -e pixl_core/
-python -m pip install -e cli/
+uv sync --package pixl-cli
 ```
 
 Note, the CLI currently [needs to be installed in editable mode](https://github.com/SAFEHR-data/PIXL/issues/318).
 
-## Development
+## Developer setup
 
 [Follow the developer setup instructions](./docs/setup/developer.md).
 

bin/README.md

@@ -1,6 +1,24 @@
 ## 'PIXL/bin' Directory Contents
 
-### Subdirectories
+<details>
+<summary>
+<h3> Subdirectories with links to the relevant README </h3> 
+
+</summary>
 
 [linters](./linters/README.md)
 
+</details>
+
+<details>
+<summary>
+<h3> Files </h3> 
+
+</summary>
+
+| **User docs** |
+| :--- | 
+README.md
+
+</details>
+

bin/linters/README.md

@@ -1,6 +1,16 @@
+A directory that contains the files used for linting.
+
 ## 'PIXL/bin/linters' Directory Contents
 
-### Files
+<details>
+<summary>
+<h3> Files </h3> 
+
+</summary>
+
+| **Code** | **User docs** |
+| :--- | :--- |
+| check_headers_exist.sh | README.md |
 
-check_headers_exist.sh
+</details>
 

cli/README.md

@@ -9,15 +9,13 @@ stopped cleanly.
 * Python version 3.11 (matching python versions in [pixl-ci](../.github/workflows/main.yml) and [dev](../docs/setup/developer.md#installation-of-pixl-modules)).
 * [Docker](https://docs.docker.com/get-docker/) with version `>=27.0.3`
 * [Docker Compose](https://docs.docker.com/compose/install/#installation-scenarios) with version `>=v2.28.1-desktop.1`
-* We recommend installing PIXL project in specific virtual environment using a environment
-management tool such as [conda](https://docs.conda.io/en/latest/) or
-[virtualenv](https://virtualenv.pypa.io/en/latest/). 
+* [uv](https://docs.astral.sh/uv/) to install PIXL in a virtual environment
 See detailed instructions [here](../docs/setup/developer.md#setting-up-python-virtual-environment)
 
 ## Installation
 Activate your python virtual environment and install `PIXL` project in editable mode by running
 ```bash
-python -m pip install -e ../pixl_core -e .
+uv sync
 ```
 
 ## Usage
@@ -130,7 +128,7 @@ are currently available, you can use the `pixl --help` command:
 ### Local installation
 Activate your python environment and install project locally in editable mode with the development and testing dependencies by running
 ```bash
-python -m pip install -e ../pixl_core -e ../pytest-pixl -e ".[test]" -e ".[dev]"
+uv sync
 ```
 
 ### Running tests
@@ -145,15 +143,29 @@ pytest -vs tests/test_docker_commands.py #e.g., for particular tests
 
 ## 'PIXL/cli' Directory Contents
 
-### Subdirectories
+<details>
+<summary>
+<h3> Subdirectories with links to the relevant README </h3> 
+
+</summary>
 
 [src](./src/README.md)
 
 [tests](./tests/README.md)
 
-### Files
+</details>
+
+<details>
+<summary>
+<h3> Files </h3> 
+
+</summary>
+
+| **Configuration** | **User docs** |
+| :--- | :--- |
+| pyproject.toml | README.md |
+
+</details>
 
-pyproject.toml
 
-README.md
 

cli/pyproject.toml

@@ -4,18 +4,17 @@ version = "0.2.0rc0"
 authors = [{ name = "PIXL authors" }]
 description = "PIXL command line interface"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = ["Programming Language :: Python :: 3"]
 dependencies = [
     "core==0.2.0rc0",
     "click==8.1.7",
-    "tqdm==4.66.4",
+    "tqdm==4.67.1",
 ]
 
 [project.optional-dependencies]
 test = [
     "core[test]==0.2.0rc0",
-    "pytest-mock==3.14.*",
 ]
 dev = [
     "core[dev]==0.2.0rc0",
@@ -25,8 +24,13 @@ dev = [
 pixl = "pixl_cli.main:cli"
 
 [build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling>=1.0.0"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+dev-mode-dirs = [
+    "src"
+]
 
 [tool.coverage.report]
 exclude_also = [

cli/src/README.md

@@ -1,6 +1,26 @@
+This directory contains the source files for the PIXL commands line interface.
+
 ## 'PIXL/cli/src' Directory Contents
 
-### Subdirectories
+<details>
+<summary>
+<h3> Subdirectories with links to the relevant README </h3> 
+
+</summary>
 
 [pixl_cli](./pixl_cli/README.md)
 
+</details>
+
+<details>
+<summary>
+<h3> Files </h3> 
+
+</summary>
+
+| **User docs** |
+| :--- |
+README.md
+
+</details>
+