Merge branch 'main' into milanmlft/rm-pixl_config

.github/workflows/main.yml

@@ -33,9 +33,6 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Ensure copyright and license header are present
-        run: ./.github/linters/check_headers_exist.sh
-
       - name: Run pre-commit
         uses: pre-commit/[email protected]
         with:

.pre-commit-config.yaml

@@ -30,3 +30,9 @@ repos:
         entry: mypy
         args: ['--config-file=setup.cfg']
         additional_dependencies: ['mypy', 'types-PyYAML', 'types-requests', 'types-python-slugify', 'types-psycopg2']
+      - id: copyright-headers
+        name: copyright-headers
+        language: script
+        types_or: [python, shell, yaml, dockerfile]
+        entry: bin/linters/check_headers_exist.sh
+

README.md

@@ -142,7 +142,7 @@ setfacl -R -m d:g::rwX /gae/pixl_dev
 
 ### 1. Choose deployment environment
 
-This is one of dev|test|staging|prod and referred to as `<environment>` in the docs.
+This is one of `dev|test|staging|prod` and referred to as `<environment>` in the docs.
 
 ### 2. Initialise environment configuration
 

.github/linters/check_headers_exist.sh → bin/linters/check_headers_exist.sh

@@ -12,15 +12,15 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
+set -euo pipefail
 
-for ext in ".yml" ".yaml" ".sh" "Dockerfile" ".py"
-do
-    # shellcheck disable=SC2044
-    for path in $(find . -name "*$ext")
-    do
-        if ! grep -q "Copyright" "$path"; then
-            echo -e "\n\e[31m»»» ⚠️  No copyright/license header in $path"
-            exit 1
-        fi
-    done || exit 1
+for f in "$@"; do
+    if ! grep -q '#.*Copyright.*University College London Hospitals NHS Foundation Trust' "$f"; then
+        echo "No copyright notice found in $f"
+        exit 1
+    fi
+    if ! grep -q '#.*Licensed under the Apache License, Version 2.0' "$f"; then
+        echo "No licence notice found in $f"
+        exit 1
+    fi
 done

cli/README.md

@@ -20,7 +20,7 @@ management tool such as [conda](https://docs.conda.io/en/latest/) or
 Then install in editable mode by running
 
 ```bash
-pip install -e ../pixl_core/ .
+pip install -e ../pixl_core/ -e .
 ```
 
 ## Usage
@@ -136,7 +136,7 @@ Commands:
 Install locally in editable mode with the development and testing dependencies by running
 
 ```bash
-pip install -e ../pixl_core/ .[test]
+pip install -e ../pixl_core/ -e .[test]
 ```
 
 ### Running tests

pixl_core/README.md

@@ -24,7 +24,7 @@ pip install -e .
 ## Testing
 
 ```bash
-pip install -e .[test] && pip install ../pytest-pixl
+pip install -e .[test] && pip install -e ../pytest-pixl
 pytest
 ```
 

pixl_dcmd/README.md

@@ -20,7 +20,7 @@ Specifically, the `pixl_dcmd` package provides the following functionality:
 Install the Python dependencies with
 
 ```bash
-pip install -e ../pixl_core/ .[test,dev]
+pip install -e ../pixl_core/ -e .[test,dev]
 ```
 
 ## Test

pixl_ehr/README.md

@@ -27,13 +27,13 @@ On Windows, follow [these instructions](https://www.postgresqltutorial.com/postg
 Then install the Python dependencies with
 
 ```bash
-pip install -e ../pixl_core/ .
+pip install -e ../pixl_core/ -e .
 ```
 
 ## Test
 
 ```bash
-pip install -e ../pixl_core/ .[test]
+pip install -e ../pixl_core/ -e .[test]
 pytest -m "not processing"
 ```
 

pixl_imaging/README.md

@@ -12,7 +12,7 @@ for the requested imaging study, if it didn't already exist.
 ## Installation
 
 ```bash
-pip install -e ../pixl_core/ .
+pip install -e ../pixl_core/ -e .
 ```
 
 ## Test