Add MLWH cache hack

Dockerfile.dev

@@ -1,6 +1,6 @@
-FROM ghcr.io/wtsi-npg/ub-18.04-baton-irods-4.2.11:latest
+FROM ghcr.io/wtsi-npg/ub-22.04-baton-irods-4.3.4:latest
 
-ARG PYTHON_VERSION=3.12
+ARG PYTHON_VERSION=3.14
 
 ENV DEBIAN_FRONTEND=noninteractive
 
@@ -18,6 +18,7 @@ RUN apt-get update && \
     make \
     libbz2-dev \
     libncurses-dev \
+    libsqlite3-dev \
     libreadline-dev \
     libssl-dev \
     zlib1g-dev
@@ -28,7 +29,7 @@ RUN echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) ma
     tee /etc/apt/sources.list.d/renci-irods.list && \
     apt-get update && \
     apt-get install -q -y --no-install-recommends \
-    irods-icommands="4.2.11-1~$(lsb_release -sc)"
+    irods-icommands="4.3.4-0~$(lsb_release -sc)"
 
 WORKDIR /app
 
@@ -53,7 +54,7 @@ COPY requirements.txt test-requirements.txt /app/
 RUN pip install --no-cache-dir -r requirements.txt && \
     pip install --no-cache-dir -r test-requirements.txt
 
-COPY . /app/
+COPY . /app
 
 RUN pip install --no-cache-dir . && \
     git status && \
@@ -65,4 +66,4 @@ USER appuser
 
 ENTRYPOINT ["/app/docker/entrypoint.sh"]
 
-CMD ["/bin/bash", "-c", "sleep infinity"]
+CMD ["/bin/bash"]

README.md

@@ -62,12 +62,12 @@ To run the tests in a container, you will need to have Docker installed.
 
 With this in place, you can run the tests with the following command:
 
-    docker-compose run app pytest --it
+    docker compose run app pytest --it
 
 There will be a delay the first time this is run because the Docker image will be built.
 To pre-build the image, you can run:
 
-    docker-compose build
+    docker compose build
 
 ## Creating a release
 
@@ -148,4 +148,4 @@ string.
 
 ## Architecture
 
-- `publish-directory` removes public permissions unless explicitly specified by `--group public` to be able to publish privately whilst having iRODS inheritance enabled on sequencing runs collections ([ADR 1](/docs/decisions/adr-01-publish-directory-removes-public-permissions-by-default.md))
+- `publish-directory` removes public permissions unless explicitly specified by `--group public` to be able to publish privately whilst having iRODS inheritance enabled on sequencing runs collections ([ADR 1](/docs/decisions/adr-01-publish-directory-removes-public-permissions-by-default.md))

docker-compose.yml

@@ -19,7 +19,7 @@ services:
   irods-server:
     platform: linux/amd64
     container_name: irods-server
-    image: "ghcr.io/wtsi-npg/ub-16.04-irods-4.2.7:latest"
+    image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3.4:latest"
     ports:
       - "127.0.0.1:1247:1247"
       - "127.0.0.1:20000-20199:20000-20199"
@@ -37,10 +37,8 @@ services:
       context: .
       dockerfile: Dockerfile.dev
     restart: always
-    volumes:
-      - "./tests/.irods:/home/appuser/.irods/"
     environment:
-      IRODS_ENVIRONMENT_FILE: "/home/appuser/.irods/irods_environment.json"
+      IRODS_ENVIRONMENT_FILE: "/app/tests/.irods/irods_environment.json"
       IRODS_PASSWORD: "irods"
     depends_on:
       irods-server:

docker/install_pyenv.sh

@@ -2,7 +2,7 @@
 
 set -ex
 
-PYENV_RELEASE_VERSION=${PYENV_RELEASE_VERSION:="2.4.16"}
+PYENV_RELEASE_VERSION=${PYENV_RELEASE_VERSION:="2.6.16"}
 export PYENV_GIT_TAG="v${PYENV_RELEASE_VERSION}"
 
 PYENV_ROOT=${PYENV_ROOT:-"$HOME/.pyenv"}

pyproject.toml

@@ -18,7 +18,7 @@ dynamic = ["version"]
 dependencies = [
     "npg-python-lib >= 1.0.0,<2",
     "npg_id_generation >=5.0.1",
-    "partisan >=4.0.2,<5",
+    "partisan >=4.1,<5",
     "pymysql >=1.1.1",
     "python-dateutil >=2.9.0,<3",
     "rich >=13.6.0",

requirements.txt

@@ -1,6 +1,6 @@
 cryptography==46.0.5
 npg_id_generation@https://github.com/wtsi-npg/npg_id_generation/releases/download/5.0.1/npg_id_generation-5.0.1.tar.gz
-npg-python-lib@https://github.com/wtsi-npg/npg-python-lib/releases/download/1.1.0/npg_python_lib-1.1.0.tar.gz
+npg-python-lib@https://github.com/wtsi-npg/npg-python-lib/releases/download/1.2.0/npg_python_lib-1.2.0.tar.gz
 partisan@https://github.com/wtsi-npg/partisan/releases/download/4.1.2/partisan-4.1.2.tar.gz
 pymysql==1.1.2
 python-dateutil==2.9.0.post0