Add put method for Collections

Change defaults for checksum-related API method keywords to False in
order to make behaviour and responsibility for the decision clearer.
API callers are now responsible for setting these flags to True where
they are needed.

Separate checksum retrieval, updates and verification more clearly.

Add a checkum keyword to DataObject::list.

Add checksum size/consistency check for zero-length data objects.

Dockerfile.dev

@@ -17,6 +17,7 @@ RUN apt-get update && \
     git \
     make \
     libbz2-dev \
+    libffi-dev \
     libncurses-dev \
     libreadline-dev \
     libssl-dev \
@@ -43,6 +44,8 @@ COPY ./docker/install_pyenv.sh /app/docker/install_pyenv.sh
 
 RUN /app/docker/install_pyenv.sh
 
+ENV MAKE_OPTS="-j 8"
+
 RUN pyenv install "$PYTHON_VERSION"
 RUN pyenv global "$PYTHON_VERSION"
 

README.md

@@ -265,7 +265,7 @@ distinguish between these circumstances.
 ## Requirements
 
 - The `baton-do` executable from the [baton](https://github.com/wtsi-npg/baton)
-  iRODS client distribution.
+  iRODS client distribution. Version >=4.3.1 is required.
 - The unit tests use the
   [iRODS client icommands](https://github.com/irods/irods_client_icommands)
   clients. These are not required during normal operation.

docker-compose.yml

@@ -3,7 +3,7 @@ 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-18.04-irods-4.2.11:latest"
     ports:
       - "127.0.0.1:1247:1247"
       - "127.0.0.1:20000-20199:20000-20199"
@@ -26,6 +26,7 @@ services:
     environment:
       IRODS_ENVIRONMENT_FILE: "/home/appuser/.irods/irods_environment.json"
       IRODS_PASSWORD: "irods"
+      IRODS_VERSION: "4.2.11"
     depends_on:
       irods-server:
         condition: service_healthy