Move user-facing docs to the docs-rework PR (#739)

The README front door, the container.md 'Running on a cluster' section, and the
basic_execution.md MPI docs are relocated to #739, which owns the full docs
story (cluster docs now live in a dedicated clusters.md, so keeping the
walkthrough here too would duplicate it). This PR keeps only the code/infra and
the CLAUDE.md build-loop note that the container changes here introduce.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: cailmdaley

README.rst

@@ -1,55 +1,22 @@
 ShapePipe
 =========
 
-|CI| |CD| |python312| |release|
+|CI| |CD| |python39| |release|
 
 .. |CI| image:: https://github.com/CosmoStat/shapepipe/workflows/CI/badge.svg
   :target: https://github.com/CosmoStat/shapepipe/actions?query=workflow%3ACI
 
 .. |CD| image:: https://github.com/CosmoStat/shapepipe/actions/workflows/pages/pages-build-deployment/badge.svg
   :target: https://github.com/CosmoStat/shapepipe/actions/workflows/pages/pages-build-deployment
 
-.. |python312| image:: https://img.shields.io/badge/python-3.12-green.svg
-  :target: https://www.python.org/
+.. |python39| image:: https://img.shields.io/badge/python-3.9-green.svg
+  :target: https://www.python.org/‰
 
 .. |release| image:: https://img.shields.io/github/v/release/CosmoStat/shapepipe
   :target: https://github.com/CosmoStat/shapepipe/releases/latest
 
 ShapePipe is a galaxy shape measurement pipeline developed within the
-CosmoStat lab at CEA Paris-Saclay. It runs the full chain from raw survey
-images to calibrated shear catalogues — object detection, PSF modelling, and
-shape measurement — and produced the first UNIONS cosmic-shear release.
+CosmoStat lab at CEA Paris-Saclay.
 
-Quickstart
-----------
-
-ShapePipe ships as a container image, so you can run the bundled example
-pipeline — a single CFIS tile through the full chain — without installing
-anything:
-
-.. code-block:: bash
-
-    # Apptainer (HPC, no root needed):
-    apptainer exec docker://ghcr.io/cosmostat/shapepipe:develop-runtime shapepipe_run_example
-
-    # ...or Docker:
-    docker run --rm ghcr.io/cosmostat/shapepipe:develop-runtime shapepipe_run_example
-
-The image is published on every push to the `GitHub Container Registry
-<https://github.com/CosmoStat/shapepipe/pkgs/container/shapepipe>`_:
-``:develop`` tracks the integration branch, release tags (e.g. ``:v1.1.0``) a
-stable cut, and the ``-runtime`` suffix selects the slim batch image over the
-full interactive one.
-
-Documentation
--------------
-
-Full documentation lives at https://cosmostat.github.io/shapepipe. Good places
-to start:
-
-- `Installation <https://cosmostat.github.io/shapepipe/installation.html>`_ — getting ShapePipe onto your machine or cluster.
-- `Basic execution <https://cosmostat.github.io/shapepipe/basic_execution.html>`_ and `configuration <https://cosmostat.github.io/shapepipe/configuration.html>`_ — running ``shapepipe_run`` and writing pipeline configs.
-- `Container workflow <https://cosmostat.github.io/shapepipe/container.html>`_ — the two image targets, the ``pyproject.toml`` / ``uv.lock`` / ``Dockerfile`` layers, and how to run on a SLURM cluster (with a worked candide example).
-
-If you use ShapePipe in academic work, please cite Guinot et al. (2022) and
-Farrens et al. (2022).
+See the `documentation <https://cosmostat.github.io/shapepipe>`_ for details
+on how to install and run ShapePipe.

docs/source/basic_execution.md

@@ -37,33 +37,11 @@ shapepipe_run -c <PATH TO CONFIG FILE>
 ## Running the Pipeline with MPI
 
 ShapePipe can also use [mpi4py](https://mpi4py.readthedocs.io/en/stable/)
-to spread work across multiple nodes of a cluster. Set `MODE = mpi` in the
-`[EXECUTION]` section of the config and launch with an MPI runner:
+for managing parallel processes on clusters with multiple nodes.
+The `shapepipe_run` script can be run with MPI as follows
 
 ```bash
-mpiexec -n <NUMBER OF RANKS> shapepipe_run -c <PATH TO CONFIG FILE>
+mpiexec -n <NUMBER OF CORES> shapepipe_run
 ```
 
-where `<NUMBER OF RANKS>` is the number of MPI processes to start.
-
-### Through the container (the supported way on a cluster)
-
-On a cluster you run ShapePipe from the published image as a standard Apptainer
-*hybrid* MPI job: the **host** `mpirun`/`mpiexec` launches one container rank per
-slot, and the OpenMPI bundled in the image wires the ranks together.
-
-```bash
-# one-time: pull the runtime image
-apptainer pull shapepipe.sif docker://ghcr.io/cosmostat/shapepipe:develop-runtime
-
-# load a host MPI in the same family as the image's OpenMPI (5.0.x), then launch
-module load openmpi
-mpirun -n <NUMBER OF RANKS> \
-    apptainer exec --bind "$PWD:$PWD" shapepipe.sif \
-    shapepipe_run -c <PATH TO CONFIG FILE>
-```
-
-The image ships **OpenMPI 5.0.x** so that its PMIx matches modern cluster
-launchers. The host and container MPI must be compatible: if you see *N* copies
-of `rank 0 of 1` instead of one *N*-rank job, load a host OpenMPI in the 5.0.x
-family. See `example/pbs/candide_mpi.sh` for a complete SLURM batch script.
+where `<NUMBER OF CORES>` is the number of cores to allocate to the run.

docs/source/container.md

@@ -91,44 +91,6 @@ in, all because something tries to write under `/app` or `$HOME`:
 If you bypass `/tmp` (e.g. with a custom apptainer profile) you may need
 to override these manually.
 
-## Running on a cluster (SLURM)
-
-On a batch cluster you pull the slim `runtime` image once to a SIF, then
-submit a job that runs `shapepipe_run` through it. The repo ships ready
-SLURM scripts for the **candide** cluster in `example/pbs/` —
-`candide_smp.sh` (single node) and `candide_mpi.sh` (multi-node hybrid
-MPI) — that you can copy and adapt. The example below runs the bundled
-single-tile pipeline end to end:
-
-```bash
-# 1. Keep the SIF and Apptainer's scratch off the quota-limited $HOME.
-#    On candide a pull under $HOME fails with "disk quota exceeded";
-#    point both at a roomy data partition instead.
-export DATA=/n17data/$USER                 # adjust to your data partition
-export APPTAINER_CACHEDIR=$DATA/.apptainer
-
-# 2. Pull the runtime image (~850 MB).
-apptainer pull "$DATA/shapepipe-runtime.sif" \
-    docker://ghcr.io/cosmostat/shapepipe:develop-runtime
-
-# 3. Submit the example pipeline. SPDIR is your local clone; it is
-#    bind-mounted at the same path inside the container so the config's
-#    $SPDIR-relative input/output directories resolve identically in and
-#    out of the container.
-SP_IMAGE="$DATA/shapepipe-runtime.sif" SPDIR="/path/to/shapepipe" \
-    sbatch example/pbs/candide_smp.sh
-```
-
-Both job scripts read `SP_IMAGE` (the SIF) and `SPDIR` (the clone) from
-the environment, so the same script serves the example and a real run —
-point the config inside the script at your own pipeline. The MPI script
-additionally needs the host's OpenMPI to match the container's PMIx wire
-protocol; it `module load`s a compatible OpenMPI (the image ships the
-5.0.x series), and the script's header comments explain the contract.
-
-Adapting to another SLURM cluster is mostly the `#SBATCH` directives and
-the `module load` line — the `apptainer exec` invocation carries over.
-
 ## Three configuration layers
 
 Three files determine what the image contains. Each has a clear role; the