CosmoStat · cailmdaley · Sep 28, 2026 · Sep 28, 2026 · Sep 28, 2026 · Sep 28, 2026
diff --git a/CLAUDE.md b/CLAUDE.md
@@ -81,19 +81,35 @@ Full detail: `docs/source/installation.md` and `docs/source/container.md`.
 
 - `src/shapepipe/` — the package (src-layout). `modules/` holds the pipeline
   modules and their `*_runner.py` wrappers; `pipeline/` is execution and file
-  I/O; `utilities/`; `canfar/` is CANFAR/cluster job orchestration. Console entry
-  points (`shapepipe_run`, `summary_run`, `canfar_*`) are defined under
+  I/O; `utilities/`; `canfar/` monitors CANFAR sessions. Console entry
+  points (`shapepipe_run`, `canfar_*`, `plot_coverage_map`) are defined under
   `[project.scripts]`.
 - `tests/` — the whole test suite, one discovery root: `module/` (per-module
   unit/property/integration tests), `unit/` (structural), `science/` (fast
   guardrails), `cluster/` (candide-only), `helpers/` (shared library code).
   See `tests/README.md`.
+- `workflow/` — **the production orchestration**: a Snakemake workflow over the
+  same `shapepipe_run` calls. `bin/sp` is the entry point (`run`, `report`,
+  `container`, `cancel`); `Snakefile` plus `rules/{prepare,exposure,tile}.smk`
+  are the rule graph; `scripts/` holds the plain Python each rule
+  shells out to; `config.yaml` declares one run (tile list, the scratch and
+  persistent roots, the container); `config/cfis/` holds the committed ini
+  chain; `profiles/nibi/config.yaml` is the SLURM executor profile. Deep
+  reference: `workflow/README.md`. User-facing: `docs/source/workflow.md`.
 - `example/` — a runnable example pipeline (`example/config.ini`) on a single
   CFIS tile; doubles as the CI smoke test.
 - `scripts/` — shell / Python / notebook helpers (`sh/`, `python/`, `jupyter/`),
   symlinked onto `$PATH` inside the image.
 - `docs/` — Sphinx sources; the API docs are generated from docstrings.
 
+**There is no concept of a catalogue version in the code.** Nothing branches on
+`v1.3`..`v1.6` or `v2.0`, and there are no sky patches (`P1`..`P9`): a campaign
+is a tile list, and the version of a catalogue is the git tag of the code that
+produced it. The pre-Snakemake bash job
+layer (`scripts/sh/run_job_sp_canfar_v2.0.bash`, `job_sp_canfar_v2.0.bash`,
+`job_list_help.bash`, `functions.sh`) stays — it is version-free, and
+sp_validation's image-simulation workflow calls it.
+
 ## Development workflow
 
 **We are in rapid iteration.** Changes that require re-running the pipeline are fine; a PR that changes science defaults (detection parameters, cuts, module options) does not need a completed rerun to be accepted — state what we expect the rerun to show, and do the rerun when it comes up.

diff --git a/Dockerfile b/Dockerfile
@@ -86,7 +86,7 @@
        --disable-dlopen --disable-sphinx && \
    make -j"$(nproc)" && make install && \
    cd / && rm -rf /tmp/openmpi-*
 ENV PATH="/opt/ompi/bin:${PATH}" \
    LD_LIBRARY_PATH="/opt/ompi/lib:${LD_LIBRARY_PATH}"

 # uv — fast reproducible Python deps installer. pyproject.toml + uv.lock
@@ -139,6 +139,7 @@
     uv pip install --no-deps -e . && \
     for ext in .py .sh .bash; do \
         for script in /app/scripts/*/*$ext; do \
+            [ -e "$script" ] || continue; \
             link_name=$(basename $script $ext); \
             ln -s $script /usr/local/bin/$link_name; \
         done; \

diff --git a/README.rst b/README.rst
@@ -49,7 +49,8 @@ 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>`_ — what's in the image and the ``pyproject.toml`` / ``uv.lock`` / ``Dockerfile`` layers.
-- `Running on a cluster <https://cosmostat.github.io/shapepipe/clusters.html>`_ — pulling the image and submitting jobs, with worked candide (SLURM) and CANFAR examples.
+- `Running on a cluster <https://cosmostat.github.io/shapepipe/clusters.html>`_ — pulling the image and submitting jobs, with a worked candide (SLURM) example.
+- `The Snakemake workflow <https://cosmostat.github.io/shapepipe/workflow.html>`_ — the production orchestration for a whole tile list, driven by ``workflow/bin/sp``.
 
 If you use ShapePipe in academic work, please cite Guinot et al. (2022) and
 Farrens et al. (2022).
diff --git a/bin/canfar_submit_job.py b/bin/canfar_submit_job.py
diff --git a/bin/summary_run.py b/bin/summary_run.py
diff --git a/docs/source/clusters.md b/docs/source/clusters.md
@@ -1,10 +1,9 @@
 # Running on a Cluster
 
 ShapePipe runs the same way on every cluster: **through the container**. You
-pull the image once, bind-mount your clone, and run `shapepipe_run` (or the
-CANFAR submission tooling) inside it — there is no environment to install or
-activate on the host. This page covers the shared pattern, then the specifics
-for each supported machine.
+pull the image once, bind-mount your clone, and run `shapepipe_run` inside it —
+there is no environment to install or activate on the host. This page covers
+the shared pattern, then the specifics for each supported machine.
 
 For what is *inside* the image and how it is built, see
 [Container Workflow](container.md).
@@ -67,32 +66,12 @@ over unchanged.
 
 ## CANFAR
 
-CANFAR submission does not go through a batch scheduler. Instead you submit
-container jobs to CANFAR's headless system with the `canfar_submit_job` console
-script (backed by the `canfar` library), and watch them with `canfar_monitor` /
-`canfar_monitor_log`. Pipeline steps are **bit-coded** through `-j` (the same
-scheme as `scripts/sh/job_sp_canfar.bash`), the PSF model is chosen with
-`-p psfex|mccd`, and `-V` selects the image version:
+ShapePipe has no CANFAR submission path. Production orchestration is the
+Snakemake workflow in `workflow/` — see `workflow/README.md`. It is SLURM-only and has no CANFAR execution mode, so a
+CANFAR campaign means moving to a SLURM site (nibi, candide).
 
-```bash
-# Submit pipeline step(s) for the configured tiles (bit-coded -j).
-canfar_submit_job -j 1 -p psfex -V 1.1
-
-# Monitor sessions/jobs and stream logs.
-canfar_monitor
-canfar_monitor_log
-```
-
-The full production run — input preparation, the per-step `-j` table, and
-post-processing — is documented in the
-[CANFAR production walkthrough](pipeline_canfar.md).
-
-```{note}
-The CANFAR production submission scripts (`scripts/sh/job_sp_canfar*.bash`) still
-run under the pre-container environment and are slated for the same
-container-first cleanup the candide scripts received. Treat the walkthrough as
-the current-but-evolving production procedure.
-```
+`canfar_monitor` and `canfar_monitor_log` stay: they list, filter and destroy
+CANFAR sessions, independently of how those sessions were started.
 
 ## ccin2p3
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -104,6 +104,10 @@
 
 myst_enable_extensions = ["html_image"]
 
+# Generate slug anchors for h1-h3 so in-page links like
+# `[Mask images](#mask-images)` resolve instead of warning.
+myst_heading_anchors = 3
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for

diff --git a/docs/source/dependencies.md b/docs/source/dependencies.md
@@ -34,8 +34,7 @@ Data access &amp; infrastructure (CANFAR / UNIONS):
 | Package | Purpose |
 |---------|---------|
 | [vos](https://github.com/opencadc/vostools) | CADC / CANFAR VOSpace access |
-| [skaha](https://github.com/shinybrar/skaha) | CANFAR Science Platform sessions |
-| canfar | CANFAR container-job submission |
+| canfar | CANFAR session monitoring |
 | [astroquery](https://astroquery.readthedocs.io/) | external catalogue queries |
 | [cs_util](https://github.com/CosmoStat/cs_util) | shared CosmoStat utilities |
 | [sqlitedict](https://github.com/RaRe-Technologies/sqlitedict) | on-disk pipeline state |